diff --git a/data/covid/preprints-summary.csv b/data/covid/preprints-summary.csv index 798bf0b5..50de4e1b 100644 --- a/data/covid/preprints-summary.csv +++ b/data/covid/preprints-summary.csv @@ -1,46 +1,46 @@ -infectious diseases,epidemiology,orthopedics,genomics,microbiology,radiology and imaging,Total,surgery,dentistry and oral medicine,ophthalmology,occupational and environmental health,biochemistry,scientific communication and education,evolutionary biology,intensive care and critical care medicine,immunology,biophysics,health economics,neurology,health informatics,public and global health,dermatology,genetic and genomic medicine,primary care research,health policy,pathology,pharmacology and therapeutics,hiv aids,allergy and immunology,psychiatry and clinical psychology,molecular biology,respiratory medicine,oncology,month,emergency medicine,geriatric medicine,systems biology,health systems and quality improvement,bioinformatics,pediatrics,cardiovascular medicine,obstetrics and gynecology -1,,,,,,4,,,,,,,,,1,,,,1,,,,,,,,,,,,1,,Oct-23,,,,,,,, -1,,,,,,1,,,,,,,,,,,,,,,,,,,,,,,,,,,Sep-23,,,,,,,, -,4,,,,,7,,,,1,,,,,,,,,,1,,,1,,,,,,,,,,Aug-23,,,,,,,, -,3,,,,,7,,,,,,,,,,,,,,1,,1,,,,,,,,,,,Jul-23,,,,2,,,, -2,1,1,,,,7,,,,1,,1,,,,,,,1,,,,,,,,,,,,,,Jun-23,,,,,,,, -1,2,,,,,6,,,,,,,,,1,,,,,1,,,,,,,,,,,1,,May-23,,,,,,,, -1,,,,,,3,,,,,,,,,,,,,,2,,,,,,,,,,,,,Apr-23,,,,,,,, -3,2,,,,,9,,,,1,,,,,,,,,,2,,,,,,,,,1,,,,Mar-23,,,,,,,, -,4,,,,,8,,,,,,,,,,,,1,,2,,,,,,,,,,,1,,Feb-23,,,,,,,, -1,5,,,,,6,,,,,,,,,,,,,,,,,,,,,,,,,,,Jan-23,,,,,,,, -4,3,,,,,12,,,,,,,,,,,,,,1,,,,1,1,,,,,,2,,Dec-22,,,,,,,, -4,,,,,,4,,,,,,,,,,,,,,,,,,,,,,,,,,,Nov-22,,,,,,,, -2,1,,,,,6,,,,,,,,,,,,,,2,,,,,,,,,,,,,Oct-22,,,,,,,1, -2,1,,,1,,9,,,,2,,,,,,,,,,1,,,,,,,,,,,1,,Sep-22,,,,,,1,, -3,4,,,,,10,,,,,,,,,,,,,,3,,,,,,,,,,,,,Aug-22,,,,,,,, -3,2,,,,,8,,,,,,,,,1,,,,1,,,,,,,,,,,,,,Jul-22,,,,,,1,, -4,6,,,,,18,,,,,,,,,,,,,1,1,,1,,,,,,,5,,,,Jun-22,,,,,,,, -5,2,,,1,,14,,,,,,,,,,,1,,,1,,,1,,,,,,2,,,,May-22,,,,1,,,, -3,5,,,1,,16,,,,1,,,,,,,1,,,1,,,,,,,,,,,1,,Apr-22,,,,2,,,1, -4,9,,,,,17,,,,,,,1,,,,,,,,,,1,,,,,,1,,1,,Mar-22,,,,,,,, -4,6,,,,,12,,,,,,,,,,,,1,,1,,,,,,,,,,,,,Feb-22,,,,,,,, -3,5,,,,,14,,,,1,,,,,1,,,,2,1,,,,,,,,,,,,,Jan-22,,,,,,,1, -8,10,,,,,22,,,,,,,,,,,,1,,,,,1,,,,,,,,,,Dec-21,,,,,,1,1, -4,9,,1,,,24,,,,,,,,1,,1,,1,,3,,,1,,,,,,1,,,,Nov-21,,,,2,,,, -3,4,,,,,11,,,,,,,,,,,,,,,,,,,,,,,2,,,,Oct-21,,1,,,,1,, -4,6,,,,,16,,,,,,,,1,,,,,1,2,,,,,,1,,,,,,,Sep-21,,,,,,,1, -3,2,,,,,13,,,,1,,,,1,,,,,1,3,,,,,,,,,,,1,,Aug-21,,,,,,,1, -12,3,,,,,25,,,,,,,,1,,,,,,4,,1,,,,,,,,,2,,Jul-21,1,,,,,1,, -7,6,,,,,27,,,,1,,,,1,1,,,1,1,4,,,1,,,,,1,1,,,,Jun-21,,,,1,,1,, -7,11,,,,,22,,,,,,,,,,,,,,1,1,1,,,,,,,1,,,,May-21,,,,,,,, -7,3,,,1,,19,,,,2,,,,,,,,,1,1,,,1,,,,,1,1,,,,Apr-21,,,,1,,,, -17,5,,,,1,38,1,,,,1,,,,,,,1,2,5,,1,,,,,,,1,,,,Mar-21,,2,,,,1,, -9,9,,,,,23,1,,,,,,,,,,1,,1,1,,,,,,,,,,,,,Feb-21,,,,1,,,, -8,4,,,,,22,,1,,,,,,1,,,,,,3,,,1,1,,,,,1,,,,Jan-21,,1,,1,,,, -4,4,,2,1,,23,,,,,,,,,,,,,3,3,,,1,,,,,,2,,,,Dec-20,,,,1,,,2, -12,5,,,,,26,,,,,,,,,1,,,,1,5,,,,1,,,,,,,,,Nov-20,,,,,1,,, -12,6,,,,,30,,,,,,,,1,1,,,,1,,,,1,1,,,,,3,,,1,Oct-20,,1,1,,1,,, -8,6,,,1,,26,,,,,,,,1,,,,,1,3,,,1,,,,1,,2,,,,Sep-20,2,,,,,,, -12,6,,,,,27,,,,1,,,,,,,,,,2,,1,,,,,,,,1,,,Aug-20,2,,,1,,,,1 -8,10,,1,,,28,,,,,,,,1,1,,,,,4,,,,,,,,,1,,1,,Jul-20,,,,,,,1, -10,7,,,,,36,,,1,,,,,3,1,,,,1,3,,,,1,,,,,4,,1,1,Jun-20,,1,,1,1,,, -10,8,,,,,36,,,,1,,,,1,,,1,,1,8,,,,,,,,,,,1,1,May-20,,1,,,1,,2, -7,7,,1,,,19,,,,,,,,,,,,,,1,,2,,,,,,,,,,,Apr-20,,,,1,,,, -1,4,,,,,8,,,,,,,,,,,,,,3,,,,,,,,,,,,,Mar-20,,,,,,,, -,4,,,,,6,,,,,,,,,,,,,,2,,,,,,,,,,,,,Feb-20,,,,,,,, +molecular biology,geriatric medicine,public and global health,immunology,pathology,psychiatry and clinical psychology,health policy,hiv aids,systems biology,occupational and environmental health,health systems and quality improvement,respiratory medicine,oncology,evolutionary biology,allergy and immunology,radiology and imaging,Total,month,biophysics,dentistry and oral medicine,microbiology,pharmacology and therapeutics,scientific communication and education,bioinformatics,infectious diseases,surgery,dermatology,primary care research,orthopedics,genetic and genomic medicine,health economics,neurology,biochemistry,cardiovascular medicine,ophthalmology,health informatics,pediatrics,epidemiology,genomics,intensive care and critical care medicine,emergency medicine +,,,1,,,,,,,,1,,,,,4,Oct-23,,,,,,,1,,,,,,,,,,,,,1,,, +,,,,,,,,,,,,,,,,1,Sep-23,,,,,,,1,,,,,,,,,,,,,,,, +,,1,,,,,,,1,,,,,,,7,Aug-23,,,,,,,,,,1,,,,,,,,,,4,,, +,,1,,,,,,,,1,,,,,,5,Jul-23,,,,,,,,,,,,,,,,,,,,3,,, +,,,,,,,,,1,,,,,,,7,Jun-23,,,,,1,,2,,,,1,,,,,,,1,,1,,, +,,1,1,,,,,,,,1,,,,,6,May-23,,,,,,,1,,,,,,,,,,,,,2,,, +,,2,,,,,,,,,,,,,,3,Apr-23,,,,,,,1,,,,,,,,,,,,,,,, +,,2,,,1,,,,1,,,,,,,9,Mar-23,,,,,,,3,,,,,,,,,,,,,2,,, +,,2,,,,,,,,,1,,,,,8,Feb-23,,,,,,,,,,,,,,1,,,,,,4,,, +,,,,,,,,,,,,,,,,6,Jan-23,,,,,,,1,,,,,,,,,,,,,5,,, +,,1,,1,,1,,,,,2,,,,,12,Dec-22,,,,,,,4,,,,,,,,,,,,,3,,, +,,,,,,,,,,,,,,,,4,Nov-22,,,,,,,4,,,,,,,,,,,,,,,, +,,2,,,,,,,,,,,,,,6,Oct-22,,,,,,,2,,,,,,,,,1,,,,1,,, +,,1,,,,,,,2,,1,,,,,9,Sep-22,,,1,,,,2,,,,,,,,,,,,1,1,,, +,,3,,,,,,,,,,,,,,10,Aug-22,,,,,,,3,,,,,,,,,,,,,4,,, +,,,1,,,,,,,,,,,,,8,Jul-22,,,,,,,3,,,,,,,,,,,1,1,2,,, +,,1,,,5,,,,,,,,,,,17,Jun-22,,,,,,,3,,,,,1,,,,,,1,,6,,, +,,1,,,2,,,,,1,,,,,,14,May-22,,,1,,,,5,,,1,,,1,,,,,,,2,,, +,,1,,,,,,,1,2,1,,,,,16,Apr-22,,,1,,,,3,,,,,,1,,,1,,,,5,,, +,,,,,1,,,,,,1,,1,,,18,Mar-22,,,,,,,5,,,1,,,,,,,,,,9,,, +,,1,,,,,,,,,,,,,,11,Feb-22,,,,,,,4,,,,,,,1,,,,,,5,,, +,,1,1,,,,,,1,,,,,,,13,Jan-22,,,,,,,2,,,,,,,,,1,,2,,5,,, +,,1,,,,,,,,,,,,,,24,Dec-21,,,1,,,,8,,,1,,,,1,,1,,,1,10,,, +,,2,,,1,,,,,2,,,,,,24,Nov-21,1,,,,,,5,,,1,,,,1,,,,,,9,1,1, +,1,,,,2,,,,,,,,,,,11,Oct-21,,,,,,,3,,,,,,,,,,,,1,4,,, +,,1,,,,,,,,,,,,,,16,Sep-21,,,,1,,,5,,,,,,,,,1,,1,,6,,1, +,,3,,,,,,,1,,1,,,,,13,Aug-21,,,,,,,3,,,,,,,,,1,,1,,2,,1, +,,4,,,,,,,,,2,1,,,,25,Jul-21,,,,,,,12,,,,,1,,,,,,,1,2,,1,1 +,,4,1,,1,,,,1,1,,,,1,,28,Jun-21,,,,,,,7,,,1,,,,1,,,,1,1,7,,1, +,,1,,,1,,,,,,,,,,,24,May-21,,,,,,,8,,1,,,1,,,,,,1,,11,,, +,,1,,,1,,,,2,1,,,,1,,20,Apr-21,,,1,,,,7,,,1,,,,,,,,1,,4,,, +,2,5,,,1,,,,,,,,,,1,37,Mar-21,,,,,,,15,1,,,,1,,1,1,,,2,1,6,,, +,,1,,,,,,,,1,,,,,,22,Feb-21,,,,,,,8,1,,,,,1,,,1,,1,,8,,, +,1,2,1,,1,1,,,,1,,,,,,22,Jan-21,,1,,,,,8,,,1,,,,,,,,,,4,,1, +,,3,,,2,,,,,1,,,,,,22,Dec-20,,,1,,,,4,,,,,,,,,2,,3,,4,2,, +,,5,1,,,1,,,,,,,,,,25,Nov-20,,,,,,1,10,,,,,,,,,,,1,,6,,, +,1,,1,,3,1,,1,,,,1,,,,30,Oct-20,,,,,,1,12,,,1,,,,,,,,1,,6,,1, +,,3,,,2,,1,,,,,,,,,26,Sep-20,,,1,,,,7,,,1,,,,,,,,1,,6,,1,3 +1,,2,,,,,,,1,1,,,,,,25,Aug-20,,,,,,,12,,,,,1,,,,,,,,5,,,2 +,,4,1,,1,,,,,,1,,,,,27,Jul-20,,,,,,,8,,,,,,,,,1,,,,10,1,, +,1,3,1,,4,1,,,,1,1,1,,,,36,Jun-20,,,,,,1,10,,,,,,,,,1,1,,,7,,3, +,1,8,,,,,,,1,,1,1,,,,36,May-20,,,,,,1,10,,,,,,1,,,2,,1,,8,,1, +,,1,,,,,,,,1,,,,,,17,Apr-20,,,,,,,7,,,,,2,,,,,,,,5,1,, +,,3,,,,,,,,,,,,,,8,Mar-20,,,,,,,1,,,,,,,,,,,,,4,,, +,,2,,,,,,,,,,,,,,7,Feb-20,,,,,,,1,,,,,,,,,,,,,4,,, diff --git a/data/covid/preprints.csv b/data/covid/preprints.csv index 4238543f..a5b7d701 100644 --- a/data/covid/preprints.csv +++ b/data/covid/preprints.csv @@ -1,20 +1,12 @@ site,doi,date,link,title,authors,affiliations,abstract,category,match_type,author_similarity,affiliation_similarity -bioRxiv,10.1101/2023.10.22.563481,2023-10-24,https://biorxiv.org/cgi/content/short/2023.10.22.563481,Microfluidic antibody profiling after repeated SARS-CoV-2 vaccination links antibody affinity and concentration to impaired immunity and variant escape in patients on anti-CD-20 therapy,Ashley Priddey; Michael Xin Hua Chen-Xu; Daniel James Cooper; Serena MacMillan; Georg Meisl; Catherine K Xu; Myra Hosmillo; Ian G Goodfellow; Rafael Kollyfas; Rainer Doffinger; John R Bradley; Irina I Mohorianu; Rachel Jones; Tuomas P.J. Knowles; Rona Smith; Vasilis Kosmoliaptsis,"Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK and NIHR Blood and Transplant Research Unit in Organ D","Background: Patients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients. Methods: We performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30). Results: Rituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination. Discussion: Our results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.",immunology,fuzzy,100,100 -medRxiv,10.1101/2023.10.12.23296948,2023-10-13,https://medrxiv.org/cgi/content/short/2023.10.12.23296948,"A nationwide study of 331 rare diseases among 58 million individuals: prevalence, demographics, and COVID-19 outcomes",Johan H Thygesen; HUAYU ZHANG; Hanane Issa; Jinge Wu; Tuankasfee Hama; Ana-Catarina Pinho-Gomes; Tudor Groza; Sara Khalid; Richard Lumbers; Mevhibe Hocaoglu; Kamlesh Khunti; Rouven Priedon; Amitava Banerjee; Nikolas Pontikos; Christopher Tomlinson; Ana Torralbo; Paul Taylor; Cathie Sudlow; Spiros Denaxas; Harry Hemingway; Honghan Wu,"Institute of Health Informatics, University College London, London, UK; Advanced Care Research Centre, Usher Institute, University of Edinburgh, Edinburgh, UK.; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, UK; Institute of Health Informatics, University College London, London, UK; Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, Kings College London, London, UK; College of Life Sciences, University of Leicester, Leicester, UK; Health Data Research UK, London, UK; Institute of Health Informatics, University College London, London, UK; UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Health Data Research UK, London, UK; British Heart Foundation Data Science Centre, London, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edin; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK","BackgroundThe Global Burden of Disease study has provided key evidence to inform clinicians, researchers, and policy makers across common diseases, but no similar effort with single study design exists for hundreds of rare diseases. Consequently, many rare conditions lack population-level evidence including prevalence and clinical vulnerability. This has led to the absence of evidence-based care for rare diseases, prominently in the COVID-19 pandemic. +medRxiv,10.1101/2023.10.26.23297598,2023-10-26,https://medrxiv.org/cgi/content/short/2023.10.26.23297598,Assessing the causal effect of air pollution on risk of SARS-CoV-2 infection,Annalan Mathew Dwight Navaratnam; Sarah Beale; Yamina Boukari; Vincent Nguyen; Wing Lam Erica Fong; Isobel Braithwaite; Thomas Edward Byrne; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Parth Patel; Madhumita Shrotri; Alexei Yavlinsky; Andrew Hayward; Haneen Khreis; Robert W Aldridge,University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCL; University College London; University College London; University College London; University College London; University College London; UCL; University of Cambridge; UCL,"Introduction Emerging evidence suggests association of air pollution exposure with risk of SARS-CoV-2 infection, but many of these findings are limited by study design, lack of individual-level covariate data or are specific to certain subpopulations. We aim to evaluate causal effects of air pollution on risk of infection, whilst overcoming these limitations. Methods Concentrations for black carbon(BC), particulate matter 10(PM10), particulate matter 2.5(PM2.5), nitrogen dioxide(NO2) and oxides of nitrogen(NOx) from the Department of Environment, Food and Rural Affairs (DEFRA) and Effect of Low-level Air Pollution: A Study in Europe (ELAPSE) were linked to postcodes of 53,683 Virus Watch study participants. The primary outcome was first SARS-CoV-2 infection, between 1st September 2020 and 30th April 2021. Regression analysis used modified Poisson with robust estimates, clustered by household, adjusting for individual (e.g., age, sex, ethnicity) and environmental covariates(e.g., population density, region) to estimate total and direct effects. Results Single pollutant analysis showed the direct effect of higher risk of SARS-CoV-2 infection with increased exposure to PM2.5(RR1.11,95%CI 1.08;1.15), PM10(RR1.06,95%CI 1.04;1.09), NO2(RR1.04,95%CI 1.04;1.05) and NOx(RR1.02,95%CI 1.02;1.02) per 1g/m3 increment with DEFRA 2015-19 data. Sensitivity analyses altering covariates, exposure window and modelled air pollution data source produced similar estimates. Higher risk of SARS-CoV-2 per 10-5m-1 increment of BC (RR1.86, 95%CI 1.62;2.14) was observed using ELAPSE data. Conclusion Long term exposure to higher concentrations of air pollutions increases the risk of SARS-CoV-2 infection, highlighting that adverse health effects of air pollution is not only limited to non-communicable diseases.",epidemiology,fuzzy,100,100 +bioRxiv,10.1101/2023.10.22.563481,2023-10-24,https://biorxiv.org/cgi/content/short/2023.10.22.563481,Microfluidic antibody profiling after repeated SARS-CoV-2 vaccination links antibody affinity and concentration to impaired immunity and variant escape in patients on anti-CD-20 therapy,Ashley Priddey; Michael Xin Hua Chen-Xu; Daniel James Cooper; Serena MacMillan; Georg Meisl; Catherine K Xu; Myra Hosmillo; Ian G Goodfellow; Rafael Kollyfas; Rainer Doffinger; John R Bradley; Irina I Mohorianu; Rachel Jones; Tuomas P.J. Knowles; Rona Smith; Vasilis Kosmoliaptsis,"Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK and NIHR Blood and Transplant Research Unit in Organ D","BackgroundPatients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients. -MethodThis study used electronic health records (EHRs) of more than 58 million people in England, linking nine National Health Service datasets spanning healthcare settings for people alive on Jan 23, 2020. Starting with all rare diseases listed in Orphanet, we quality assured and filtered down to analyse 331 conditions with ICD-10 or SNOMED-CT mappings clinically validated in our dataset. We report 1) population prevalence, clinical and demographic details of rare diseases, and 2) investigate differences in mortality with SARs-CoV-2. +MethodsWe performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30). -FindingsAmong 58,162,316 individuals, we identified 894,396 with at least one rare disease. Prevalence data in Orphanet originates from various sources with varying degrees of precision. Here we present reproducible age and gender-adjusted estimates for all 331 rare diseases, including first estimates for 186 (56.2%) without any reported prevalence estimate in Orphanet. We identified 49 rare diseases significantly more frequent in females and 62 in males. Similarly we identified 47 rare diseases more frequent in Asian as compared to White ethnicity and 22 with higher Black to white ratios as compared to similar ratios in population controls. 37 rare diseases were overrepresented in the white population as compared to both Black and Asian ethnicities. In total, 7,965 of 894,396 (0.9%) of rare-disease patients died from COVID-19, as compared to 141,287 of 58,162,316 (0.2%) in the full study population. Eight rare diseases had significantly increased risks for COVID-19-related mortality in fully vaccinated individuals, with bullous pemphigoid (8.07[3.01-21.62]) being worst affected. +ResultsRituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination. -InterpretationOur study highlights that National-scale EHRs provide a unique resource to estimate detailed prevalence, clinical and demographic data for rare diseases. Using COVID-19-related mortality analysis, we showed the power of large-scale EHRs in providing insights to inform public health decision-making for these often neglected patient populations. - -FundingBritish Heart Foundation Data Science Centre, led by Health Data Research UK. - -Research in contextO_ST_ABSEvidence before the studyC_ST_ABSWe have previously published the largest study looking at COVID-19 across rare diseases, but with a sample size of 158 COVID-19 infected rare disease patients and 125 unaffected relatives, from Genomics England, the power of that study was limited. We searched PubMed from database inception to Apr 21, 2023, for publications using the search terms ""COVID-19"" or ""SARS-CoV-2"" and ""rare disease"" or ""ORPHANET"", without language restrictions. There are many studies examining the severity of COVID-19 in rare disease patients. However, to date, most studies have focused on a single or a few rare diseases associated with severity of COVID-19, and not taken a comprehensive rare disease wide approach. So far no studies have examined the impact of vaccination on mortality in rare disease patients. Moreover, the sample size used to examine rare diseases is limited in most studies. The largest study we identified included 168,680 individuals but only focused on autoimmune rheumatic disease. - -Added value of this studyIn this study we use national scale EHR data from England to report age and gender adjusted point prevalence for 331 rare diseases, with clinically-validated ICD-10 and/or SNOMED-CT code lists. Among these, 186 (56.2%) diseases did not have existing point prevalence data available in Orphanet. To our knowledge, this is the first time that rare diseases have been examined on a national scale, encompassing a population of over 58 million people. The large sample size provides sufficient statistical power to detect and describe enough carriers of even very rare conditions <1 case per million. Our analysis of COVID-related mortality has demonstrated the clinical relevance of national data for rare diseases. Specifically, we identified eight rare conditions that are associated with a significantly increased risk of mortality from COVID-19, even among fully vaccinated individuals. - -Implication of all the available evidenceThese findings provide robust reproducible prevalence, gender, and ethnicity estimates for disease that may often have been under prioritised, and where such information in most cases was not previously available. Our COVID-19 mortality findings highlight the need for targeted policy and support addressing the high level of vulnerability of these patients to COVID-19.",health informatics,fuzzy,100,100 +DiscussionOur results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.",immunology,fuzzy,100,100 medRxiv,10.1101/2023.10.11.23296866,2023-10-12,https://medrxiv.org/cgi/content/short/2023.10.11.23296866,"SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort",Elisabeth Dietz; Emma Elizabeth Pritchard; Koen Pouwels; Muhammad Ehsaan; Joshua Blake; Charlotte Gaughan; Eric Haduli; Hugh Boothe; Karina-Doris Vihta; Tim Peto; Nicole Stoesser; Philippa Matthews; Nick Taylor; Ian Diamond; Ruth Studley; Emma Rourke; Paul Birrell; Daniela De Angelis; Tom Fowler; Conall Watson; David W Eyre; Thomas House; Ann Sarah Walker,University of Oxford; University of Oxford; University of Oxford; Berkshire and Surrey Pathology Services; University of Cambridge; Office of National Statistics; Berkshire and Surrey Pathology Services; Berkshire and Surrey Pathology Services; University of Oxford; University of Oxford; University of Oxford; The Francis Crick Institute; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Cambridge; University of Cambridge; UK Health Security Agency; UK Health Security Agency; University of Oxford; University of Manchester; University of Oxford,"BackgroundSyndromic surveillance often relies on patients presenting to healthcare. Community cohorts, although more challenging to recruit, could provide additional population-wide insights, particularly with SARS-CoV-2 co-circulating with other respiratory viruses. MethodsWe estimated positivity and incidence of SARS-CoV-2, influenza A/B, and RSV, and trends in self-reported symptoms including influenza-like illness (ILI), over the 2022/23 winter season in a broadly representative UK community cohort (COVID-19 Infection Survey), using negative-binomial generalised additive models. We estimated associations between test positivity and each of symptoms and influenza vaccination, using adjusted logistic and multinomial models. @@ -133,18 +125,6 @@ C_LI How this study might affect research, practice or policyO_LIAlternative explanations for the rise in economic inactivity need to be investigated such as long-term sickness. C_LIO_LIPossible biases introduced by linkage consent need considering when using linked healthcare data. C_LI",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2023.07.25.23293143,2023-07-27,https://medrxiv.org/cgi/content/short/2023.07.25.23293143,The Cost of Keeping Patients Waiting: Retrospective Treatment-Control Study of Additional Healthcare Utilisation for UK Patients Awaiting Elective Treatment Following COVID-19,Charlotte James; Rachel Denholm; Richard M Wood,University of Bristol; University of Bristol; UK National Health Service (BNSSG ICB),"ObjectiveThe COVID-19 pandemic has led to increased waiting times for elective treatments in many countries. This study seeks to address a deficit in the literature concerning the effect of long waits on the wider consumption of healthcare resources. - -MethodsWe carried out a retrospective treatment-control study in a healthcare system in South West England from 15 June 2021 to 15 December 2021. We compared weekly contacts with health services of patients waiting over 18 weeks for treatment ( Treatments) and people not on a waiting list ( Controls). Controls were matched to Treatments based on age, sex, deprivation and multimorbidity. Treatments were stratified by the clinical specialty of the awaited treatment, with healthcare usage assessed over various healthcare settings. T-tests assessed whether there was an increase in healthcare utilisation and bootstrap resampling was used to estimate the magnitude of any differences. - -ResultsA total of 44,616 patients were waiting over 18 weeks (the constitutional target in England) for treatment during the study period. Evidence suggests increases (p < 0.05) in healthcare utilisation for all specialties. Patients in the Cardiothoracic Surgery specialty had the largest increase, requiring 17.9 [4.3, 33.8] additional contacts with secondary care and 17.3 [-1.1, 34.1] additional prescriptions per year. - -ConclusionPeople waiting for treatment consume higher levels of healthcare than comparable individuals not on a waiting list. These findings are relevant for clinicians and managers in better understanding patient need and reducing harm. Results also highlight the possible false economy in failing to promptly resolve long elective waits. - -HighlightsO_LILong waits for elective care can result in additional healthcare needs to manage symptoms up to the point of definitive treatment. While previous studies indicate some association, these mainly consider only a single elective specialty and are limited in the range of healthcare settings covered. -C_LIO_LIThe large number of long-wait pathways produced as a consequence of COVID-19 disruption allows for a more holistic analysis, covering the full range of elective treatment specialties and wider healthcare impacts across primary, secondary, mental health, and community care, as well as emergency service calls and prescriptions. -C_LIO_LIAnalysis of 44,616 elective care pathways reveals evidence of increases in wider healthcare consumption additional to that expected for similar patients not awaiting elective treatment. This suggests a false economy in failing to promptly resolve elective pathways, which should be reflected by healthcare providers in long-term resource allocation decisions. -C_LI",health systems and quality improvement,fuzzy,100,100 medRxiv,10.1101/2023.07.19.23292289,2023-07-23,https://medrxiv.org/cgi/content/short/2023.07.19.23292289,Can computer simulation support strategic service planning? Modelling a large integrated mental health system on recovery from COVID-19,Livia LP Pierotti; Jennifer Cooper; Charlotte James; Rachel Denholm; Kenah Cassels; Emma Gara; Richard Wood,"University of Bristol; University of Bristol; University of Bristol; University of Bristol; Bristol, North Somerset and South Gloucestershire Integrated Care Board, UK National Health Service; Bristol, North Somerset and South Gloucestershire Integrated Care Board, UK National Health Service; Bristol, North Somerset and South Gloucestershire Integrated Care Board, UK National Health Service. HDR UK Southwest.","BackgroundCOVID-19 has had a significant impact on peoples mental health and mental health services. During the first year of the pandemic, existing demand was not fully met while new demand was generated, resulting in large numbers of people requiring support. To support mental health services to recover without being overwhelmed, it was important to know where services will experience increased pressure, and what strategies could be implemented to mitigate this. MethodsWe implemented a computer simulation model of patient flow through an integrated mental health service in Southwest England covering General Practice (GP), community-based talking therapies (IAPT), acute hospital care, and specialist care settings. The model was calibrated on data from 1 April 2019 to 1 April 2021. Model parameters included patient demand, service-level length of stay, and probabilities of transitioning to other care settings. We used the model to compare do nothing (baseline) scenarios to what if (mitigation) scenarios, including increasing capacity and reducing length of stay, for two future demand trajectories from 1 April 2021 onwards. @@ -179,7 +159,6 @@ Key PointsQuestion: What health conditions are associated with increased risk of Findings: Certain groups were found to be at overall higher risk of postbooster COVID-19 death (e.g., learning disability or Down Syndrome) and certain groups were found to have significantly higher relative risk of COVID-19 death compared to other non-COVID-19 causes (e.g., cancer of the blood or bone marrow). Meaning: This work has implications for prioritisation of vaccination booster doses worldwide. We highlight which groups with health conditions are at elevated risk of postbooster COVID-19 death.",public and global health,fuzzy,100,100 -medRxiv,10.1101/2023.06.29.23292056,2023-07-01,https://medrxiv.org/cgi/content/short/2023.06.29.23292056,Genome-wide Association Study of Long COVID,Vilma Lammi; Tomoko Nakanishi; Samuel E Jones; Shea J Andrews; Juha Karjalainen; Beatriz Cortes; Heath E O'Brien; Brian E Fulton-Howard; Hele H Haapaniemi; Axel Schmidt; Ruth E Mitchell; Abdou Mousas; Massimo Mangino; Alicia Huerta-Chagoya; Nasa Sinnott-Armstrong; Elizabeth T Cirulli; Marc Vaudel; Alex SF Kwong; Amit K Maiti; Minttu M Marttila; Chiara Batini; Francesca Minnai; Anna R Dearman; CA Robert Warmerdam; Celia B Sequeros; Thomas W Winkler; Daniel M Jordan; Lindsay Guare; Ekaterina Vergasova; Eirini Marouli; Pasquale Striano; Ummu Afeera Zainulabid; Ashutosh Kumar; Hajar Fauzan Ahmad; Ryuya Edahiro; Shuhei Azekawa; - Long COVID Host Genetics Initiative; - FinnGen; - DBDS Genomic Consortium; - GEN-COVID Multicenter Study; Joseph J Grzymski; Makoto Ishii; Yukinori Okada; Noam D Beckmann; Meena Kumari; Ralf Wagner; Iris M Heid; Catherine John; Patrick J Short; Per Magnus; Karina Banasik; Frank Geller; Lude H Franke; Alexander Rakitko; Emma L Duncan; Alessandra Renieri; Konstantinos K Tsilidis; Rafael de Cid; Ahmadreza Niavarani; Teresa Tusie-Luna; Shefali S Verma; George Davey Smith; Nicholas J Timpson; Mark J Daly; Andrea Ganna; Eva C Schulte; J Brent Richards; Kerstin U Ludwig; Michael Hultstrom; Hugo Zeberg; Hanna M Ollila,Institute for Molecular Medicine Finland (FIMM); Department of Human Genetics; Institute for Molecular Medicine Finland (FIMM); University of California San Francisco; Institute for Molecular Medicine Finland (FIMM); Genomes for Life-GCAT lab; Sano Genetics Limited; Genetics and Genomic Sciences; Institute for Molecular Medicine Finland (FIMM); Institute of Human Genetics; Centre for Clinical Brain Sciences; Department of Hygiene and Epidemiology; Department of Twin Research; Departamento de Medicina Genomica y Toxicologia Ambiental; Herbold Computational Biology Program; Helix; Mohn Center for Diabetes Precision Medicine; University of Bristol; Department of Genetics and Genomics; University of Helsinki; Department of Population Health Sciences; Institute for Biomedical Technologies - National Research Council; Institute for Social and Economic Research; Department of Genetics; Novo Nordisk Foundation Center for Protein Research; Department of Genetic Epidemiology; Charles Bronfman Institute for Personalized Medicine; Department of Pathology and Laboratory Medicine; Genotek Ltd.; William Harvey Research Institute; IRCCS G; Department of Internal Medicine; Department of Anatomy; Faculty of Industrial Sciences and Technology; Department of Statistical Genetics; Division of Pulmonary Medicine; ; ; ; ; Center for Genomic Medicine; Division of Pulmonary Medicine; Department of Statistical Genetics; Charles Bronfman Institute for Personalized Medicine; Institute for Social and Economic Research; Institute of Medical Microbiology & Hygiene; Department of Genetic Epidemiology; Department of Population Health Sciences; Sano Genetics Limited; Centre for Fertility and Health; Novo Nordisk Foundation Center for Protein Research; Statens Serum Institute; Department of Genetics; Genotek Ltd.; Department of Twin Research and Genetic Epidemiology; Medical Genetics; Department of Hygiene and Epidemiology; Genomes for Life-GCAT lab; Digestive Oncology Research Center; Instituto de Investigaciones Biomedicas Unam/ Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran; Department of Pathology and Laboratory Medicine; MRC Integrative Epidemiology Unit at the University of Bristol; MRC Integrative Epidemiology Unit at the University of Bristol; Institute for Molecular Medicine Finland (FIMM); Institute for Molecular Medicine Finland (FIMM); Institute of Psychiatric Phenomics & Genomics; Department of Human Genetics; Institute of Human Genetics; Anaesthesiology and Intensive Care Medicine; Department of Evolutionary Genetics; Institute for Molecular Medicine Finland (FIMM),"Infections can lead to persistent or long-term symptoms and diseases such as shingles after varicella zoster, cancers after human papillomavirus, or rheumatic fever after streptococcal infections1, 2. Similarly, infection by SARS-CoV-2 can result in Long COVID, a condition characterized by symptoms of fatigue and pulmonary and cognitive dysfunction3-5. The biological mechanisms that contribute to the development of Long COVID remain to be clarified. We leveraged the COVID-19 Host Genetics Initiative6, 7 to perform a genome-wide association study for Long COVID including up to 6,450 Long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We identified the first genome-wide significant association for Long COVID at the FOXP4 locus. FOXP4 has been previously associated with COVID-19 severity6, lung function8, and cancers9, suggesting a broader role for lung function in the pathophysiology of Long COVID. While we identify COVID-19 severity as a causal risk factor for Long COVID, the impact of the genetic risk factor located in the FOXP4 locus could not be solely explained by its association to severe COVID-19. Our findings further support the role of pulmonary dysfunction and COVID-19 severity in the development of Long COVID.",genetic and genomic medicine,fuzzy,100,100 medRxiv,10.1101/2023.06.30.23292079,2023-06-30,https://medrxiv.org/cgi/content/short/2023.06.30.23292079,Synthesis and new evidence from the PROTECT UK National Core Study: Determining occupational risks of SARS-CoV-2 infection and COVID-19 mortality,Sarah Rhodes; Sarah Beale; Mark Cherrie; William Mueller; Fiona Holland; Melissa Matz; Ioannis Basinas; Jack D Wilkinson; Matthew Gittins; Bernardine Farrell; Andrew Hayward; Neil Pearce; Martie van Tongeren,University of Manchester; University College London; Institute of Occupational Medicine; Institute of Occupational Medicine; University of Manchester; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester; University of Manchester; University of Manchester; UCL; London School of Hygiene and Tropical Medicine; University of Manchester,"IntroductionThe PROTECT National Core Study was funded by the UK Health and Safety Executive (HSE) to investigate routes of transmission for SARS-CoV-2 and variation between settings. MethodsA workshop was organised in Oct 2022.We brought together evidence from five published epidemiological studies that compared risks of SARS-CoV-2 infection or COVID-19 mortality by occupation or sector funded by PROTECT relating to three non-overlapping data sets, plus additional unpublished analyses relating to the Omicron period. We extracted descriptive study level data and model results. We investigated risk across four pandemic waves using forest plots for key occupational groups by time-period. @@ -1011,13 +990,6 @@ Method12,965 healthcare staff (clinical and non-clinical) were recruited from 18 ResultsPMIEs were significantly associated with adverse mental health symptoms across healthcare staff. Specific work factors were significantly associated with experiences of moral injury, including being redeployed, lack of PPE, and having a colleague die of COVID-19. Nurses who reported symptoms of mental disorders were more likely to report all forms of PMIEs than those without symptoms (AOR 2.7; 95% CI 2.2, 3.3). Doctors who reported symptoms were only more likely to report betrayal events, such as breach of trust by colleagues (AOR 2.7, 95% CI 1.5, 4.9). ConclusionsA considerable proportion of NHS healthcare staff in both clinical and non-clinical roles report exposure to PMIEs during the COVID-19 pandemic. Prospective research is needed to identify the direction of causation between moral injury and mental disorder as well as continuing to monitor the longer term outcomes of exposure to PMIEs.",psychiatry and clinical psychology,fuzzy,100,100 -medRxiv,10.1101/2022.06.14.22276391,2022-06-16,https://medrxiv.org/cgi/content/short/2022.06.14.22276391,Factors associated with COVID-19 vaccine uptake in people with kidney disease: an OpenSAFELY cohort study,- The OpenSAFELY Collaborative; Edward PK Parker; John Tazare; William J Hulme; Christopher Bates; Rupert Beale; Edward J Carr; Jonathan Cockburn; Helen J Curtis; Louis Fisher; Amelia CA Green; Sam Harper; Frank Hester; Elsie MF Horne; Fiona Loud; Susan Lyon; Viyaasan Mahalingasivam; Amir Mehrkar; Linda Nab; John Parry; Shalini Santhakumaran; Retha Steenkamp; Jonathan AC Sterne; Alex J Walker; Elizabeth J Williamson; Michelle Willicombe; Bang Zheng; Ben Goldacre; Dorothea Nitsch; Laurie A Tomlinson,"-; London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK; The Francis Crick Institute, London, NW1 1AT, UK; UCL Department of Renal Medicine, Royal Free Hospital, London, UK; The Francis Crick Institute, London, NW1 1AT, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK; Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK; NIHR Bristol Biomedical Research Centre, Bristol, UK; Kidney Care UK, Alton, UK; Patient Council, UK Kidney Association, Bristol, UK; London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK; UK Renal Registry, Bristol, UK; UK Renal Registry, Bristol, UK; Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK; NIHR Bristol Biomedical Research Centre, Bristol, UK; H; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, Du Cane Road London, W12 0NN, UK; London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; UK Renal Registry, Bristol, UK; London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK","BackgroundKidney disease is a significant risk factor for COVID-19-related mortality. Achieving high COVID-19 vaccine coverage among people with kidney disease is therefore a public health priority. - -MethodsWith the approval of NHS England, we performed a retrospective cohort study using the OpenSAFELY-TPP platform. Individual-level routine clinical data from 24 million people in England were included. A cohort of individuals with stage 3-5 chronic kidney disease (CKD) or receiving renal replacement therapy (RRT) at the start of the COVID-19 vaccine roll-out was identified based on evidence of reduced estimated glomerular filtration rate or inclusion in the UK Renal Registry. Individual-level factors associated with vaccine uptake were explored via Cox proportional hazards models. - -Results948,845 people with stage 3-5 CKD or receiving RRT were included. Cumulative vaccine coverage as of 11th May 2022 was 97.5%, 97.0%, and 93.5% for doses 1, 2, and 3, respectively, and 61.1% among individuals with one or more indications for receipt of a fourth dose. Delayed 3-dose vaccine uptake was associated with non-White ethnicity, social deprivation, and severe mental illness - associations that were consistent across CKD stages and in RRT recipients. Similar associations were observed for 4-dose uptake, which was also delayed among care home residents. - -ConclusionAlthough high primary and booster dose coverage has been achieved among people with kidney disease in England, key disparities in vaccine uptake remain across demographic groups. Identifying how to address these disparities remains a priority to reduce the risk of severe disease in this vulnerable patient group.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.06.09.22276232,2022-06-14,https://medrxiv.org/cgi/content/short/2022.06.09.22276232,"HEALTHCARE UTILISATION IN PATIENTS WITH LONG-TERM CONDITIONS DURING THE COVID-19 PANDEMIC: A POPULATION BASED STUDY ACROSS GREATER MANCHESTER, UK",Camilla Sammut-Powell; Richard Williams; Matthew Sperrin; Owain Thomas; Niels Peek; Stuart W Grant,"Division of Informatics, Imaging and Data Science, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Division of Informatics, Imaging and Data Science, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Division of Informatics, Imaging and Data Science, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Langworthy Medical Practice, Salford, UK; Division of Informatics, Imaging and Data Science, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; 6. Division of Cardiovascular Sciences, University of Manchester, ERC, Manchester University Hospitals Foundation Trust, Manchester, M23 9LT, UK.","BackgroundThe COVID-19 pandemic has placed an unprecedented demand on global healthcare resources. Data on whole population healthcare utilisation (HCU) across both primary and secondary care during the COVID-19 pandemic are lacking. AimTo describe primary and secondary HCU stratified by LTCs and deprivation, during the first 19 months of COVID-19 pandemic across a large urban area in the United Kingdom. @@ -1346,6 +1318,13 @@ ConclusionThere is no evidence of an association between COVID-19 vaccination an What is already known on this topicSeveral studies have highlighted the association between COVID-19 vaccination and the risk of myocarditis, myopericarditis, and other cardiac problems, especially in young people, but associated risk of mortality is unclear. Since younger people have lower risk of COVID-19 hospitalisation and mortality, the mortality risk associated with vaccination is potentially more important to them in balancing the risk and benefit of vaccination. What this study addsAlthough there is a risk of myocarditis or myopericarditis with COVID-19, there is no evidence of increased risk of cardiac or all-cause mortality following COVID-19 vaccination in young people aged 12 to 29. Given the increased risk of mortality following SARS-CoV-2 infection in this group, the risk-benefit analysis favours COVID-19 vaccination for this age group.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2022.03.23.22272804,2022-03-23,https://medrxiv.org/cgi/content/short/2022.03.23.22272804,Waning effectiveness of BNT162b2 and ChAdOx1 COVID-19 vaccines over six months since second dose: a cohort study using linked electronic health records,Elsie MF Horne; William J Hulme; Ruth H Keogh; Tom M Palmer; Elizabeth J Williamson; Edward PK Parker; Amelia Green; Venexia Walker; Alex J Walker; Helen Curtis; Louis Fisher; Brian MacKenna; Richard Croker; Lisa Hopcroft; Robin Y Park; Jon Massey; Jessica Morely; Amir Mehrkar; Sebastian Bacon; David Evans; Peter Inglesby; Caroline E Morton; George Hickman; Simon Davy; Tom Ward; Iain Dillingham; Ben Goldacre; Miguel A Hernan; Jonathan AC Sterne,University of Bristol; Univeristy of Oxford; London School of Hygiene and Tropical Medicine; University of Bristol; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Univeristy of Oxford; University of Bristol; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Harvard University; University of Bristol,"BackgroundThe rate at which COVID-19 vaccine effectiveness wanes over time is crucial for vaccination policies, but is incompletely understood with conflicting results from different studies. + +MethodsThis cohort study, using the OpenSAFELY-TPP database and approved by NHS England, included individuals without prior SARS-CoV-2 infection assigned to vaccines priority groups 2-12 defined by the UK Joint Committee on Vaccination and Immunisation. We compared individuals who had received two doses of BNT162b2 or ChAdOx1 with unvaccinated individuals during six 4-week comparison periods, separately for subgroups aged 65+ years; 16-64 years and clinically vulnerable; 40-64 years and 18-39 years. We used Cox regression, stratified by first dose eligibility and geographical region and controlled for calendar time, to estimate adjusted hazard ratios (aHRs) comparing vaccinated with unvaccinated individuals, and quantified waning vaccine effectiveness as ratios of aHRs per-4-week period. The outcomes were COVID-19 hospitalisation, COVID-19 death, positive SARS-CoV-2 test, and non-COVID-19 death. + +FindingsThe BNT162b2, ChAdOx1 and unvaccinated groups comprised 1,773,970, 2,961,011 and 2,433,988 individuals, respectively. Waning of vaccine effectiveness was similar across outcomes and vaccine brands: e.g. in the 65+ years subgroup ratios of aHRs versus unvaccinated for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test ranged from 1.23 (95% CI 1.15-1.32) to 1.27 (1.20-1.34) for BNT162b2 and 1.16 (0.98-1.37) to 1.20 (1.14-1.27) for ChAdOx1. Despite waning, rates of COVID-19 hospitalisation and COVID-19 death were substantially lower among vaccinated individuals compared to unvaccinated individuals up to 26 weeks after second dose, with estimated aHRs <0.20 (>80% vaccine effectiveness) for BNT162b2, and <0.26 (>74%) for ChAdOx1. By weeks 23-26, rates of SARS-CoV-2 infection in fully vaccinated individuals were similar to or higher than those in unvaccinated individuals: aHRs ranged from 0.85 (0.78-0.92) to 1.53 (1.07-2.18) for BNT162b2, and 1.21 (1.13-1.30) to 1.99 (1.94-2.05) for ChAdOx1. + +InterpretationThe rate at which estimated vaccine effectiveness waned was strikingly consistent for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test, and similar across subgroups defined by age and clinical vulnerability. If sustained to outcomes of infection with the Omicron variant and to booster vaccination, these findings will facilitate scheduling of booster vaccination doses.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.03.18.22272607,2022-03-21,https://medrxiv.org/cgi/content/short/2022.03.18.22272607,"Multi-organ impairment and Long COVID: a 1-year prospective, longitudinal cohort study",Andrea Dennis; Daniel J Cuthbertson; Dan Wootton; Michael Crooks; Mark Gabbay; Nicole Eichert; Sofia Mouchti; Michele Pansini; Adriana Roca-Fernandez; Helena Thomaides-Brears; Matt Kelly; Matthew Robson; Lyth Hishmeh; Emily Attree; Melissa J Heightman; Rajarshi Banerjee; Amitava Banerjee,Perspectum Ltd; University of Liverpool; University of Liverpool; University of Hull; University of Liverpool; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Diagnostics; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Long COVID SoS; UKDoctors#Longcovid; UCLH; Perspectum Ltd; University College London,"ImportanceMulti-organ impairment associated with Long COVID is a significant burden to individuals, populations and health systems, presenting challenges for diagnosis and care provision. Standardised assessment across multiple organs over time is lacking, particularly in non-hospitalised individuals. ObjectiveTo determine the prevalence of organ impairment in Long COVID patients at 6 and at 12 months after initial symptoms and to explore links to clinical presentation. @@ -1602,7 +1581,6 @@ DiscussionApproximately 4 in 5 participants with prior PCR-confirmed infection w FundingThe research costs for the study have been supported by the MRC Grant Ref: MC_PC 19070 awarded to UCL on 30 March 2020 and MRC Grant Ref: MR/V028375/1 awarded on 17 August 2020. The study also received $15,000 of Facebook advertising credit to support a pilot social media recruitment campaign on 18th August 2020. The study also received funding from the UK Government Department of Health and Social Cares Vaccine Evaluation Programme to provide monthly Thriva antibody tests to adult participants. This study was supported by the Wellcome Trust through a Wellcome Clinical Research Career Development Fellowship to RA [206602].",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.02.01.22270235,2022-02-02,https://medrxiv.org/cgi/content/short/2022.02.01.22270235,Hospitalisation for COVID-19 predicts long lasting cerebrovascular impairment: A prospective observational cohort study,Kamen A Tsvetanov; Lennart R B Spindler; Emmanuel A Stamatakis; Virginia FJ Newcombe; Victoria C Lupson; Doris A Chatfield; Anne E Manktelow; Joanne G Outtrim; Anne Elmer; Nathalie Kingston; John R Bradley; Edward T Bullmore; James B Rowe; David K Menon; - the Cambridge NeuroCOVID Group; - the NIHR COVID-19 BioResource; - the Cambridge NIHR Clinical Research Facility; - the CITIID-NIHR BioResource COVID-19 collaboration,"Department of Clinilcal Neurosciences, University of Cambridge, Cambridge, UK; Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.; Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University Cambridge, Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University Cambridge, Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University Cambridge, Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University Cambridge, Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University Cambridge, Cambridge, UK.; Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK.; Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.; Department of Psychiatry, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.; Medical Research Council Cognition and Brain Sciences Unit, Department of Psychiatry, Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University Cambridge, Cambridge, UK.; -; -; -; -","Human coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has multiple neurological consequences, but its long-term effect on brain health is still uncertain. The cerebrovascular consequences of COVID-19 may also affect brain health. Here we assess cerebrovascular health in 45 hospitalised patients using the resting state fluctuation amplitudes (RSFA) from functional magnetic resonance imaging, in relation to disease severity and in contrast with 42 controls. Widespread changes in frontoparietal RSFA were related to the severity of the acute COVID-19 episode, as indexed by COVID-19 WHO Progression Scale, inflammatory and coagulatory biomarkers. This relationship was not explained by chronic cardiorespiratory dysfunction, age, or sex. Exploratory analysis suggests that the level of cerebrovascular dysfunction is associated with cognitive, mental, and physical health at follow-up. The principal findings were consistent across univariate and multivariate approaches. The results indicate chronic cerebrovascular impairment following severe acute COVID-19, with the potential for long-term consequences on cognitive function and mental wellbeing.",neurology,fuzzy,100,100 -medRxiv,10.1101/2022.01.31.22269194,2022-02-01,https://medrxiv.org/cgi/content/short/2022.01.31.22269194,"An outbreak of SARS-CoV-2 in a public-facing office in England, 2021",Barry Atkinson; Karin van Veldhoven; Ian Nicholls; Matthew Coldwell; Adam Clarke; Gillian Frost; Christina J Atchison; Amber I Raja; Allan M Bennett; Derek Morgan; Neil Pearce; Tony Fletcher; Elizabeth B Brickley; Yiqun Chen,UK Health Security Agency; London School of Hygiene & Tropical Medicine; UK Health Security Agency; Health and Safety Executive; Health and Safety Executive; Health and Safety Executive; UK Health Security Agency; London School of Hygiene & Tropical Medicine; UK Health Security Agency; Health and Safety Executive; London School of Hygiene & Tropical Medicine; UK Health Security Agency; London School of Hygiene & Tropical Medicine; Health and Safety Executive,"Between August-September 2021, an outbreak of SARS-CoV-2, with an attack rate of 55% (22/40 workers), occurred in a public-facing office in England. To identify workplace and worker-related risk factors, a comprehensive investigation involving surface sampling, environmental assessment, molecular and serological testing, and worker questionnaires was performed in September - October 2021. The results affirm the utility of surface sampling to identify SARS-CoV-2 control deficiencies and the importance of evolving, site-specific risk assessments with layered COVID-19 mitigation strategies.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.01.28.22270013,2022-01-29,https://medrxiv.org/cgi/content/short/2022.01.28.22270013,Agility and sustainability: A qualitative evaluation of COVID-19 Non-pharmaceutical Interventions (NPIs) in the UK logistics sector,Hua Wei; Sarah A Daniels; Carl A Whitfield; Yang Han; David W Denning; Ian Hall; Martyn Regan; Arpana Verma; Martie J van Tongeren,The University of Manchester; The University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester,"BackgroundThe emergence of SARS-CoV-2 triggered a chain of public health responses that radically changed our way of living and working. Non-healthcare sectors, such as the logistics sector, play a key role in such responses. This research aims to qualitatively evaluate the non-pharmaceutical interventions (NPIs) implemented in the UK logistics sector during the COVID-19 pandemic. MethodsWe conducted nine semi-structured interviews in July-August 2020 and May-June 2021. In total 11 interviewees represented six companies occupying a range of positions in the UKs logistics sector, including takeaway food delivery, large and small goods delivery and home appliance installation, and logistics technology providers. Inductive thematic analysis was completed using NVivo12 to generate emerging themes and subthemes. Themes/subthemes relevant to interventions were mapped deductively onto an adapted Hierarchy of Control (HoC) framework, focusing on delivery workers. Themes/subthemes relevant to the process of implementation were analyzed to understand the barriers and facilitators of rapid responses. @@ -1632,13 +1610,6 @@ MethodsWe developed a rapid online survey of risk mitigation behaviours during t ResultsOver 95% of survey respondents (NALSPAC=2,686 and NTwins=6,155) reported some risk mitigation behaviours, with vaccination and using home testing kits reported most frequently. Less than half of those respondents reported that their behaviour was due to ""plan B"". We estimate that without risk mitigation behaviours, the Omicron variant is consistent with an effective reproduction number between 2.5 and 3.5. Due to the reduced vaccine effectiveness against infection with the Omicron variant, our modelled estimates suggest that between 55% and 60% of the English population could be infected during the current wave, translating into between 15,000 and 46,000 cumulative deaths, depending on assumptions about vaccine effectiveness. We estimate that voluntary risk reduction measures could reduce the effective reproduction number to between 1.8 and 2.2 and reduce the cumulative number of deaths by up to 24%. ConclusionsWe conclude that voluntary measures substantially reduce the projected impact of the SARS-CoV-2 Omicron variant, but that voluntary measures alone would be unlikely to completely control transmission.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2022.01.26.22269877,2022-01-27,https://medrxiv.org/cgi/content/short/2022.01.26.22269877,The impacts of increased global vaccine sharing on the COVID-19 pandemic; a retrospective modelling study,Sam Moore; Edward M Hill; Louise J Dyson; Michael J Tildesley; Matt J Keeling,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"BackgroundThe SARS-CoV-2 pandemic has generated considerable morbidity and mortality world-wide. While the protection offered by vaccines (and booster doses) offers a method of mitigating the worst effects, by the end of 2021 the distribution of vaccine was highly heterogeneous with some countries achieving over 90% coverage in adults by the end of 2021, while others have less than 2%. In part, this is due to the availability of sufficient vaccine, although vaccine hesitancy also plays a role. - -MethodsWe use an age-structured model of SARS-CoV-2 dynamics, matched to national data from 152 countries, to investigate the global impact of different vaccine sharing protocols during 2021. We assume a direct relationship between the emergence of variants with increased transmissibility and the cumulative amount of global infection, such that lower global prevalence leads to a lower reproductive number within each country. We compare five vaccine sharing scenarios, from the current situation, through sharing once a particular within-country threshold is reached (e.g. all over 40s have received 2 doses), to full sharing where all countries achieve equal age-dependent vaccine deployment. - -FindingsCompared to the observed distribution of vaccine uptake, we estimate full vaccine sharing would have generated a 1.5% (PI -0.1 - 4.5%) reduction in infections and a 11.3% (PI 0.6 - 23.2%) reduction in mortality globally by January 2022. The greatest benefit of vaccine sharing would have been experienced by low and middle income countries, who see an average 5.2% (PI 2.5% - 10.4%) infection reduction and 26.8% (PI 24.1% - 31.3%) mortality reduction. Many high income countries, that have had high vaccine uptake (most notably Canada, Chile, UK and USA), suffer increased infections and mortality under most of the sharing protocols investigated, assuming no other counter measures had been taken. However, if reductions in vaccine supply in these countries had been offset by prolonged use of non-pharmaceutical intervention measures, we predict far greater reductions in global infection and mortality of 64.5% (PI 62.6% - 65.4%) and 62.8% (PI 44.0% - 76.3%), respectively. - -InterpretationBy itself, our results suggest that although more equitable vaccine distribution would have had limited impact on overall infection numbers, vaccine sharing would have substantially reduced global mortality by providing earlier protection of the most vulnerable. If increased vaccine sharing from high income nations had been combined with slower easing of non pharmaceutical interventions to compensate for this, a large reduction in both infection and mortality globally would be expected, confounded by a lower risk of new variants arising.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.01.26.22269885,2022-01-27,https://medrxiv.org/cgi/content/short/2022.01.26.22269885,SARS-CoV-2 anti-spike antibody levels following second dose of ChAdOx1 nCov-19 or BNT162b2 in residents of long-term care facilities in England (VIVALDI),Oliver Stirrup; Maria Krutikov; Gokhan Tut; Tom Palmer; David Bone; Rachel Bruton; Christopher Fuller; Borscha Azmi; Tara Lancaster; Panagiota Sylla; Nayandeep Kaur; Eliska Spalkova; Christopher Bentley; Umayr Amin; Azar Jadir; Samuel Hulme; Rebecca Giddings; Hadjer Nacer-Laidi; Verity Baynton; Aidan Irwin-Singer; Andrew Hayward; Paul Moss; Andrew Copas; Laura Shallcross,"University College London; University College London; University of Birmingham, Medical School; UCL Institute for Global Health; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; UCL Institute of Health Informatics; UCL Institute of Health Informatics; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; Institute of Immunology and Immunotherapy, University of Birmingham; UCL Institute of Health Informatics; UCL Institute of Health Informatics; UK Department of Health and Social Care; UK Department of Health and Social Care; UCL; University of Birmingham; UCL Institute for Global Health; UCL","BackgroundGeneral population studies have shown strong humoral response following SARS-CoV-2 vaccination with subsequent waning of anti-spike antibody levels. Vaccine-induced immune responses are often attenuated in frail and older populations such as Long-Term Care Facility (LTCF) residents but published data are scarce. MethodsVIVALDI is a prospective cohort study in England which links serial blood sampling in LTCF staff and residents to routine healthcare records. We measured quantitative titres of SARS-CoV-2 anti-spike antibodies in residents and staff following second vaccination dose with ChAdOx1 nCov-19 (Oxford-AstraZeneca) or BNT162b2 (Pfizer-BioNTech). We investigated differences in peak antibody levels and rates of decline using linear mixed effects models. @@ -1754,6 +1725,7 @@ MethodTrial emulation was conducted by pooling results from six cohorts whose re ResultsAcross six cohorts, there were a total of 21,283 participants who were eligible and vaccinated with either ChAdOx1 (n = 13,813) or BNT162b2 (n = 7,470) with a median follow-up time of 266 days (IQR: 235 - 282). By November 12th 2021, 750 (5.4%) adults who had ChAdOx1 as their vaccine experienced a SARS-CoV-2 infection, compared to 296 (4.0%) who had BNT162b2. We found that people who received ChAdOx1 vaccinations had 10.54 per 1000 people higher cumulative incidence for SARS-CoV-2 infection compared to BNT162b2 for infections during a maximum of 315 days of follow-up. When adjusted for age at vaccination, sex, minority ethnic status, index of multiple deprivation, and clinical vulnerability status, we found a pooled adjusted hazard ratio of 1.35 [HR: 1.35, 95%CI: 1.15 - 1.58], demonstrating a 35% increase in SARS-CoV-2 infections in people who received ChAdOx1 compared to BNT162b2. DiscussionWe found evidence of greater effectiveness of receiving BNT162b2 compared to ChAdOx1 vaccines against SARS-CoV-2 infection in England and Wales during a time period when Delta became the most prevalent variant of concern. Our findings demonstrate the importance of booster (third) doses to maintain protection and suggest that these should be prioritised to those who received ChAdOx1 as their primary course.",epidemiology,fuzzy,100,100 +bioRxiv,10.1101/2021.12.17.473248,2021-12-21,https://biorxiv.org/cgi/content/short/2021.12.17.473248,"SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion",Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta,"University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge","The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.",microbiology,fuzzy,100,100 medRxiv,10.1101/2021.12.20.21268098,2021-12-21,https://medrxiv.org/cgi/content/short/2021.12.20.21268098,"Therapies for Long COVID in non-hospitalised individuals - from symptoms, patient-reported outcomes, and immunology to targeted therapies (The TLC Study): Study protocol",Shamil Haroon; Krishnarajah Nirantharakumar; Sarah Hughes; Anuradhaa Subramanian; Olalekan Lee Aiyegbusi; Elin Haf Davies; Puja Myles; Tim Williams; Grace Turner; Joht Singh Chandan; Christel McMullan; Janet Lord; David Wraith; Kirsty McGee; Alastair Denniston; Tom Taverner; Louise Jackson; Elizabeth Sapey; Georgios Gkoutos; Krishna Gokhale; Edward Leggett; Clare Iles; Christopher Frost; Gary McNamara; Amy Bamford; Tom Marshall; Dawit Zemedikun; Gary Price; Steven Marwaha; Nikita Simms-Williams; Kirsty Brown; Anita Walker; Karen Jones; Karen Matthews; Jennifer Camaradou; Michael Saint-Cricq; Sumita Kumar; Yvonne Alder; David Stanton; Lisa Agyen; Megan Baber; Hannah Blaize; Melanie Calvert,University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University ofBirmingham; University of Birmingham; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; Aparito; Aparito; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; N/A; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; University ofBirmingham,"IntroductionIndividuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies. Methods and analysisA cohort of 4000 non-hospitalised individuals with a past COVID-19 diagnosis and 1000 matched controls will be selected from anonymised primary care records from the Clinical Practice Research Datalink (CPRD) and invited by their general practitioners to participate on a digital platform (Atom5). Individuals will report symptoms, quality of life, work capability, and patient reported outcome measures. Data will be collected monthly for one year. @@ -1838,6 +1810,13 @@ Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe systematically s Added value of this studyIn a diverse population of adults post-hospital admission with COVID-19, our large UK prospective multi-centre study reports several novel findings: the minority felt fully recovered at one year with minimal recovery from five months across any health domain; female sex and obesity are associated with being less likely to feel fully recovered at one year; several inflammatory mediators were increased in individuals with the most severe physical, mental health, and cognitive impairments compared to individuals with milder ongoing impairments. Implications of all the available evidenceBoth pharmacological and non-pharmacological interventions are urgently needed to improve the ongoing burden following hospitalisation for COVID-19 both for individuals and healthcare systems; our findings support the use of a precision medicine approach with potential treatable traits of systemic inflammation and obesity.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.12.13.21267368,2021-12-15,https://medrxiv.org/cgi/content/short/2021.12.13.21267368,Acute COVID-19 severity and 16-month mental morbidity trajectories in patient populations of six nations,Ingibjorg Magnusdottir; Aniko Lovik; Anna Bara Unnarsdottir; Daniel L. McCartney; Helga Ask; Kadri Koiv; Lea Arregui Nordahl Christoffersen; Sverre Urnes Johnson; Andrew M McIntosh; Anna K. Kahler; Archie Campbell; Arna Hauksdottir; Chloe Fawns-Ritchie; Christian Erikstrup; Dorte Helenius; Drew Altschul; Edda Bjork Thordardottir; Elias Eythorsson; Emma M. Frans; Gunnar Tomasson; Harpa Lind Jonsdottir; Harpa Runarsdottir; Henrik Hjalgrim; Hronn Hardardottir; Juan Gonzalez-Hijon; Karina Banasik; Khoa Manh Dinh; Li Lu; Lili Milani; Lill Trogstad; Maria Didriksen; Omid V. Ebrahimi; Patrick F. Sullivan; Per Minor Magnus; Qing Shen; Ragnar Nesvag; Reedik Magi; Runolfur Palsson; Sisse Rye Ostrowski; Thomas Werge; Asle Hoffart; David J. Porteous; Fang Fang; Johanna Jakobsdottir; Kelli Lehto; Ole A. Andreassen; Ole B.V. Pedersen; Thor Aspelund; Unnur Anna Valdimarsdottir,"Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Division of Psychiatry, University of Edinburgh, Edinburgh, UK; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Edinburgh, Edinburgh, UK; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Faculty of Psychology, University of Iceland School of Health Sciences, Reykjavik, Iceland; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Danish Cancer Society Research Center, Copenhagen, Denmark; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA; Centre of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway.; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Clinical Immunology, Zealand University Hospital, Denmark; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland","BACKGROUNDThe aim of this multinational study was to assess the development of adverse mental health symptoms among individuals diagnosed with COVID-19 in the general population by acute infection severity up to 16 months after diagnosis. + +METHODSParticipants consisted of 247 249 individuals from seven cohorts across six countries (Denmark, Estonia, Iceland, Norway, Scotland, and Sweden) recruited from April 2020 through August 2021. We used multivariable Poisson regression to contrast symptom-prevalence of depression, anxiety, COVID-19 related distress, and poor sleep quality among individuals with and without a diagnosis of COVID-19 at entry to respective cohorts by time (0-16 months) from diagnosis. We also applied generalised estimating equations (GEE) analysis to test differences in repeated measures of mental health symptoms before and after COVID-19 diagnosis among individuals ever diagnosed with COVID-19 over time. + +FINDINGSA total of 9979 individuals (4%) were diagnosed with COVID-19 during the study period and presented overall with a higher symptom burden of depression (prevalence ratio [PR] 1{middle dot}18, 95% confidence interval [95% CI] 1{middle dot}03-1{middle dot}36) and poorer sleep quality (1{middle dot}13, 1{middle dot}03-1{middle dot}24) but not with higher levels of symptoms of anxiety or COVID-19 related distress compared with individuals without a COVID-19 diagnosis. While the prevalence of depression and COVID-19 related distress attenuated with time, the trajectories varied significantly by COVID-19 acute infection severity. Individuals diagnosed with COVID-19 but never bedridden due to their illness were consistently at lower risks of depression and anxiety (PR 0{middle dot}83, 95% CI 0{middle dot}75-0{middle dot}91 and 0{middle dot}77, 0{middle dot}63-0{middle dot}94, respectively), while patients bedridden for more than 7 days were persistently at higher risks of symptoms of depression and anxiety (PR 1{middle dot}61, 95% CI 1{middle dot}27-2{middle dot}05 and 1{middle dot}43, 1{middle dot}26-1{middle dot}63, respectively) throughout the 16-month study period. + +CONCLUSIONAcute infection severity is a key determinant of long-term mental morbidity among COVID-19 patients.",public and global health,fuzzy,100,92 medRxiv,10.1101/2021.12.14.21267460,2021-12-15,https://medrxiv.org/cgi/content/short/2021.12.14.21267460,Differential Risk of SARS-CoV-2 Infection by Occupation: Evidence from the Virus Watch prospective cohort study in England and Wales,Sarah Beale; Susan J Hoskins; Thomas Edward Byrne; Erica Wing Lam Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan MD Navaratnam; Vincent Nguyen; Parth Patel; Alexei Yavlinsky; Anne Johnson; Martie Van Tongeren; Robert W Aldridge; Andrew Hayward,University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University of Manchester; University College London; University College London,"BackgroundWorkers differ in their risk of SARS-CoV-2 infection according to their occupation, but the direct contribution of occupation to this relationship is unclear. This study aimed to investigate how infection risk differed across occupational groups in England and Wales up to April 2022, after adjustment for potential confounding and stratification by pandemic phase. MethodsData from 15,190 employed/self-employed participants in the Virus Watch prospective cohort study were used to generate risk ratios for virologically- or serologically-confirmed SARS-CoV-2 infection using robust Poisson regression, adjusting for socio-demographic and health-related factors and non-work public activities. We calculated attributable fractions (AF) amongst the exposed for belonging to each occupational group based on adjusted risk ratios (aRR). @@ -1947,6 +1926,13 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSTo identify existin Added value of this studyUsing data from one of the largest UK citizen science epidemiological initiatives, we describe and compare illness (symptom duration, burden, profile, risk of long illness, and hospital attendance) in symptomatic community-based adults presenting when either the Alpha or Delta variant was the predominant circulating strain of SARS-CoV-2 in the UK. We assess evidence of transmission, reinfection, and vaccine effectiveness. Our data show that the seven most common symptoms with Delta infection were the same as with Alpha infection. Risks of illness duration [≥]7 days and [≥]28 days, and of requiring hospital care, were not increased. In line with previous research, we found increased transmissibility of Delta vs. previous variants; and no evidence of increased re-infection rates. Our data support high vaccine efficacy of BNT162b2 and ChAdOx1 nCoV-19 formulations against Delta variant infection. Overall, our study adds quantitative information regarding meaningful clinical differences in COVID-19 due to Delta vs. other variants. Implications of all the available evidenceOur observational data confirm that COVID-19 disease in UK in adults is generally comparable to infection with the Alpha variant, including in elderly individuals. Our data contribute to epidemiological surveillance from the wider UK population and may capture information from COVID-19 presentation within the community that might be missed in healthcare-based surveillance. Our data may be useful in informing healthcare service planning, vaccination policies, and measures for social protection.",epidemiology,fuzzy,94,100 +medRxiv,10.1101/2021.11.22.21266692,2021-11-24,https://medrxiv.org/cgi/content/short/2021.11.22.21266692,Serological responses to COVID-19 booster vaccine in England,Georgina Ireland; Heather Whitaker; Shamez N Ladhani; Frances Baawuah; Vani Subbarao; Ezra Linley; Lenesha Warrener; Michelle O'Brien; Corrine Whillock; Paul Moss; Mary E Ramsay; Gayatri Amirthalingam; Kevin E Brown,"UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; Brondesbury Medical Centre, Kilburn, London, United Kingdom; UK Health Security Agency; University of Birmingham; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency","IntroductionThere are limited data on immune responses after COVID-19 vaccine boosters in individuals receiving primary immunisation with BNT162b2 (Pfizer-BioNTech) or AZD1222 (AstraZeneca). + +MethodsA prospective, cohort study to assess SARS-CoV-2 antibody responses before and after booster vaccination with BNT162b2 in adults receiving either (i) two BNT162b2 doses <30 days apart (BNT162b2-control), (ii) two BNT162b2 doses [≥]30 days apart (BNT162b2-extended) or (iii) two AZD1222 doses [≥]30 days apart (AZD1222-extended) in London, England. SARS-CoV-2 spike protein antibody geometric mean titres (GMTs) before and 2-4 weeks after booster were compared. + +ResultsOf 750 participants, 626 provided serum samples for up to 38 weeks after their second vaccine dose. Antibody GMTs peaked at 2-4 weeks after the second dose, before declining by 68% at 36-38 weeks after dose 2 for BNT162b2-control participants, 85% at 24-29 weeks for BNT162b2-extended participants and 78% at 24-29 weeks for AZD1222-extended participants. Antibody GMTs was highest in BNT162b2-extended participants (942 [95%CI, 797-1113]) than AZD1222-extended (183 [124-268]) participants at 24-29 weeks or BNT162b2-control participants at 36-38 weeks (208; 95%CI, 150-289). At 2-4 weeks after booster, GMTs were significantly higher than after primary vaccination in all three groups: 18,104 (95%CI, 13,911-23,560; n=47) in BNT162b2-control (76.3-fold), 13,980 (11,902-16,421; n=118) in BNT162b2-extended (15.9-fold) and 10,799 (8,510-13,704; n=43) in AZD1222-extended (57.2-fold) participants. BNT162b2-control participants (median:262 days) had a longer interval between primary and booster doses than BNT162b2-extended or AZD1222-extended (both median:186 days) participants. + +ConclusionsWe observed rapid serological responses to boosting with BNT162b2, irrespective of vaccine type or schedule used for primary immunisation, with higher post-booster responses with longer interval between primary immunisation and boosting. Boosters will not only provide additional protection for those at highest risk of severe COVID-19 but also prevent infection and, therefore, interrupt transmission, thereby reducing infections rates in the population. Ongoing surveillance will be important for monitoring the duration of protection after the booster.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.11.22.21266512,2021-11-24,https://medrxiv.org/cgi/content/short/2021.11.22.21266512,Association of COVID-19 with arterial and venous vascular diseases: a population-wide cohort study of 48 million adults in England and Wales,Rochelle Knight; Venexia Walker; Samantha Ip; Jennifer A Cooper; Thomas Bolton; Spencer Keene; Rachel Denholm; Ashley Akbari; Hoda Abbasizanjani; Fatemeh Torabi; Efosa Omigie; Sam Hollings; Teri-Louise North; Renin Toms; Emanuele Di Angelantonio; Spiros Denaxas; Johan H Thygesen; Christopher Tomlinson; Ben Bray; Craig J Smith; Mark Barber; George Davey Smith; Nishi Chaturvedi; Cathie Sudlow; William N Whiteley; Angela Wood; Jonathan A C Sterne; - CVD-COVID-UK/COVID-IMPACT consortium; - Longitudinal Health and Wellbeing COVID-19 National Core Study,University of Bristol; University of Bristol; University of Cambridge; University of Bristol; University of Cambridge; University of Cambridge; University of Bristol; Swansea University; Swansea University; Swansea University; NHS Digital; NHS Digital; University of Bristol; University of Bristol; University of Cambridge; University College London; University College London; University College London; Kings College London; University of Manchester; Glasgow Caledonian University; University of Bristol; University College London; Health Data Research UK; University of Edinburgh; University of Cambridge; University of Bristol; ; ,"ImportanceThe long-term effects of COVID-19 on the incidence of vascular diseases are unclear. ObjectiveTo quantify the association between time since diagnosis of COVID-19 and vascular disease, overall and by age, sex, ethnicity, and pre-existing disease. @@ -2020,19 +2006,6 @@ FindingsComparing the least deprived and predominantly White areas with most dep InterpretationAt the area level, IMD and BAME% are both associated with an increased COVID-19 burden in terms of prevalence (disease spread) and test positivity (disease monitoring), and the strength of association varies over the course of the pandemic. The consistency of results across the two outcome measures suggests that community level characteristics such as deprivation and ethnicity have a differential impact on disease exposure or susceptibility rather than testing access and habits. FundingsEPSRC, MRC, The Alan Turing Institute, NIH, UKHSA, DHSC, NIHR",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.11.08.21265312,2021-11-09,https://medrxiv.org/cgi/content/short/2021.11.08.21265312,"Understanding COVID-19 trajectories from a nationwide linked electronic health record cohort of 56 million people: phenotypes, severity, waves & vaccination",Johan H Thygesen; Christopher R Tomlinson; Sam Hollings; Mehrdad A Mizani; Alex Handy; Ashley Akbari; Amitava Banerjee; Jennifer A Cooper; Alvina G Lai; Kezhi Li; Bilal A Mateen; Naveed Sattar; Reecha Sofat; Ana Torralbo; Honghan Wu; Angela Wood; Jonathan AC Sterne; Christina Pagel; William Whiteley; Cathie Sudlow; Harry Hemingway; Spiros Denaxas; - CVD-COVID-UK Consortium,"Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; NHS Digital, Leeds, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Population Data Science and Health Data Research UK, Swansea University, Swansea, UK; Institute of Health Informatics, University College London, London, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; The Wellcome Trust, London, UK; Institute of Cardiovascular & Medical Sciences, University of Glasgow, Glasgow, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Clinical Operational Research Unit, University College London, London, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; ","BackgroundUpdatable understanding of the onset and progression of individuals COVID-19 trajectories underpins pandemic mitigation efforts. In order to identify and characterize individual trajectories, we defined and validated ten COVID-19 phenotypes from linked electronic health records (EHR) on a nationwide scale using an extensible framework. - -MethodsCohort study of 56.6 million people in England alive on 23/01/2020, followed until 31/05/2021, using eight linked national datasets spanning COVID-19 testing, vaccination, primary & secondary care and death registrations data. We defined ten COVID-19 phenotypes reflecting clinically relevant stages of disease severity using a combination of international clinical terminologies (e.g. SNOMED-CT, ICD-10) and bespoke data fields; positive test, primary care diagnosis, hospitalisation, critical care (four phenotypes), and death (three phenotypes). Using these phenotypes, we constructed patient trajectories illustrating the transition frequency and duration between phenotypes. Analyses were stratified by pandemic waves and vaccination status. - -FindingsWe identified 3,469,528 infected individuals (6.1%) with 8,825,738 recorded COVID-19 phenotypes. Of these, 364,260 (11%) were hospitalised and 140,908 (4%) died. Of those hospitalised, 38,072 (10%) were admitted to intensive care (ICU), 54,026 (15%) received non-invasive ventilation and 21,404 (6%) invasive ventilation. Amongst hospitalised patients, first wave mortality (30%) was higher than the second (23%) in non-ICU settings, but remained unchanged for ICU patients. The highest mortality was for patients receiving critical care outside of ICU in wave 1 (51%). 13,083 (9%) COVID-19 related deaths occurred without diagnoses on the death certificate, but within 30 days of a positive test while 10,403 (7%) of cases were identified from mortality data alone with no prior phenotypes recorded. We observed longer patient trajectories in the second pandemic wave compared to the first. - -InterpretationOur analyses illustrate the wide spectrum of severity that COVID-19 displays and significant differences in incidence, survival and pathways across pandemic waves. We provide an adaptable framework to answer questions of clinical and policy relevance; new variant impact, booster dose efficacy and a way of maximising existing data to understand individuals progression through disease states. - -Research in ContextO_ST_ABSEvidence before the studyC_ST_ABSWe searched PubMed on October 14, 2021, for publications with the terms ""COVID-19"" or ""SARS-CoV-2"", ""severity"", and ""electronic health records"" or ""EHR"" without date or language restrictions. Multiple studies explore factors associated with severity of COVID-19 infection, and model predictions of outcome for hospitalised patients. However, most work to date focused on isolated facets of the healthcare system, such as primary or secondary care only, was conducted in subpopulations (e.g. hospitalised patients) of limited sample size, and often utilized dichotomised outcomes (e.g. mortality or hospitalisation) ignoring the full spectrum of disease. We identified no studies which comprehensively detailed severity of infections while describing disease severity across pandemic waves, vaccination status, and patient trajectories. - -Added value of this studyTo our knowledge, this is the first study providing a comprehensive view of COVID-19 across pandemic waves using national data and focusing on severity, vaccination, and patient trajectories. Drawing on linked electronic health record (EHR) data on a national scale (56.6 million people alive and registered with GP in England), we describe key demographic factors, frequency of comorbidities, impact of the two main waves in England, and effect of full vaccination on COVID-19 severities. Additionally, we identify and describe patient trajectory networks which illustrate the main transition pathways of COVID-19 patients in the healthcare system. Finally, we provide reproducible COVID-19 phenotyping algorithms reflecting clinically relevant stages of disease severity i.e. positive tests, primary care diagnoses, hospitalisation, critical care treatments (e.g. ventilatory support) and mortality. - -Implications of all the available evidenceThe COVID-19 phenotypes and trajectory analysis framework outlined produce a reproducible, extensible and repurposable means to generate national-scale data to support critical policy decision making. By modelling patient trajectories as a series of interactions with healthcare systems, and linking these to demographic and outcome data, we provide a means to identify and prioritise care pathways associated with adverse outcomes and highlight healthcare system touch points which may act as tangible targets for intervention.",public and global health,fuzzy,100,100 medRxiv,10.1101/2021.11.05.21265977,2021-11-09,https://medrxiv.org/cgi/content/short/2021.11.05.21265977,"Waning, Boosting and a Path to Endemicity for SARS-CoV-2.",Matt J Keeling; Amy C Thomas; Edward M Hill; Robin N Thompson; Louise Dyson; Michael Tildesley; Sam Moore,University of Warwick; University of Bristol; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"In many countries, an extensive vaccination programme has substantially reduced the public-health impact of SARS-CoV-2, limiting the number of hospital admissions and deaths compared to an unmitigated epidemic. Ensuring a low-risk transition from the current situation to one in which SARS-CoV-2 is endemic requires maintenance of high levels of population immunity. The observed waning of vaccine efficacy over time suggests that booster doses may be required to maintain population immunity especially in the most vulnerable groups. Here, using data and models for England, we consider the dynamics of COVID-19 over a two-year time-frame, and the role that booster vaccinations can play in mitigating the worst effects. We find that boosters are necessary to suppress the imminent wave of infections that would be generated by waning vaccine efficacy. Projecting further into the future, the optimal deployment of boosters is highly sensitive to their long-term action. If protection from boosters wanes slowly (akin to protection following infection) then a single booster dose to the over 50s may be all that is needed over the next two-years. However, if protection wanes more rapidly (akin to protection following second dose vaccination) then annual or even biannual boosters are required to limit subsequent epidemic peaks an reduce the pressure on public health services.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.11.05.21264590,2021-11-08,https://medrxiv.org/cgi/content/short/2021.11.05.21264590,Prone positioning of patients with moderate hypoxia due to COVID-19: A multicenter pragmatic randomized trial,Mike Fralick; Michael Colacci; Laveena Munshi; Kevin Venus; Lee Fidler; Haseena Hussein; Karen Britto; Rob Fowler; Bruno da Costa; Irfan Dhalla; Richard Dunbar-Yaffe; Laura Branfield Day; Thomas MacMillan; Jonathan Zipursky; Travis Carpenter; Terence Tang; Amanda Cooke; Rachel Hensel; Melissa Bregger; Alexis Gordon; Erin Worndl; Stephanie Go; Keren Mandelzweig; Lana Castellucci; Daniel Tamming; Fahad Razak; Amol Verma; - COVID PRONE Investigators,University of Toronto; University of Toronto - Department of Medicine; Sinai Health System; University Health Network; Sunnybrook Health Sciences Centre; William Osler Health System; William Osler Health System; Sunnybrook Health Sciences Centre; St. Michael's Hospital; Unity Health Toronto; University Health Network; University of Toronto; University of Toronto; Sunnybrook Health Sciences Centre; University of Toronto; Trillium Health Partners; Beth Israel Deaconess Medical Center; Beth Israel Deaconess Medical Center; Northwestern University Feinberg School of Medicine; Scarborough Health Network; Scarborough Health Network; Humber River Hospital; Humber River Hospital; Ottawa Hospital Research Institute; Unity Health Toronto; University of Toronto; University of Toronto; ,"ObjectivesTo assess the effectiveness of prone positioning to reduce the risk of death or respiratory failure in non-critically ill patients hospitalized with COVID-19 @@ -2269,6 +2242,7 @@ Methods and findingsWe performed a rapid systematic review, searching Medline, E 49 observational studies (15 peer-reviewed papers and 34 preprints) reported primary outcomes for eight drug groups hypothesised to be deleterious. Meta-analysis showed that acute inpatient corticosteroid use was associated with increased mortality (OR 2.22, 95% CI 1.26-3.90), however this result appeared to have been biased by confounding via indication. One subgroup analysis indicated an association between immunosuppressant use and susceptibility to COVID-19 among case control and cross-sectional studies (OR 1.29, 95% CI 1.19-1.40) but this was not found with cohort studies (OR 1.11, 95% CI 0.86-1.43). Studies which adjusted for multiple confounders showed that people taking angiotensin-converting-enzyme inhibitors (ACEIs) or angiotensin-II-receptor blockers (ARBs) required a lower level of care (OR 0.85, 95% CI 0.74-0.98). Furthermore, studies which combined these two drug groups in their analysis demonstrated an association with a lower mortality (OR 0.68, 95% CI 0.55-0.85). ConclusionsWe found minimal high quality or consistent evidence that any drug groups increase susceptibility, severity or mortality in COVID-19. Converse to initial hypotheses, we found some evidence that regular use of ACEIs and ARBs prior to infection may be effective in reducing the level of care required, such as requiring intensive care, in patients with COVID-19.",pharmacology and therapeutics,fuzzy,100,100 +medRxiv,10.1101/2021.09.13.21263487,2021-09-16,https://medrxiv.org/cgi/content/short/2021.09.13.21263487,SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population,Jia Wei; Koen B. Pouwels; Nicole Stoesser; Philippa C. Matthews; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John I Bell; John N Newton; Jeremy Farrar; Alison Howarth; Brian D. Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W. Crook; Tim E.A. Peto; A.Sarah Walker; David W. Eyre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.09.13.21262360,2021-09-16,https://medrxiv.org/cgi/content/short/2021.09.13.21262360,Efficacy of two doses of COVID-19 vaccine against severe COVID-19 in those with risk conditions and residual risk to the clinically extremely vulnerable: the REACT-SCOT case-control study,Paul M McKeigue; David McAllister; Chris Robertson; Sharon J Hutchinson; Stuart McGurnaghan; Diane Stockton; Helen M Colhoun,University of Edinburgh; University of Glasgow; University of Strathclyde; Glasgow Caledonian University; University of Edinburgh; Public Health Scotland; University of Edinburgh,"ObjectivesTo determine whether COVID-19 efficacy varies with clinical risk category and to investigate risk factors for severe COVID-19 in those who have received two doses of vaccine. DesignMatched case-control study (REACT-SCOT). @@ -2351,13 +2325,6 @@ MethodsWe analysed prevalence trends and their drivers using reverse transcripti ResultsWe observed sustained exponential growth with an average doubling time in round 13 of 25 days (lower Credible Interval of 15 days) and an increase in average prevalence from 0.15% (0.12%, 0.18%) in round 12 to 0.63% (0.57%, 0.18%) in round 13. The rapid growth across and within rounds appears to have been driven by complete replacement of Alpha variant by Delta, and by the high prevalence in younger less-vaccinated age groups, with a nine-fold increase between rounds 12 and 13 among those aged 13 to 17 years. Prevalence among those who reported being unvaccinated was three-fold higher than those who reported being fully vaccinated. However, in round 13, 44% of infections occurred in fully vaccinated individuals, reflecting imperfect vaccine effectiveness against infection despite high overall levels of vaccination. Using self-reported vaccination status, we estimated adjusted vaccine effectiveness against infection in round 13 of 49% (22%, 67%) among participants aged 18 to 64 years, which rose to 58% (33%, 73%) when considering only strong positives (Cycle threshold [Ct] values < 27); also, we estimated adjusted vaccine effectiveness against symptomatic infection of 59% (23%, 78%), with any one of three common COVID-19 symptoms reported in the month prior to swabbing. Sex (round 13 only), ethnicity, household size and local levels of deprivation jointly contributed to the risk of higher prevalence of swab-positivity. DiscussionFrom end May to beginning July 2021 in England, where there has been a highly successful vaccination campaign with high vaccine uptake, infections were increasing exponentially driven by the Delta variant and high infection prevalence among younger, unvaccinated individuals despite double vaccination continuing to effectively reduce transmission. Although slower growth or declining prevalence may be observed during the summer in the northern hemisphere, increased mixing during the autumn in the presence of the Delta variant may lead to renewed growth, even at high levels of vaccination.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.09.03.21263083,2021-09-07,https://medrxiv.org/cgi/content/short/2021.09.03.21263083,Suicide and self-harm in low- and middle- income countries during the COVID-19 pandemic: A systematic review,Duleeka Kniipe; Ann John; Prianka Padmanathan; Emily Eyles; Dana Dekel; Julian Higgins; Jason Bantjes; Rakhi Dandona; Catherine Macleod-Hall; Luke A McGuinness; Lena Schmidt; Roger Webb; David Gunnell,"Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; South Asian Clinical Toxicology Research Collaboration, Faculty of Medic; Population Data Science, Swansea University Medical School, Swansea, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; Population Data Science, Swansea University Medical School, Swansea, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; National Institute of Health Research Biomedical Research Centre, Unive; Institute for Life Course Health Research, Department of Global Health, Faculty of medicine and Health Sciences, Stellenbosch University, South Africa.; Public Health Foundation of India, Gurugram, India; Institute for Health Metrics and Evaluation, University of Washington, Seattle, USA; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; Sciome LLC, Research Triangle Park, NC, United States.; Division of Psychology & Mental Health, University of Manchester, Manchester, UK; National Institute of Health Research Greater Manchester Patient Safety Transl; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; National Institute of Health Research Biomedical Research Centre, Unive","There is widespread concern over the potential impact of the COVID-19 pandemic on suicide and self-harm globally, particularly in low- and middle-income countries (LMIC) where the burden of these behaviours is greatest. We synthesised the evidence from the published literature on the impact of the pandemic on suicide and self-harm in LMIC. - -This review is nested within a living systematic review that continuously identifies published evidence (all languages) through a comprehensive automated search of multiple databases (PubMed; Scopus; medRxiv, PsyArXiv; SocArXiv; bioRxiv; the WHO COVID-19 database; and the COVID-19 Open Research Dataset by Semantic Scholar (up to 11/2020), including data from Microsoft Academic, Elsevier, arXiv and PubMed Central.) All articles identified by the 4th August 2021 were screened. Papers reporting on data from a LMIC and presenting evidence on the impact of the pandemic on suicide or self-harm were included. - -A total of 22 studies from LMIC were identified representing data from 12 countries. There was an absence of data from Africa. The reviewed studies mostly report on the early months of COVID-19 and were generally methodologically poor. Few studies directly assessed the impact of the pandemic. The most robust evidence, from time-series studies, indicate either a reduction or no change in suicide and self-harm behaviour. - -As LMIC continue to experience repeated waves of the virus and increased associated mortality, against a backdrop of vaccine inaccessibility and limited welfare support, continued efforts are needed to track the indirect impact of the pandemic on suicide and self-harm in these countries.",public and global health,fuzzy,100,100 medRxiv,10.1101/2021.09.02.21263017,2021-09-05,https://medrxiv.org/cgi/content/short/2021.09.02.21263017,Monitoring populations at increased risk for SARS-CoV-2 infection in the community,Emma Pritchard; Joel Jones; Karina Vihta; Nicole Stoesser; Philippa C Matthews; David W Eyre; Thomas House; John I Bell; John N Newton; Jeremy Farrar; Derrick Crook; Susan Hopkins; Duncan Cook; Emma Rourke; Ruth Studley; Ian Diamond; Tim Peto; Koen B Pouwels; A Sarah Walker,University of Oxford; Office for National Statistics; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Manchester; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; Public Health England; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; University of Oxford; University of Oxford,"BackgroundThe COVID-19 pandemic is rapidly evolving, with emerging variants and fluctuating control policies. Real-time population screening and identification of groups in whom positivity is highest could help monitor spread and inform public health messaging and strategy. MethodsTo develop a real-time screening process, we included results from nose and throat swabs and questionnaires taken 19 July 2020-17 July 2021 in the UKs national COVID-19 Infection Survey. Fortnightly, associations between SARS-CoV-2 positivity and 60 demographic and behavioural characteristics were estimated using logistic regression models adjusted for potential confounders, considering multiple testing, collinearity, and reverse causality. @@ -2520,6 +2487,13 @@ QuestionDoes the association between BMI and COVID-19 mortality vary by ethnicit FindingsIn this study of 12.6 million adults, BMI was associated with COVID-19 in all ethnicities, but with stronger associations in ethnic minority populations such that the risk of COVID-19 mortality for a BMI of 40 kg/m2 in white ethnicities was observed at a BMI of 30.1 kg/m2, 27.0 kg/m2, and 32.2 kg/m2 in black, South Asian and other ethnicities, respectively. MeaningBMI is a stronger risk factor for COVID-19 mortality in ethnic minorities. Obesity management is therefore a priority in these populations.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.07.20.21260558,2021-07-22,https://medrxiv.org/cgi/content/short/2021.07.20.21260558,Intentions to participate in cervical and colorectal cancer screening during the COVID-19 pandemic: a mixed-methods study,Rebecca Wilson; Harriet Quinn-Scoggins; Yvonne Moriarty; Jacqueline Hughes; Mark Goddard; Rebecca Cannings-John; Victoria Whitelock; Katriina L Whitaker; Detelina Grozeva; Julia Townson; Kirstie Osborne; Stephanie Smits; Michael Robling; Julie Hepburn; Graham Moore; Ardiana Gjini; Kate Brain; Jo Waller,"Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cancer Research UK; University of Surrey; Cardiff University; Cardiff University; Cancer Research UK; Cardiff University; Cardiff University; Public Involvement Community, Health and Care Research Wales; Cardiff University; Public Health Wales; Cardiff University; Kings College London","Worldwide, cancer screening faced significant disruption in 2020 due to the COVID-19 pandemic. If this has led to changes in public attitudes towards screening and reduced intention to participate, there is a risk of long-term adverse impact on cancer outcomes. In this study, we examined previous participation and future intentions to take part in cervical and colorectal cancer (CRC) screening following the first national lockdown in the UK. + +Overall, 7543 adults were recruited to a cross-sectional online survey in August-September 2020. Logistic regression analyses were used to identify correlates of strong screening intentions among 2,319 participants eligible for cervical screening and 2,502 eligible for home-based CRC screening. Qualitative interviews were conducted with a sub-sample of 30 participants. Verbatim transcripts were analysed thematically. + +Of those eligible, 74% of survey participants intended to attend cervical screening and 84% intended to complete home-based CRC screening when next invited. Thirty percent and 19% of the cervical and CRC samples respectively said they were less likely to attend a cancer screening appointment now than before the pandemic. Previous non-participation was the strongest predictor of low intentions for cervical (aOR 26.31, 95% CI: 17.61-39.30) and CRC (aOR 67.68, 95% CI: 33.91-135.06) screening. Interview participants expressed concerns about visiting healthcare settings but were keen to participate when screening programmes resumed. + +Intentions to participate in future screening were high and strongly associated with previous engagement in both programmes. As screening services recover, it will be important to monitor participation and to ensure people feel safe to attend.",oncology,fuzzy,100,98 medRxiv,10.1101/2021.07.19.21260782,2021-07-22,https://medrxiv.org/cgi/content/short/2021.07.19.21260782,Does COVID-19 vaccination improve mental health? A difference-in-difference analysis of the UnderstandingCoronavirus in America study,Jonathan Koltai; Julia Raifman; Jacob Bor; Martin McKee; David Stuckler,University of New Hampshire; Boston University; Boston University; London School of Hygiene and Tropical Medicine; Bocconi University,"BackgroundMental health problems increased during the COVID-19 pandemic. Knowledge that one is less at risk after being vaccinated may alleviate distress, but this hypothesis remains unexplored. Here we test whether psychological distress declined in those vaccinated against COVID-19 in the US and whether changes in perceived risk mediated any association. MethodsA nationally-representative cohort of U.S. adults (N=5,792) in the Understanding America Study were interviewed every two weeks from March 2020 to June 2021 (28 waves). Difference-in-difference regression tested whether getting vaccinated reduced distress (PHQ-4 scores), with mediation analysis used to identify potential mechanisms, including perceived risks of infection, hospitalization, and death. @@ -2653,15 +2627,6 @@ FindingsThe within-school reproduction number, Rschool, has remained below 1 fro InterpretationSecondary school control strategies involving mass testing have the potential to control within-school transmission while substantially reducing absences compared to an isolation of close contacts policy.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.07.12.21260360,2021-07-15,https://medrxiv.org/cgi/content/short/2021.07.12.21260360,The impact of hypoxia on B cells in COVID-19,Prasanti Kotagiri; Federica Mescia; Aimee Hanson; Lorinda Turner; Laura Bergamaschi; Ana Penalver; Nathan Richoz; Stephen Moore; Brian Ortmann; Benjamin Dunmore; Helene Ruffieux; Michael Morgan; Zewen Kelvin Tuong; Rachael Bashford Rogers; Myra Hosmillo; Stephen Baker; Anne Elmer; Ian Goodfellow; Ravindra Gupta; Nathalie Kingston; Paul Lehner; Nicholas Matheson; Sylvia Richardson; Caroline Saunders; Michael Weekes; Berthold Gottgens; Mark Toshner; Christoph Hess; Patrick Maxwell; Menna Clatworthy; James A Nathan; John Bradley; Paul Lyons; Natalie Burrows; Kenneth G C Smith,Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Oxford University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University; Cambridge University,"Prominent early features of COVID-19 include severe, often clinically silent, hypoxia and a pronounced reduction in B cells, the latter important in defence against SARS-CoV-2. This brought to mind the phenotype of mice with VHL-deficient B cells, in which Hypoxia-Inducible Factors are constitutively active, suggesting hypoxia might drive B cell abnormalities in COVID-19. We demonstrated the breadth of early and persistent defects in B cell subsets in moderate/severe COVID-19, including reduced marginal zone-like, memory and transitional B cells, changes we also observed in B cell VHL-deficient mice. This was corroborated by hypoxia-related transcriptional changes in COVID-19 patients, and by similar B cell abnormalities in mice kept in hypoxic conditions, including reduced marginal zone and germinal center B cells. Thus hypoxia might contribute to B cell pathology in COVID-19, and in other hypoxic states. Through this mechanism it may impact on COVID-19 outcome, and be remediable through early oxygen therapy.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.07.07.21253295,2021-07-08,https://medrxiv.org/cgi/content/short/2021.07.07.21253295,Mortality among Care Home Residents in England during the first and second waves of the COVID-19 pandemic: an analysis of 4.3 million adults over the age of 65,Anna Schultze; Emily Nightingale; David Evans; William J Hulme; Alicia Rosello; Chris Bates; Jonathan Cockburn; Brian MacKenna; Helen J Curtis; Caroline E Morton; Richard Croker; Seb Bacon; Helen I McDonald; Christopher T. Rentsch; Krishnan Bhaskaran; Rohini Mathur; Laurie A Tomlinson; Elizabeth J Williamson; Harriet Forbes; John Tazare; Daniel J Grint; Alex J Walker; Peter Inglesby; Nicholas J DeVito; Amir Mehrkar; George Hickman; Simon Davy; Tom Ward; Louis Fisher; Amelia CA Green; Kevin Wing; Angel YS Wong; Robert McManus; John Parry; Frank Hester; Sam Harper; Stephen JW Evans; Ian J Douglas; Liam Smeeth; Rosalind M Eggo; Ben Goldacre; David A Leon,"London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT","BackgroundResidents in care homes have been severely impacted by the COVID-19 pandemic. We describe trends in risk of mortality among care home residents compared to residents in private homes in England. - -MethodsOn behalf of NHS England, we used OpenSAFELY-TPP, an analytics platform running across the linked electronic health records of approximately a third of the English population, to calculate monthly age-standardised risks of death due to all causes and COVID-19 among adults aged >=65 years between 1/2/2019 and 31/03/2021. Care home residents were identified using linkage to the Care and Quality Commission. - -FindingsWe included 4,329,078 people aged 65 years or older on the 1st of February 2019, 2.2% of whom were classified as residing in a care or nursing home. Age-standardised mortality risks were approximately 10 times higher among care home residents compared to non-residents in February 2019 residents (CMF = 10.59, 95%CI = 9.51, 11.81 among women, CMF = 10.82, 95%CI = 9.89, 11.84 among men). This increased to more than 17 times in April 2020 (CMF = 17.52, 95%CI = 16.38, 18.74 among women, CMF = 18.12, 95%CI = 17.17 - 19.12 among men) before returning to pre-pandemic levels in June 2020. CMFs did not increase during the second wave, despite a rise in the absolute age-standardised COVID-19 mortality risks. - -InterpretationThe first COVID-19 wave had a disproportionate impact on care home residents in England compared to older private home residents. A degree of immunity, improved protective measures or changes in the underlying frailty of the populations may explain the lack of an increase in the relative mortality risks during the second wave. The care home population should be prioritised for measures aimed at controlling the spread of COVID-19. - -FundingMedical Research Council MR/V015737/1",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.07.07.21260137,2021-07-08,https://medrxiv.org/cgi/content/short/2021.07.07.21260137,Anxiety and depression symptoms after COVID-19 infection: results from the COVID Symptom Study app,Kerstin Klaser; Ellen J Thompson; Long H Nguyen; Carole H Sudre; Michela Antonelli; Benjamin Murray; Liane S Canas; Erika Molteni; Mark S Graham; Eric Kerfoot; Liyuan Chen; Jie Deng; Anna May; Christina Hu; Andy Guest; Somesh Selvachandran; David A Drew; Marc Modat; Andrew T Chan; Jonathan Wolf; Timothy D Spector; Alexander Hammers; Emma L Duncan; Sebastien Ourselin; Claire J Steves,"King's College London; King's College London; Massachusetts General Hospital and Harvard Medical School; King's College London, University College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Limited; Zoe Limited; Zoe Limited; Zoe Limited; Massachusetts General Hospital; King's College London; Massachusetts General Hospital and Harvard Medical School; Zoe Limited; King's College London; King's College London; King's College London; King's College London; King's College London","BackgroundMental health issues have been reported after SARS-CoV-2 infection. However, comparison to prevalence in uninfected individuals and contribution from common risk factors (e.g., obesity, comorbidities) have not been examined. We identified how COVID-19 relates to mental health in the large community-based COVID Symptom Study. MethodsWe assessed anxiety and depression symptoms using two validated questionnaires in 413,148 individuals between February and April 2021; 26,998 had tested positive for SARS-CoV-2. We adjusted for physical and mental pre-pandemic comorbidities, BMI, age, and sex. @@ -2821,6 +2786,15 @@ Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed Added value of this studyImmune interference and safety are always a concern when two vaccines are administered at the same time. This is the first study to demonstrate the safety and immunogenicity profile and clinical vaccine efficacy of a COVID-19 vaccine when co-administered with a seasonal influenza vaccine. Implications of all the available evidenceThis study provides much needed information to help guide national immunisation policy decision making on the critical issue of concomitant use of COVID-19 vaccines with influenza vaccines.",allergy and immunology,fuzzy,95,100 +medRxiv,10.1101/2021.06.08.21258533,2021-06-12,https://medrxiv.org/cgi/content/short/2021.06.08.21258533,The impact of co-circulating pathogens on SARS-CoV-2/COVID-19 surveillance. How concurrent epidemics may decrease true SARS-CoV-2 percent positivity.,Aleksandra Kovacevic; Rosalind M Eggo; Marc Baguelin; Matthieu Domenech de Cellès; Lulla Opatowski,Institut Pasteur; London School of Hygiene & Tropical Medicine; Imperial College London; Max Planck Institute for Infection Biology; Univ Versailles Saint Quentin / Institut Pasteur / Inserm,"BackgroundCirculation of non-SARS-CoV-2 respiratory viruses during the COVID-19 pandemic may alter quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures. Here, we assess the impact of an increased circulation of other respiratory viruses on the monitoring of positivity rates of SARS-CoV-2 and interpretation of surveillance data. + +MethodsUsing a multi-pathogen Susceptible-Exposed-Infectious-Recovered (SEIR) transmission model formalizing co-circulation of SARS-CoV-2 and another respiratory we assess how an outbreak of secondary virus may inflate the number of SARS-CoV-2 tests and affect the interpretation of COVID-19 surveillance data. Using simulation, we assess to what extent the use of multiplex PCR tests on a subsample of symptomatic individuals can support correction of the observed SARS-CoV-2 percent positive during other virus outbreaks and improve surveillance quality. + +ResultsModel simulations demonstrated that a non-SARS-CoV-2 epidemic creates an artificial decrease in the observed percent positivity of SARS-CoV-2, with stronger effect during the growth phase, until the peak is reached. We estimate that performing one multiplex test for every 1,000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percent positive. + +ConclusionsThis study highlights that co-circulating respiratory viruses can disrupt SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex PCR, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance. + +SummaryCOVID-19 surveillance indicators may be impacted by increased co-circulation of other respiratory viruses delaying control measure implementation. Continued surveillance through multiplex PCR testing in a subsample of the symptomatic population may play a role in fixing this problem.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.06.08.21258546,2021-06-12,https://medrxiv.org/cgi/content/short/2021.06.08.21258546,Inequalities in healthcare disruptions during the Covid-19 pandemic: Evidence from 12 UK population-based longitudinal studies,Jane Maddock; Sam Parsons; Giorgio Di Gessa; Michael J Green; Ellen J Thompson; Anna J Stevenson; Alex S.F. Kwong; Eoin McElroy; Gillian Santorelli; Richard J Silverwood; Gabriella Captur; Nish Chaturvedi; Claire J Steves; Andrew Steptoe; Praveetha Patalay; George B Ploubidis; Srinivasa Vittal Katikireddi,University College London; University College London; University College London; University of Glasgow; King's College London; University of Edinburgh; University of Bristol; University of Leicester; Bradford Institute for Health Research; University College London; University College London; University College London; King's College London; University College London; University College London; University College London; University of Glasgow,"BackgroundHealth systems worldwide have faced major disruptions due to COVID-19 which could exacerbate health inequalities. The UK National Health Service (NHS) provides free healthcare and prioritises equity of delivery, but the pandemic may be hindering the achievement of these goals. We investigated associations between multiple social characteristics (sex, age, occupational social class, education and ethnicity) and self-reported healthcare disruptions in over 65,000 participants across twelve UK longitudinal studies. MethodsParticipants reported disruptions from March 2020 up to late January 2021. Associations between social characteristics and three types of self-reported healthcare disruption (medication access, procedures, appointments) and a composite of any of these were assessed in logistic regression models, adjusting for age, sex and ethnicity where relevant. Random-effects meta-analysis was conducted to obtain pooled estimates. @@ -2927,6 +2901,15 @@ MethodsVirus Watch is a large community cohort with prospective daily recording FindingsWe included results from 8213 swabbed illnesses, 944 of which tested positive for SARS-CoV-2. All symptoms were more common in test positive than test negative illnesses and symptoms were also more severe and of longer duration. Common symptoms such as cough, headache, fatigue, muscle aches, and loss of appetite occurred early in the course of illness but were also very common in test-negative illnesses. In contrast, high temperature and loss of or altered sense of smell or taste were less frequently identified in swab positive illnesses but were markedly more common than in swab negative illnesses. The current UK definition had a sensitivity and specificity of 81% and 47% respectively for symptomatic COVID-19 compared to 93% and 26% for the broader definition. On average, cases met the broader case definition 0.3 days earlier than the current definition. 1.7-fold more illnesses met the broader definition than the current case definition. InterpretationCOVID-19 is difficult to distinguish from other respiratory infections and common ailments on the basis of symptoms. Broadening the list of symptoms used to encourage engagement with TTI could moderately increase the number of infections identified and shorten delays to isolation, but with a large increase in the number of tests needed and the number of unwell individuals and contacts who are advised to self-isolate whilst awaiting results, and subsequently test negative for SARS-CoV-2.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.05.18.21257267,2021-05-18,https://medrxiv.org/cgi/content/short/2021.05.18.21257267,"Colchicine in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial",Peter W Horby; Mark Campbell; Enti Spata; Jonathan R Emberson; Natalie Staplin; Guilherme Pessoa-Amorim; Leon Peto; Martin Wiselka; Laura Wiffen; Simon Tiberi; Ben Caplin; Caroline Wroe; Christopher Green; Paul Hine; Benjamin Prudon; Tina George; Andrew Wight; J Kenneth Baillie; Buddha Basnyat; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Faust; Raph L Hamers; Thomas Jaki; Edmund Juszczak; Katie Jeffery; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; Richard Haynes; Martin J Landray,"Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and International Severe Acute Res; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and Nuffield Department of Populat; Department of Infectious Diseases, University Hospital Leicester, Leicester, United Kingdom; Portsmouth Hospitals University NHS Foundation Trust, Portsmouth, United Kingdom; Department of Infection, Barts Health NHS Trust, London, United Kingdom; Department of Renal Medicine, University College London, London, United Kingdom and Royal Free London NHS Trust, London, United Kingdom; James Cook University Hospital, Middlesbrough, United Kingdom; University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom; Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom; North Tees and Hartlepool NHS Foundation Trust, Hartlepool, United Kingdom; Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom; Wirral University Teaching Hospital NHS Foundation Trust, Birkenhead, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Oxford University Clinical Research Unit -Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Course Sciences, King?s College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia and Faculty of Medicine, University of Indonesia, Jakarta, Indonesia and Centre for Tropical Medicine ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom and MRC Biostatistics Unit, University of Cambridge, Cambridge, United; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom and Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Notting; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit & Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un","BackgroundColchicine has been proposed as a treatment for COVID-19 on the basis of its anti-inflammatory actions. + +MethodsIn this randomised, controlled, open-label trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care alone or usual standard of care plus colchicine twice daily for 10 days or until discharge (or one of the other treatment arms) using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936). + +FindingsBetween 27 November 2020 and 4 March 2021, 5610 patients were randomly allocated to receive colchicine and 5730 patients to receive usual care alone. Overall, 1173 (21%) patients allocated to colchicine and 1190 (21%) patients allocated to usual care died within 28 days (rate ratio 1.01; 95% confidence interval [CI] 0.93-1.10; p=0.77). Consistent results were seen in all pre-specified subgroups of patients. There was no significant difference in duration of hospitalisation (median 10 days vs. 10 days) or the proportion of patients discharged from hospital alive within 28 days (70% vs. 70%; rate ratio 0.98; 95% CI 0.94-1.03; p=0.44). Among those not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (25% vs. 25%; risk ratio 1.02; 95% CI 0.96-1.09; p=0.47). + +InterpretationIn adults hospitalised with COVID-19, colchicine was not associated with reductions in 28-day mortality, duration of hospital stay, or risk of progressing to invasive mechanical ventilation or death. + +FundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056). Wellcome Trust (Grant Ref: 222406/Z/20/Z) through the COVID-19 Therapeutics Accelerator.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.05.17.21256818,2021-05-18,https://medrxiv.org/cgi/content/short/2021.05.17.21256818,Local prevalence of transmissible SARS-CoV-2 infection : an integrative causal model for debiasing fine-scale targeted testing data,George Nicholson; Brieuc CL Lehmann; Tullia Padellini; Koen B Pouwels; Radka Jersakova; James Lomax; Ruairidh E King; Ann-Marie Mallon; Peter J Diggle; Sylvia Richardson; Marta Blangiardo; Chris Holmes,University of Oxford; University of Oxford; Imperial College London; University of Oxford; The Alan Turing Institute; The Alan Turing Institute; MRC Harwell Institute; MRC Harwell Institute; Lancaster University; MRC Biostatistics Unit; Imperial College London; University of Oxford,"Targeted surveillance testing schemes for SARS-CoV-2 focus on certain subsets of the population, such as individuals experiencing one or more of a prescribed list of symptoms. These schemes have routinely been used to monitor the spread of SARS-CoV-2 in countries across the world. The number of positive tests in a given region can provide local insights into important epidemiological parameters, such as prevalence and effective reproduction number. Moreover, targeted testing data has been used inform the deployment of localised non-pharmaceutical interventions. However, surveillance schemes typically suffer from ascertainment bias; the individuals who are tested are not necessarily representative of the wider population of interest. Here, we show that data from randomised testing schemes, such as the REACT study in the UK, can be used to debias fine-scale targeted testing data in order to provide accurate localised estimates of the number of infectious individuals. We develop a novel, integrative causal framework that explicitly models the process underlying the selection of individuals for targeted testing. The output from our model can readily be incorporated into longitudinal analyses to provide local estimates of the reproduction number. We apply our model to characterise the size of the infectious population in England between June 2020 and January 2021. Our local estimates of the effective reproduction number are predictive of future changes in positive case numbers. We also capture local increases in both prevalence and effective reproductive number in the South East from November 2020 to December 2020, reflecting the spread of the Kent variant. Our results illustrate the complementary roles of randomised and targeted testing schemes. Preparations for future epidemics should ensure the rapid deployment of both types of schemes to accurately monitor the spread of emerging and ongoing infectious diseases.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.05.15.21257017,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.15.21257017,Extended interval BNT162b2 vaccination enhances peak antibody generation in older people,Helen M Parry; Rachel Bruton; Christine Stephens; Kevin Brown; Gayatri Amirthalingam; Bassam Hallis; Ashley Otter; Jianmin Zuo; Paul Moss,"University of Birmingham, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; National infection Service, Public Health England, Colindale, London NW9 5EQ, UK; National infection Service, Public Health England, Colindale, London NW9 5EQ, UK; National infection Service, Public Health England, Porton Down, Salisbury, SP4 OJG, UK; National infection Service, Public Health England, Porton Down, Salisbury, SP4 OJG, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK","ObjectivesTo assess the relative immunogenicity of standard or extended interval BNT162b2 vaccination. @@ -3048,6 +3031,9 @@ MethodsThe Virus Watch study is a household community cohort of acute respirator ResultsThe proportion of participants with a positive SARS-CoV-2 PCR result was highest in the overcrowded group (6.6%; 73/1,102) and lowest in the under-occupied group (2.9%; 682/23,219). In a mixed effects logistic regression model that included age, sex, ethnicity, household income and geographical region, we found strong evidence of an increased odds of having a positive PCR SARS-CoV-2 antigen result (Odds Ratio 3.72; 95% CI: 1.92, 7.13; p-value < 0.001) and increased odds of having a positive SARS-CoV-2 antibody result in individuals living in overcrowded houses (2.96; 95% CI: 1.13, 7.74; p-value =0.027) compared to people living in under-occupied houses. The proportion of variation at the household level was 9.91% and 9.97% in the PCR and antibody models respectively. DiscussionPublic health interventions to prevent and stop the spread of SARS-CoV-2 should consider the much greater risk of infection for people living in overcrowded households and pay greater attention to reducing household transmission. There is an urgent need to better recognise housing as a leading determinant of health in the context of a pandemic and beyond.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.05.05.21256668,2021-05-09,https://medrxiv.org/cgi/content/short/2021.05.05.21256668,COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland,Sofia de la Fuente Garcia; Fasih Haider; Saturnino Luz,The University of Edinburgh; The University of Edinburgh; The University of Edinburgh,"The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively. + +Clinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.",health informatics,fuzzy,100,100 medRxiv,10.1101/2021.05.05.21256649,2021-05-08,https://medrxiv.org/cgi/content/short/2021.05.05.21256649,Illness duration and symptom profile in a large cohort of symptomatic UK school-aged children tested for SARS-CoV-2,Erika Molteni; Carole Helene Sudre; Liane Santos Canas; Sunil S Bhopal; Robert C Hughes; Michela S Antonelli; Benjamin Murray; Kerstin Klaser; Eric Kerfoot; Liyuan Chen; Jie Deng; Christina Hu; Somesh Selvachandran; Kenneth Read; Joan Capdevila Pujol; Alexander Hammers; Timothy Spector; Sebastien Ourselin; Claire J Steves; Marc Modat; Michael Absoud; Emma L Duncan,King's College London; University College London; King's College London; King's College London; Newcastle University; London School of Hygiene & Tropical Medicine; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; ZOE Global Ltd; Zoe Global Ltd; ZOE Global Ltd; Zoe Global Ltd; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Evelina Hospital London; King's College London,"BackgroundIn children, SARS-CoV-2 is usually asymptomatic or causes a mild illness of short duration. Persistent illness has been reported; however, its prevalence and characteristics are unclear. We aimed to determine illness duration and characteristics in symptomatic UK school-aged children tested for SARS-CoV-2 using data from the COVID Symptom Study, the largest UK citizen participatory epidemiological study to date. MethodsData from 258,790 children aged 5-17 years were reported by an adult proxy between 24 March 2020 and 22 February 2021. Illness duration and symptom profiles were analysed for all children testing positive for SARS-CoV-2 for whom illness duration could be determined, considered overall and within younger (5-11 years) and older (12-17 years) groups. Data from symptomatic children testing negative for SARS-CoV-2, matched 1:1 for age, gender, and week of testing, were also assessed. @@ -3097,6 +3083,13 @@ What this study addsO_LIIn 70,464 people with atrial fibrillation, at the thresh C_LIO_LIThis might be explained by OACs preventing severe COVID-19 outcomes, or more cautious behaviours and environmental factors reducing the risk of SARS-CoV-2 infection in those taking OACs. C_LIO_LIIn 372,746 people with non-valvular atrial fibrillation, there was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin compared with DOACs. C_LI",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.04.26.21255732,2021-04-28,https://medrxiv.org/cgi/content/short/2021.04.26.21255732,Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales,Sarah Beale; Isobel Braithwaite; Annalan MD Navaratnam; Pia Hardelid; Alison Rodger; Anna Aryee; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative,"University College London; University College London; University College London; University College London; University College London; Royal Free London NHS Foundation Trust,; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ","BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation. + +MethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period. + +ResultsRelative to participants in the least deprived areas, participants in the most deprived areas persistently exhibited elevated risk of exposure to vehicle sharing (aRR range across time points 1.73-8.52), public transport (aRR 3.13-5.73), work or education outside of the household (aRR 1.09-1.21), essential shops (aRR 1.09-1.13) and non-household contacts (aRR 1.15-1.19) across multiple survey periods. + +ConclusionDifferential exposure to essential public activities in deprived communities is likely to contribute to inequalities in infection risk and outcomes during the COVID-19 pandemic. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.04.24.21255968,2021-04-27,https://medrxiv.org/cgi/content/short/2021.04.24.21255968,MORTALITY OF CARE HOME RESIDENTS AND COMMUNITY-DWELLING CONTROLS DURING THE COVID-19 PANDEMIC IN 2020: MATCHED COHORT STUDY,Martin C Gulliford; A Toby Prevost; Andrew Clegg; Emma C Rezel-Potts,King's College London; King's College London; University of Leeds; King's College London,"ObjectiveTo estimate mortality of care home (CH) residents, and matched community-dwelling controls, during the Covid-19 pandemic from primary care electronic health records. DesignMatched cohort study @@ -3305,23 +3298,6 @@ ResultsWe identified two models for prediction of mortality (referred to as Xie The performance of the models was variable. For prediction of mortality Xie had good discrimination at OUH with an area under the receiver-operating characteristic (AUROC) 0.87 [95 % confidence interval (CI) 0.79-0.95] and acceptable discrimination at KCH, AUROC 0.79 [0.76-0.82]. In prediction of severe disease, Allenbach had acceptable discrimination (OUH AUROC 0.81 [0.74-0.88] and KCH AUROC 0.72 [0.68-0.75]). The Zhang models had moderate to poor discrimination. Initial calibration was poor for all models but improved with recalibration. ConclusionsThe performance of the four prediction models was variable. The Xie model had the best discrimination for mortality, while the Allenbach model had acceptable results for prediction of severe disease.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.03.26.21254391,2021-03-26,https://medrxiv.org/cgi/content/short/2021.03.26.21254391,Vaccine effectiveness of the first dose of ChAdOx1 nCoV-19 and BNT162b2 against SARS-CoV-2 infection in residents of Long-Term Care Facilities (VIVALDI study),Madhumita Shrotri; Maria Krutikov; Tom Palmer; Rebecca Giddings; Borscha Azmi; Sathyavani Subbarao; Christopher Fuller; Aidan Irwin-Singer; Daniel Davies; Gokhan Tut; Jamie Lopez Bernal; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross,"University College London; University College London; University College London; University College London; University College London; Public Health England; University College London; Department of Health and Social Care, UK; Palantir Technologies UK Ltd; University of Birmingham; Public Health England; University of Birmingham; University College London; University College London; University College London","BackgroundThe effectiveness of SARS-CoV-2 vaccines in frail older adults living in Long-Term Care Facilities (LTCFs) is uncertain. We estimated protective effects of the first dose of ChAdOx1 and BNT162b2 vaccines against infection in this population. - -MethodsCohort study comparing vaccinated and unvaccinated LTCF residents in England, undergoing routine asymptomatic testing (8 December 2020 - 15 March 2021). We estimated the relative hazard of PCR-positive infection using Cox proportional hazards regression, adjusting for age, sex, prior infection, local SARS-CoV-2 incidence, LTCF bed capacity, and clustering by LTCF. - -ResultsOf 10,412 residents (median age 86 years) from 310 LTCFs, 9,160 were vaccinated with either ChAdOx1 (6,138; 67%) or BNT162b2 (3,022; 33%) vaccines. A total of 670,628 person days and 1,335 PCR-positive infections were included. Adjusted hazard ratios (aHRs) for PCR-positive infection relative to unvaccinated residents declined from 28 days following the first vaccine dose to 0{middle dot}44 (0{middle dot}24, 0{middle dot}81) at 28-34 days and 0{middle dot}38 (0{middle dot}19, 0{middle dot}77) at 35-48 days. Similar effect sizes were seen for ChAdOx1 (aHR 0{middle dot}32 [0{middle dot}15-0{middle dot}66] and BNT162b2 (aHR 0{middle dot}35 [0{middle dot}17, 0{middle dot}71]) vaccines at 35-48 days. Mean PCR cycle threshold values were higher, implying lower infectivity, for infections [≥]28 days post-vaccination compared with those prior to vaccination (31{middle dot}3 vs 26{middle dot}6, p<0{middle dot}001). - -InterpretationThe first dose of BNT162b2 and ChAdOx1 vaccines was associated with substantially reduced SARS-CoV-2 infection risk in LTCF residents from 4 weeks to at least 7 weeks. - -FundingUK Government Department of Health and Social Care. - -Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe conducted a systematic search for studies which evaluated SARS-CoV-2 vaccine effectiveness in residents of long-term care facilities (LTCFs) published between 01/01/2020 and 11/03/2021. We used variations of search terms for ""COVID-19"" AND ""vaccine effectiveness"" OR ""vaccine efficacy"" AND ""care homes"" OR ""long term care facilities"" OR ""older people"" on Ovid MEDLINE and MedRxiv. We identified one pre-print article regarding LTCFs in Denmark, which reported that a single dose of BNT162b was ineffective against SARS-CoV-2 infection in residents, however, participants received the second vaccine dose 24 days following the first dose on average, which is likely to be too soon to capture the protective effects of a single vaccine dose. Additionally, we identified two pre-print reports of studies evaluating vaccine effectiveness against symptomatic infection and hospitalisation amongst older adults in the community. The first of these found 81% vaccine effectiveness against COVID-19-related hospitalisation at 28-34 days following a single dose of BNT162b or ChAdOx1 in [≥]80-year-olds. The second of these found vaccine effectiveness against symptomatic infection of 60% at 28-34 days and 73% at 35+ days following a single dose of ChAdOx1 in [≥]70-year-olds. No studies were identified that focused on the effectiveness of a single vaccine dose against infection amongst LTCF residents at more than 4 weeks post-vaccination, a particularly important question in the context of the UK policy decision to extend the dose interval beyond 3 weeks. - -Added value of this studyWe conducted a prospective cohort study of 10,412 residents aged [≥]65 years, from 310 LTCFs across England, to investigate the protective effect of the first dose of the ChAdOx1 and BNT162b vaccines against SARS-CoV-2 infection in frail older adults. We retrieved results from routine monthly PCR testing, as well as outbreak and clinical testing for SARS-CoV-2, thereby capturing data on asymptomatic as well as symptomatic infections, which we linked to vaccination records. We estimated vaccine effectiveness to be 56% (19-76%) at 28-34 days, and 62% (23-81%) at 35-48 days following a single dose of ChAdOx1 or BNT162. Our findings suggest that the risk of SARS-CoV-2 infection is substantially reduced from 28 days following the first dose of either vaccine and that this effect is maintained for at least 7 weeks, with similar protection offered by both vaccine types. We also found that PCR cycle threshold (Ct) values, which are negatively associated with the ability to isolate virus, were significantly higher in infections occurring at [≥] 28days post vaccination compared to those occurring in the unvaccinated period, suggesting that vaccination may reduce onward transmission of SARS-CoV-2 in breakthrough infections. To the best of our knowledge, our findings constitute the first real-world evidence on vaccine effectiveness against infection for ChAdOx1, in any age group. We can also infer that both vaccines are effective against the B.1.1.7 variant, because our analysis period coincided with the rapid emergence of B.1.1.7 in England during the second wave of the pandemic. - -Implications of all the available evidenceOur findings add to the growing body of evidence on the protective effect of the BNT162b vaccines in residents of LTCFs and demonstrate the effectiveness of ChAdOx1 in this vulnerable population. Evaluating single-dose vaccine efficacy has become increasingly important in light of extended dosing intervals that have been implemented in order to maximise vaccine coverage across high-risk groups. Further work is required to evaluate the effectiveness of the first vaccine dose after 8-12 weeks, as well as following the second dose, and to evaluate the long-term impact of vaccination on SARS-CoV-2 infection, transmission and mortality in LTCFs. This will inform policy decisions regarding the ongoing need for disease control measures in LTCF such as visitor restrictions, which continue to have a detrimental impact on the wellbeing of residents, their relatives, and staff. - -Supplementary material attached.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.03.22.21254057,2021-03-24,https://medrxiv.org/cgi/content/short/2021.03.22.21254057,"Physical, cognitive and mental health impacts of COVID-19 following hospitalisation: a multi-centre prospective cohort study",Rachael Andrea Evans; Hamish McAuley; Ewen M Harrison; Aarti Shikotra; Amisha Singapuri; Marco Sereno; Omer Elneima; Annemarie B Docherty; Nazir I Lone; Olivia C Leavy; Luke Daines; J Kenneth Baillie; Jeremy S Brown; Trudie Chalder; Anthony De Soyza; Nawar Diar Bakerly; Nicholas Easom; John R Geddes; Neil J Greening; Nick Hart; Liam G Heaney; Simon Heller; Luke Howard; Joseph Jacob; R Gisli Jenkins; Caroline Jolley; Steven Kerr; Onn M Kon; Keir Lewis; Janet M Lord; Gerry P McCann; Stefan Neubauer; Peter JM Openshaw; Paul Pfeffer; Matthew Rowland; Malcolm G Semple; Sally J Singh; Aziz Sheikh; David Thomas; Mark Toshner; James D Chalmers; Ling-Pei Ho; Alex Horsley; Michael Marks; Krisnah Poinasamy; Louise V Wain; Christopher E Brightling,"University of Leicester; The Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, United Kingdom; The Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; The Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; The Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; The Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, United Kingdom; Usher Institute, University of Edinburgh, Edinburgh, United Kingdom; Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, United Kingdom; Department of Health Sciences, University of Leicester, Leicester, United Kingdom; Usher Institute, University of Edinburgh, Edinburgh, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, United Kingdom; Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom; Population Health Sciences Institute, Newcastle University, Newcastle Upon Tyne, United Kingdom; Newcastle upon Tyne Teaching Hospitals Trust, Newcastle upon Ty; Manchester Metropolitan University, Manchester, United Kingdom; Salford Royal NHS Foundation Trust, Manchester, United Kingdom; Infection Research Group, Hull University Teaching Hospitals, Hull, United Kingdom; NIHR Oxford Health BRC, Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, United Kingdom; Oxford Health NHS Foundation Trust, Oxford, ; The Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; Lane Fox Respiratory Service, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom; Wellcome-Wolfson Institute for Experimental Medicine, Queens University Belfast, United Kingdom; Belfast Health & Social Care Trust, Belfast, United Kingdom; Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom; Imperial College Healthcare NHS Trust, London, United Kingdom; Centre for Medical Image Computing, University College London, London, United Kingdom; Lungs for Living Research Centre, University College London, London, Unit; National Heart and Lung Institute, Imperial College London, London, United Kingdom; Centre for Human and Applied Physiological Sciences, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, Lond; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Respiratory Medicine, Imperial College Healthcare NHS Trust, London, United Kingdom; National Heart and Lung Institute, Imperial College London, London, United ; Hywel Dda University Health Board, Wales, United Kingdom; University of Swansea, Wales, United Kingdom;(3) Respiratory Innovation Wales, Wales, United Kingdom; Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom; Department of Cardiovascular Sciences, University of Leicester, Leicester, United Kingdom; Leicester NIHR Biomedical Research Centre, University of Leicester, L; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom; NIHR Biomedical Research Centre, John Radcl; National Heart and Lung Institute, Imperial College London, London, United Kingdom; Barts Health NHS Trust, London, United Kingdom; Queen Mary University of London, London, United Kingdom; Kadoorie Centre for Critical Care Research, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, U; The Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; Usher Institute, University of Edinburgh, Edinburgh, United Kingdom; Immunology and Inflammation, Imperial College, London, United Kingdom; Cambridge NIHR BRC, Cambridge, United Kingdom; NIHR Cambridge Clinical Research Facility, Cambridge, United Kingdom; University of Dundee, Ninewells Hospital and Medical School, Dundee, United Kingdom; MRC Human Immunology Unit, University of Oxford, Oxford, United Kingdom; Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom; Department of Clinical Research, London School of Hygiene & Tropical Medicine Keppel Street, London, United Kingdom; Hospital for Tropical Diseases, University ; Asthma UK and British Lung Foundation, London, United Kingdom; Department of Health Sciences, University of Leicester, Leicester, United Kingdom; The Institute for Lung Health, Leicester NIHR Biomedical Research Centre, Uni; The Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom","BackgroundThe impact of COVID-19 on physical and mental health, and employment following hospitalisation is poorly understood. MethodsPHOSP-COVID is a multi-centre, UK, observational study of adults discharged from hospital with a clinical diagnosis of COVID-19 involving an assessment between two- and seven-months later including detailed symptom, physiological and biochemical testing. Multivariable logistic regression was performed for patient-perceived recovery with age, sex, ethnicity, body mass index (BMI), co-morbidities, and severity of acute illness as co-variates. Cluster analysis was performed using outcomes for breathlessness, fatigue, mental health, cognition and physical function. @@ -3351,29 +3327,6 @@ ResultsThere were 5810 SARS-CoV-2 RNA positive cases comprising inpatients (n=23 ConclusionsAutomated EHR data extraction linked with SARS-CoV-2 genome sequence data provides valuable insight into the evolving characteristics of cases admitted to hospital with COVID-19. The proportion of cases with hypoxia on admission was greater in those infected with the B.1.1.7 variant, which supports evidence the B.1.1.7 variant is associated with more severe disease. The number of nosocomial cases was similar in both waves despite introduction of many infection control interventions before wave two, an observation requiring further investigation.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.03.15.21253542,2021-03-24,https://medrxiv.org/cgi/content/short/2021.03.15.21253542,Comparison between one and two dose SARS-CoV-2 vaccine prioritisation for a fixed number of vaccine doses,Edward M Hill; Matt J Keeling,University of Warwick; University of Warwick,"The swift development of SARS-CoV-2 vaccines has been met with worldwide commendation. How-ever, in the context of an ongoing pandemic there is an interplay between infection and vaccination. Whilst infection can grow exponentially, vaccination rates are generally limited by supply and logistics. With the first SARS-CoV-2 vaccines receiving medical approval requiring two doses, there has been scrutiny on the spacing between doses; an elongated period between doses allows more of the population to receive a first vaccine dose in the short-term generating wide-spread partial immunity. Focusing on data from England, we investigated prioritisation of a one dose or two dose vaccination schedule given a fixed number of vaccine doses and with respect to a measure of maximising averted deaths. We optimised outcomes for two different estimates of population size and relative risk of mortality for at-risk groups within the Phase 1 vaccine priority order. Vaccines offering relatively high protection from the first dose favour strategies that prioritise giving more people one dose, although with increasing vaccine supply eventually those eligible and accepting vaccination will receive two doses. Whilst optimal dose timing can substantially reduce the overall mortality risk, there needs to be careful consideration of the logistics of vaccine delivery.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.03.18.21253888,2021-03-23,https://medrxiv.org/cgi/content/short/2021.03.18.21253888,"Long Covid in adults discharged from UK hospitals after Covid-19: A prospective, multicentre cohort study using the ISARIC WHO Clinical Characterisation Protocol.",Louise Sigfrid; Tom M Drake; Ellen Pauley; Edwin C Jesudason; Piero Olliaro; Wei Shen Lim; Annelise Gillesen; Colin Berry; David Lowe; Joanne McPeake; Nazir Lone; Muge Cevik; Daniel Munblit; Anna Casey; Peter Bannister; Clark D Russell; Lynsey Goodwin; Antonia Ho; Lance Turtle; Margret E O'Hara; Claire Hastie; Chloe Donohue; Rebecca Spencer; Cara Donegan; Alison Gummery; Janet Harrison; Hayley Hardwick; Claire E Hastie; Gail Carson; Laura Merson; John Kenneth Baillie; Peter Openshaw; Ewen M Harrison; Annemarie Docherty; Malcolm G Semple; Janet T Scott,"ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK; Centre for Medical Informatics, University of Edinburgh, Edinburgh, UK; University of Edinburgh Medical School, Edinburgh, UK.; NHS Lothian, Edinburgh, UK,; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, UK.; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK; NHS Greater Glasgow and Clyde, Emergency Department, Glasgow, UK; School of Medicine, Dentistry and Nursing, University of Glasgow, UK; Usher Institute, University of Edinburgh, Edinburgh, UK; University of St Andrews; Sechenov First Moscow State Medical University, Imperial College London, Imperial College London, RSMU; Medical Student, Brighton and Sussex Medical School, UK; Brighton & Sussex Medical School, Brighton, UK; Centre for Inflammation Research, University of Edinburgh, UK; Institute of Infection, Veterinary and Ecological Studies, Univeristy of Liverpool. Tropical and Infectious Diseases Unit, North Manchester General Hospital, De; University of Glasgow, Glasgow, UK; NIHR Health Protection Research Unit in emerging and zoonotic infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L; Long COVID Support, Birmingham, UK; Long COVID Support, Birmingham, UK; Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK; Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK.; Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK.; Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK.; National Institute of Health Research (NIHR) Health Protection research Unit in Emerging and Zoonotic Infections, Liverpool, UK. 2. Institute of Infection and G; National Institute of Health Research (NIHR) Health Protection research Unit in Emerging and Zoonotic Infections, Liverpool, UK. 2. Institute of Infection and G; Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK.; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK; Roslin Institute, University of Edinburgh, Edinburgh, UK; National Heart and Lung Institute, Imperial College, London UK.; Director Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK.; Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK. 2. Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK; Health Protection Research Unit In Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK 2. ; MRC-University of Glasgow Center for Virus research","Structured AbstractO_ST_ABSObjectivesC_ST_ABSThe long-term consequences of severe Covid-19 requiring hospital admission are not well characterised. The objective of this study was to establish the long-term effects of Covid-19 following hospitalisation and the impact these may have on patient reported outcome measures. - -DesignA multicentre, prospective cohort study with at least 3 months follow-up of participants admitted to hospital between 5th February 2020 and 5th October 2020. - -Setting31 hospitals in the United Kingdom. - -Participants327 hospitalised participants discharged alive from hospital with confirmed/high likelihood SARS-CoV-2 infection. - -Main outcome measures and comparisonsThe primary outcome was self-reported recovery at least ninety days after initial Covid-19 symptom onset. Secondary outcomes included new symptoms, new or increased disability (Washington group short scale), breathlessness (MRC Dyspnoea scale) and quality of life (EQ5D-5L). We compared these outcome measures across age, comorbidity status and in-hospital Covid-19 severity to identify groups at highest risk of developing long-term difficulties. Multilevel logistic and linear regression models were built to adjust for the effects of patient and centre level risk factors on these outcomes. - -ResultsIn total 53.7% (443/824) contacted participants responded, yielding 73.8% (327/443) responses with follow-up of 90 days or more from symptom onset. The median time between symptom onset of initial illness and completing the participant questionnaire was 222 days (Interquartile range (IQR) 189 to 269 days). In total, 54.7% (179/327) of participants reported they did not feel fully recovered. Persistent symptoms were reported by 93.3% (305/325) of participants, with fatigue the most common (82.8%, 255/308), followed by breathlessness (53.5%, 175/327). 46.8% (153/327) reported an increase in MRC dyspnoea scale of at least one grade. New or worse disability was reported by 24.2% (79/327) of participants. Overall (EQ5D-5L) summary index was significantly worse at the time of follow-up (median difference 0.1 points on a scale of 0 to 1, IQR: -0.2 to 0.0). Females under the age of 50 years were five times less likely to report feeling recovered (adjusted OR 5.09, 95% CI 1.64 to 15.74), were more likely to have greater disability (adjusted OR 4.22, 95% CI 1.12 to 15.94), twice as likely to report worse fatigue (adjusted OR 2.06, 95% CI 0.81 to 3.31) and seven times more likely to become more breathless (adjusted OR 7.15, 95% CI 2.24 to 22.83) than men of the same age. - -ConclusionsSurvivors of Covid-19 experienced long-term symptoms, new disability, increased breathlessness, and reduced quality of life. These findings were present even in young, previously healthy working age adults, and were most common in younger females. Policymakers should fund further research to identify effective treatments for long-Covid and ensure healthcare, social care and welfare support is available for individuals with long-Covid. - -Section 1: What is already known on this topicO_LILong-term symptoms after hospitalisation for Covid-19 have been reported, but it is not clear what impact this has on quality of life. -C_LIO_LIIt is not known which patient groups are most likely to have long-term persistent symptoms following hospitalisation for Covid-19, or if this differs by disease severity. -C_LI - -Section 2: What this study addsO_LIMore than half of patients reported not being fully recovered 7 months after onset of Covid-19 symptoms. -C_LIO_LIPreviously healthy participants and those under the age of 50 had higher odds of worse long-term outcomes compared to older participants and those with comorbidities. -C_LIO_LIYounger women and those with more severe acute disease in-hospital had the worst long-term outcomes. -C_LIO_LIPolicy makers need to ensure there is long-term support for people experiencing long-Covid and should plan for lasting long-term population morbidity. Funding for research to understand mechanisms underlying long-Covid and identify potential interventions for testing in randomised trials is urgently required. -C_LI",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.03.20.21254010,2021-03-22,https://medrxiv.org/cgi/content/short/2021.03.20.21254010,Older biological age is associated with adverse COVID-19 outcomes: A cohort study in UK Biobank,Qingning Wang; Veryan Codd; Zahra Raisi-Estabragh; Crispin Musicha; Bountziouka Vasiliki; Stephen Kaptoge; Elias Allara; Emanuele Di Angelantonio; Adam S Butterworth; Angela M Wood; John R Thompson; Steffen E Petersen; Nicholas C Harvey; John N Danesh; Nilesh J Samani; Christopher P Nelson,Univeristy of Leicester; Univeristy of Leicester; Queen Mary University of London; Univeristy of Leicester; Univeristy of Leicester; Univeristy of Cambridge; Univeristy of Cambridge; Univeristy of Cambridge; Univeristy of Cambridge; Univeristy of Cambridge; Univeristy of Leicester; Queen Mary University of London; University of Southampton; Univeristy of Cambridge; Univeristy of Leicester; University of Leicester,"BackgroundOlder chronological age is the most powerful risk factor for adverse coronavirus disease-19 (COVID-19) outcomes. It is uncertain, however, whether older biological age, as assessed by leucocyte telomere length (LTL), is also associated with COVID-19 outcomes. MethodsWe associated LTL values obtained from participants recruited into UK Biobank (UKB) during 2006-2010 with adverse COVID-19 outcomes recorded by 30 November 2020, defined as a composite of any of the following: hospital admission, need for critical care, respiratory support, or mortality. Using information on 131 LTL-associated genetic variants, we conducted exploratory Mendelian randomisation (MR) analyses in UKB to evaluate whether observational associations might reflect cause-and-effect relationships. @@ -3430,6 +3383,7 @@ Added value of this studyThrough prospective collection of symptom and test repo Implications of all the available evidenceDespite the UK having a simple set of symptom-based testing criteria, with tests made freely available through nationalised healthcare, a quarter of individuals with qualifying symptoms do not get tested. Our findings suggest testing uptake may be limited by individuals not acting on mild or transient symptoms, not recognising the testing criteria, and not knowing where to get tested. Improved messaging may help address this testing gap, with opportunities to target individuals of older age or fewer years of education. Messaging may prove even more valuable in countries with more fragmented testing infrastructure or more nuanced testing criteria, where knowledge barriers are likely to be greater.",public and global health,fuzzy,94,100 bioRxiv,10.1101/2021.03.14.435295,2021-03-16,https://biorxiv.org/cgi/content/short/2021.03.14.435295,3D genomic capture of regulatory immuno-genetic profiles in COVID-19 patients for prognosis of severe COVID disease outcome,Ewan Hunter; Christina Koutsothanasi; Adam Wilson; Francisco Coroado Santos; Matthew Salter; Ryan Powell; Ann Dring; Paulina Brajer; Benedict Egan; Jurjen Westra; Aroul Ramadass; William Messner; Amanda Brunton; Zoe Lyski; Rama Vancheeswaran; Andrew Barlow; Dmitri Pchejetski; Alexandre Akoulitchev,"Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oregon Health & Science University, Portland, OR; Oregon Health & Science University, Portland, OR; Oregon Health & Science University, Portland, OR; West Hertfordshire NHS Trust, Watford, UK; West Hertfordshire NHS Trust, Watford, UK; Norwich Medical School, University of East Anglia; Oxford BioDynamics Plc, Oxford UK","Human infection with the SARS-CoV-2 virus leads to coronavirus disease (COVID-19). A striking characteristic of COVID-19 infection in humans is the highly variable host response and the diverse clinical outcomes, ranging from clinically asymptomatic to severe immune reactions leading to hospitalization and death. Here we used a 3D genomic approach to analyse blood samples at the time of COVID diagnosis, from a global cohort of 80 COVID-19 patients, with different degrees of clinical disease outcomes. Using 3D whole genome EpiSwitch(R) arrays to generate over 1 million data points per patient, we identified a distinct and measurable set of differences in genomic organization at immune-related loci that demonstrated prognostic power at baseline to stratify patients with mild forms of illness and those with severe forms that required hospitalization and intensive care unit (ICU) support. Further analysis revealed both well established and new COVID-related dysregulated pathways and loci, including innate and adaptive immunity; ACE2; olfactory, G{beta}{psi}, Ca2+ and nitric oxide (NO) signalling; prostaglandin E2 (PGE2), the acute inflammatory cytokine CCL3, and the T-cell derived chemotactic cytokine CCL5. We identified potential therapeutic agents for mitigation of severe disease outcome, with several already being tested independently, including mTOR inhibitors (rapamycin and tacrolimus) and general immunosuppressants (dexamethasone and hydrocortisone). Machine learning algorithms based on established EpiSwitch(R) methodology further identified a subset of 3D genomic changes that could be used as prognostic molecular biomarker leads for the development of a COVID-19 disease severity test.",biochemistry,fuzzy,92,100 medRxiv,10.1101/2021.03.09.21253012,2021-03-15,https://medrxiv.org/cgi/content/short/2021.03.09.21253012,The local and systemic response to SARS-CoV-2 infection in children and adults,Masahiro Yoshida; Kaylee B Worlock; Ni Huang; Rik GH Lindeboom; Colin R Butler; Natsuhiko Kumasaka; Cecilia Dominguez Conde; Lira Mamanova; Liam Bolt; Laura Richardson; Krzysztof Polanski; Elo Madissoon; Josephine L Barnes; Jessica Allen-Hyttinen; Eliz Kilich; Brendan C Jones; Angus de Wilton; Anna Wilbrey-Clark; Waradon Sungnak; Jan Patrick Prett; Elena Prigmore; Henry Yung; Puja Mehta; Aarash Saleh; Anita Saigal; Vivian Chu; Jonathan M Cohen; Clare Cane; Aikaterini Iordanidou; Soichi Shibuya; Ann-Kathrin Reuschl; A. Christine Argento; Richard G Wunderink; Sean B Smith; Taylor A Poor; Catherine A Gao; Jane E Dematte; - NU SCRIPT Study Investigators; Gary Reynolds; Muzlifah Haniffa; Georgina S Bowyer; Matthew Coates; Menna R Clatworthy; Fernando J Calero-Nieto; Berthold Gottgens; Neil J Sebire; Clare Jolly; Paolo de Coppi; Claire M Smith; Alexander V Misharin; Sam M Janes; Sarah A Teichmann; Marko Z Nikolic; Kerstin B Meyer,"UCL Respiratory, Division of Medicine, University College London, London, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; UCL Great Ormond Street Institute of Child Health, London, UK; Wellcome Trust Sanger Institute; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; UCL Great Ormond Street Institute of Child Health, London, UK; University College London Hospital Trust; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; Royal Free Hospital, London, UK; Royal Free Hospital, London, UK; Royal Free Hospital, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; Royal Free Hospital, London, UK; Royal Free Hospital, London, UK; UCL Great Ormond Street Institute of Child Health, London, UK; Division of Infection and Immunity, University College London, London, UK; Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, USA; Northwestern University Feinberg School of Medicine; Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, USA; Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, USA; Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, USA; Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, USA; ; Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK; Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; University of Cambridge, Department of Medicine; University of Cambride, Department of Medicine; Wellcome Trust & MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge UK; Wellcome Trust & MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge UK; NIHR Great Ormond Street BRC and Institute of Child Health, London, UK; Division of Infection and Immunity, University College London, UK; UCL Great Ormond Street Institute of Child Health, London, UK; UCL Great Ormond Street Institute of Child Health, London, UK; Northwestern University; UCL Respiratory, Division of Medicine, University College London, London, UK; Wellcome Sanger Institute, Cambridge, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; Wellcome Sanger Institute, Cambridge, UK","While a substantial proportion of adults infected with SARS-CoV-2 progress to develop severe disease, children rarely manifest respiratory complications. Therefore, understanding differences in the local and systemic response to SARS-CoV-2 infection between children and adults may provide important clues about the pathogenesis of SARS-CoV-2 infection. To address this, we first generated a healthy reference multi-omics single cell data set from children (n=30) in whom we have profiled triple matched samples: nasal and tracheal brushings and PBMCs, where we track the developmental changes for 42 airway and 31 blood cell populations from infancy, through childhood to adolescence. This has revealed the presence of naive B and T lymphocytes in neonates and infants with a unique gene expression signature bearing hallmarks of innate immunity. We then contrast the healthy reference with equivalent data from severe paediatric and adult COVID-19 patients (total n=27), from the same three types of samples: upper and lower airways and blood. We found striking differences: children with COVID-19 as opposed to adults had a higher proportion of innate lymphoid and non-clonally expanded naive T cells in peripheral blood, and a limited interferon-response signature. In the airway epithelium, we found the highest viral load in goblet and ciliated cells and describe a novel inflammatory epithelial cell population. These cells represent a transitional regenerative state between secretory and ciliated cells; they were found in healthy children and were enriched in paediatric and adult COVID-19 patients. Epithelial cells display an antiviral and neutrophil-recruiting gene signature that is weaker in severe paediatric versus adult COVID-19. Our matched blood and airway samples allowed us to study the spatial dynamics of infection. Lastly, we provide a user-friendly interface for this data1 as a highly granular reference for the study of immune responses in airways and blood in children.",pediatrics,fuzzy,100,100 +medRxiv,10.1101/2021.03.12.21253484,2021-03-13,https://medrxiv.org/cgi/content/short/2021.03.12.21253484,Limits of lockdown: characterising essential contacts during strict physical distancing,Amy C Thomas; Leon Danon; Hannah Christensen; Kate Northstone; Daniel Smith; Emily J Nixon; Adam Trickey; Gibran Hemani; Sarah Sauchelli; Adam Finn; Nicholas J Timpson; Ellen Brooks-Pollock,"University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; NIHR Bristol Biomedical Research Centre, University of Bristol; University of Bristol; University of Bristol; University of Bristol","COVID-19 has exposed health inequalities within countries and globally. The fundamental determining factor behind an individuals risk of infection is the number of social contacts they make. In many countries, physical distancing measures have been implemented to control transmission of SARS-CoV-2, reducing social contacts to a minimum. Characterising unavoidable social contacts is key for understanding the inequalities behind differential risks and planning vaccination programmes. We utilised an existing English longitudinal birth cohort, which is broadly representative of the wider population (n=6807), to explore social contact patterns and behaviours when strict physical distancing measures were in place during the UKs first lockdown in March-May 2020. Essential workers, specifically those in healthcare, had 4.5 times as many contacts as non-essential workers [incident rate ratio = 4.42 (CI95%: 3.88-5.04)], whilst essential workers in other sectors, mainly teaching and the police force had three times as many contacts [IRR = 2.84 (2.58-3.13)]. The number of individuals in a household, which is conflated by number of children, increases essential social contacts by 40%. Self-isolation effectively reduces numbers of contacts outside of the home, but not entirely. Together, these findings will aid the interpretation of epidemiological data and impact the design of effective SARS-CoV-2 control strategies, such as vaccination, testing and contact tracing.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.03.10.21253173,2021-03-12,https://medrxiv.org/cgi/content/short/2021.03.10.21253173,"High household transmission of SARS-CoV-2 in the United States: living density, viral load, and disproportionate impact on communities of color",Carla Cerami; Tyler Rapp; Feng-Chang Lin; Kathleen Tompkins; Christopher Basham; Meredith Smith Muller; Maureen Whittelsey; Haoming Zhang; Srijana Bhattarai Chhetri; Judy Smith; Christy Litel; Kelly Lin; Mehal Churiwal; Salman Khan; Faith Claman; Rebecca Rubinstein; Katie Mollan; David Wohl; Lakshmanane Premkumar; Jonathan J. Juliano; Jessica T Lin,"MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; University of North Carolina School of Medicine; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA","BackgroundFew prospective studies of SARS-CoV-2 transmission within households have been reported from the United States, where COVID-19 cases are the highest in the world and the pandemic has had disproportionate impact on communities of color. Methods and FindingsThis is a prospective observational study. Between April-October 2020, the UNC CO-HOST study enrolled 102 COVID-positive persons and 213 of their household members across the Piedmont region of North Carolina, including 45% who identified as Hispanic/Latinx or non-white. Households were enrolled a median of 6 days from onset of symptoms in the index case. Secondary cases within the household were detected either by PCR of a nasopharyngeal (NP) swab on study day 1 and weekly nasal swabs (days 7, 14, 21) thereafter, or based on seroconversion by day 28. After excluding household contacts exposed at the same time as the index case, the secondary attack rate (SAR) among susceptible household contacts was 60% (106/176, 95% CI 53%-67%). The majority of secondary cases were already infected at study enrollment (73/106), while 33 were observed during study follow-up. Despite the potential for continuous exposure and sequential transmission over time, 93% (84/90, 95% CI 86%-97%) of PCR-positive secondary cases were detected within 14 days of symptom onset in the index case, while 83% were detected within 10 days. Index cases with high NP viral load (>10^6 viral copies/ul) at enrollment were more likely to transmit virus to household contacts during the study (OR 4.9, 95% CI 1.3-18 p=0.02). Furthermore, NP viral load was correlated within families (ICC=0.44, 95% CI 0.26-0.60), meaning persons in the same household were more likely to have similar viral loads, suggesting an inoculum effect. High household living density was associated with a higher risk of secondary household transmission (OR 5.8, 95% CI 1.3-55) for households with >3 persons occupying <6 rooms (SAR=91%, 95% CI 71-98%). Index cases who self-identified as Hispanic/Latinx or non-white were more likely to experience a high living density and transmit virus to a household member, translating into an SAR in minority households of 70%, versus 52% in white households (p=0.05). @@ -3719,7 +3673,6 @@ medRxiv,10.1101/2021.02.10.21251484,2021-02-16,https://medrxiv.org/cgi/content/s Our results show that absences as a result of COVID-19 infection rose steadily following the re-opening of schools in September. Cases in teachers were seen to decline during the November lockdown, particularly in those regions that had previously been in tier 3, the highest level of control at the time. Cases in secondary school pupils increased for the first two weeks of the November lockdown, before decreasing. Since the introduction of the tier system, the number of absences owing to confirmed infection in primary schools was observed to be significantly lower than in secondary schools across all regions and tiers. In December, we observed a large rise in the number of absences per school in secondary school settings in the South East and Greater London, but such rises were not observed in other regions or in primary school settings. We conjecture that the increased transmissibility of the new variant in these regions may have contributed to this rise in cases in secondary schools. Finally, we observe a positive correlation between cases in the community and cases in schools in most regions, with weak evidence suggesting that cases in schools lag behind cases in the surrounding community. We conclude that there is not significant evidence to suggest that schools are playing a significant role in driving spread in the community and that careful monitoring may be required as schools re-open to determine the effect associated with open schools upon community incidence.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.02.10.21251480,2021-02-12,https://medrxiv.org/cgi/content/short/2021.02.10.21251480,Symptom reporting in over 1 million people: community detection of COVID-19,Joshua Elliott; Matthew Whitaker; Barbara Bodinier; Steven Riley; Helen Ward; Graham Cooke; Ara Darzi; Marc Chadeau-Hyam; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London,,infectious diseases,fuzzy,96,100 medRxiv,10.1101/2021.02.11.21251587,2021-02-12,https://medrxiv.org/cgi/content/short/2021.02.11.21251587,Assessing the impact of secondary school reopening strategies on within-school COVID-19 transmission and absences: a modelling study,Trystan Leng; Edward M Hill; Robin N Thompson; Michael J Tildesley; Matt J Keeling; Louise J Dyson,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,,infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.02.11.21249258,2021-02-11,https://medrxiv.org/cgi/content/short/2021.02.11.21249258,"Tocilizumab in patients admitted to hospital with COVID-19 (RECOVERY): preliminary results of a randomised, controlled, open-label, platform trial",Peter W Horby; Mark Campbell; Natalie Staplin; Enti Spata; Jonathan R Emberson; Guilherme Pessoa-Amorim; Leon Peto; Christopher E Brightling; Rahuldeb Sarkar; Koshy Thomas; Vandana Jeebun; Abdul Ashish; Redmond Tully; David Chadwick; Muhammad Sharafat; Richard Stewart; Banu Rudran; J Kenneth Baillie; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Furst; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; Richard Haynes; Martin J Landray,"Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; Medway Foundation NHS Trust, Gillingham, United Kingdom; King?s College London, London, United Kingdom; Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom; Department of Respiratory Medicine, North Tees & Hartlepool NHS Foundation Trust, Stockton-on-Tees, United Kingdom; Wrightington Wigan and Leigh NHS Foundation Trust, Wigan, United Kingdom; Royal Oldham Hospital, Northern Care Alliance, Oldham, United Kingdom; Centre for Clinical Infection, James Cook University Hospital, Middlesbrough, United Kingdom; North West Anglia NHS Foundation Trust, Peterborough, United Kingdom; Milton Keynes University Hospital, Milton Keynes, United Kingdom; Luton & Dunstable University Hospital, Luton, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Sciences, Kings College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Foundation Trust, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit and Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom","Findings: Between 23 April 2020 and 25 January 2021, 4116 adults were included in the assessment of tocilizumab, including 562 (14%) patients receiving invasive mechanical ventilation, 1686 (41%) receiving non-invasive respiratory support, and. 1868 (45%) receiving no respiratory support other than oxygen. Median CRP was 143 [IQR 107-205] mg/L and 3385 (82%) patients were receiving systemic corticosteroids at randomisation. Overall, 596 (29%) of the 2022 patients allocated tocilizumab and 694 (33%) of the 2094 patients allocated to usual care died within 28 days (rate ratio 0.86; 95% confidence interval [CI] 0.77-0.96; p=0.007). Consistent results were seen in all pre-specified subgroups of patients, including those receiving systemic corticosteroids. Patients allocated to tocilizumab were more likely to be discharged from hospital alive within 28 days (54% vs. 47%; rate ratio 1.23; 95% CI 1.12-1.34; p<0.0001). Among those not receiving invasive mechanical ventilation at baseline, patients allocated tocilizumab were less likely to reach the composite endpoint of invasive mechanical ventilation or death (33% vs. 38%; risk ratio 0.85; 95% CI 0.78-0.93; p=0.0005). Interpretation: In hospitalised COVID-19 patients with hypoxia and systemic inflammation, tocilizumab improved survival and other clinical outcomes regardless of the level of respiratory support received and in addition to the use of systemic corticosteroids.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.02.08.21250525,2021-02-09,https://medrxiv.org/cgi/content/short/2021.02.08.21250525,"COVID-19 infection and outcomes in a population-based cohort of 17,173 adults with intellectual disabilities compared with the general population",Angela Henderson; Micheal Fleming; Sally-Ann Cooper; Jill Pell; Craig Melville; Daniel MacKay; Christopher Hatton; Deborah Kinnear,University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; Manchester Metropolitan University; University of Glasgow,"ObjectivesTo compare COVID-19 infection, severe infection, mortality, case-fatality, and excess deaths, among adults with intellectual disabilities and those without. @@ -3788,21 +3741,13 @@ ResultsWave 2 patients were younger, more ethnically diverse, had less co-morbid ConclusionPrior to new SARS-CoV-2 variants, outcomes for hospitalised patients with COVID-19 were improving but with similar intensive care needs.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.02.03.21251054,2021-02-05,https://medrxiv.org/cgi/content/short/2021.02.03.21251054,Age-related heterogeneity in Neutralising antibody responses to SARS-CoV-2 following BNT162b2 vaccination,Dami Collier; Isabella Ferreira; Rawlings Datir; Prasanti Kotagiri; Eleanor Lim; Bo Meng; - The CITIID-NIHR Bioresource COVID-19 Collaboration; Anne Elmer; Nathalie Kingston; Barbara Graves; Barbara Graves; Kenneth GC Smith; John Bradley; Paul Lyons; Lourdes Ceron-Gutierrez; Gabriela Barcenas-Morales; Michelle Linterman; Laura McCoy; Rainer Doffinger; Mark Wills; Ravindra K Gupta,UCL; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; -; Cambridge; NIHR; NIHR; Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; Babraham Institute; UCL; University of Cambridge; University of Cambridge; University of Cambridge,"Two dose mRNA vaccination provides excellent protection against SARS-CoV-2. However, there are few data on vaccine efficacy in elderly individuals above the age of 801. Additionally, new variants of concern (VOC) with reduced sensitivity to neutralising antibodies have raised fears for vulnerable groups. Here we assessed humoral and cellular immune responses following vaccination with mRNA vaccine BNT162b22 in elderly participants prospectively recruited from the community and younger health care workers. Median age was 72 years and 51% were females amongst 140 participants. Neutralising antibody responses after the first vaccine dose diminished with increasing age, with a marked drop in participants over 80 years old. Sera from participants below and above 80 showed significantly lower neutralisation potency against B.1.1.7, B.1.351 and P.1. variants of concern as compared to wild type. Those over 80 were more likely to lack any neutralisation against VOC compared to younger participants following first dose. The adjusted odds ratio for inadequate neutralisation activity against the B.1.1.7, P.1 and B.1.351 variant in the older versus younger age group was 4.3 (95% CI 2.0-9.3, p<0.001), 6.7 (95% CI 1.7-26.3, p=0.008) and 1.7 (95% CI 0.5-5.7, p=0.41). Binding IgG and IgA antibodies were lower in the elderly, as was the frequency of SARS-CoV-2 Spike specific B-memory cells. We observed a trend towards lower somatic hypermutation in participants with suboptimal neutralisation, and elderly participants demonstrated clear reduction in class switched somatic hypermutation, driven by the IgA1/2 isotype. SARS-CoV-2 Spike specific T-cell IFN{gamma} and IL-2 responses fell with increasing age, and both cytokines were secreted primarily by CD4 T cells. We conclude that the elderly are a high risk population that warrant specific measures in order to mitigate against vaccine failure, particularly where variants of concern are circulating.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.02.03.21251004,2021-02-05,https://medrxiv.org/cgi/content/short/2021.02.03.21251004,Ethnic differences in COVID-19 mortality during the first two waves of the Coronavirus Pandemic: a nationwide cohort study of 29 million adults in England,Vahe Nafilyan; Nazrul Islam; Rohini Mathur; Daniel Ayoubkhani; Amitava Banerjee; Myer Glickman; Ben Humberstone; Ian DIamond; Kamlesh Khunti,"Office for National Statistics; Nuffield Department of Population Health, Big Data Institute, University of Oxford; London School of Hygiene and Tropical Medicine; Office for National Statistics; University College London; Office for National Statistics; Office for National Statistics; Office for National Statistics; Diabetes Research Centre, University of Leicester","BackgroundEthnic minorities have experienced disproportionate COVID-19 mortality rates in the UK and many other countries. We compared the differences in the risk of COVID-19 related death between ethnic groups in the first and second waves the of COVID-19 pandemic in England. We also investigated whether the factors explaining differences in COVID-19 death between ethnic groups changed between the two waves. - -MethodsUsing data from the Office for National Statistics Public Health Data Asset on individuals aged 30-100 years living in private households, we conducted an observational cohort study to examine differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and second wave (from 1st September to 28th December 2020). We estimated age-standardised mortality rates (ASMR) in the two waves stratified by ethnic groups and sex. We also estimated hazard ratios (HRs) for ethnic-minority groups compared with the White British population, adjusted for geographical factors, socio-demographic characteristics, and pre-pandemic health conditions. - -ResultsThe study population included over 28.9 million individuals aged 30-100 years living in private households. In the first wave, all ethnic minority groups had a higher risk of COVID-19 related death compared to the White British population. In the second wave, the risk of COVID-19 death remained elevated for people from Pakistani (ASMR: 339.9 [95% CI: 303.7 - 376.2] and 166.8 [141.7 - 191.9] deaths per 100,000 population in men and women) and Bangladeshi (318.7 [247.4 - 390.1] and 127.1 [91.1 - 171.3] in men and women)background but not for people from Black ethnic groups. Adjustment for geographical factors explained a large proportion of the differences in COVID-19 mortality in the first wave but not in the second wave. Despite an attenuation of the elevated risk of COVID-19 mortality after adjusting for sociodemographic characteristics and health status, the risk was substantially higher in people from Bangladeshi and Pakistani background in both the first and the second waves. - -ConclusionBetween the first and second waves of the pandemic, the reduction in the difference in COVID-19 mortality between people from Black ethnic background and people from the White British group shows that ethnic inequalities in COVID-19 mortality can be addressed. The continued higher rate of mortality in people from Bangladeshi and Pakistani background is alarming and requires focused public health campaign and policy changes. - -*VN and NI contributed equally to this paper +medRxiv,10.1101/2021.02.02.21251043,2021-02-05,https://medrxiv.org/cgi/content/short/2021.02.02.21251043,COVID-19 infection and subsequent thromboembolism: A self-controlled case series analysis of a population cohort,Frederick Ho; Kenneth Man; Mark Toshner; Colin Church; Carlos Celis-Morales; Ian Wong; Colin Berry; Naveed Sattar; Jill Pell,University of Glasgow; UCL; University of Cambridge; NHS Greater Glasgow and Clyde; University of Glasgow; UCL; University of Glasgow; University of Glasgow; University of Glasgow,"ObjectiveAn unexpectedly large number of people infected with Covid-19 had experienced a thrombotic event. This study aims to assess the associations between Covid-19 infection and thromboembolism including myocardial infarction (MI), ischaemic stroke, deep-vein thrombosis (DVT), and pulmonary embolism (PE). -Research in contextO_ST_ABSEvidence before this studyC_ST_ABSA recent systematic review by Pan and colleagues demonstrated that people of ethnic minority background in the UK and the USA have been disproportionately affected by the Coronavirus (COVID-19) pandemic, compared to White populations. While several studies have investigated whether adjusting for socio-demographic and economic factors and medical history reduces the estimated difference in risk of mortality and hospitalisation, the reasons for the differences in the risk of experiencing harms from COVID-19 are still being explored during the course of the pandemic. Studies so far have analysed the ethnic differences in COVID-19 mortality in the first wave of the pandemic. The evidence on the temporal trend of ethnic inequalities in COVID-19 mortality, especially those from the second wave of the pandemic, is scarce. +Patients and MethodsA self-controlled case-series study was conducted covering the whole of Scotlands general population. The study population comprised individuals with confirmed (positive test) Covid-19 and at least one thromboembolic event between March 2018 and October 2020. Their incidence rates during the risk interval (5 days before to 56 days after the positive test) and the control interval (the remaining periods) were compared intra-personally. -Added value of this studyUsing data from the Office for National Statistics (ONS) Public Health Data Asset on 29 million adults aged 30-100 years living in private households in England, we conducted an observational cohort study to examine the differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and second wave (from 1st September to 28th December 2020). We find that in the first wave all ethnic minority groups were at elevated risk of COVID-19 related death compared to the White British population. In the second wave, the differences in the risk of COVID-19 related death attenuated for Black African and Black Caribbean groups, remained substantially higher in people from Bangladeshi background, and worsened in people from Pakistani background. We also find that some of the factors explaining these differences in mortality have changed in the two waves. +ResultsAcross Scotland, 1,449 individuals tested positive for Covid-19 and experienced a thromboembolic event. The risk of thromboembolism was significantly elevated over the whole risk period but highest in the 7 days following the positive test (IRR 12.01, 95% CI 9.91-14.56) in all included individuals. The association was also present in individuals not originally hospitalised for Covid-19 (IRR 4.07, 95% CI 2.83-5.85). Risk of MI, stroke, PE and DVT were all significantly higher in the week following a positive test. The risk of PE and DVT was particularly high and remained significantly elevated even 56 days following the test. -Implications of all the available evidenceThe risk of COVID-19 mortality during the first wave of the pandemic was elevated in people from ethnic minority background. An appreciable reduction in the difference in COVID-19 mortality in the second wave of the pandemic between people from Black ethnic background and people from the White British group is reassuring, but the continued higher rate of mortality in people from Bangladeshi and Pakistani background is alarming and requires focused public health campaign and policy response. Focusing on treating underlying conditions, although important, may not be enough in reducing the inequalities in COVID-19 mortality. Focused public health policy as well as community mobilisation and participatory public health campaign involving community leaders may help reduce the existing and widening inequalities in COVID-19 mortality.",epidemiology,fuzzy,100,100 +ConclusionConfirmed Covid-19 infection was associated with early elevations in risk with MI, ischaemic stroke, and substantially stronger and prolonged elevations with DVT and PE both in hospital and community settings. Clinicians should consider thromboembolism, especially PE, among people with Covid-19 in the community.",cardiovascular medicine,fuzzy,100,100 medRxiv,10.1101/2021.02.03.21250974,2021-02-05,https://medrxiv.org/cgi/content/short/2021.02.03.21250974,Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US,Estee Y Cramer; Evan L Ray; Velma K Lopez; Johannes Bracher; Andrea Brennen; Alvaro J Castro Rivadeneira; Aaron Gerding; Tilmann Gneiting; Katie H House; Yuxin Huang; Dasuni Jayawardena; Abdul H Kanji; Ayush Khandelwal; Khoa Le; Anja Muehlemann; Jarad Niemi; Apurv Shah; Ariane Stark; Yijin Wang; Nutcha Wattanachit; Martha W Zorn; Youyang Gu; Sansiddh Jain; Nayana Bannur; Ayush Deva; Mihir Kulkarni; Srujana Merugu; Alpan Raval; Siddhant Shingi; Avtansh Tiwari; Jerome White; Neil F Abernethy; Spencer Woody; Maytal Dahan; Spencer Fox; Kelly Gaither; Michael Lachmann; Lauren Ancel Meyers; James G Scott; Mauricio Tec; Ajitesh Srivastava; Glover E George; Jeffrey C Cegan; Ian D Dettwiller; William P England; Matthew W Farthing; Robert H Hunter; Brandon Lafferty; Igor Linkov; Michael L Mayo; Matthew D Parno; Michael A Rowland; Benjamin D Trump; Yanli Zhang-James; Samuel Chen; Stephen V Faraone; Jonathan Hess; Christopher P Morley; Asif Salekin; Dongliang Wang; Sabrina M Corsetti; Thomas M Baer; Marisa C Eisenberg; Karl Falb; Yitao Huang; Emily T Martin; Ella McCauley; Robert L Myers; Tom Schwarz; Daniel Sheldon; Graham Casey Gibson; Rose Yu; Liyao Gao; Yian Ma; Dongxia Wu; Xifeng Yan; Xiaoyong Jin; Yu-Xiang Wang; YangQuan Chen; Lihong Guo; Yanting Zhao; Quanquan Gu; Jinghui Chen; Lingxiao Wang; Pan Xu; Weitong Zhang; Difan Zou; Hannah Biegel; Joceline Lega; Steve McConnell; VP Nagraj; Stephanie L Guertin; Christopher Hulme-Lowe; Stephen D Turner; Yunfeng Shi; Xuegang Ban; Robert Walraven; Qi-Jun Hong; Stanley Kong; Axel van de Walle; James A Turtle; Michal Ben-Nun; Steven Riley; Pete Riley; Ugur Koyluoglu; David DesRoches; Pedro Forli; Bruce Hamory; Christina Kyriakides; Helen Leis; John Milliken; Michael Moloney; James Morgan; Ninad Nirgudkar; Gokce Ozcan; Noah Piwonka; Matt Ravi; Chris Schrader; Elizabeth Shakhnovich; Daniel Siegel; Ryan Spatz; Chris Stiefeling; Barrie Wilkinson; Alexander Wong; Sean Cavany; Guido Espana; Sean Moore; Rachel Oidtman; Alex Perkins; David Kraus; Andrea Kraus; Zhifeng Gao; Jiang Bian; Wei Cao; Juan Lavista Ferres; Chaozhuo Li; Tie-Yan Liu; Xing Xie; Shun Zhang; Shun Zheng; Alessandro Vespignani; Matteo Chinazzi; Jessica T Davis; Kunpeng Mu; Ana Pastore y Piontti; Xinyue Xiong; Andrew Zheng; Jackie Baek; Vivek Farias; Andreea Georgescu; Retsef Levi; Deeksha Sinha; Joshua Wilde; Georgia Perakis; Mohammed Amine Bennouna; David Nze-Ndong; Divya Singhvi; Ioannis Spantidakis; Leann Thayaparan; Asterios Tsiourvas; Arnab Sarker; Ali Jadbabaie; Devavrat Shah; Nicolas Della Penna; Leo A Celi; Saketh Sundar; Russ Wolfinger; Dave Osthus; Lauren Castro; Geoffrey Fairchild; Isaac Michaud; Dean Karlen; Matt Kinsey; Luke C. Mullany; Kaitlin Rainwater-Lovett; Lauren Shin; Katharine Tallaksen; Shelby Wilson; Elizabeth C Lee; Juan Dent; Kyra H Grantz; Alison L Hill; Joshua Kaminsky; Kathryn Kaminsky; Lindsay T Keegan; Stephen A Lauer; Joseph C Lemaitre; Justin Lessler; Hannah R Meredith; Javier Perez-Saez; Sam Shah; Claire P Smith; Shaun A Truelove; Josh Wills; Maximilian Marshall; Lauren Gardner; Kristen Nixon; John C. Burant; Lily Wang; Lei Gao; Zhiling Gu; Myungjin Kim; Xinyi Li; Guannan Wang; Yueying Wang; Shan Yu; Robert C Reiner; Ryan Barber; Emmanuela Gaikedu; Simon Hay; Steve Lim; Chris Murray; David Pigott; Heidi L Gurung; Prasith Baccam; Steven A Stage; Bradley T Suchoski; B. Aditya Prakash; Bijaya Adhikari; Jiaming Cui; Alexander Rodriguez; Anika Tabassum; Jiajia Xie; Pinar Keskinocak; John Asplund; Arden Baxter; Buse Eylul Oruc; Nicoleta Serban; Sercan O Arik; Mike Dusenberry; Arkady Epshteyn; Elli Kanal; Long T Le; Chun-Liang Li; Tomas Pfister; Dario Sava; Rajarishi Sinha; Thomas Tsai; Nate Yoder; Jinsung Yoon; Leyou Zhang; Sam Abbott; Nikos I Bosse; Sebastian Funk; Joel Hellewell; Sophie R Meakin; Katharine Sherratt; Mingyuan Zhou; Rahi Kalantari; Teresa K Yamana; Sen Pei; Jeffrey Shaman; Michael L Li; Dimitris Bertsimas; Omar Skali Lami; Saksham Soni; Hamza Tazi Bouardi; Turgay Ayer; Madeline Adee; Jagpreet Chhatwal; Ozden O Dalgic; Mary A Ladd; Benjamin P Linas; Peter Mueller; Jade Xiao; Yuanjia Wang; Qinxia Wang; Shanghong Xie; Donglin Zeng; Alden Green; Jacob Bien; Logan Brooks; Addison J Hu; Maria Jahja; Daniel McDonald; Balasubramanian Narasimhan; Collin Politsch; Samyak Rajanala; Aaron Rumack; Noah Simon; Ryan J Tibshirani; Rob Tibshirani; Valerie Ventura; Larry Wasserman; Eamon B O'Dea; John M Drake; Robert Pagano; Quoc T Tran; Lam Si Tung Ho; Huong Huynh; Jo W Walker; Rachel B Slayton; Michael A Johansson; Matthew Biggerstaff; Nicholas G Reich,"University of Massachusetts, Amherst; University of Massachusetts, Amherst; Centers for Disease Control and Prevention; Chair of Econometrics and Statistics, Karlsruhe Institute of Technology; Computational Statistics Group, Heidelberg Institute for Theoretical Studies; IQT; University of Massachusetts, Amherst; University of Massachusetts, Amherst; Institute of Stochastics, Karlsruhe Institute of Technology; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; Institute of Mathematical Statistics and Actuarial Science, University of Bern; Iowa State University; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; University of Massachusetts, Amherst; Unaffiliated; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; Wadhwani Institute of Artificial Intelligence; University of Washington; University of Texas at Austin; Texas Advanced Computing Center; University of Texas at Austin; Texas Advanced Computing Center; Santa Fe Institute; University of Texas at Austin; University of Texas at Austin; University of Texas at Austin; University of Southern California; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; US Army Engineer Research and Development Center; State University of New York Upstate Medical University; State University of New York Upstate Medical University; State University of New York Upstate Medical University; State University of New York Upstate Medical University; State University of New York Upstate Medical University; Syracuse University; State University of New York Upstate Medical University; University of Michigan - Ann Arbor; Trinity University, San Antonio; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Michigan - Ann Arbor; University of Massachusetts, Amherst; University of Massachusetts, Amherst; Northeastern University; University of California, San Diego; University of Washington; University of California, San Diego; University of California, San Diego; University of California at Santa Barbara; University of California at Santa Barbara; University of California at Santa Barbara; University of California, Merced; Jilin University; University of Science and Technology of China; University of California, Los Angeles; University of California, Los Angeles; University of California, Los Angeles; University of California, Los Angeles; University of California, Los Angeles; University of California, Los Angeles; University of Arizona; University of Arizona; Construx; Signature Science, LLC; Signature Science, LLC; Signature Science, LLC; Signature Science, LLC; Rensselaer Polytechnic Institute; University of Washington; Unaffiliated; Arizona State University; Brown University; Manhasset Secondary School; Brown University; Predictive Science, Inc; Predictive Science, Inc; Imperial College, London; Predictive Science, Inc; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; Oliver Wyman; University of Notre Dame; University of Notre Dame; University of Notre Dame; University of Chicago; University of Notre Dame; University of Notre Dame; Masaryk University; Masaryk University; Microsoft; Microsoft; Microsoft; Microsoft; Microsoft; Microsoft; Microsoft; Microsoft; Microsoft; ISI Foundation; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University; Operations Research Center, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Sloan School of Management, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Sloan School of Management, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Massachusetts Institute of Technology; Massachusetts Institute of Technology; Massachusetts Institute of Technology; New York University; Massachusetts Institute of Technology; Massachusetts Institute of Technology; Massachusetts Institute of Technology; Institute for Data, Systems, and Society, Massachusetts Institute of Technology; Institute for Data, Systems, and Society, Massachusetts Institute of Technology; Institute for Data, Systems, and Society, Massachusetts Institute of Technology; Laboratory for Computational Physiology, Massachusetts Institute of Technology; Laboratory for Computational Physiology, Massachusetts Institute of Technology; River Hill High School; SAS Institute Inc; Los Alamos National Laboratory; Los Alamos National Laboratory; Los Alamos National Laboratory; Los Alamos National Laboratory; TRIUMF; University of Victoria; Johns Hopkins University Applied Physics Lab; Johns Hopkins University Applied Physics Lab; Johns Hopkins University Applied Physics Lab; Johns Hopkins University Applied Physics Lab; Johns Hopkins University Applied Physics Lab; Johns Hopkins University Applied Physics Lab; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins University; Johns Hopkins Bloomberg School of Public Health; Unaffiliated; University of Utah; Johns Hopkins Bloomberg School of Public Health; Ecole Polytechnique Federale de Lausanne; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins Bloomberg School of Public Health; Unaffiliated; Johns Hopkins Bloomberg School of Public Health; Johns Hopkins Bloomberg School of Public Health; Unaffiliated; Johns Hopkins University; Johns Hopkins University; Johns Hopkins University; Unaffiliated; Iowa State University; Iowa State University; Iowa State University; Iowa State University; Clemson University; College of William & Mary; Iowa State University; University of Virginia; University of Washington; University of Washington; University of Washington; University of Washington; University of Washington; University of Washington; University of Washington; IEM, Inc.; IEM, Inc.; IEM, Inc.; IEM, Inc.; Georgia Institute of Technology; University of Iowa; Georgia Institute of Technology; Georgia Institute of Technology; Georgia Institute of Technology; Virginia Tech; Georgia Institute of Technology; Georgia Insitute of Technology; Metron, Inc.; Georgia Insitute of Technology; Georgia Insitute of Technology; Georgia Insitute of Technology; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Google Cloud; Harvard University; Google Cloud; Google Cloud; Google Cloud; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; The University of Texas at Austin; The University of Texas at Austin; Columbia University; Columbia University; Columbia University; Operations Research Center, Massachusetts Institute of Technology; Sloan School of Management, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Operations Research Center, Massachusetts Institute of Technology; Emory University Medical School; Georgia Insitute of Technology; MGH; MGH; Value Analytics Labs; MGH; Boston University School of Medicine; MGH; Georgia Insitute of Technology; Columbia University; Columbia University; Columbia University; UNC Chapel Hill; Carnegie Mellon University; University of Southern California; Carnegie Mellon University; Carnegie Mellon University; Carnegie Mellon University; University of British Columbia; Stanford University; Carnegie Mellon University; Stanford University; Carnegie Mellon University; University of Washington; Carnegie Mellon University; Stanford University; Carnegie Mellon University; Carnegie Mellon University; University of Georgia; University of Georgia; Unaffiliated; Walmart Inc.; Dalhousie University; Virtual Power System Inc.; Centers for Disease Control and Prevention; Centers for Disease Control and Prevention; Centers for Disease Control and Prevention; Centers for Disease Control and Prevention; University of Massachusetts, Amherst","Short-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. Starting in April 2020, the US COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized tens of millions of specific predictions from more than 90 different academic, industry, and independent research groups. A multi-model ensemble forecast that combined predictions from dozens of different research groups every week provided the most consistently accurate probabilistic forecasts of incident deaths due to COVID-19 at the state and national level from April 2020 through October 2021. The performance of 27 individual models that submitted complete forecasts of COVID-19 deaths consistently throughout this year showed high variability in forecast skill across time, geospatial units, and forecast horizons. Two-thirds of the models evaluated showed better accuracy than a naive baseline model. Forecast accuracy degraded as models made predictions further into the future, with probabilistic error at a 20-week horizon 3-5 times larger than when predicting at a 1-week horizon. This project underscores the role that collaboration and active coordination between governmental public health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks. Significance StatementThis paper compares the probabilistic accuracy of short-term forecasts of reported deaths due to COVID-19 during the first year and a half of the pandemic in the US. Results show high variation in accuracy between and within stand-alone models, and more consistent accuracy from an ensemble model that combined forecasts from all eligible models. This demonstrates that an ensemble model provided a reliable and comparatively accurate means of forecasting deaths during the COVID-19 pandemic that exceeded the performance of all of the models that contributed to it. This work strengthens the evidence base for synthesizing multiple models to support public health action.",epidemiology,fuzzy,100,100 @@ -3851,26 +3796,6 @@ Our estimates of sensitivity and specificity are likely to be higher than would Implications of all the available evidenceWhen used in epidemiological studies of antibody prevalence, the estimates of sensitivity and specificity provided in this study can be used to adjust for test errors. Increased precision in error rates will translate to increased precision in seroprevalence estimates. If lateral flow devices were used for individual risk assessment, devices with maximum specificity would be preferable. However, if, for an example, 20% of the tested population had antibodies, we estimate that around 1 in 20 positive results on the most specific device would be incorrect.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.01.28.21250606,2021-01-31,https://medrxiv.org/cgi/content/short/2021.01.28.21250606,REACT-1 round 8 final report: high average prevalence with regional heterogeneity of trends in SARS-CoV-2 infection in the community in England during January 2021,Steven Riley; Oliver Eales; Caroline E. Walters; Haowei Wang; Kylie E. C. Ainslie; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear","In early January 2021, England entered its third national lockdown of the COVID-19 pandemic to reduce numbers of deaths and pressure on healthcare services, while rapidly rolling out vaccination to healthcare workers and those most at risk of severe disease and death. REACT-1 is a survey of SARS-CoV-2 prevalence in the community in England, based on repeated cross-sectional samples of the population. Between 6th and 22nd January 2021, out of 167,642 results, 2,282 were positive giving a weighted national prevalence of infection of 1.57% (95% CI, 1.49%, 1.66%). The R number nationally over this period was estimated at 0.98 (0.92, 1.04). Prevalence remained high throughout, but with suggestion of a decline at the end of the study period. The average national trend masked regional heterogeneity, with robustly decreasing prevalence in one region (South West) and increasing prevalence in another (East Midlands). Overall prevalence at regional level was highest in London at 2.83% (2.53%, 3.16%). Although prevalence nationally was highest in the low-risk 18 to 24 year old group at 2.44% (1.96%, 3.03%), it was also high in those over 65 years who are most at risk, at 0.93% (0.82%, 1.05%). Large household size, living in a deprived neighbourhood, and Black and Asian ethnicity were all associated with higher levels of infections compared to smaller households, less deprived neighbourhoods and other ethnicities. Healthcare and care home workers, and other key workers, were more likely to test positive compared to other workers. If sustained lower prevalence is not achieved rapidly in England, pressure on healthcare services and numbers of COVID-19 deaths will remain unacceptably high.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.01.25.21249942,2021-01-30,https://medrxiv.org/cgi/content/short/2021.01.25.21249942,Development and external validation of prognostic models for COVID-19 to support risk stratification in secondary care,Nicola J Adderley; Thomas Taverner; Malcolm Price; Christopher Sainsbury; David Greenwood; Joht Singh Chandan; Yemisi Takwoingi; Rashan Haniffa; Isaac Hosier; Carly Welch; Dhruv Parekh; Suzy Gallier; Krishna M Gokhale; Alastair K Denniston; Elizabeth Sapey; Krishnarajah Nirantharakumar,University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Oxford; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham,"ObjectivesExisting UK prognostic models for patients admitted to hospital with COVID-19 are limited by reliance on comorbidities, which are under-recorded in secondary care, and lack of imaging data among the candidate predictors. Our aims were to develop and externally validate novel prognostic models for adverse outcomes (death, intensive therapy unit (ITU) admission) in UK secondary care; and externally validate the existing 4C score. - -DesignCandidate predictors included demographic variables, symptoms, physiological measures, imaging, laboratory tests. Final models used logistic regression with stepwise selection. - -SettingModel development was performed in data from University Hospitals Birmingham (UHB). External validation was performed in the CovidCollab dataset. - -ParticipantsPatients with COVID-19 admitted to UHB January-August 2020 were included. - -Main outcome measuresDeath and ITU admission within 28 days of admission. - -Results1040 patients with COVID-19 were included in the derivation cohort; 288 (28%) died and 183 (18%) were admitted to ITU within 28 days of admission. Area under the receiver operating curve (AUROC) for mortality was 0.791 (95%CI 0.761-0.822) in UHB and 0.767 (95%CI 0.754-0.780) in CovidCollab; AUROC for ITU admission was 0.906 (95%CI 0.883-0.929) in UHB and 0.811 (95%CI 0.795-0.828) in CovidCollab. Models showed good calibration. Addition of comorbidities to candidate predictors did not improve model performance. AUROC for the 4C score in the UHB dataset was 0.754 (95%CI 0.721-0.786). - -ConclusionsThe novel prognostic models showed good discrimination and calibration in derivation and external validation datasets, and outperformed the existing 4C score. The models can be integrated into electronic medical records systems to calculate each individual patients probability of death or ITU admission at the time of hospital admission. Implementation of the models and clinical utility should be evaluated. - -Article SummaryO_ST_ABSStrengths and limitations of this studyC_ST_ABSO_LIWe developed novel prognostic models predicting mortality and ITU admission within 28 days of admission for patients hospitalised with COVID-19, using a large routinely collected dataset gathered at admission with a wide range of possible predictors (demographic variables, symptoms, physiological measures, imaging, laboratory test results). -C_LIO_LIThese novel models showed good discrimination and calibration in both derivation and external validation cohorts, and outperformed the existing ISARIC model and 4C score in the derivation dataset. We found that addition of comorbidities to the set of candidate predictors included in model derivation did not improve model performance. -C_LIO_LIIf integrated into hospital electronic medical records systems, the model algorithms will provide a predicted probability of mortality or ITU admission for each patient based on their individual data at, or close to, the time of admission, which will support clinicians decision making with regard to appropriate patient care pathways and triage. This information might also assist clinicians in explaining complex prognostic assessments and decisions to patients and their relatives. -C_LIO_LIA limitation of the study was that in the external validation cohort we were unable to examine all of the predictors included in the original full UHB model due to only a reduced set of candidate predictors being available in CovidCollab. Nevertheless, the reduced model performed well and the results suggest it may be applicable in a wide range of datasets where only a reduced set of predictor variables is available. -C_LIO_LIFurthermore, it was not possible to carry out stratified analysis by ethnicity as the UHB dataset contained too few patients in most of the strata, and no ethnicity data was available in the CovidCollab dataset. -C_LI",public and global health,fuzzy,100,100 medRxiv,10.1101/2021.01.28.21250680,2021-01-29,https://medrxiv.org/cgi/content/short/2021.01.28.21250680,"The effect of SARS-CoV-2 variant B.1.1.7 on symptomatology, re-infection and transmissibility",Mark S Graham; Carole H Sudre; Anna May; Michela Antonelli; Benjamin Murray; Thomas Varsavsky; Kerstin Klaser; Liane Dos Santos Canas; Erika Molteni; Marc Modat; David Alden Drew; Long Alden Nguyen; Lorenzo Polidori; Somesh Selvachandran; Christina Hu; Joan Capdevila Pujol; - The COVID-19 Genomics UK (COG-UK) consortium; Alexander Hammers; Andrew T Chan; Jonathan Wolf; Timothy Spector; Claire Steves; Sebastien Ourselin,King's College London; MRC Unit for Lifelong Health and Ageing; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Massachusetts General Hospital; Massachusetts General Hospital and Harvard Medical School; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; ; King's College London; Massachusetts General Hospital; Zoe Global Limited; King's College London; King's College London; King's College London,"BackgroundSARS-CoV-2 variant B.1.1.7 was first identified in December 2020 in England. It is not known if the new variant presents with variation in symptoms or disease course, if previously infected individuals may become reinfected with the new variant, or how the variants increased transmissibility affects measures to reduce its spread. MethodsUsing longitudinal symptom reports from 36,920 users of the COVID Symptom Study app testing positive for Covid-19 between 28 September and 27 December 2020, we performed an ecological study to examine the association between the regional proportion of B.1.1.7 and reported symptoms, disease course, rates of reinfection, and transmissibility. @@ -3959,6 +3884,7 @@ RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSPublic policy measu Added value of this studyCommissioned by the Chief Medical Officer for England, we validated the novel clinical risk prediction model (QCovid) to identify risks of short-term severe outcomes due to COVID-19. We used national linked datasets from general practice, death registry and hospital episode data for a population-representative sample of over 34 million adults. The risk models have excellent discrimination in men and women (Harrells C statistic>0.9) and are well calibrated. QCovid represents a new, evidence-based opportunity for population risk-stratification. Implications of all the available evidenceQCovid has the potential to support public health policy, from enabling shared decision making between clinicians and patients in relation to health and work risks, to targeted recruitment for clinical trials, and prioritisation of vaccination, for example.",public and global health,fuzzy,100,100 +bioRxiv,10.1101/2021.01.25.428136,2021-01-25,https://biorxiv.org/cgi/content/short/2021.01.25.428136,mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge,Michelle Meyer; Yuan Wang; Darin Edwards; Gregory R Smith; Aliza B Rubenstein; Palaniappan Ramanathan; Chad E Mire; Colette Pietzsch; Xi Chen; Yongchao Ge; Wan Sze Cheng; Carole Henry; Angela Woods; LingZhi Ma; Guillaume B. E. Stewart-Jones; Kevin W Bock; Minai Mahnaz; Bianca M Nagata; Sivakumar Periasamy; Pei-Yong Shi; Barney S Graham; Ian N Moore; Irene Ramos; Olga G. Troyanskaya; Elena Zaslavsky; Andrea Carfi; Stuart C Sealfon; Alexander Bukreyev,"University of Texas Medical Branch; Princeton University; Moderna Inc; Icahn School of Medicine at Mount Sinai; Icahn School of Medicine at Mount Sinai; University of Texas Medical Branch; University of Texas Medical Branch; University of Texas Medical Branch; Flatiron Institute, Simons Foundation; Icahn School of Medicine at Mount Sinai; Icahn School of Medicine at Mount Sinai; Moderna Inc; Moderna Inc; Moderna Inc; Moderna Inc; National Institute of Health; National Institutes of Health; National Institutes of Health; University of Texas Medical Branch; University of Texas Medical Branch; National Institutes of Health; National Institutes of Health; Icahn School of Medicine at Mount Sinai; Princeton University; Icahn School of Medicine at Mount Sinai; Moderna Inc; Icahn School of Medicine at Mount Sinai; University of Texas Medical Branch at Galveston","The mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase 3 results. Human studies, however, cannot provide the controlled response to infection and complex immunological insight that are only possible with preclinical studies. Hamsters are the only model that reliably exhibit more severe SARS-CoV-2 disease similar to hospitalized patients, making them pertinent for vaccine evaluation. We demonstrate that prime or prime-boost administration of mRNA-1273 in hamsters elicited robust neutralizing antibodies, ameliorated weight loss, suppressed SARS-CoV-2 replication in the airways, and better protected against disease at the highest prime-boost dose. Unlike in mice and non-human primates, mRNA-1273- mediated immunity was non-sterilizing and coincided with an anamnestic response. Single-cell RNA sequencing of lung tissue permitted high resolution analysis which is not possible in vaccinated humans. mRNA-1273 prevented inflammatory cell infiltration and the reduction of lymphocyte proportions, but enabled antiviral responses conducive to lung homeostasis. Surprisingly, infection triggered transcriptome programs in some types of immune cells from vaccinated hamsters that were shared, albeit attenuated, with mock-vaccinated hamsters. Our results support the use of mRNA-1273 in a two-dose schedule and provides insight into the potential responses within the lungs of vaccinated humans who are exposed to SARS-CoV-2.",immunology,fuzzy,96,94 medRxiv,10.1101/2021.01.21.20240887,2021-01-22,https://medrxiv.org/cgi/content/short/2021.01.21.20240887,"The psychosocial impact of the COVID-19 pandemic on 4,378 UK healthcare workers and ancillary staff: initial baseline data from a cohort study collected during the first wave of the pandemic.",Danielle Lamb; Sam Gnanapragasam; Neil Greenberg; Rupa Bhundia; Ewan Carr; Matthew Hotopf; Reza Razavi; Rosalind Raine; Sean Cross; Amy Dewar; Mary Docherty; Sarah Dorrington; Stephani Hatch; Charlotte Wilson-Jones; Daniel Leightley; Ira Madan; Sally Marlow; Isabel McMullen; Anne Marie Rafferty; Martin Parsons; Catherine Polling; Danai Serfioti; Helen Gaunt; Peter Aitken; Joanna Morris-Bone; Chloe Simela; Veronica French; Rachel Harris; Sharon A.M. Stevelink; Simon Wessely,"Department of Applied Health Research, UCL, 1-19 Torrington Place, London, WC1E 7HB; South London and Maudsley NHS Foundation Trust, London, UK; Health Protection Research Unit, King's College London, Weston Education Centre, 10 Cutcombe Road, London, SE5 9RJ; Department of Psychological Medicine, King's College London, London, UK.; Department of Biostatistics and Health Informatics, King's College London, London, UK; National Institute of Health Research Biomedical Research Centre at the South London and Maudsley NHS Foundation Trust.; 1 Lambeth Palace Rd, South Bank, London, SE1 7EU; Dept of Applied Health Research, UCL; Department of Psychological Medicine, King's College Hospital. Denmark Hill. SE5 9RS; Guy's and St Thomas' NHS Foundation Trust; Department of Psychological Medicine, King's College Hospital. Denmark Hill. SE5 9RS; Institute of Psychiatry, Psychology and Neuroscience, King's College London; Institute of Psychiatry, Psychology and Neuroscience, King's College London; Institute of Psychiatry, Psychology and Neuroscience, King's College London; King's Centre for Military Health Research, Department of Psychological Medicine, King's College London, London, UK. AND Department of Psychological Medicine, K; Guy's and St Thomas' NHS Foundation Trust, London; Institute of Psychiatry, Psychology and Neuroscience, King's College London; Department of Psychological Medicine, King's College Hospital, South London and Maudsley NHS Foundation Trust; Adult Nursing, King's College London; Mental Health Liaison Team, King's College Hospital; Institute of Psychiatry, Psychology and Neuroscience, King's College London; King's Centre for Military Health Research, King's College London, Room 307, Weston Education Centre, 10 Cutcombe Road, London SE5 9RJ; University Hospital of Leciester NHS Trust. Groby Road Leciester LE4 9QP; Devon Partnership NHS Trust, Trust HQ, R&D, Dryden Road, Exeter, Devon, EX2 5AF; Avon & Wiltshire Mental Health Partnership NHS Trust, R&D, Fromeside, Blackberry Hill Hospital, Bristol, BS16 1EG; Guy's and St Thomas' NHS Foundation Trust, London; Nottinghamshire Healthcare NHS Foundation Trust; Cornwall Partnership Foundation NHS Trust/ Research and Innovation Team; King's Centre for Military Health Research, Department of Psychological Medicine, King's College London, London, UK. AND Department of Psychological Medicine, K; Department of Psychological Medicine, King's College London, Weston Education, Denmark Hill, London, SE5 9JR","ObjectivesThis study reports preliminary findings on the prevalence of, and factors associated with, mental health and wellbeing outcomes of healthcare workers during the early months (April-June) of the COVID-19 pandemic in the UK. MethodsPreliminary cross-sectional data were analysed from a cohort study (n=4,378). Clinical and non-clinical staff of three London-based NHS Trusts (UK), including acute and mental health Trusts, took part in an online baseline survey. The primary outcome measure used is the presence of probable common mental disorders (CMDs), measured by the General Health Questionnaire (GHQ-12). Secondary outcomes are probable anxiety (GAD-7), depression (PHQ-9), Post-Traumatic Stress Disorder (PTSD) (PCL-6), suicidal ideation (CIS-R), and alcohol use (AUDIT). Moral injury is measured using the Moray Injury Event Scale (MIES). @@ -4189,23 +4115,6 @@ FindingsBetween 7 April and 27 November 2020, 2582 patients were randomly alloca InterpretationIn patients hospitalised with COVID-19, azithromycin did not provide any clinical benefit. Azithromycin use in patients hospitalised with COVID-19 should be restricted to patients where there is a clear antimicrobial indication. FundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056).",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.12.11.20247742,2020-12-14,https://medrxiv.org/cgi/content/short/2020.12.11.20247742,Changes in cardiovascular disease monitoring in English primary care during the COVID-19 pandemic: an observational cohort study,Clare R Bankhead; Sarah Lay-Flurrie; Brian D Nicholson; James P Sheppard; Chris P Gale; Harshana Liyanage; Dylan McGagh; Mark Minchin; Rafael Perera; Julian Sherlock; Margaret Smith; Nicholas PB Thomas; Cynthia Wright Drakesmith; Simon D de Lusignan; Richard Hobbs,University of Oxford; University of Oxford; Nuffield Department of Primary Care Health Sciences; University of Oxford; University of Leeds; University of Oxford; University of Oxford; National Institute for Health and Care Excellence; University of Oxford; University of Oxford; University of Oxford; Royal College of General Practitioners; University of Oxford; University of Oxford; University of Oxford,"ObjectiveTo quantify the impact and recovery in cardiovascular disease monitoring in primary care associated with the first COVID-19 lockdown. - -DesignRetrospective nationwide primary care cohort study, utilising data from 1st January 2018 to 27th September 2020. - -SettingWe extracted primary care electronic health records data from 514 primary care practices in England contributing to the Oxford Royal College of General Practitioners Clinical Informatics Digital Hub (ORCHID). These practices were representative of English primary care across urban and non-urban practices. - -ParticipantsThe ORCHID database included 6,157,327 active patients during the study period, and 13,938,390 patient years of observation (final date of follow-up 27th September 2020). The mean (SD) age was 38{+/-}24 years, 49.4% were male and the majority were of white ethnicity (65% [21.9% had unknown ethnicity]) - -ExposureThe primary exposure was the first national lockdown in the UK, starting on 23rd March 2020. - -Main outcome measuresRecords of cholesterol, blood pressure, HbA1c and International Normalised Ratio (INR) measurement derived from coded entries in the primary care electronic health record. - -ResultsRates of cholesterol, blood pressure, HbA1c and INR recording dropped by 23-87% in the week following the first UK national lockdown, compared with the previous week. The largest decline was seen in cholesterol (IRR 0.13, 95% CI 0.11 to 0.15) and smallest for INR (IRR 0.77, 95% CI 0.72 to 0.81). - -Following the immediate drop, rates of recorded tests increased on average by 5-9% per week until 27th September 2020. However, the number of recorded measures remained below that expected for the time of year, reaching 51.8% (95% CI 51.8 to 51.9%) for blood pressure, 63.7%, (95% CI 63.7% to 63.8%) for cholesterol measurement and 70.3% (95% CI 70.2% to 70.4%) for HbA1c. Rates of INR recording declined throughout the previous two years, a trend that continued after lockdown. There were no differences in the times series trends based on sex, age, ethnicity or deprivation. - -ConclusionsCardiovascular disease monitoring in English primary care declined substantially from the time of the first UK lockdown. Despite a consistent recovery in activity, there is still a substantial shortfall in the numbers of recorded measurements to those expected. Strategies are required to ensure cardiovascular disease monitoring is maintained during the COVID-19 pandemic.",primary care research,fuzzy,100,100 medRxiv,10.1101/2020.12.10.20247155,2020-12-14,https://medrxiv.org/cgi/content/short/2020.12.10.20247155,Self-harm presentations to Emergency Departments and Place of Safety during the first wave of the UK COVID-19 pandemic: South London and Maudsley data on service use from February to June 2020.,Eleanor Nuzum; Evangelia Martin; Gemma Morgan; Rina Dutta; Christoph Mueller; Catherine Polling; Megan Pritchard; Sumithra Velupillai; Robert Stewart,South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic has had a substantial impact on both mental health service delivery, and the ways in which people are accessing these services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for around 1.2m residents in South London) have highlighted increased use of virtual contacts by mental health teams, with dropping numbers of face-to-face contacts over the first wave of the pandemic. There has been concern that the impact of the COVID-19 pandemic would lead to higher mental health emergencies, particularly instances of self-harm. However, with people advised to stay at home during the first wave lockdown, it is as yet unclear whether this impacted mental health service presentations. Taking advantage of SLaMs Clinical Records Interactive Search (CRIS) data resource with daily updates of information from its electronic mental health records, this paper describes overall presentations to Emergency Department (ED) mental health liaison teams, and those with self-harm. The paper focussed on three periods: i) a pre-lockdown period 1st February to 15th March, ii) a lockdown period 16th March to 10th May and iii) a post-lockdown period 11th May to 28th June. In summary, all attendances to EDs for mental health support decreased during the lockdown period, including those with self-harm. All types of self-harm decreased during lockdown, with self-poisoning remaining the most common. Attendances to EDs for mental health support increased post-lockdown, although were only just approaching pre-lockdown levels by the end of June 2020.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2020.12.05.20241927,2020-12-11,https://medrxiv.org/cgi/content/short/2020.12.05.20241927,Neutralising antibodies drive Spike mediated SARS-CoV-2 evasion,Steven A Kemp; Dami A Collier; Rawlings Datir; Isabella ATM Ferreira; Salma Gayed; Aminu Jahun; Myra Hosmillo; Chloe Rees-Spear; Petra Mlcochova; Ines Ushiro Lumb; David Roberts; Anita Chandra; Nigel Temperton; - The COVID-19 Genomics UK (COG-UK) Consortium; Katherine Sharrocks; Elizabeth Blane; - The CITIID-NIHR BioResource COVID-19 Collaboration; John A Briggs; Marit van Gils; Ken G Smith; John R Bradley; Chris Smith; Rainer Doffinger; Lourdes Ceron-Gutierrez; Gabriela Barcenas-Morales; David Pollock; Richard Goldstein; Anna Smielewska; Jordan P Skittrall; Theo Gouliouris; Ian G Goodfellow; Effrossyni Gkrania-Klotsas; Chris JR Illingworth; Laura E McCoy; Ravindra K Gupta,"Division of Infection and Immunity, University College London, London, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.; Department of Pathology, University of Cambridge, Cambridge; Department of Pathology, University of Cambridge, Cambridge; Division of Infection and Immunity, University College London, London, UK.; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; Public Health England, Colindale, London, UK; Public Health England, Colindale, London, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, UK; -; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.; Department of Medicine, University of Cambridge, Cambridge, UK.; -; Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.; University of Amsterdam; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; NIHR Cambridge Clinical Research Facility, Cambridge, UK.; Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK; Addenbrookes Hospital; Addenbrookes Hospital; Addenbrookes Hospital; University of Colorado School of Medicine; Division of Infection & Immunity, University College London, UK; Department of Virology, Cambridge University NHS Hospitals Foundation Trust; Clinical Microbiology and Public Health Laboratory, Addenbrookes Hospital, Cambridge, UK; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.; Department of Pathology, University of Cambridge, Cambridge; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.; MRC Biostatistics Unit, University of Cambridge, Cambridge, UK; Division of Infection and Immunity, University College London, London, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.","SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2, and amino acid variation in Spike is increasingly appreciated. Given both vaccines and therapeutics are designed around Wuhan-1 Spike, this raises the theoretical possibility of virus escape, particularly in immunocompromised individuals where prolonged viral replication occurs. Here we report chronic SARS-CoV-2 with reduced sensitivity to neutralising antibodies in an immune suppressed individual treated with convalescent plasma, generating whole genome ultradeep sequences by both short and long read technologies over 23 time points spanning 101 days. Although little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days, N501Y in Spike was transiently detected at day 55 and V157L in RdRp emerged. However, following convalescent plasma we observed large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and{Delta} H69/{Delta}V70 in the S1 N-terminal domain NTD of the Spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype diminished in frequency, before returning during a final, unsuccessful course of convalescent plasma. In vitro, the Spike escape double mutant bearing{Delta} H69/{Delta}V70 and D796H conferred decreased sensitivity to convalescent plasma, whilst maintaining infectivity similar to wild type. D796H appeared to be the main contributor to decreased susceptibility, but incurred an infectivity defect. The{Delta} H69/{Delta}V70 single mutant had two-fold higher infectivity compared to wild type and appeared to compensate for the reduced infectivity of D796H. Consistent with the observed mutations being outside the RBD, monoclonal antibodies targeting the RBD were not impacted by either or both mutations, but a non RBD binding monoclonal antibody was less potent against{Delta} H69/{Delta}V70 and the double mutant. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy associated with emergence of viral variants with reduced susceptibility to neutralising antibodies.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.12.08.20246231,2020-12-11,https://medrxiv.org/cgi/content/short/2020.12.08.20246231,Artificial intelligence-enabled analysis of UK and US public attitudes on Facebook and Twitter towards COVID-19 vaccinations,Amir Hussain; Ahsen Tahir; Zain Hussain; Zakariya Sheikh; Mandar Gogate; Kia Dashtipour; Azhar Ali; Aziz Sheikh,"Edinburgh Napier University, UK; Edinburgh Napier University, UK; Edinburgh Medical School, College of Medicine and Veterinary Medicine, University of Edinburgh, UK; Edinburgh Medical School, College of Medicine and Veterinary Medicine, University of Edinburgh, UK; Edinburgh Napier University, UK; Edinburgh Napier University, UK; NHS Forth Medical Group, UK & Harvard T.H. Chan School of Public Health, USA; Usher Institute, Edinburgh Medical School, University of Edinburgh, UK","BackgroundGlobal efforts towards the development and deployment of a vaccine for SARS-CoV-2 are rapidly advancing. We developed and applied an artificial-intelligence (AI)-based approach to analyse social-media public sentiment in the UK and the US towards COVID-19 vaccinations, to understand public attitude and identify topics of concern. @@ -4308,6 +4217,7 @@ C_LIO_LIOptimal symptom combinations maximise case capture considering available C_LIO_LIImplications for COVID-19 vaccine efficacy trials and wider public health C_LI",health informatics,fuzzy,100,100 medRxiv,10.1101/2020.11.19.20234120,2020-11-23,https://medrxiv.org/cgi/content/short/2020.11.19.20234120,Actionable druggable genome-wide Mendelian randomization identifies repurposingopportunities for COVID-19,Liam Gaziano; Claudia Giambartolomei; Alexandre C Pereira; Anna Gaulton; Daniel C Posner; Sonja A Swanson; Yuk Lam Ho; Sudha K Iyengar; Nicole M Kosik; Marijana Vujkovic; David R Gagnon; A Patricia Bento; Pedro Beltrao; Inigo Barrio Hernandez; Lars Ronnblom; Niklas Hagberg; Christian Lundtoft; Claudia Langenberg; Maik Pietzner; Dennis Valentine; Elias Allara; Praveen Surendran; Stephen Burgess; Jing Hua Zhao; James E Peters; Bram P Prins; John Danesh; Poornima Devineni; Yunling Shi; Kristine E Lynch; Scott L DuVall; Helene Garcon; Lauren Thomann; Jin J Zhou; Bryan R Gorman; Jennifer E Huffman; Christopher J O'Donnell; Philip S Tsao; Jean C Beckham; Saiju Pyarajan; Sumitra Muralidhar; Grant D Huang; Rachel Ramoni; Adriana M Hung; Kyong-Mi Chang; Yan V Sun; Jacob Joseph; Andrew R Leach; Todd L Edwards; Kelly Cho; J Michael Gaziano; Adam S Butterworth; Juan P Casas,"VA Boston Healthcare System, University of Cambridge; Instituto Italiano di Tecnologia, University of California Los Angeles; University of Sao Paulo, Harvard University; European Molecular Biology Laboratory, European Bioinformatics Institute; VA Boston Healthcare System; Erasmus Medical Center; VA Boston Healthcare System; Case Western Reserve University and Louis Stoke Cleveland VAMC; VA Boston Healthcare System; The Corporal Michael J. Crescenz VA Medical Center, the University of Pennsylvania Perelman School of Medicine; Boston University, VA Boston Healthcare System; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; Uppsala University; Uppsala University; Uppsala University; Charite University Medicine Berlin, Universityof Cambridge; Universityof Cambridge; University College London; University of Cambridge; Wellcome Genome Campus and University of Cambridge; University of Cambridge; University of Cambridge; Imperial College London; Wellcome Genome Campus and University of Cambridge; University of Cambridge; VA Boston Healthcare System; VA Boston Healthcare System; VA Salt Lake City Health Care System, University of Utah; VA Salt Lake City Health Care System, University of Utah; VA Boston Healthcare System; VA Boston Healthcare System; University of Arizona, Phoenix VA Health Care System; VA Boston Healthcare System; VA Boston Healthcare System; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Palo Alto Health Care System, Stanford University School of Medicine; Durham VA Medical Center, Duke University School of Medicine; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs, Vanderbilt University; The Corporal Michael J. Crescenz VA Medical Center, University of Pennsylvania; Atlanta VA Health Care System, Emory University Rollins School of Public Health; VA Boston Healthcare System and Brigham & Women's Hospital; European Molecular Biology Laboratory, European Bioinformatics Institute; Department of Veterans Affairs Tennessee Valley Healthcare System, Vanderbilt Genetics Institute Vanderbilt University Medical Center; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; University of Cambridge, Wellcome Genome Campus and University of Cambridge; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School","Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization (MR) analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2: P=1.6x10-6, IFNAR2: P=9.8x10-11, and IL-10RB: P=1.9x10-14) using cis-eQTL genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared eQTL signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.11.19.20234849,2020-11-22,https://medrxiv.org/cgi/content/short/2020.11.19.20234849,Community factors and excess mortality in first wave of the COVID-19 pandemic.,Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.11.18.20233932,2020-11-20,https://medrxiv.org/cgi/content/short/2020.11.18.20233932,REACT-1 round 6 updated report: high prevalence of SARS-CoV-2 swab positivity with reduced rate of growth in England at the start of November 2020,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E. Walters; Haowei Wang; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear","BackgroundEngland is now in the midst of its second wave of the COVID-19 pandemic. Multiple regions of the country are at high infection prevalence and all areas experienced rapid recent growth of the epidemic during October 2020. MethodsREACT-1 is a series of community surveys of SARS-CoV-2 RT-PCR swab-positivity in England designed to monitor the spread of the epidemic and thus increase situational awareness. Round 6 of REACT-1 commenced swab-collection on 16th October. A prior interim report included data from 16th to 25th October for 85,971 participants. Here, we report data for the entire round on 160,175 participants with swab results obtained up to 2nd November 2020. @@ -4322,13 +4232,13 @@ MethodsWe use a data-driven approach to parameterise an individual-based network ResultsThe progress of the epidemic can be significantly hindered by instructing a significant proportion of the workforce to work from home. Furthermore, if required to be present at the workplace, asynchronous work patterns can help to reduce infections when compared with scenarios where all workers work on the same days, particularly for longer working weeks. When assessing COVID-secure workplace measures, we found that smaller work teams and a greater reduction in transmission risk reduced the probability of large, prolonged outbreaks. Finally, following isolation guidance and engaging with contact tracing without other measures is an effective tool to curb transmission, but is highly sensitive to adherence levels. ConclusionsIn the absence of sufficient adherence to non-pharmaceutical interventions, our results indicate a high likelihood of SARS-CoV-2 spreading widely throughout a worker population. Given the heterogeneity of demographic attributes across worker roles, in addition to the individual nature of controls such as contact tracing, we demonstrate the utility of a network model approach to investigate workplace-targeted intervention strategies and the role of test, trace and isolation in tackling disease spread.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.11.18.20234369,2020-11-19,https://medrxiv.org/cgi/content/short/2020.11.18.20234369,Antibodies to SARS-CoV-2 are associated with protection against reinfection,Sheila F Lumley; Nicole E Stoesser; Philippa C Matthews; Alison Howarth; Stephanie B Hatch; Brian D Marsden; Stuart Cox; Tim James; Fiona Warren; Liam J Peck; Thomas G Ritter; Zoe de Toledo; Laura Warren; David Axten; Richard J Cornall; E Yvonne Jones; David I Stuart; Gavin Screaton; Daniel Ebner; Sarah Hoosdally; Meera Chand; - Oxford University Hospitals Staff Testing Group; Derrick W Crook; Christopher P Conlon; Koen B Pouwels; A Sarah Walker; Tim EA Peto; Susan Hopkins; Tim M Walker; Katie Jeffery; David W Eyre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; Oxford University Hospitals; Oxford University Hospitals; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; Oxford University Hospitals; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Public Health England; ; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Public Health England; University of Oxford; University of Oxford; University of Oxford,"BackgroundIt is critical to understand whether infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) protects from subsequent reinfection. +medRxiv,10.1101/2020.11.18.20225029,2020-11-20,https://medrxiv.org/cgi/content/short/2020.11.18.20225029,The Invasive Respiratory Infection Surveillance (IRIS) Initiative reveals significant reductions in invasive bacterial infections during the COVID-19 pandemic,Angela B Brueggemann; Melissa J Jansen van Rensburg; David Shaw; Noel D McCarthy; Keith A Jolley; Martin CJ Maiden; Mark PG van der Linden,University of Oxford; University of Oxford; University of Oxford; University of Warwick; University of Oxford; University of Oxford; University Hospital RWTH Aachen,"BackgroundStreptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis are leading causes of invasive diseases including bacteraemic pneumonia and meningitis, and of secondary infections post-viral respiratory disease. They are typically transmitted via respiratory droplets. We investigated rates of invasive disease due to these pathogens during the early phase of the COVID-19 pandemic. -MethodsWe investigated the incidence of SARS-CoV-2 PCR-positive results in seropositive and seronegative healthcare workers (HCWs) attending asymptomatic and symptomatic staff testing at Oxford University Hospitals, UK. Baseline antibody status was determined using anti-spike and/or anti-nucleocapsid IgG assays and staff followed for up to 30 weeks. We used Poisson regression to estimate the relative incidence of PCR-positive results and new symptomatic infection by antibody status, accounting for age, gender and changes in incidence over time. +MethodsLaboratories in 26 countries across six continents submitted data on cases of invasive disease due to S pneumoniae, H influenzae and N meningitidis from 1 January 2018 to 31 May 2020. Weekly cases in 2020 vs 2018-2019 were compared. Streptococcus agalactiae data were collected from nine laboratories for comparison to a non-respiratory pathogen. The stringency of COVID-19 containment measures was quantified by the Oxford COVID-19 Government Response Tracker. Changes in population movements were assessed by Google COVID-19 Community Mobility Reports. Interrupted time series modelling quantified changes in rates of invasive disease in 2020 relative to when containment measures were imposed. -ResultsA total of 12219 HCWs participated and had anti-spike IgG measured, 11052 were followed up after negative and 1246 after positive antibody results including 79 who seroconverted during follow up. 89 PCR-confirmed symptomatic infections occurred in seronegative individuals (0.46 cases per 10,000 days at risk) and no symptomatic infections in those with anti-spike antibodies. Additionally, 76 (0.40/10,000 days at risk) anti-spike IgG seronegative individuals had PCR-positive tests in asymptomatic screening, compared to 3 (0.21/10,000 days at risk) seropositive individuals. Overall, positive baseline anti-spike antibodies were associated with lower rates of PCR-positivity (with or without symptoms) (adjusted rate ratio 0.24 [95%CI 0.08-0.76, p=0.015]). Rate ratios were similar using anti-nucleocapsid IgG alone or combined with anti-spike IgG to determine baseline status. +FindingsAll countries experienced a significant, sustained reduction in invasive diseases due to S pneumoniae, H influenzae and N meningitidis, but not S agalactiae, in early 2020, which coincided with the introduction of COVID-19 containment measures in each country. Similar impacts were observed across most countries despite differing stringency in COVID-19 control policies. There was no evidence of a specific effect due to enforced school closures. -ConclusionsPrior SARS-CoV-2 infection that generated antibody responses offered protection from reinfection for most people in the six months following infection. Further work is required to determine the long-term duration and correlates of post-infection immunity.",infectious diseases,fuzzy,100,100 +InterpretationThe introduction of COVID-19 containment policies and public information campaigns likely reduced transmission of these bacterial respiratory pathogens, leading to a significant reduction in life-threatening invasive diseases in many countries worldwide.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.11.12.20229955,2020-11-15,https://medrxiv.org/cgi/content/short/2020.11.12.20229955,Mobile consulting (mConsulting) as an option for accessing healthcare services for communities in remote rural areas and urban slums in low- and middle- income countries: A mixed methods study,Bronwyn Harris; Motunrayo Ajisola; Raisa Alam; Jocelyn Antsley Watkins; Theodoros N Arvanitis; Pauline Bakibinga; Beatrice Chipwaza; Nazratun Nayeem Choudhury; Olufunke Fayhun; Peter Kibe; Akinyinka Omigbodun; Eme Owoaje; Senga Pemba; Rachel Potter; Narjis Rizvi; Jackie Sturt; Jonathan A.K Cave; Romaina Iqbal; Caroline Kabaria; Albino Kalolo; Catherine Kyobutungi; Richard J Lilford; Titus Mashanya; Sylvester Ndegese; Omar Rahman; Saleem Sayani; Rita Yusuf; Frances Griffiths,"Warwick Medical School, University of Warwick, UK; Department of Sociology, Faculty of Social Sciences, University of Ibadan, Ibadan, Oyo State, Nigeria; Centre for Health, Population and Development, Independent University Bangladesh, Dhaka, Bangladesh; Warwick Medical School, University of Warwick, UK; Institute of Digital Healthcare, WMG, University of Warwick, UK; African Population and Health Research Center, Nairobi, Kenya; St Francis University College of Health and Allied Sciences, Tanzania; Centre for Health, Population and Development, Independent University Bangladesh, Dhaka, Bangladesh; Department of Sociology, Faculty of Social Sciences, University of Ibadan, Ibadan, Oyo State, Nigeria; African Population and Health Research Center, Nairobi, Kenya; Department of Obstetrics and Gynaecology, Faculty of Clinical Sciences, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria; Department of Community Medicine, Faculty of Public Health, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria; St Francis University College of Health and Allied Sciences, Tanzania; Clinical Trials Unit Warwick Medical School, University of Warwick, University of Warwick, UK; Community Health Sciences Department, Aga Khan University, Karachi, Pakistan; King's College London, Florence Nightingale Faculty of Nursing and Midwifery, London, UK; Department of Economics, University of Warwick, UK; Community Health Sciences Department, Aga Khan University, Karachi, Pakistan; African Population and Health Research Center, Nairobi, Kenya; St Francis University College of Health and Allied Sciences, Tanzania; African Population and Health Research Center, Nairobi, Kenya; Institute of Applied Health Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK; St Francis University College of Health and Allied Sciences, Tanzania; St Francis University College of Health and Allied Sciences, Tanzania; University of Liberal Arts Bangladesh, Dhaka, Bangladesh; Aga Khan Development Network Digital Health Resource Centre (Asia and Africa), Aga Khan University, Karachi, Pakistan; Centre for Health, Population and Development, Independent University Bangladesh, Dhaka, Bangladesh; Warwick Medical School, University of Warwick, UK","ObjectiveRemote or mobile consulting (mConsulting) is being promoted to strengthen health systems, deliver universal health coverage and facilitate safe clinical communication during COVID-19 and beyond. We explored whether mConsulting is a viable option for communities with minimal resources in low- and middle-income countries (LMICs). MethodsWe reviewed evidence published since 2018 about mConsulting in LMICs and undertook a scoping study (pre-COVID) in two rural settings (Pakistan, Tanzania) and five urban slums (Kenya, Nigeria, Bangladesh), using policy/document review, secondary analysis of survey data (from the urban sites), and thematic analysis of interviews/workshops with community members, healthcare workers, digital/telecommunications experts, mConsulting providers, local and national decision-makers. Project advisory groups guided the study in each country. @@ -4343,7 +4253,6 @@ MethodsThe EHS is an ongoing and deeply-phenotyped prospective cohort study that ResultsA total of 563 participants (49 years mean age; 60% women) had available information on the standard EHS questionnaire, the clinical and biochemical measurements, and the COVID-19-related questionnaire. Percentages of poor, moderate and good knowledge status regarding COVID-19 were 4.5%, 10.0% and 85.6%, respectively. The majority of participants showed absolute or moderate trust in the Greek health authorities for the management of the epidemic (90.1%), as well as in the Greek Government (84.7%) and the official national sources of information (87.4%). Trust in the authorities was weaker in younger participants and those who joined the study after the lifting of lockdown measures (p-value[≤]0.001). None of the factors examined was associated with participants level of knowledge after correction for multiple testing. ConclusionsHigh level of knowledge about the COVID-19 pandemic and trust in the Greek authorities was observed, possibly due to the plethora of good quality publicly available information and the timely management of the pandemic at its early stages in Greece. Information campaigns for the COVID-19 pandemic should be encouraged even after the lifting of lockdown measures to increase public awareness.",public and global health,fuzzy,100,100 -medRxiv,10.1101/2020.11.11.20229500,2020-11-13,https://medrxiv.org/cgi/content/short/2020.11.11.20229500,Association of social distancing and masking with risk of COVID-19,Sohee Kwon; Amit D. Joshi; Chun-Han Lo; David Alden Drew; Long Nguyen; Chuan-Guo Guo; Wenjie Ma; Raaj S. Mehta; Erica T. Warner; Christina M. Astley; Jordi Merino; Benjamin Murray; Jonathan Wolf; Sebastien Ourselin; Claire Steves; Timothy Spector; Jaime E. Hart; Mingyang Song; Trang VoPham; Andrew T. Chan,Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Boston Children's Hospital; Massachusetts General Hospital; King's College London; Zoe Global Limited; King's College London; King's College London; King's College London; Harvard T.H. Chan School of Public Health; Massachusetts General Hospital; Fred Hutchinson Cancer Research Center; Massachusetts General Hospital,"Given the continued burden of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) disease (COVID-19) across the U.S., there is a high unmet need for data to inform decision-making regarding social distancing and universal masking. We examined the association of community-level social distancing measures and individual masking with risk of predicted COVID-19 in a large prospective U.S. cohort study of 198,077 participants. Individuals living in communities with the greatest social distancing had a 31% lower risk of predicted COVID-19 compared with those living in communities with poor social distancing. Self-reported masking was associated with a 63% reduced risk of predicted COVID-19 even among individuals living in a community with poor social distancing. These findings provide support for the efficacy of mask-wearing even in settings of poor social distancing in reducing COVID-19 transmission. In the current environment of relaxed social distancing mandates and practices, universal masking may be particularly important in mitigating risk of infection.",infectious diseases,fuzzy,94,100 medRxiv,10.1101/2020.11.10.20229278,2020-11-13,https://medrxiv.org/cgi/content/short/2020.11.10.20229278,Changing probability of experiencing food insecurity by socioeconomic and demographic groups during the COVID-19 pandemic in the UK,Jonathan Koltai; Veronica Toffolutti; Martin McKee; David Stuckler,Bocconi University; Bocconi University; The London School of Hygiene & Tropical Medicine; Bocconi University,"BackgroundFood supply concerns have featured prominently in the UK response to the COVID-19 pandemic. We assess changes in food insecurity in the UK population from April to July 2020. MethodWe analyze 11,095 respondents from the April through July waves of the Understanding Society COVID-19 longitudinal study survey linked with Wave 9 of the UK Understanding Society study. Food insecurity was defined as having used a food bank in the last 4 weeks; being hungry but not eating in the last week; or not able to eat healthy and nutritious food in the last week. Unadjusted estimates to examine changes in population prevalence and logistic regression were used to assess the association between employment transitions and food insecurity. @@ -4385,7 +4294,6 @@ C_LI How might this impact on clinical practice or future developments?O_LIVariable shielding behaviour amongst patients with IMIDs may be an important confounder when considering differential COVID-19 risk between therapy types, so should be accounted for in analyses where possible. C_LI",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.11.06.20227108,2020-11-07,https://medrxiv.org/cgi/content/short/2020.11.06.20227108,Primary school staff reflections on school closures due to COVID-19 and recommendations for the future: a national qualitative survey,Emily Marchant; Charlotte Todd; Michaela James; Tom Crick; Russell Dwyer; Sinead Brophy,Swansea University; Swansea University; Swansea University; Swansea University; St Thomas Community Primary School; Swansea University,"School closures due to the COVID-19 global pandemic are likely to have a range of negative consequences spanning the domains of child development, education and health, in addition to the widening of inequalities and inequities. Research is required to improve understanding of the impact of school closures on the education, health and wellbeing of pupils and school staff, the challenges posed during reopening and importantly to identify how countries can return to in-school education and to inform policy. This qualitative study aimed to reflect on the perspectives and experiences of primary school staff (pupils aged 3-11) in Wales regarding school closures and the initial reopening of schools and to identify recommendations for the future. A total of 208 school staff completed a national online survey through the HAPPEN primary school network, consisting of questions about school closures (March to June 2020), the phased reopening of schools (June to July 2020) and a return to full-time education. Thematic analysis of survey responses highlighted that primary school staff perceive that gaps in learning, health and wellbeing have increased and inequalities have widened during school closures. Findings from this study identified five recommendations; (i) prioritise the health and wellbeing of pupils and staff; (ii) focus on enabling parental engagement and support; (iii) improve digital competence amongst pupils, teachers and parents; (iv) consider opportunities for smaller class sizes and additional staffing; and (v) improve the mechanism of communication between schools and families, and between government and schools.",public and global health,fuzzy,100,100 -medRxiv,10.1101/2020.11.05.20223289,2020-11-06,https://medrxiv.org/cgi/content/short/2020.11.05.20223289,Longitudinal proteomic profiling of high-risk patients with COVID-19 reveals markers of severity and predictors of fatal disease,Jack Gisby; Candice L Clarke; Nicholas Medjeral-Thomas; Talat H Malik; Artemis Papadaki; Paige M Mortimer; Norzawani B Buang; Shanice Lewis; Marie Pereira; Frederic Toulza; Ester Fagnano; Marie-Anne Mawhin; Emma E Dutton; Lunnathaya Tapeng; Arianne C Richard; Paul Kirk; Jacques Behmoaras; Eleanor Sandhu; Stephen P McAdoo; Maria F Prendecki; Matthew C Pickering; Marina Botto; Michelle Willicombe; David C Thomas; James E. Peters,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; University of Cambridge; MRC Biostatistics Unit University of Cambridge; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"End-stage kidney disease (ESKD) patients are at high risk of severe COVID-19. We measured 436 circulating proteins in serial blood samples from hospitalised and non-hospitalised ESKD patients with COVID-19 (n=256 samples from 55 patients). Comparison to 51 non-infected patients revealed 221 differentially expressed proteins, with consistent results in a separate subcohort of 46 COVID-19 patients. 203 proteins were associated with clinical severity, including IL6, markers of monocyte recruitment (e.g. CCL2, CCL7), neutrophil activation (e.g. proteinase-3) and epithelial injury (e.g. KRT19). Machine learning identified predictors of severity including IL18BP, CTSD, GDF15, and KRT19. Survival analysis with joint models revealed 69 predictors of death. Longitudinal modelling with linear mixed models uncovered 32 proteins displaying different temporal profiles in severe versus non-severe disease, including integrins and adhesion molecules. These data implicate epithelial damage, innate immune activation, and leucocyte-endothelial interactions in the pathology of severe COVID-19 and provide a resource for identifying drug targets.",infectious diseases,fuzzy,100,100 bioRxiv,10.1101/2020.11.06.369439,2020-11-06,https://biorxiv.org/cgi/content/short/2020.11.06.369439,Allosteric hotspots in the main protease of SARS-CoV-2,Léonie Strömich; Nan Wu; Mauricio Barahona; Sophia N Yaliraki,Imperial College London; Imperial College London; Imperial College London; Imperial College London,"AO_SCPLOWBSTRACTC_SCPLOWInhibiting the main protease of SARS-CoV-2 is of great interest in tackling the COVID-19 pandemic caused by the virus. Most efforts have been centred on inhibiting the binding site of the enzyme. However, considering allosteric sites, distant from the active or orthosteric site, broadens the search space for drug candidates and confers the advantages of allosteric drug targeting. Here, we report the allosteric communication pathways in the main protease dimer by using two novel fully atomistic graph theoretical methods: Bond-to-bond propensity analysis, which has been previously successful in identifying allosteric sites without a priori knowledge in benchmark data sets, and, Markov transient analysis, which has previously aided in finding novel drug targets in catalytic protein families. We further score the highest ranking sites against random sites in similar distances through statistical bootstrapping and identify four statistically significant putative allosteric sites as good candidates for alternative drug targeting.",bioinformatics,fuzzy,100,100 medRxiv,10.1101/2020.11.01.20224014,2020-11-04,https://medrxiv.org/cgi/content/short/2020.11.01.20224014,MODELLING PRESYMPTOMATIC INFECTIOUSNESS IN COVID-19,Russell Cheng; Christopher Dye; John Dagpunar; Brian Williams,University of Southampton; Oxford University; University of Southampton; Stellenbosch University,"This paper considers SEPIR, the extension of an existing parametric SEIR continuous simulation compartment model. Both models can be fitted to real data as they include parameters that can simply be estimated from the data. However SEPIR deploys an additional presymptomatic (also called asymptomatic) infectious stage that is not included in SEIR but which is known to exist in COVID-19. This stage is also parametrised and so can be fitted to data. Both SEPIR and the existing SEIR model assume a homogeneous mixing population, an idealisation that is unrealistic in practice when dynamically varying control strategies are deployed against virus. This means that if either model is to represent more than just a single period in the behaviour of the epidemic, then the parameters of the model will have to be time dependent. This issue is also discussed in this paper.",epidemiology,fuzzy,93,100 medRxiv,10.1101/2020.11.02.20223891,2020-11-04,https://medrxiv.org/cgi/content/short/2020.11.02.20223891,Performance characteristics of a rapid SARS-CoV-2 antigen detection assay at a public plaza testing site in San Francisco,Genay Pilarowski; Paul Lebel; Sara Sunshine; Jamin Liu; Emily Crawford; Carina Marquez; Luis Rubio; Gabriel Chamie; Jackie Martinez; James Peng; Douglas Black; Wesley Wu; John Pak; Matthew T Laurie; Diane Jones; Steve Miller; Jon Jacobo; Susana Rojas; Susy Rojas; Robert Nakamura; Valerie Tulier-Laiwa; Maya Petersen; Diane V Havlir; - The CLIAHUB Consortium; Joseph DeRisi,"Department of Pathology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA and Department of Microbiology and Immunology, University of California San Francisco, CA 94143; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA; Unidos en Salud, San Francisco, CA 94143, USA; Department of Laboratory Medicine, University of California San Francisco CA 94131, USA; Latino Task Force-COVID-19, San Francisco, CA 94110, USA; Latino Task Force-COVID-19, San Francisco, CA 94110, USA; Latino Task Force-COVID-19, San Francisco, CA 94110, USA; California Department of Public Health, Microbial Diseases Laboratory, Richmond, CA, 94804, USA; Latino Task Force-COVID-19, San Francisco, CA 94110, USA; Division of Epidemiology and Biostatistics, University of California, Berkeley, Berkeley, CA 94720, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; ; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA and Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA","We evaluated the performance of the Abbott BinaxNOW Covid-19 rapid antigen test to detect virus among persons, regardless of symptoms, at a public plaza site of ongoing community transmission. Titration with cultured clinical SARS-CoV-2 yielded a human observable threshold between 1.6x104-4.3x104 viral RNA copies (cycle threshold (Ct) of 30.3-28.8 in this assay). Among 878 subjects tested, 3% (26/878) were positive by RT-PCR, of which 15/26 had a Ct<30, indicating high viral load. 40% (6/15) of Ct<30 were asymptomatic. Using this Ct<30 threshold for Binax-CoV2 evaluation, the sensitivity of the Binax-CoV2 was 93.3% (14/15), 95% CI: 68.1-99.8%, and the specificity was 99.9% (855/856), 95% CI: 99.4-99.9%.",infectious diseases,fuzzy,92,100 @@ -4682,7 +4590,6 @@ MethodsRepeated cross-sectional surveys of random samples of the population aged ResultsOver the 9 days for which data are available, we find 363 positives from 84,610 samples giving a weighted prevalence to date of 0.55% (0.47%, 0.64%) in round 5. This implies that 411,000 (351,000, 478,000) people in England are virus-positive under the assumption that the swab assay is 75% sensitive. Using data from the most recent two rounds, we estimate a doubling time of 10.6 (9.4, 12.0) days covering the period 20th August to 26th September, corresponding to a reproduction number R of 1.47 (1.40, 1.53). Using data only from round 5 we estimate a reproduction number of 1.06 (0.74, 1.46) with probability of 63% that R is greater than 1. Between rounds 4 and 5 there was a marked increase in unweighted prevalence at all ages. In the most recent data, prevalence was highest in the 18 to 24 yrs age group at 0.96% (0.68%, 1.36%). At 65+ yrs prevalence increased [~]7-fold between rounds 4 and 5 from 0.04% (0.03%, 0.07%) to 0.29% (0.23%, 0.37%). Prevalence increased in all regions between rounds 4 and 5, giving the highest unweighted prevalence in round 5 in the North West at 0.86% (0.69%, 1.06%). In London, prevalence increased [~]5-fold from 0.10% (0.06%, 0.17%) to 0.49% (0.36%, 0.68%). Regional R values ranged from 1.32 (1.16,1.50) in Yorkshire and the Humber to 1.63 (1.42, 1.88) in the East Midlands over the same period. In the most recent data, there was extensive clustering in the North West, Midlands and in and around London with pockets of clustering in other regions including the South West, North East and East of England. Odds of swab-positivity were [~]2-fold higher in people of Asian and Black ethnicity compared with white participants. ConclusionRapid growth has led to high prevalence of SARS-CoV-2 virus in England among all regions and age groups, including those age groups at highest risk. Although there is evidence of a recent deceleration in the epidemic, current levels of prevalence will inevitably result in additional hospitalisations and mortality in coming weeks. A re-doubling of public health efforts is needed to return to a declining phase of the epidemic.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.09.28.20202929,2020-09-29,https://medrxiv.org/cgi/content/short/2020.09.28.20202929,T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses,Ane Ogbe; Barbara Kronsteiner; Donal T Skelly; Matthew Pace; Anthony Brown; Emily Adland; Kareena Adair; Hossain Delowar Akhter; Mohammad Ali; Serat-E Ali; Adrienn Angyal; M. Azim Ansari; Carolina V Arancibia-Carcamo; Helen Brown; Senthil Chinnakannan; Christopher P Conlon; Catherine de Lara; Thushan de Silva; Christina Dold; Tao Dong Dong; Timothy Donnison; David W Eyre; Amy Flaxman; Helen A Fletcher; Joshua Gardner; James T Grist; Carl-Philipp Hackstein; Kanoot Jaruthamsophon; Katie Jeffrey; Teresa Lambe; Lian Lee; Wenqin Li; Nicholas Lim; Philippa C Matthews; Alexander J Mentzer; Shona C Moore; Dean J Naisbitt; Monday Ogese; Graham Ogg; Peter Openshaw; Munir Pirmohamed; Andrew J Pollard; Narayan Ramamurthy; Patpong Rongkard; Sarah Rowland-Jones; Oliver L Sampson; Gavin Screaton; Alessandro Sette; Lizzie Stafford; Craig Thompson; Paul J Thomson; Ryan Thwaites; Vinicius Vieira; Daniela Weiskopf; Panagiota Zacharopoulou; - Oxford Immunology Network Covid-19 Response T cell Consortium; - Oxford Protective T cell Immunology for COVID-19 (OPTIC) Clinical team; Lance Turtle; Paul Klenerman; Philip Goulder; John Frater; Eleanor Barnes; Susanna Dunachie,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Liverpool; University of Liverpool; University of Oxford; Imperial College; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; La Jolla Institute for Immunology; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Liverpool; Imperial College; University of Oxford; La Jolla Institute for Immunology; University of Oxford; ; ; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"A major issue in identification of protective T cell responses against SARS-CoV-2 lies in distinguishing people infected with SARS-CoV-2 from those with cross-reactive immunity generated by exposure to other coronaviruses. We characterised SARS-CoV-2 T cell immune responses in 168 PCR-confirmed SARS-CoV-2 infected subjects and 118 seronegative subjects without known SARS-CoV-2 exposure using a range of T cell assays that differentially capture immune cell function. Strong ex vivo ELISpot and proliferation responses to multiple antigens (including M, NP and ORF3) were found in those who had been infected by SARS-CoV-2 but were rare in pre-pandemic and unexposed seronegative subjects. However, seronegative doctors with high occupational exposure and recent COVID-19 compatible illness showed patterns of T cell responses characteristic of infection, indicating that these readouts are highly sensitive. By contrast, over 90% of convalescent or unexposed people showed proliferation and cellular lactate responses to spike subunits S1/S2, indicating pre-existing cross-reactive T cell populations. The detection of T cell responses to SARS-CoV-2 is therefore critically dependent on the choice of assay and antigen. Memory responses to specific non-spike proteins provides a method to distinguish recent infection from pre-existing immunity in exposed populations.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.09.26.20202150,2020-09-28,https://medrxiv.org/cgi/content/short/2020.09.26.20202150,Comparison of mental health service activity before and shortly after UK social distancing responses to the COVID-19 pandemic: February-March 2020,Robert Stewart; Evangelia Martin; Ioannis Bakolis; Matthew Broadbent; Nicola Byrne; Sabine Landau,King's College London; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; South London and Maudsley NHS Foundation Trust; King's College London,"This study sought to provide an early description of mental health service activity before and after national implementation of social distancing for COVID-19. A time series analysis was carried out of daily service-level activity on data from a large mental healthcare provider in southeast London, from 01.02.2020 to 31.03.2020, comparing activity before and after 16.03.2020: i) inpatient admissions, discharges and numbers, ii) contact numbers and daily caseloads (Liaison, Home Treatment Teams, Community Mental Health Teams); iii) numbers of deaths for past and present patients. Daily face-to-face contact numbers fell for liaison, home treatment and community services with incomplete compensatory rises in non-face-to-face contacts. Daily caseloads fell for all services, apart from working age and child/adolescent community teams. Inpatient numbers fell 13.6% after 16th March, and daily numbers of deaths increased by 61.8%.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2020.09.25.20201731,2020-09-27,https://medrxiv.org/cgi/content/short/2020.09.25.20201731,Antihypertensive Medications and COVID-19 Diagnosis and Mortality: Population-based Case-Control Analysis in the United Kingdom,Emma Rezel-Potts; Abdel Douiri; Phil J Chowienczyk; Martin C Gulliford,King's College London; King's College London; King's College London; King's College London,"ObjectivesTo evaluate antihypertensive medications and COVID-19 diagnosis and mortality, accounting for healthcare seeking behaviour. @@ -4805,6 +4712,15 @@ MethodsIn this analysis of the Bug Watch prospective community cohort study, we ResultsThe baseline incidence of cough or fever in the UK is expected to rise rapidly from 154,554 (95%CI 103,083 - 231,725) cases per day in August 2020 to 250,708 (95%CI 181,095 - 347,080) in September, peaking at 444,660 (95%CI 353,084 - 559,988) in December. If 80% of baseline cough or fever cases request tests, average daily UK testing demand would exceed current capacity for five consecutive months (October 2020 to February 2021), with a peak demand of 147,240 (95%CI 73,978 - 239,502) tests per day above capacity in December 2020. ConclusionsOur results show that current national COVID-19 testing capacity is likely to be exceeded by demand due to baseline cough and fever alone. This study highlights that the UKs response to the COVID-19 pandemic must ensure that a high proportion of people with symptoms request tests, and that testing capacity is immediately scaled up to meet this high predicted demand.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.09.01.20185793,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.01.20185793,Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study,Katie Biggs; Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Matthew Bursnall; Amanda Loban; Simon Waterhouse; Richard Simmonds; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter,University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust,"ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection. + +MethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome. + +ResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse outcome. C-statistics were 0.80 (95% confidence interval 0.73-0.87) for the WHO algorithm, 0.80 (0.71-0.90) for POPS, 0.76 (0.67-0.85) for COAST, and 0.71 (0.59-0.82) for SFHPC. Using pre-specified thresholds, the WHO algorithm had the highest sensitivity (0.85) and lowest specificity (0.75), but POPS and COAST could optimise sensitivity (0.96 and 0.92 respectively) at the expense of specificity (0.25 and 0.38 respectively) by using a threshold of any score above zero instead of the pre-specified threshold. + +ConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive. + +RegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533",emergency medicine,fuzzy,100,100 medRxiv,10.1101/2020.09.02.20186502,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.02.20186502,Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection,Thibaut Jombart; Stephane Ghozzi; Dirk Schumacher; Quentin Leclerc; Mark Jit; Stefan Flasche; Felix Greaves; Tom Ward; Rosalind M Eggo; Emily Nightingale; Sophie Meakin; Oliver J Brady; - Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group; Graham Medley; Michael Hohle; John Edmunds,"London School of Hygiene and Tropical Medicine (LSHTM); Department of Epidemiology, Helmholtz Centre for Infection Research, Brunswick, Lower Saxony, Germany; R Epidemics Consortium; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; LSHTM; Joint Biosecurity Centre; Joint Biosecurity Centre; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; LSHTM; London School of Hygiene and Tropical Medicine; ; LSHTM; Department of Mathematics, Stockholm University, Sweden; LSHTM","As several countries gradually release social distancing measures, rapid detection of new localised COVID-19 hotspots and subsequent intervention will be key to avoiding large-scale resurgence of transmission. We introduce ASMODEE (Automatic Selection of Models and Outlier Detection for Epidemics), a new tool for detecting sudden changes in COVID-19 incidence. Our approach relies on automatically selecting the best (fitting or predicting) model from a range of user-defined time series models, excluding the most recent data points, to characterise the main trend in an incidence. We then derive prediction intervals and classify data points outside this interval as outliers, which provides an objective criterion for identifying departures from previous trends. We also provide a method for selecting the optimal breakpoints, used to define how many recent data points are to be excluded from the trend fitting procedure. The analysis of simulated COVID-19 outbreaks suggest ASMODEE compares favourably with a state-of-art outbreak-detection algorithm while being simpler and more flexible. We illustrate our method using publicly available data of NHS Pathways reporting potential COVID-19 cases in England at a fine spatial scale, for which we provide a template automated analysis pipeline. ASMODEE is implemented in the free R package trendbreaker.",health informatics,fuzzy,100,100 medRxiv,10.1101/2020.09.02.20186817,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.02.20186817,Revealing the extent of the COVID-19 pandemic in Kenya based on serological and PCR-test data,John Ojal; Samuel PC Brand; Vincent Were; Emelda A Okiro; Ivy Kadzo Kombe; Caroline Mburu; Rabia Aziza; Morris Ogero; Ambrose Agweyu; George M Warimwe; Sophie Uyoga; Ifedayo M. O Adetifa; John Anthony Scott; Edward Otieno; Lynette I Ochola-Oyier; Charles Nyaigoti Agoti; Kadondi Kasera; Patrick Amoth; Mercy Mwangangi; Rashid Aman; Wangari Ng'ang'a; Benjamin Tsofa; Philip Bejon; Edwine Barasa; Matt J Keeling; D James Nokes,"Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya and London School of Hygiene and Tropical Medicine; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK.; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK.; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; KEMRI Wellcome Trust Research Programme; KEMRI-Wellcome Trust Research Programme; London School of Hygiene & Tropical Medicine; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Presidential Policy & Strategy Unit, The Presidency, Government of Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK; KEMRI-Wellcome Trust Research Programme, Kenya and School of Life Sciences, University of Warwick, UK","Policy makers in Africa need robust estimates of the current and future spread of SARS-CoV-2. Data suitable for this purpose are scant. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya. We estimate that the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 34 - 41% of residents infected, and will peak elsewhere in the country within 2-3 months. Despite this penetration, reported severe cases and deaths are low. Our analysis suggests the COVID-19 disease burden in Kenya may be far less than initially feared. A similar scenario across sub-Saharan Africa would have implications for balancing the consequences of restrictions with those of COVID-19.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.09.01.20183822,2020-09-02,https://medrxiv.org/cgi/content/short/2020.09.01.20183822,Trust and Transparency in times of Crisis: Results from an Online Survey During the First Wave (April 2020) of the COVID-19 Epidemic in the UK,Luisa Enria; Naomi Waterlow; Nina Trivedy Rogers; Hannah Brindle; Sham Lal; Rosalind M Eggo; Shelley Lees; Chrissy h Roberts,London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; UCL; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine (LSHTM),"BackgroundThe success of a governments COVID-19 control strategy relies on public trust and broad acceptance of response measures. We investigated public perceptions of the UK governments COVID-19 response, focusing on the relationship between trust and transparency, during the first wave (April 2020) of the COVID-19 pandemic in the United Kingdom. @@ -4996,21 +4912,6 @@ Main outcomeHospitalisation with COVID-19 ResultsThe cohort comprised 158,445 healthcare workers, the majority being patient facing (90,733 / 158,445; 57.3%), and 229,905 household members. Of all COVID-19 hospitalisations in the working age population (18-65-year-old), 17.2% (360 / 2,097) were in healthcare workers or their households. Adjusting for age, sex, ethnicity, socio-economic deprivation and comorbidity, the risk of COVID-19 hospitalisation in non-patient facing healthcare workers and their households was similar to the risk in the general population (hazards ratio [HR] 0.81; 95%CI 0.52-1.26 and 0.86; 95%CI 0.49-1.51 respectively). In models adjusting for the same covariates however, patient facing healthcare workers, compared to non-patient facing healthcare workers, were at higher risk (HR 3.30; 95%CI 2.13-5.13); so too were household members of patient facing healthcare workers (HR 1.79; 95%CI 1.10-2.91). On sub-dividing patient-facing healthcare workers into those who worked in front-door, intensive care and non-intensive care aerosol generating settings and other, those in front door roles were at higher risk (HR 2.09; 95%CI 1.49-2.94). For most patient facing healthcare workers and their households, the estimated absolute risk of COVID-19 hospitalisation was less than 0.5% but was 1% and above in older men with comorbidity. ConclusionsHealthcare workers and their households contribute a sixth of hospitalised COVID-19 cases. Whilst the absolute risk of hospitalisation was low overall, patient facing healthcare workers and their households had 3- and 2-fold increased risks of COVID-19 hospitalisation.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2020.08.03.20167122,2020-08-04,https://medrxiv.org/cgi/content/short/2020.08.03.20167122,Ethnic minority groups in England and Wales - factors affecting the size and timing of elevated COVID-19 mortality: a retrospective cohort study linking Census and death records,Daniel Ayoubkhani; Vahe Nafilyan; Chris White; Peter Goldblatt; Charlotte Gaughan; Louisa Blackwell; Nicky Rogers; Amitava Banerjee; Kamlesh Khunti; Myer Glickman; Ben Humberstone; Ian Diamond,"Office for National Statistics; Office for National Statistics; Office for National Statistics; UCL Institute for Health Equity; Office for National Statistics; Office for National Statistics; Office for National Statistics; Institute of Health Informatics, University College London; Diabetes Research Centre, University of Leicester; Office for National Statistics; Office for National Statistics; Office for National Statistics","ObjectivesTo estimate population-level associations between ethnicity and coronavirus disease 2019 (COVID-19) mortality, and to investigate how ethnicity-specific mortality risk evolved over the course of the pandemic. - -DesignRetrospective cohort study using linked administrative data. - -SettingEngland and Wales, deaths occurring 2 March to 15 May 2020. - -ParticipantsRespondents to the 2011 Census of England and Wales aged [≤]100 years and enumerated in private households, linked to death registrations and adjusted to account for emigration before the outcome period, who were alive on 1 March 2020 (n=47,872,412). - -Main outcome measureDeath related to COVID-19, registered by 29 May 2020. - -Statistical methodsWe estimated hazard ratios (HRs) for ethnic minority groups compared with the White population using Cox regression models, controlling for geographical, demographic, socio-economic, occupational, and self-reported health factors. HRs were estimated on the full outcome period and separately for pre- and post-lockdown periods in the UK. - -ResultsIn the age-adjusted models, people from all ethnic minority groups were at elevated risk of COVID-19 mortality; the HRs for Black males and females were 3.13 [95% confidence interval: 2.93 to 3.34] and 2.40 [2.20 to 2.61] respectively. However, in the fully adjusted model for females, the HRs were close to unity for all ethnic groups except Black (1.29 [1.18 to 1.42]). For males, COVID-19 mortality risk remained elevated for the Black (1.76 [1.63 to 1.90]), Bangladeshi/Pakistani (1.35 [1.21 to 1.49]) and Indian (1.30 [1.19 to 1.43]) groups. The HRs decreased after lockdown for all ethnic groups, particularly Black and Bangladeshi/Pakistani females. - -ConclusionsDifferences in COVID-19 mortality between ethnic groups were largely attenuated by geographical and socio-economic factors, although some residual differences remained. Lockdown was associated with reductions in excess mortality risk in ethnic minority populations, which has major implications for a second wave of infection or local spikes. Further research is needed to understand the causal mechanisms underpinning observed differences in COVID-19 mortality between ethnic groups.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.08.04.20163782,2020-08-04,https://medrxiv.org/cgi/content/short/2020.08.04.20163782,Fitting models to the COVID-19 outbreak and estimating R,Matt J Keeling; Louise Dyson; Glen Guyver-Fletcher; Alex Holmes; Malcolm G Semple; - ISARIC4C Investigators; Michael J Tildesley; Edward M Hill,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Liverpool; ; University of Warwick; University of Warwick,"The COVID-19 pandemic has brought to the fore the need for policy makers to receive timely and ongoing scientific guidance in response to this recently emerged human infectious disease. Fitting mathematical models of infectious disease transmission to the available epidemiological data provides a key statistical tool for understanding the many quantities of interest that are not explicit in the underlying epidemiological data streams. Of these, the effective reproduction number, R, has taken on special significance in terms of the general understanding of whether the epidemic is under control (R < 1). Unfortunately, none of the epidemiological data streams are designed for modelling, hence assimilating information from multiple (often changing) sources of data is a major challenge that is particularly stark in novel disease outbreaks. Here, focusing on the dynamics of the first-wave (March-June 2020), we present in some detail the inference scheme employed for calibrating the Warwick COVID-19 model to the available public health data streams, which span hospitalisations, critical care occupancy, mortality and serological testing. We then perform computational simulations, making use of the acquired parameter posterior distributions, to assess how the accuracy of short-term predictions varied over the timecourse of the outbreak. To conclude, we compare how refinements to data streams and model structure impact estimates of epidemiological measures, including the estimated growth rate and daily incidence.",infectious diseases,fuzzy,100,100 @@ -5029,21 +4930,6 @@ ResultsThere were 34 692 patients included in the derivation dataset (mortality ConclusionsWe have developed and validated an easy-to-use risk stratification score based on commonly available parameters at hospital presentation. This outperformed existing scores, demonstrated utility to directly inform clinical decision making, and can be used to stratify inpatients with covid-19 into different management groups. The 4C Mortality Score may help clinicians identify patients with covid-19 at high risk of dying during current and subsequent waves of the pandemic. Study registrationISRCTN66726260",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.07.30.20164921,2020-08-01,https://medrxiv.org/cgi/content/short/2020.07.30.20164921,Estrogen and COVID-19 symptoms: associations in women from the COVID Symptom Study,Ricardo Costeira; Karla A Lee; Benjamin Murray; Colette Christiansen; Juan Castillo-Fernandez; Mary Ni Lochlainn; Joan Capdevila Pujol; Iain Buchan; Louise C Kenny; Jonathan Wolf; Janice Rymer; Sebastien Ourselin; Claire Steves; Timothy Spector; Louise Newson; Jordana Bell,King's College London; Department of Twin Research and Genetic Epidemiology; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; University of Liverpool; University of Liverpool; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London; Newson HealthMenopause & Wellbeing Centre; King's College London,"BackgroundMen and older women have been shown to be at higher risk of adverse COVID-19 outcomes. Animal model studies of SARS-CoV and MERS suggest that the age and sex difference in COVID-19 symptom severity may be due to a protective effect of the female sex hormone estrogen. Females have shown an ability to mount a stronger immune response to a variety of viral infections because of more robust humoral and cellular immune responses. - -ObjectivesWe sought to determine whether COVID-19 positivity increases in women entering menopause. We also aimed to identify whether premenopausal women taking exogenous hormones in the form of the combined oral contraceptive pill (COCP) and post-menopausal women taking hormone replacement therapy (HRT) have lower predicted rates of COVID-19, using our published symptom-based model. - -DesignThe COVID Symptom Study developed by Kings College London and Zoe Global Limited was launched in the UK on 24th March 2020. It captured self-reported information related to COVID-19 symptoms. Data used for this study included records collected between 7th May - 15th June 2020. - -Main outcome measuresWe investigated links between COVID-19 rates and 1) menopausal status, 2) COCP use and 3) HRT use, using symptom-based predicted COVID-19, tested COVID-19, and disease severity based on requirement for hospital attendance or respiratory support. - -ParticipantsFemale users of the COVID Symptom Tracker Application in the UK, including 152,637 women for menopause status, 295,689 for COCP use, and 151,193 for HRT use. Analyses were adjusted for age, smoking and BMI. - -ResultsPost-menopausal women aged 40-60 years had a higher rate of predicted COVID (P=0.003) and a corresponding range of symptoms, with consistent, but not significant trends observed for tested COVID-19 and disease severity. Women aged 18-45 years taking COCP had a significantly lower predicted COVID-19 (P=8.03E-05), with a reduction in hospital attendance (P=0.023). Post-menopausal women using HRT or hormonal therapies did not exhibit consistent associations, including increased rates of predicted COVID-19 (P=2.22E-05) for HRT users alone. - -ConclusionsOur findings support a protective effect of estrogen on COVID-19, based on positive association between predicted COVID-19 and menopausal status, and a negative association with COCP use. HRT use was positively associated with COVID-19 symptoms; however, the results should be considered with caution due to lack of data on HRT type, route of administration, duration of treatment, and potential comorbidities. - -Trial registrationThe App Ethics has been approved by KCL ethics Committee REMAS ID 18210, review reference LRs-19/20-18210",obstetrics and gynecology,fuzzy,94,100 medRxiv,10.1101/2020.07.30.20165134,2020-08-01,https://medrxiv.org/cgi/content/short/2020.07.30.20165134,"Improving COVID-19 critical care mortality over time in England: A national cohort study, March to June 2020",John Dennis; Andrew McGovern; Sebastian Vollmer; Bilal A Mateen,University of Exeter; University of Exeter; University of Warwick; The Alan Turing Institute,"ObjectivesTo determine the trend in mortality risk over time in people with severe COVID-19 requiring critical care (high intensive unit [HDU] or intensive care unit [ICU]) management. MethodsWe accessed national English data on all adult COVID-19 specific critical care admissions from the COVID-19 Hospitalisation in England Surveillance System (CHESS), up to the 29th June 2020 (n=14,958). The study period was 1st March until 30th May, meaning every patient had 30 days of potential follow-up available. The primary outcome was in-hospital 30-day all-cause mortality. Hazard ratios for mortality were estimated for those admitted each week using a Cox proportional hazards models, adjusting for age (non-linear restricted cubic spline), sex, ethnicity, comorbidities, and geographical region. @@ -5107,15 +4993,6 @@ ConclusionsOxygen saturation on room air and patient age are strong predictors o medRxiv,10.1101/2020.07.22.20159772,2020-07-25,https://medrxiv.org/cgi/content/short/2020.07.22.20159772,Projecting contact matrices in 177 geographical regions: an update and comparison with empirical data for the COVID-19 era,Kiesha Prem; Kevin van Zandvoort; Petra Klepac; Rosalind M Eggo; Nicholas G Davies; - Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group; Alex R Cook; Mark Jit,"London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; ; Saw Swee Hock School of Public Health, National University of Singapore; London School of Hygiene & Tropical Medicine","Mathematical models have played a key role in understanding the spread of directly-transmissible infectious diseases such as Coronavirus Disease 2019 (COVID-19), as well as the effectiveness of public health responses. As the risk of contracting directly-transmitted infections depends on who interacts with whom, mathematical models often use contact matrices to characterise the spread of infectious pathogens. These contact matrices are usually generated from diary-based contact surveys. However, the majority of places in the world do not have representative empirical contact studies, so synthetic contact matrices have been constructed using more widely available setting-specific survey data on household, school, classroom, and workplace composition combined with empirical data on contact patterns in Europe. In 2017, the largest set of synthetic contact matrices to date were published for 152 geographical locations. In this study, we update these matrices with the most recent data and extend our analysis to 177 geographical locations. Due to the observed geographic differences within countries, we also quantify contact patterns in rural and urban settings where data is available. Further, we compare both the 2017 and 2020 synthetic matrices to out-of-sample empirically-constructed contact matrices, and explore the effects of using both the empirical and synthetic contact matrices when modelling physical distancing interventions for the COVID-19 pandemic. We found that the synthetic contact matrices reproduce the main traits of the contact patterns in the empirically-constructed contact matrices. Models parameterised with the empirical and synthetic matrices generated similar findings with few differences observed in age groups where the empirical matrices have missing or aggregated age groups. This finding means that synthetic contact matrices may be used in modelling outbreaks in settings for which empirical studies have yet to be conducted. Author summaryThe risk of contracting a directly transmitted infectious disease such as the Coronavirus Disease 2019 (COVID-19) depends on who interacts with whom. Such person-to-person interactions vary by age and locations--e.g., at home, at work, at school, or in the community--due to the different social structures. These social structures, and thus contact patterns, vary across and within countries. Although social contact patterns can be measured using contact surveys, the majority of countries around the world, particularly low- and middle-income countries, lack nationally representative contact surveys. A simple way to present contact data is to use matrices where the elements represent the rate of contact between subgroups such as age groups represented by the columns and rows. In 2017, we generated age- and location-specific synthetic contact matrices for 152 geographical regions by adapting contact pattern data from eight European countries using country-specific data on household size, school and workplace composition. We have now updated these matrices with the most recent data (Demographic Household Surveys, World Bank, UN Population Division) extending the coverage to 177 geographical locations, covering 97.2% of the worlds population. We also quantified contact patterns in rural and urban settings. When compared to out-of-sample empirically-measured contact patterns, we found that the synthetic matrices reproduce the main features of these contact patterns.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2020.07.19.20156869,2020-07-25,https://medrxiv.org/cgi/content/short/2020.07.19.20156869,Paired nasopharyngeal and deep lung testing for SARS-CoV2 reveals a viral gradient in critically ill patients: a multi-centre study,Islam Hamed; Nesreen Shaban; Marwan Nassar; Sam Love; Martin D Curran; Stephen Webb; Huina Yang; Anthony Rostron; Katherine Watson; Vilas Navapurkar; Razeenn Mahroof; Andrew Conway Morris,"John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK; John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK; John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK; John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK; Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom; Royal Papworth Hospital, Cambridge, UK; Royal Papworth Hospital, Cambridge, UK; Sunderland Royal Hospital, South Tyneside and Sunderland NHS Foundation Trust, UK; Sunderland Royal Hospital, South Tyneside and Sunderland NHS Foundation Trust, UK; John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK; John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK; University of Cambridge","Samples for diagnostic tests for SARS-CoV-2 can be obtained from the upper (nasopharyngeal/oropharyngeal swabs) or lower respiratory tract (sputum or tracheal aspirate or broncho-alveolar lavage - BAL). Data from different testing sites indicates different rates of positivity. Reverse-transcriptase polymerase chain reaction (RT-PCR) allows for semi-quantitative estimates of viral load as time to crossing threshold (Ct) is inversely related to viral load. - -ObjectivesThe objective of our study was to evaluate SARS-CoV2 RNA loads between paired nasopharyngeal (NP) and deep lung (endotracheal aspirate or BAL) samples from critically ill patients. - -MethodsSARS-CoV-2 RT-PCR results were retrospectively reviewed for 51 critically ill patients from 5 intensive care units in 3 hospitals ; Addenbrookes Hospital Cambridge (3 units), Royal Papworth Cambridge (1 unit), and Royal Sunderland Hospital (1 unit). At the times when paired NP and deep lung samples were obtained, one patient had been on oxygen only, 6 patients on non-invasive ventilation, 18 patients on ECMO, and 26 patients mechanically ventilated. - -ResultsResults collected showed significant gradient between NP and deep lung viral loads. Median Ct value was 29 for NP samples and 24 for deep lung samples. Of 51 paired samples, 16 were negative (below limit of detection) on NP swabs but positive (above limit of detection) on deep lung sample, whilst 2 were negative on deep sample but positive on NP (both patients were on ECMO). - -ConclusionsIt has been suggested that whilst SARS-CoV1 tends to replicate in the lower respiratory tract, SARS-CoV2 replicates more vigorously in the upper respiratory tract. These data challenge that assumption. These data suggest that viral migration to, and proliferation in, the lower respiratory tract may be a key factor in the progression to critical illness and the development of severe acute respiratory syndrome (SARS). Factors which promote this migration should be examined for association with severe COVID-19. From a practical point of view, patients with suspected severe COVID-19 should have virological samples obtained from the lower respiratory tract where-ever possible, as upper respiratory samples have a significant negative rate.",intensive care and critical care medicine,fuzzy,100,100 medRxiv,10.1101/2020.07.22.20159632,2020-07-24,https://medrxiv.org/cgi/content/short/2020.07.22.20159632,Excess mortality during the COVID-19 outbreak in Italy: a two-stage interrupted time series analysis,Matteo Scortichini; Rochelle Schneider dos Santos; Francesca De' Donato; Manuela De Sario; Paola Michelozzi; Marina Davoli; Pierre Masselot; Francesco Sera; Antonio Gasparrini,London School of Hygiene and Tropical Medicine; LSHTM; Lazio Regional Health Service; Lazio Regional Health Service; Lazio Regional Health Service; Lazio Regional Health Service; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine,"BackgroundItaly was the first country outside China to experience the impact of the COVID-19 pandemic, which resulted in a significant health burden. This study presents an analysis of the excess mortality across the 107 Italian provinces, stratified by sex, age group, and period of the outbreak. MethodsThe analysis was performed using a two-stage interrupted time series design using daily mortality data for the period January 2015 - May 2020. In the first stage, we performed province-level quasi-Poisson regression models, with smooth functions to define a baseline risk while accounting for trends and weather conditions and to flexibly estimate the variation in excess risk during the outbreak. Estimates were pooled in the second stage using a mixed-effects multivariate meta-analysis. @@ -5413,9 +5290,6 @@ ResultsHospital cohort: significantly higher prevalence of delirium in the frail ConclusionsThis is the first study demonstrating higher prevalence of delirium as a COVID-19 symptom in older adults with frailty compared to other older adults. This emphasises need for systematic frailty assessment and screening for delirium in acutely ill older patients in hospital and community settings. Clinicians should suspect COVID-19 in frail adults with delirium.",geriatric medicine,fuzzy,94,100 medRxiv,10.1101/2020.06.13.20130419,2020-06-16,https://medrxiv.org/cgi/content/short/2020.06.13.20130419,Mental health service activity during COVID-19 lockdown: South London and Maudsley data on working age community and home treatment team services and mortality from February to mid-May 2020,Robert Stewart; Evangelia Martin; Matthew Broadbent,King's College London; King's College London; South London and Maudsley NHS Foundation Trust,"The lockdown and social distancing policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare; however, there has been relatively little quantification of this. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for home treatment teams (HTTs) and working age adult community mental health teams (CMHTs) from 1st February to 15th May 2020 at the South London and Maudsley NHS Trust (SLaM), a large mental health service provider for 1.2m residents in south London. In addition daily deaths are described for all current and previous SLaM service users over this period and the same dates in 2019. In summary, comparing periods before and after 16th March 2020 the CMHT sector showed relatively stable caseloads and total contact numbers, but a substantial shift from face-to-face to virtual contacts, while HTTs showed the same changeover but reductions in caseloads and total contacts (although potentially an activity rise again during May). Number of deaths for the two months between 16th March and 15th May were 2.4-fold higher in 2020 than 2019, with 958 excess deaths.",psychiatry and clinical psychology,fuzzy,100,100 -medRxiv,10.1101/2020.06.12.20129056,2020-06-16,https://medrxiv.org/cgi/content/short/2020.06.12.20129056,Symptom clusters in Covid19: A potential clinical prediction tool from the COVID Symptom study app,Carole H Sudre; Karla Lee; Mary Ni Lochlainn; Thomas Varsavsky; Benjamin Murray; Mark S. Graham; Cristina Menni; Marc Modat; Ruth C.E. Bowyer; Long H Nguyen; David Alden Drew; Amit D Joshi; Wenjie Ma; Chuan Guo Guo; Chun Han Lo; Sajaysurya Ganesh; Abubakar Buwe; Joan Capdevila Pujol; Julien Lavigne du Cadet; Alessia Visconti; Maxim Freydin; Julia S. El Sayed Moustafa; Mario Falchi; Richard Davies; Maria F. Gomez; Tove Fall; M. Jorge Cardoso; Jonathan Wolf; Paul W Franks; Andrew T Chan; Timothy D Spector; Claire J Steves; Sebastien Ourselin,King's College London; Department of Twin Research and Genetic Epidemiology; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; Lund University; Lund University; King's College London; Zoe Global Limited; Lund University; Massachusetts General Hospital; King's College London; King's College London; King's College London,"As no one symptom can predict disease severity or the need for dedicated medical support in COVID-19, we asked if documenting symptom time series over the first few days informs outcome. Unsupervised time series clustering over symptom presentation was performed on data collected from a training dataset of completed cases enlisted early from the COVID Symptom Study Smartphone application, yielding six distinct symptom presentations. Clustering was validated on an independent replication dataset between May 1-May 28th, 2020. Using the first 5 days of symptom logging, the ROC-AUC of need for respiratory support was 78.8%, substantially outperforming personal characteristics alone (ROC-AUC 69.5%). Such an approach could be used to monitor at-risk patients and predict medical resource requirements days before they are required. - -One sentence summaryLongitudinal clustering of symptoms can predict the need for respiratory support in severe COVID-19.",health informatics,fuzzy,94,100 bioRxiv,10.1101/2020.06.16.153817,2020-06-16,https://biorxiv.org/cgi/content/short/2020.06.16.153817,The IMEx Coronavirus interactome: an evolving map of Coronaviridae-Host molecular interactions,Livia Perfetto; Chiara Pastrello; Noemi Del-Toro; Margaret Duesbury; Marta Iannuccelli; Max Kotlyar; Luana Licata; Birgit Meldal; Kalpana Panneerselvam; Simona Panni; Negin Rahimzadeh; Sylvie Ricard-Blum; Lukasz Salwinski; Anjali Shrivastava; Gianni Cesareni; Matteo Pellegrini; Sandra Orchard; Igor Jurisica; Henning Hermjakob; Pablo Porras,"European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI); Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, University Health Network, 5KD-407, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Can; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK. UCLA-DOE Institute, UCLA, ; Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy; Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, University Health Network, 5KD-407, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Can; Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.; Department of Biology, Ecology and Earth Sciences, Universita della Calabria, Rende, Italy; UCLA-DOE Institute, UCLA, Los Angeles, USA. Providence John Wayne Cancer Institute, Santa Monica, USA; Univ Lyon, University Claude Bernard Lyon 1, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry (ICBMS), UMR 5246, F-69622 Vil; UCLA-DOE Institute, UCLA, Los Angeles, USA; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.; Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy; Department of Molecular, Cell and Developmental Biology, UCLA, Los Angeles, USA; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.; Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, University Health Network, 5KD-407, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Can; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.; European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.","The current Coronavirus Disease 2019 (COVID-19) pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has spurred a wave of research of nearly unprecedented scale. Among the different strategies that are being used to understand the disease and develop effective treatments, the study of physical molecular interactions enables studying fine-grained resolution of the mechanisms behind the virus biology and the human organism response. Here we present a curated dataset of physical molecular interactions, manually extracted by IMEx Consortium curators focused on proteins from SARS-CoV-2, SARS-CoV-1 and other members of the Coronaviridae family. Currently, the dataset comprises over 2,200 binarized interactions extracted from 86 publications. The dataset can be accessed in the standard formats recommended by the Proteomics Standards Initiative (HUPO-PSI) at the IntAct database website (www.ebi.ac.uk/intact), and will be continuously updated as research on COVID-19 progresses.",bioinformatics,fuzzy,100,100 medRxiv,10.1101/2020.06.12.20129494,2020-06-14,https://medrxiv.org/cgi/content/short/2020.06.12.20129494,Impact on mental health care and on mental health service users of the COVID-19 pandemic: a mixed methods survey of UK mental health care staff,Sonia Johnson; Christian Dalton-Locke; Norha Vera San Juan; Una Foye; Sian Oram; Alexandra Papamichail; Sabine Landau; Rachel Rowan Olive; Tamar Jeynes; Prisha Shah; Luke Sheridan Rains; Brynmor Lloyd-Evans; Sarah Carr; Helen Killaspy; Steve Gillard; Alan Simpson; - The COVID-19 Mental Health Policy Research Unit Group,"NIHR Mental Health Policy Research Unit, Division of Psychiatry, University College London, London, UK; NIHR Mental Health Policy Research Unit, Division of Psychiatry, University College London, London, UK; NIHR Mental Health Policy Research Unit, Institute of Psychiatry, Psychology & Neuroscience, King s College London, London, UK; NIHR Mental Health Policy Research Unit, Institute of Psychiatry, Psychology & Neuroscience, King s College London, London, UK; NIHR Mental Health Policy Research Unit, Institute of Psychiatry, Psychology & Neuroscience, King s College London, London, UK; NIHR Mental Health Policy Research Unit, Institute of Psychiatry, Psychology & Neuroscience, King s College London, London, UK; NIHR Mental Health Policy Research Unit, Institute of Psychiatry, Psychology & Neuroscience, King s College London, London, UK; Division of Psychiatry (NIHR Mental Health Policy Research Unit COVID-19 Co-Production Group), University College London, London, UK; Division of Psychiatry (NIHR Mental Health Policy Research Unit COVID-19 Co-Production Group), University College London, London, UK; Division of Psychiatry (NIHR Mental Health Policy Research Unit COVID-19 Co-Production Group), University College London, London, UK; NIHR Mental Health Policy Research Unit, Division of Psychiatry, University College London, London, UK; NIHR Mental Health Policy Research Unit, Division of Psychiatry, University College London, London, UK; School of Social Policy/ Institute for Mental Health, University of Birmingham, Birmingham, UK; 1. NIHR Mental Health Policy Research Unit, Division of Psychiatry, University College London, London, UK; Population Health Research Institute, St George s, University of London, London, UK; NIHR Mental Health Policy Research Unit, Institute of Psychiatry, Psychology & Neuroscience, King s College London, London, UK; ","PurposeThe COVID-19 pandemic has potential to disrupt and burden the mental health care system, and to magnify inequalities experienced by mental health service users. @@ -5449,6 +5323,15 @@ C_LI What do these findings mean?O_LIIndividuals with [≥]2 LTCs, especially if these are cardiometabolic in nature, should be particularly stringent in adhering to preventive measures, such as physical distancing and hand hygiene. C_LIO_LIOur findings have implications for clinicians, occupational health and employers when considering work-place environments, appropriate advice for patients, and adaptations that might be required to protect such staff, identified here, as higher risk. C_LI",epidemiology,fuzzy,100,91 +medRxiv,10.1101/2020.06.10.20127175,2020-06-11,https://medrxiv.org/cgi/content/short/2020.06.10.20127175,Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.,Amitava Banerjee; Suliang Chen; Laura Pasea; Alvina Lai; Michail Katsoulis; Spiros Denaxas; Vahe Nafilyan; Bryan Williams; Wai Keong Wong; Ameet Bakhai; Kamlesh Khunti; Deenan Pillay; Mahdad Noursadeghi; Honghan Wu; Nilesh Pareek; Daniel Bromage; Theresa Mcdonagh; Jonathan Byrne; James T Teo; Ajay Shah; Ben Humberstone; Liang V Tang; Anoop SV Shah; Andrea Rubboli; Yutao Guo; Yu Hu; Cathie LM Sudlow; Gregory YH Lip; Harry Hemingway,"University College London; University College London; University College London; University College London; UCL; University College London; Office for National Statistics; UCL; University College London Hospitals NHS Trust; Royal Free Hospitals NHS Trust; University of Leicester; UCL; UCL; UCL; King's College Hospital; Kings College London; Kings College London; Kings London NHS Trust; Kings College Hospital NHS Foundation Trust; King's College London; Office for National Statistics; Huazhong University of Science and Technology, Wuhan, China; University of Edinburgh; Ospedale S. Maria delle Croci, Ravenna, Italy; PLA General Hospital, Beijing, China.; Huazhong University of Science and Technology, Wuhan, China.; University of Edinburgh; University of Liverpool; UCL","BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both ""direct"", through infection, and ""indirect"", through changes in healthcare. + +MethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(""direct"" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For ""indirect"" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020. + +FindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths. + +InterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic. + +FundingNIHR, HDR UK, Astra Zeneca",cardiovascular medicine,fuzzy,100,100 bioRxiv,10.1101/2020.06.11.145920,2020-06-11,https://biorxiv.org/cgi/content/short/2020.06.11.145920,SARS-CoV-2 mRNA Vaccine Development Enabled by Prototype Pathogen Preparedness,Kizzmekia S. Corbett; Darin Edwards; Sarah R. Leist; Olubukola M. Abiona; Seyhan Boyoglu-Barnum; Rebecca A. Gillespie; Sunny Himansu; Alexandra Schafer; Cynthia T. Ziwawo; Anthony T. DiPiazza; Kenneth H. Dinnon; Sayda M. Elbashir; Christine A. Shaw; Angela Woods; Ethan J. Fritch; David R. Martinez; Kevin W. Bock; Mahnaz Minai; Bianca M. Nagata; Geoffrey B. Hutchinson; Kapil Bahl; Dario Garcia-Dominguez; LingZhi Ma; Isabella Renzi; Wing-Pui Kong; Stephen D. Schmidt; Lingshu Wang; Yi Zhang; Laura J. Stevens; Emily Phung; Lauren A. Chang; Rebecca J. Loomis; Nedim Emil Altaras; Elisabeth Narayanan; Mihir Metkar; Vlad Presnyak; Catherine Liu; Mark K. Louder; Wei Shi; Kwanyee Leung; Eun Sung Yang; Ande West; Kendra L. Gully; Nianshuang Wang; Daniel Wrapp; Nicole A. Doria-Rose; Guillaume Stewart-Jones; Hamilton Bennett; Martha C. Nason; Tracy J. Ruckwardt; Jason S. McLellan; Mark R. Denison; James D. Chappell; Ian N. Moore; Kaitlyn M. Morabito; John R. Mascola; Ralph S. Baric; Andrea Carfi; Barney S Graham,"Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Moderna, Inc.; Department of Epidemiology; University of North Carolina at Chapel Hill; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Moderna, Inc.; Department of Epidemiology; University of North Carolina at Chapel Hill; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Epidemiology; University of North Carolina at Chapel Hill; Moderna, Inc.; Moderna, Inc.; Moderna, Inc.; Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill; Department of Epidemiology; University of North Carolina at Chapel Hill; National Institute of Allergy and Infectious Diseases; National Institutes of Health; National Institute of Allergy and Infectious Diseases; National Institutes of Health; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Moderna, Inc.; Moderna, Inc.; Moderna, Inc.; Moderna, Inc.; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Pediatrics, Vanderbilt University Medical Center; Institute for Biomedical Sciences, George Washington University; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Moderna, Inc.; Moderna, Inc.; Moderna, Inc.; Moderna, Inc.; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Epidemiology; University of North Carolina at Chapel Hill; Department of Epidemiology; University of North Carolina at Chapel Hill; Department of Molecular Biosciences; University of Texas at Austin; Department of Molecular Biosciences; University of Texas at Austin; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Moderna, Inc.; Moderna, Inc.; Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Molecular Biosciences; University of Texas at Austin; Department of Pediatrics, Vanderbilt University Medical Center; Department of Pediatrics, Vanderbilt University Medical Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Epidemiology; University of North Carolina at Chapel Hill; Department of Microbiology and Immunology, School of Medicine, University of North Caro; Moderna, Inc.; Vaccine Research Center, NIAID, NIH","A SARS-CoV-2 vaccine is needed to control the global COVID-19 public health crisis. Atomic-level structures directed the application of prefusion-stabilizing mutations that improved expression and immunogenicity of betacoronavirus spike proteins. Using this established immunogen design, the release of SARS-CoV-2 sequences triggered immediate rapid manufacturing of an mRNA vaccine expressing the prefusion-stabilized SARS-CoV-2 spike trimer (mRNA-1273). Here, we show that mRNA-1273 induces both potent neutralizing antibody and CD8 T cell responses and protects against SARS-CoV-2 infection in lungs and noses of mice without evidence of immunopathology. mRNA-1273 is currently in a Phase 2 clinical trial with a trajectory towards Phase 3 efficacy evaluation.",immunology,fuzzy,96,94 medRxiv,10.1101/2020.06.08.20120584,2020-06-09,https://medrxiv.org/cgi/content/short/2020.06.08.20120584,SARS-CoV-2 virus and antibodies in front-line Health Care Workers in an acute hospital in London: preliminary results from a longitudinal study,Catherine Houlihan; Nina Vora; Thomas Byrne; Dan Lewer; Judith Heaney; David A Moore; Rebecca Matthews; Sajida Adam; Louise Enfield; Abigail Severn; Angela McBride; Moira Jane Spyer; Rupert Beale; Peter Cherepanov; Kathleen Gaertner; Maryam Shahmanesh; - The SAFER Field Study Team; Kevin Ng; Georgina Cornish; Naomi Walker; Susan Michie; Ed Manley; Fabiana Lorencatto; - The Crick-COVID-Consortium; Richard Gilson; Sonia Gandhi; Steve Gamblin; George Kassiotis; Laura McCoy; Charles Swanton; Andrew Hayward; Eleni Nastouli,University College London Hospital; UCL; UCL; University College London; UCL; Francis Crick Institute; UCL; UCL; UCL; UCL; UCL; UCL; Francis Crick Institute; Francis Crick Institute; UCL; UCL; ; Francis Crick Institute; Francis Crick Institute; UCL; UCL; Leeds University; UCL; ; UCL; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; UCL; Francis Crick Institute; UCL; University College London,"BackgroundAlthough SARS-CoV-2 infection in Healthcare Workers (HCWs) is a public health concern, there is little description of their longitudinal antibody response in the presence or absence of SARS-CoV-2 and symptoms. We followed HCWs in an acute London hospital to measure seroconversion and RNA detection at the peak of the pandemic. @@ -5552,13 +5435,6 @@ MethodsWe report multi-center, weekly cancer diagnostic referrals and chemothera ResultsWeekly data until April 2020 demonstrate significant falls in admissions for chemotherapy (45-66% reduction) and urgent referrals for early cancer diagnosis (70-89% reduction), compared to pre-emergency levels. Under conservative assumptions of the emergency affecting only people with newly diagnosed cancer (incident cases) at COVID-19 PAE of 40%, and an RIE of 1.5, the model estimated 6,270 excess deaths at 1 year in England and 33,890 excess deaths in the US. In England, the proportion of patients with incident cancer with [≥]1 comorbidity was 65.2%. The number of comorbidities was strongly associated with cancer mortality risk. Across a range of model assumptions, and across incident and prevalent cancer cases, 78% of excess deaths occur in cancer patients with Harry [≥]1 comorbidity. ConclusionWe provide the first estimates of potential excess mortality among people with cancer and multimorbidity due to the COVID-19 emergency and demonstrate dramatic changes in cancer services. To better inform prioritization of cancer care and guide policy change, there is an urgent need for weekly data on cause-specific excess mortality, cancer diagnosis and treatment provision and better intelligence on the use of effective treatments for comorbidities.",oncology,fuzzy,100,100 -medRxiv,10.1101/2020.05.27.20114447,2020-05-28,https://medrxiv.org/cgi/content/short/2020.05.27.20114447,Automated and partially-automated contact tracing: a rapid systematic review to inform the control of COVID-19,Isobel Braithwaite; Tom Callender; Miriam Bullock; Robert W Aldridge,"UCL Public Health Data Science Research Group, Institute of Health Informatics, University College London, London, UK; Department of Applied Health Research, University College London, London, UK; UCL Collaborative Centre for Inclusion Health, University College London, London UK; UCL Public Health Data Science Group, Institute of Health Informatics, University College London, London UK","BackgroundAutomated or partially-automated contact tracing tools are being deployed by many countries to contain SARS-CoV-2; however, the evidence base for their use is not well-established. - -MethodsWe undertook a rapid systematic review of automated or partially-automated contact tracing, registered with PROSPERO (CRD42020179822). We searched PubMed, EMBASE, OVID Global Health, EBSCO COVID Portal, Cochrane Library, medRxiv, bioRxiv, arXiv and Google Advanced for articles relevant to COVID-19, SARS, MERS, influenza or Ebola from 1/1/200014/4/2020. Two authors reviewed all full-text manuscripts. One reviewer extracted data using a pre-piloted form; a second independently verified extracted data. Primary outcomes were the number or proportion of contacts (and/or subsequent cases) identified; secondary outcomes were indicators of outbreak control, app/tool uptake, resource use, cost-effectiveness and lessons learnt. The Effective Public Health Practice Project tool or CHEERS checklist were used in quality assessment. - -Findings4,033 citations were identified and 15 were included. No empirical evidence of automated contact tracings effectiveness (regarding contacts identified or transmission reduction) was identified. Four of seven included modelling studies suggested that controlling COVID-19 requires high population uptake of automated contact-tracing apps (estimates from 56% to 95%), typically alongside other control measures. Studies of partially-automated contact tracing generally reported more complete contact identification and follow-up, and greater intervention timeliness (0.5-5 hours faster), than previous systems. No meta-analyses were possible. - -InterpretationAutomated contact tracing has potential to reduce transmission with sufficient population uptake and usage. However, there is an urgent need for well-designed prospective evaluations as no studies provided empirical evidence of its effectiveness.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.05.19.20105460,2020-05-26,https://medrxiv.org/cgi/content/short/2020.05.19.20105460,"SARS-CoV-2 infection, clinical features and outcome of COVID-19 in United Kingdom nursing homes",Neil SN Graham; Cornelia Junghans; Rawlda Downes; Catherine Sendall; Helen Lai; Annie McKirdy; Paul Elliott; Robert Howard; David Wingfield; Miles Priestman; Marta Ciechonska; Loren Cameron; Marko Storch; Michael Crone; Paul Freemont; Paul Randell; Robert McLaren; Nicola Lang; Shamez Ladhani; Frances Sanderson; David J Sharp,"UK DRI Centre for Care Research and Technology, Imperial College London; Department of Primary Care and Public Health, Imperial College London; Department of Elderly Medicine, Imperial College Healthcare NHS Trust, Charing Cross Hospital, London W6 8RF, UK; Department of Elderly Medicine, Imperial College Healthcare NHS Trust, Charing Cross Hospital, London W6 8RF, UK; UK DRI Centre for Care Research and Technology, Imperial College London; 5. North West London Health Protection Team, Public Health England, 61 Colindale Avenue, Colindale, London NW9 5EQ; Department of Epidemiology and Biostatistics, Imperial College London; Division of Psychiatry, UCL, 149 Tottenham Court Road, London W1T 7NF; Department of Metabolism, Digestion & Reproduction, Imperial College London; London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London, W12 0BZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London, W12 0BZ, UK; Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London, W12 0BZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London, W12 0BZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London, W12 0BZ, UK; North West London Pathology, Charing Cross Hospital, London W6 8RF, UK; Park Medical Centre, Hammersmith, London W6 0QG; Hammersmith & Fulham Council, 3 Shortlands, Hammersmith W6 8DA; Immunisation and Countermeasures Division, Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Department of Infection, Imperial College Healthcare NHS Trust, Charing Cross Hospital, London W6 8RF, UK; UK Dementia Research Institute Centre for Care Research and Technology, Imperial College London","ObjectivesTo understand SARS-Co-V-2 infection and transmission in UK nursing homes in order to develop preventive strategies for protecting the frail elderly residents. DesignAn outbreak investigation. @@ -5683,6 +5559,9 @@ RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe interaction bet Added value of this studyData from a large UK population who are users of a symptom reporting app during the pandemic supports the hypothesis that smokers are more likely to develop symptoms consistent with COVID-19 and that they have an increased symptom burden. Implications of all the available evidenceThese population data, combined with evidence of a worse outcome in smokers hospitalised with the condition, support the contention that smoking increases individual risk from COVID-19. Support to help people to quit smoking should therefore form part of efforts to deal with the pandemic.",respiratory medicine,fuzzy,94,100 +medRxiv,10.1101/2020.05.14.20101824,2020-05-19,https://medrxiv.org/cgi/content/short/2020.05.14.20101824,Changing travel patterns in China during the early stages of the COVID-19 pandemic,Hamish Gibbs; Yang Liu; Carl AB Pearson; Christopher I Jarvis; Chris Grundy; Billy J Quilty; Charlie Diamond; Rosalind M Eggo,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine,"Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigated the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020 and discussed their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower access to care. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and have not yet led to structural reorganisation of the transportation network at the time of this study. + +One sentence summaryUnderstanding travel before, during, and after the introduction of travel restrictions in China in response to the COVID-19 Pandemic.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.05.11.20098269,2020-05-18,https://medrxiv.org/cgi/content/short/2020.05.11.20098269,Accessibility and allocation of public parks and gardens during COVID-19 social distancing in England and Wales,Niloofar Shoari; Majid Ezzati; Jill Baumgartner; Diego Malacarne; Daniela Fecht,Imperial College London; Imperial College London; McGill University; Imperial College London; Imperial College London,"Visiting parks and gardens may attenuate the adverse physical and mental health impacts of social distancing implemented to reduce the spread of COVID-19. We quantified access to public parks and gardens in urban areas of England and Wales, and the potential for park crowdedness during periods of high use. We combined data from the Office for National Statistics and Ordnance Survey to quantify (i) the number of parks within 500 and 1,000 metres of urban postcodes (i.e., availability), (ii) the distance of postcodes to the nearest park (i.e., accessibility), and (iii) per-capita space in each park for people living within 1,000m. We examined how these measures vary by city and share of homes that are flats. Around 25.4 million people can access public parks or gardens within a ten-minute walk, while 3.8 million residents live farther away; of these 21% are children and 13% are elderly. Areas with a higher share of flats on average are closer to a park but people living in these areas are potentially less able to meet social distancing requirements while in parks during periods of high use. Cities in England and Wales can provide residents with access to green space that enables outdoor exercise and play during social distancing. Cities aiming to facilitate social distancing while keeping public green spaces open might require implementing measures such as dedicated park times for different age groups or entry allocation systems that, combined with smartphone apps or drones, can monitor and manage the total number of people using the park.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.05.12.20098921,2020-05-18,https://medrxiv.org/cgi/content/short/2020.05.12.20098921,Behavioural change towards reduced intensity physical activity is disproportionately prevalent among adults with serious health issues or self-perception of high risk during the UK COVID-19 lockdown.,Nina Trivedy Rogers; Naomi Waterlow; Hannah E Brindle; Luisa Enria; Rosalind M Eggo; Shelley Lees; Chrissy h Roberts,University College London (UCL); London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Bath; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine,"ImportanceThere are growing concerns that the UK COVID-19 lockdown has reduced opportunities to maintain health through physical activity, placing individuals at higher risk of chronic disease and leaving them more vulnerable to severe sequelae of COVID-19. @@ -5993,13 +5872,6 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSAs the COVID-19 pan Added value of this studyThis study combines evidence from large international databases and new analysis of large multimorbidity studies to inform policymakers about the number of individuals that may be at increased risk of severe COVID-19 illness in different countries. We developed a tool for rapid assessments of the number and percentage of country populations that would need to be targeted under different shielding policies. Implications of all the available evidenceQuantifying how many and who is at increased risk of severe COVID-19 illness is critical to help countries design more effective interventions to protect vulnerable individuals and reduce pressure on health systems. This information can also inform a broader assessment of the health, social and economic implications of shielding various groups.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2020.04.19.20071639,2020-04-22,https://medrxiv.org/cgi/content/short/2020.04.19.20071639,How best to use limited tests? Improving COVID-19 surveillance in long-term care,David RM Smith; Audrey Duval; Koen B Pouwels; Didier Guillemot; Jerome Fernandes; Bich-Tram Huynh; Laura Temime; Lulla Opatowski,"Institut Pasteur; Institut Pasteur; University of Oxford; Institut Pasteur; Clinique de soins de suite et readaptation, Choisy-Le-Roi; Institut Pasteur; Conservatoire national des arts et metiers; Institut Pasteur","BackgroundLong-term care facilities (LTCFs) are vulnerable to COVID-19 outbreaks. Timely epidemiological surveillance is essential for outbreak response, but is complicated by a high proportion of silent (non-symptomatic) infections and limited testing resources. - -MethodsWe used a stochastic, individual-based model to simulate SARS-CoV-2 transmission along detailed inter-individual contact networks describing patient-staff interactions in real LTCF settings. We distributed nasopharyngeal swabs and RT-PCR tests using clinical and demographic indications, and evaluated the efficacy and resource-efficiency of a range of surveillance strategies, including group testing (sample pooling) and testing cascades, which couple (i) testing for multiple indications (symptoms, admission) with (ii) random daily testing. - -ResultsIn the baseline scenario, randomly introducing SARS-CoV-2 into a 170-bed LTCF led to large outbreaks, with a cumulative 86 (6-224) infections after three weeks of unmitigated transmission. Efficacy of symptom-based screening was limited by (i) lags between infection and symptom onset, and (ii) silent transmission from asymptomatic and pre-symptomatic infections. Testing upon admission detected up to 66% of patients silently infected upon LTCF entry, but missed potential introductions from staff. Random daily testing was more effective when targeting patients than staff, but was overall an inefficient use of limited resources. At high testing capacity (>1 test/10 beds/day), cascades were most effective, with a 22-52% probability of detecting outbreaks prior to any nosocomial transmission, and 38-63% prior to first onset of COVID-19 symptoms. Conversely, at low capacity (<1 test/85 beds/day), pooling randomly selected patients in a daily group test was most effective (9-15% probability of detecting outbreaks prior to transmission; 30-44% prior to symptoms). The most efficient strategy compared to the reference was to pool individuals with any COVID-like symptoms, requiring only 5-7 additional tests and 17-24 additional swabs to detect outbreaks 5-6 days earlier, prior to an additional 14-18 infections. - -ConclusionsGroup testing is an effective and efficient COVID-19 surveillance strategy for resource-limited LTCFs. Cascades are even more effective given ample testing resources. Increasing testing capacity and updating surveillance protocols accordingly could facilitate earlier detection of emerging outbreaks, informing a need for urgent intervention in settings with ongoing nosocomial transmission.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.04.16.20067504,2020-04-21,https://medrxiv.org/cgi/content/short/2020.04.16.20067504,"The effect of inter-city travel restrictions on geographical spread of COVID-19: Evidence from Wuhan, China",Billy J Quilty; Charlie Diamond; Yang Liu; Hamish Gibbs; Timothy W Russell; Christopher I Jarvis; Kiesha Prem; Carl A B Pearson; Samuel J Clifford; Stefan Flasche; CMMID COVID-19 working group; Petra Klepac; Rosalind M Eggo; Mark Jit,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; ; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine,"BackgroundTo contain the spread of COVID-19, a cordon sanitaire was put in place in Wuhan prior to the Lunar New Year, on 23 January 2020, restricting travel to other parts of China. We assess the efficacy of the cordon sanitaire to delay the introduction and onset of local transmission of COVID-19 in other major cities in mainland China. MethodsWe estimated the number of infected travellers from Wuhan to other major cities in mainland China from November 2019 to March 2020 using previously estimated COVID-19 prevalence in Wuhan and publicly available mobility data. We focused on Beijing, Chongqing, Hangzhou, and Shenzhen as four representative major cities to identify the potential independent contribution of the cordon sanitaire and holiday travel. To do this, we simulated outbreaks generated by infected arrivals in these destination cities using stochastic branching processes. We also modelled the effect of the cordon sanitaire in combination with reduced transmissibility scenarios representing the effect of local non-pharmaceutical interventions. @@ -6085,9 +5957,6 @@ What this study addsO_LIAmong individuals showing symptoms severe enough to be g C_LIO_LIWe developed a mathematical model combining symptoms to predict individuals likely to be COVID-19 positive and applied this to over 400,000 individuals in the general population presenting some of the COVID-19 symptoms. C_LIO_LIWe find that [~]13% of those presenting symptoms are likely to have or have had a COVID-19 infection. The proportion was slightly higher in women than in men but is comparable in all age groups, and corresponds to 3.4% of those who filled the app report. C_LI",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2020.04.02.20051334,2020-04-06,https://medrxiv.org/cgi/content/short/2020.04.02.20051334,Rapid implementation of mobile technology for real-time epidemiology of COVID-19,David A. Drew; Long H. Nguyen; Claire J. Steves; Jonathan Wolf; Tim D. Spector; Andrew T. Chan; COPE Consortium,Massachusetts General Hospital; Massachusetts General Hospital; King's College London; Zoe Global Limited; King's College London; Massachusetts General Hospital; ,"The rapid pace of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic (COVID-19) presents challenges to the robust collection of population-scale data to address this global health crisis. We established the COronavirus Pandemic Epidemiology (COPE) consortium to bring together scientists with expertise in big data research and epidemiology to develop a COVID-19 Symptom Tracker mobile application that we launched in the UK on March 24, 2020 and the US on March 29, 2020 garnering more than 2.25 million users to date. This mobile application offers data on risk factors, herald symptoms, clinical outcomes, and geographical hot spots. This initiative offers critical proof-of-concept for the repurposing of existing approaches to enable rapidly scalable epidemiologic data collection and analysis which is critical for a data-driven response to this public health challenge. - -One Sentence SummaryCOVID-19 symptom tracker for smartphones",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.04.02.20051284,2020-04-06,https://medrxiv.org/cgi/content/short/2020.04.02.20051284,Building an International Consortium for Tracking Coronavirus Health Status,Eran Segal; Feng Zhang; Xihong Lin; Gary King; Ophir Shalem; Smadar Shilo; William E. Allen; Yonatan H. Grad; Casey S. Greene; Faisal Alquaddoomi; Simon Anders; Ran Balicer; Tal Bauman; Ximena Bonilla; Gisel Booman; Andrew T. Chan; Ori Ori Cohen; Silvano Coletti; Natalie Davidson; Yuval Dor; David A. Drew; Olivier Elemento; Georgina Evans; Phil Ewels; Joshua Gale; Amir Gavrieli; Benjamin Geiger; Iman Hajirasouliha; Roman Jerala; Andre Kahles; Olli Kallioniemi; Ayya Keshet; Gregory Landua; Tomer Meir; Aline Muller; Long H. Nguyen; Matej Oresic; Svetlana Ovchinnikova; Hedi Peterson; Jay Rajagopal; Gunnar Ratsch; Hagai Rossman; Johan Rung; Andrea Sboner; Alexandros Sigaras; Tim Spector; Ron Steinherz; Irene Stevens; Jaak Vilo; Paul Wilmes; CCC (Coronavirus Census Collective),"Weizmann Institute of Science; Howard Hughes Medical Institute, Core Member, Broad Institute of MIT and Harvard, United States; Departments of Biostatistics and Statistics, Harvard T.H. Chan School of Public Health; Albert J. Weatherhead III University, Institute for Quantitative Social Science, Harvard University; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Society of Fellows, Harvard University, United States; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, United States; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, United States; ETH Zurich, NEXUS Personalized Health Technologies, Zurich, Switzerland; Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; Clalit Research Institute, Clalit Health Services, Israel; Mapping and Geo-Information Engineering, Civil and Environmental Engineering Faculty, The Technion, Israel; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; Regen Network, Argentina; Massachusetts General Hospital (MGH), United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Chelonia Applied Science, Switzerland; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; School of Medicine-IMRIC-Developmental Biology and Cancer Research, The Hebrew University; Massachusetts General Hospital (MGH), United States; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Institute for Quantitative Social Science, Harvard University; Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Sweden; symptometrics.org; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Department of immunology, Weizmann Institute of Science, Israel; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Department of Synthetic biology and Immunology, National Institute of Chemistry, Slovenia; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Regen Network, United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Luxembourg Institute of Socio-Economic Research and University of Luxembourg, Luxembourg; Massachusetts General Hospital (MGH), United States; School of Medical Sciences, Orebro University, Orebro, Sweden, and Turku Bioscience Centre, University of Turku and Abo Akademi University, Turku, Finland; Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; Institute of Computer Science, University of Tartu, Estonia, Estonia; Internal Medicine, Harvard Medical School, Department of Pulmonary Medicine and Critical Care, Massachusetts General Hospital (MGH), United States; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich a; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Science for Life Laboratory (SciLifeLab), Department of Immunology, Genetics and Pathology, Uppsala university, Sweden; Englander Institute for Precision Medicine and Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, USA; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Kings College, United Kingdom; Regen Network, United States; Science for Life Laboratory (SciLifeLab), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Sweden; Institute of Computer Science, University of Tartu, Estonia, Estonia; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg; ","Information is the most potent protective weapon we have to combat a pandemic, at both the individual and global level. For individuals, information can help us make personal decisions and provide a sense of security. For the global community, information can inform policy decisions and offer critical insights into the epidemic of COVID-19 disease. Fully leveraging the power of information, however, requires large amounts of data and access to it. To achieve this, we are making steps to form an international consortium, Coronavirus Census Collective (CCC, coronaviruscensuscollective.org), that will serve as a hub for integrating information from multiple data sources that can be utilized to understand, monitor, predict, and combat global pandemics. These sources may include self-reported health status through surveys (including mobile apps), results of diagnostic laboratory tests, and other static and real-time geospatial data. This collective effort to track and share information will be invaluable in predicting hotspots of disease outbreak, identifying which factors control the rate of spreading, informing immediate policy decisions, evaluating the effectiveness of measures taken by health organizations on pandemic control, and providing critical insight on the etiology of COVID-19. It will also help individuals stay informed on this rapidly evolving situation and contribute to other global efforts to slow the spread of disease. In the past few weeks, several initiatives across the globe have surfaced to use daily self-reported symptoms as a means to track disease spread, predict outbreak locations, guide population measures and help in the allocation of healthcare resources. The aim of this paper is to put out a call to standardize these efforts and spark a collaborative effort to maximize the global gain while protecting participant privacy.",infectious diseases,fuzzy,100,100 @@ -6185,3 +6054,12 @@ Added value of this studyThis study uses a mathematical model to assess the feas Implications of all the available evidenceContact tracing and isolation may not contain outbreaks of 2019-nCoV unless very high levels of contact tracing are achieved. Even in this case, if there is asymptomatic transmission, or a high fraction of transmission before onset of symptoms, this strategy may not achieve control within three months.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.01.31.20019265,2020-02-02,https://medrxiv.org/cgi/content/short/2020.01.31.20019265,Effectiveness of airport screening at detecting travellers infected with 2019-nCoV,Billy Quilty; Sam Clifford; Stefan Flasche; Rosalind M Eggo,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine,"As the number of novel coronavirus cases grows both inside and outside of China, public health authorities require evidence on the effectiveness of control measures such as thermal screening of arrivals at airports. We evaluated the effectiveness of exit and entry screening for 2019-nCoV infection. In our baseline scenario, we estimated that 46.5% (95%CI: 35.9 to 57.7) of infected travellers would not be detected, depending on the incubation period, sensitivity of exit and entry screening, and the proportion of cases which are asymptomatic. Airport screening is unlikely to detect a sufficient proportion of 2019-nCoV infected travellers to avoid entry of infected travellers. We developed an online tool so that results can be updated as new information becomes available.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.01.31.20019901,2020-02-02,https://medrxiv.org/cgi/content/short/2020.01.31.20019901,Early dynamics of transmission and control of 2019-nCoV: a mathematical modelling study,Adam J Kucharski; Timothy W Russell; Charlie Diamond; Yang Liu; CMMID nCoV working group; John Edmunds; Sebastian Funk; Rosalind M Eggo,London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine,"BackgroundAn outbreak of the novel coronavirus SARS-CoV-2 has led to 46,997 confirmed cases as of 13th February 2020. Understanding the early transmission dynamics of the infection and evaluating the effectiveness of control measures is crucial for assessing the potential for sustained transmission to occur in new areas. + +MethodsWe combined a stochastic transmission model with data on cases of novel coronavirus disease (COVID-19) in Wuhan and international cases that originated in Wuhan to estimate how transmission had varied over time during January and February 2020. Based on these estimates, we then calculated the probability that newly introduced cases might generate outbreaks in other areas. + +FindingsWe estimated that the median daily reproduction number, Rt, declined from 2.35 (95% CI: 1.15-4.77) one week before travel restrictions were introduced on 23rd January to 1.05 (95% CI: 0.413-2.39) one week after. Based on our estimates of Rt,we calculated that in locations with similar transmission potential as Wuhan in early January, once there are at least four independently introduced cases, there is a more than 50% chance the infection will establish within that population. + +InterpretationOur results show that COVID-19 transmission likely declined in Wuhan during late January 2020, coinciding with the introduction of control measures. As more cases arrive in international locations with similar transmission potential to Wuhan pre-control, it is likely many chains of transmission will fail to establish initially, but may still cause new outbreaks eventually. + +FundingWellcome Trust (206250/Z/17/Z, 210758/Z/18/Z), HDR UK (MR/S003975/1), Gates Foundation (INV-003174), NIHR (16/137/109)",infectious diseases,fuzzy,100,100 diff --git a/data/covid/preprints.exact.csv b/data/covid/preprints.exact.csv index 4f4d2477..5057a137 100644 --- a/data/covid/preprints.exact.csv +++ b/data/covid/preprints.exact.csv @@ -1,4 +1,5 @@ site,doi,date,link,title,authors,affiliations,abstract,category,match_type,author_similarity,affiliation_similarity +medRxiv,10.1101/2023.10.26.23297598,2023-10-26,https://medrxiv.org/cgi/content/short/2023.10.26.23297598,Assessing the causal effect of air pollution on risk of SARS-CoV-2 infection,Annalan Mathew Dwight Navaratnam; Sarah Beale; Yamina Boukari; Vincent Nguyen; Wing Lam Erica Fong; Isobel Braithwaite; Thomas Edward Byrne; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Parth Patel; Madhumita Shrotri; Alexei Yavlinsky; Andrew Hayward; Haneen Khreis; Robert W Aldridge,University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCL; University College London; University College London; University College London; University College London; University College London; UCL; University of Cambridge; UCL,"Introduction Emerging evidence suggests association of air pollution exposure with risk of SARS-CoV-2 infection, but many of these findings are limited by study design, lack of individual-level covariate data or are specific to certain subpopulations. We aim to evaluate causal effects of air pollution on risk of infection, whilst overcoming these limitations. Methods Concentrations for black carbon(BC), particulate matter 10(PM10), particulate matter 2.5(PM2.5), nitrogen dioxide(NO2) and oxides of nitrogen(NOx) from the Department of Environment, Food and Rural Affairs (DEFRA) and Effect of Low-level Air Pollution: A Study in Europe (ELAPSE) were linked to postcodes of 53,683 Virus Watch study participants. The primary outcome was first SARS-CoV-2 infection, between 1st September 2020 and 30th April 2021. Regression analysis used modified Poisson with robust estimates, clustered by household, adjusting for individual (e.g., age, sex, ethnicity) and environmental covariates(e.g., population density, region) to estimate total and direct effects. Results Single pollutant analysis showed the direct effect of higher risk of SARS-CoV-2 infection with increased exposure to PM2.5(RR1.11,95%CI 1.08;1.15), PM10(RR1.06,95%CI 1.04;1.09), NO2(RR1.04,95%CI 1.04;1.05) and NOx(RR1.02,95%CI 1.02;1.02) per 1g/m3 increment with DEFRA 2015-19 data. Sensitivity analyses altering covariates, exposure window and modelled air pollution data source produced similar estimates. Higher risk of SARS-CoV-2 per 10-5m-1 increment of BC (RR1.86, 95%CI 1.62;2.14) was observed using ELAPSE data. Conclusion Long term exposure to higher concentrations of air pollutions increases the risk of SARS-CoV-2 infection, highlighting that adverse health effects of air pollution is not only limited to non-communicable diseases.",epidemiology,exact,100,100 medRxiv,10.1101/2023.10.11.23296866,2023-10-12,https://medrxiv.org/cgi/content/short/2023.10.11.23296866,"SARS-CoV-2, influenza A/B and respiratory syncytial virus positivity and association with influenza-like illness and self-reported symptoms, over the 2022/23 winter season in the UK: a longitudinal surveillance cohort",Elisabeth Dietz; Emma Elizabeth Pritchard; Koen Pouwels; Muhammad Ehsaan; Joshua Blake; Charlotte Gaughan; Eric Haduli; Hugh Boothe; Karina-Doris Vihta; Tim Peto; Nicole Stoesser; Philippa Matthews; Nick Taylor; Ian Diamond; Ruth Studley; Emma Rourke; Paul Birrell; Daniela De Angelis; Tom Fowler; Conall Watson; David W Eyre; Thomas House; Ann Sarah Walker,University of Oxford; University of Oxford; University of Oxford; Berkshire and Surrey Pathology Services; University of Cambridge; Office of National Statistics; Berkshire and Surrey Pathology Services; Berkshire and Surrey Pathology Services; University of Oxford; University of Oxford; University of Oxford; The Francis Crick Institute; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Cambridge; University of Cambridge; UK Health Security Agency; UK Health Security Agency; University of Oxford; University of Manchester; University of Oxford,"BackgroundSyndromic surveillance often relies on patients presenting to healthcare. Community cohorts, although more challenging to recruit, could provide additional population-wide insights, particularly with SARS-CoV-2 co-circulating with other respiratory viruses. MethodsWe estimated positivity and incidence of SARS-CoV-2, influenza A/B, and RSV, and trends in self-reported symptoms including influenza-like illness (ILI), over the 2022/23 winter season in a broadly representative UK community cohort (COVID-19 Infection Survey), using negative-binomial generalised additive models. We estimated associations between test positivity and each of symptoms and influenza vaccination, using adjusted logistic and multinomial models. @@ -60,7 +61,6 @@ Added value of this studyThis study is the first to quantify changes in fit note Implications of all the available evidenceWhile we have likely underestimated the fit note rate due to overcounting of people in the workforce and misclassification of COVID-19 status, we still identified a substantial increased risk of receiving a fit note in people with COVID-19 compared with the general population over all years, even after adjusting for demographics and a wide range of clinical characteristics. The increased risk persisted into 2022, in an era where most people are vaccinated and the severity of COVID-19 illness is lessened. Given the high infection rates still occurring, these findings provide evidence for a substantial impact of COVID-19 on productivity and further evidence of the long-term impacts of COVID-19.",epidemiology,exact,100,100 medRxiv,10.1101/2023.08.02.23293519,2023-08-04,https://medrxiv.org/cgi/content/short/2023.08.02.23293519,Real-time epidemiological modelling during the COVID-19 emergency in Wales,Michael Gravenor; Mark Dawson; Ed Bennett; Ben Thorpe; Carla White; Alma Rahat; Daniel Archambault; Noemi Picco; Gibin Powathil; Biagio Lucini,Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University,"The sudden outbreak of the COVID-19 pandemic presented governments, policy makers and health services with an unprecedented challenge of taking real-time decisions that could keep the disease under control with non-pharmaceutical interventions, while at the same time limit as much as possible severe consequences of a very strict lockdown. Mathematical modelling has proved to be a crucial element for informing those decisions. Here we report on the rapid development and application of the Swansea Model, a mathematical model of disease spread in real time, to inform policy decisions during the COVID-19 pandemic in Wales.",epidemiology,exact,100,100 -medRxiv,10.1101/2023.06.29.23292056,2023-07-01,https://medrxiv.org/cgi/content/short/2023.06.29.23292056,Genome-wide Association Study of Long COVID,Vilma Lammi; Tomoko Nakanishi; Samuel E Jones; Shea J Andrews; Juha Karjalainen; Beatriz Cortes; Heath E O'Brien; Brian E Fulton-Howard; Hele H Haapaniemi; Axel Schmidt; Ruth E Mitchell; Abdou Mousas; Massimo Mangino; Alicia Huerta-Chagoya; Nasa Sinnott-Armstrong; Elizabeth T Cirulli; Marc Vaudel; Alex SF Kwong; Amit K Maiti; Minttu M Marttila; Chiara Batini; Francesca Minnai; Anna R Dearman; CA Robert Warmerdam; Celia B Sequeros; Thomas W Winkler; Daniel M Jordan; Lindsay Guare; Ekaterina Vergasova; Eirini Marouli; Pasquale Striano; Ummu Afeera Zainulabid; Ashutosh Kumar; Hajar Fauzan Ahmad; Ryuya Edahiro; Shuhei Azekawa; - Long COVID Host Genetics Initiative; - FinnGen; - DBDS Genomic Consortium; - GEN-COVID Multicenter Study; Joseph J Grzymski; Makoto Ishii; Yukinori Okada; Noam D Beckmann; Meena Kumari; Ralf Wagner; Iris M Heid; Catherine John; Patrick J Short; Per Magnus; Karina Banasik; Frank Geller; Lude H Franke; Alexander Rakitko; Emma L Duncan; Alessandra Renieri; Konstantinos K Tsilidis; Rafael de Cid; Ahmadreza Niavarani; Teresa Tusie-Luna; Shefali S Verma; George Davey Smith; Nicholas J Timpson; Mark J Daly; Andrea Ganna; Eva C Schulte; J Brent Richards; Kerstin U Ludwig; Michael Hultstrom; Hugo Zeberg; Hanna M Ollila,Institute for Molecular Medicine Finland (FIMM); Department of Human Genetics; Institute for Molecular Medicine Finland (FIMM); University of California San Francisco; Institute for Molecular Medicine Finland (FIMM); Genomes for Life-GCAT lab; Sano Genetics Limited; Genetics and Genomic Sciences; Institute for Molecular Medicine Finland (FIMM); Institute of Human Genetics; Centre for Clinical Brain Sciences; Department of Hygiene and Epidemiology; Department of Twin Research; Departamento de Medicina Genomica y Toxicologia Ambiental; Herbold Computational Biology Program; Helix; Mohn Center for Diabetes Precision Medicine; University of Bristol; Department of Genetics and Genomics; University of Helsinki; Department of Population Health Sciences; Institute for Biomedical Technologies - National Research Council; Institute for Social and Economic Research; Department of Genetics; Novo Nordisk Foundation Center for Protein Research; Department of Genetic Epidemiology; Charles Bronfman Institute for Personalized Medicine; Department of Pathology and Laboratory Medicine; Genotek Ltd.; William Harvey Research Institute; IRCCS G; Department of Internal Medicine; Department of Anatomy; Faculty of Industrial Sciences and Technology; Department of Statistical Genetics; Division of Pulmonary Medicine; ; ; ; ; Center for Genomic Medicine; Division of Pulmonary Medicine; Department of Statistical Genetics; Charles Bronfman Institute for Personalized Medicine; Institute for Social and Economic Research; Institute of Medical Microbiology & Hygiene; Department of Genetic Epidemiology; Department of Population Health Sciences; Sano Genetics Limited; Centre for Fertility and Health; Novo Nordisk Foundation Center for Protein Research; Statens Serum Institute; Department of Genetics; Genotek Ltd.; Department of Twin Research and Genetic Epidemiology; Medical Genetics; Department of Hygiene and Epidemiology; Genomes for Life-GCAT lab; Digestive Oncology Research Center; Instituto de Investigaciones Biomedicas Unam/ Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran; Department of Pathology and Laboratory Medicine; MRC Integrative Epidemiology Unit at the University of Bristol; MRC Integrative Epidemiology Unit at the University of Bristol; Institute for Molecular Medicine Finland (FIMM); Institute for Molecular Medicine Finland (FIMM); Institute of Psychiatric Phenomics & Genomics; Department of Human Genetics; Institute of Human Genetics; Anaesthesiology and Intensive Care Medicine; Department of Evolutionary Genetics; Institute for Molecular Medicine Finland (FIMM),"Infections can lead to persistent or long-term symptoms and diseases such as shingles after varicella zoster, cancers after human papillomavirus, or rheumatic fever after streptococcal infections1, 2. Similarly, infection by SARS-CoV-2 can result in Long COVID, a condition characterized by symptoms of fatigue and pulmonary and cognitive dysfunction3-5. The biological mechanisms that contribute to the development of Long COVID remain to be clarified. We leveraged the COVID-19 Host Genetics Initiative6, 7 to perform a genome-wide association study for Long COVID including up to 6,450 Long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We identified the first genome-wide significant association for Long COVID at the FOXP4 locus. FOXP4 has been previously associated with COVID-19 severity6, lung function8, and cancers9, suggesting a broader role for lung function in the pathophysiology of Long COVID. While we identify COVID-19 severity as a causal risk factor for Long COVID, the impact of the genetic risk factor located in the FOXP4 locus could not be solely explained by its association to severe COVID-19. Our findings further support the role of pulmonary dysfunction and COVID-19 severity in the development of Long COVID.",genetic and genomic medicine,exact,100,100 medRxiv,10.1101/2023.06.30.23292079,2023-06-30,https://medrxiv.org/cgi/content/short/2023.06.30.23292079,Synthesis and new evidence from the PROTECT UK National Core Study: Determining occupational risks of SARS-CoV-2 infection and COVID-19 mortality,Sarah Rhodes; Sarah Beale; Mark Cherrie; William Mueller; Fiona Holland; Melissa Matz; Ioannis Basinas; Jack D Wilkinson; Matthew Gittins; Bernardine Farrell; Andrew Hayward; Neil Pearce; Martie van Tongeren,University of Manchester; University College London; Institute of Occupational Medicine; Institute of Occupational Medicine; University of Manchester; London School of Hygiene and Tropical Medicine; University of Manchester; University of Manchester; University of Manchester; University of Manchester; UCL; London School of Hygiene and Tropical Medicine; University of Manchester,"IntroductionThe PROTECT National Core Study was funded by the UK Health and Safety Executive (HSE) to investigate routes of transmission for SARS-CoV-2 and variation between settings. MethodsA workshop was organised in Oct 2022.We brought together evidence from five published epidemiological studies that compared risks of SARS-CoV-2 infection or COVID-19 mortality by occupation or sector funded by PROTECT relating to three non-overlapping data sets, plus additional unpublished analyses relating to the Omicron period. We extracted descriptive study level data and model results. We investigated risk across four pandemic waves using forest plots for key occupational groups by time-period. @@ -865,7 +865,6 @@ ExposuresChAdOx1 versus BNT162b2 as a primary dose, and an mRNA booster vaccine. ResultsAcross eight cohorts, 19,692 mRNA vaccine boosted participants were analysed with 12,036 ChAdOx1 and 7,656 BNT162b2 primary courses with a median follow-up time of 73 days (IQR:54-90). Median age, clinical vulnerability status and infection rates fluctuate through time. 7.2% (n=864) of boosted adults with ChAdOx1 primary course experienced a SARS-CoV-2 infection compared to 7.6% (n=582) of those with BNT162b2 primary course during follow-up. The pooled adjusted hazard ratio was 0.99 [95%CI:0.88-1.11], demonstrating no difference between the incidence of SARs-CoV-2 infections based upon the primary vaccine course. Conclusion and RelevanceIn mRNA boosted individuals, we found no difference in protection comparing those with a primary course of BNT162b2 to those with aChAdOx1 primary course. This contrasts with pre-booster findings where previous research shows greater effectiveness of BNT162b2 than ChAdOx1 in preventing infection.",epidemiology,exact,100,100 -medRxiv,10.1101/2022.01.31.22269194,2022-02-01,https://medrxiv.org/cgi/content/short/2022.01.31.22269194,"An outbreak of SARS-CoV-2 in a public-facing office in England, 2021",Barry Atkinson; Karin van Veldhoven; Ian Nicholls; Matthew Coldwell; Adam Clarke; Gillian Frost; Christina J Atchison; Amber I Raja; Allan M Bennett; Derek Morgan; Neil Pearce; Tony Fletcher; Elizabeth B Brickley; Yiqun Chen,UK Health Security Agency; London School of Hygiene & Tropical Medicine; UK Health Security Agency; Health and Safety Executive; Health and Safety Executive; Health and Safety Executive; UK Health Security Agency; London School of Hygiene & Tropical Medicine; UK Health Security Agency; Health and Safety Executive; London School of Hygiene & Tropical Medicine; UK Health Security Agency; London School of Hygiene & Tropical Medicine; Health and Safety Executive,"Between August-September 2021, an outbreak of SARS-CoV-2, with an attack rate of 55% (22/40 workers), occurred in a public-facing office in England. To identify workplace and worker-related risk factors, a comprehensive investigation involving surface sampling, environmental assessment, molecular and serological testing, and worker questionnaires was performed in September - October 2021. The results affirm the utility of surface sampling to identify SARS-CoV-2 control deficiencies and the importance of evolving, site-specific risk assessments with layered COVID-19 mitigation strategies.",epidemiology,exact,100,100 medRxiv,10.1101/2022.01.26.22269901,2022-01-28,https://medrxiv.org/cgi/content/short/2022.01.26.22269901,The impact of the COVID-19 pandemic on health service utilisation following self-harm: a systematic review,Sarah Steeg; Ann John; David Gunnell; Nav Kapur; Dana Dekel; Lena Schmidt; Duleeka Kniipe; Ella Arensman; Keith Hawton; Julian PT Higgins; Emily Eyles; Catherine Macleod-Hall; Luke A McGuinness; Roger T Webb,University of Manchester; Swansea University; University of Bristol; University of Manchester; University of Swansea; University of Bristol; University of Bristol; University College Cork; University of Oxford; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Manchester,"BackgroundEvidence on the impacts of the pandemic on healthcare presentations for self-harm has accumulated rapidly. However, existing reviews do not include studies published beyond 2020. AimsTo systematically review evidence on health services utilisation for self-harm during the COVID-19 pandemic. @@ -968,6 +967,7 @@ MethodTrial emulation was conducted by pooling results from six cohorts whose re ResultsAcross six cohorts, there were a total of 21,283 participants who were eligible and vaccinated with either ChAdOx1 (n = 13,813) or BNT162b2 (n = 7,470) with a median follow-up time of 266 days (IQR: 235 - 282). By November 12th 2021, 750 (5.4%) adults who had ChAdOx1 as their vaccine experienced a SARS-CoV-2 infection, compared to 296 (4.0%) who had BNT162b2. We found that people who received ChAdOx1 vaccinations had 10.54 per 1000 people higher cumulative incidence for SARS-CoV-2 infection compared to BNT162b2 for infections during a maximum of 315 days of follow-up. When adjusted for age at vaccination, sex, minority ethnic status, index of multiple deprivation, and clinical vulnerability status, we found a pooled adjusted hazard ratio of 1.35 [HR: 1.35, 95%CI: 1.15 - 1.58], demonstrating a 35% increase in SARS-CoV-2 infections in people who received ChAdOx1 compared to BNT162b2. DiscussionWe found evidence of greater effectiveness of receiving BNT162b2 compared to ChAdOx1 vaccines against SARS-CoV-2 infection in England and Wales during a time period when Delta became the most prevalent variant of concern. Our findings demonstrate the importance of booster (third) doses to maintain protection and suggest that these should be prioritised to those who received ChAdOx1 as their primary course.",epidemiology,exact,100,100 +bioRxiv,10.1101/2021.12.17.473248,2021-12-21,https://biorxiv.org/cgi/content/short/2021.12.17.473248,"SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion",Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta,"University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge","The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.",microbiology,exact,100,100 medRxiv,10.1101/2021.12.20.21268098,2021-12-21,https://medrxiv.org/cgi/content/short/2021.12.20.21268098,"Therapies for Long COVID in non-hospitalised individuals - from symptoms, patient-reported outcomes, and immunology to targeted therapies (The TLC Study): Study protocol",Shamil Haroon; Krishnarajah Nirantharakumar; Sarah Hughes; Anuradhaa Subramanian; Olalekan Lee Aiyegbusi; Elin Haf Davies; Puja Myles; Tim Williams; Grace Turner; Joht Singh Chandan; Christel McMullan; Janet Lord; David Wraith; Kirsty McGee; Alastair Denniston; Tom Taverner; Louise Jackson; Elizabeth Sapey; Georgios Gkoutos; Krishna Gokhale; Edward Leggett; Clare Iles; Christopher Frost; Gary McNamara; Amy Bamford; Tom Marshall; Dawit Zemedikun; Gary Price; Steven Marwaha; Nikita Simms-Williams; Kirsty Brown; Anita Walker; Karen Jones; Karen Matthews; Jennifer Camaradou; Michael Saint-Cricq; Sumita Kumar; Yvonne Alder; David Stanton; Lisa Agyen; Megan Baber; Hannah Blaize; Melanie Calvert,University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University ofBirmingham; University of Birmingham; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; Aparito; Aparito; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; N/A; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; University ofBirmingham,"IntroductionIndividuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies. Methods and analysisA cohort of 4000 non-hospitalised individuals with a past COVID-19 diagnosis and 1000 matched controls will be selected from anonymised primary care records from the Clinical Practice Research Datalink (CPRD) and invited by their general practitioners to participate on a digital platform (Atom5). Individuals will report symptoms, quality of life, work capability, and patient reported outcome measures. Data will be collected monthly for one year. @@ -1131,19 +1131,6 @@ FindingsComparing the least deprived and predominantly White areas with most dep InterpretationAt the area level, IMD and BAME% are both associated with an increased COVID-19 burden in terms of prevalence (disease spread) and test positivity (disease monitoring), and the strength of association varies over the course of the pandemic. The consistency of results across the two outcome measures suggests that community level characteristics such as deprivation and ethnicity have a differential impact on disease exposure or susceptibility rather than testing access and habits. FundingsEPSRC, MRC, The Alan Turing Institute, NIH, UKHSA, DHSC, NIHR",epidemiology,exact,100,100 -medRxiv,10.1101/2021.11.08.21265312,2021-11-09,https://medrxiv.org/cgi/content/short/2021.11.08.21265312,"Understanding COVID-19 trajectories from a nationwide linked electronic health record cohort of 56 million people: phenotypes, severity, waves & vaccination",Johan H Thygesen; Christopher R Tomlinson; Sam Hollings; Mehrdad A Mizani; Alex Handy; Ashley Akbari; Amitava Banerjee; Jennifer A Cooper; Alvina G Lai; Kezhi Li; Bilal A Mateen; Naveed Sattar; Reecha Sofat; Ana Torralbo; Honghan Wu; Angela Wood; Jonathan AC Sterne; Christina Pagel; William Whiteley; Cathie Sudlow; Harry Hemingway; Spiros Denaxas; - CVD-COVID-UK Consortium,"Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; NHS Digital, Leeds, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Population Data Science and Health Data Research UK, Swansea University, Swansea, UK; Institute of Health Informatics, University College London, London, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; The Wellcome Trust, London, UK; Institute of Cardiovascular & Medical Sciences, University of Glasgow, Glasgow, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Clinical Operational Research Unit, University College London, London, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; ","BackgroundUpdatable understanding of the onset and progression of individuals COVID-19 trajectories underpins pandemic mitigation efforts. In order to identify and characterize individual trajectories, we defined and validated ten COVID-19 phenotypes from linked electronic health records (EHR) on a nationwide scale using an extensible framework. - -MethodsCohort study of 56.6 million people in England alive on 23/01/2020, followed until 31/05/2021, using eight linked national datasets spanning COVID-19 testing, vaccination, primary & secondary care and death registrations data. We defined ten COVID-19 phenotypes reflecting clinically relevant stages of disease severity using a combination of international clinical terminologies (e.g. SNOMED-CT, ICD-10) and bespoke data fields; positive test, primary care diagnosis, hospitalisation, critical care (four phenotypes), and death (three phenotypes). Using these phenotypes, we constructed patient trajectories illustrating the transition frequency and duration between phenotypes. Analyses were stratified by pandemic waves and vaccination status. - -FindingsWe identified 3,469,528 infected individuals (6.1%) with 8,825,738 recorded COVID-19 phenotypes. Of these, 364,260 (11%) were hospitalised and 140,908 (4%) died. Of those hospitalised, 38,072 (10%) were admitted to intensive care (ICU), 54,026 (15%) received non-invasive ventilation and 21,404 (6%) invasive ventilation. Amongst hospitalised patients, first wave mortality (30%) was higher than the second (23%) in non-ICU settings, but remained unchanged for ICU patients. The highest mortality was for patients receiving critical care outside of ICU in wave 1 (51%). 13,083 (9%) COVID-19 related deaths occurred without diagnoses on the death certificate, but within 30 days of a positive test while 10,403 (7%) of cases were identified from mortality data alone with no prior phenotypes recorded. We observed longer patient trajectories in the second pandemic wave compared to the first. - -InterpretationOur analyses illustrate the wide spectrum of severity that COVID-19 displays and significant differences in incidence, survival and pathways across pandemic waves. We provide an adaptable framework to answer questions of clinical and policy relevance; new variant impact, booster dose efficacy and a way of maximising existing data to understand individuals progression through disease states. - -Research in ContextO_ST_ABSEvidence before the studyC_ST_ABSWe searched PubMed on October 14, 2021, for publications with the terms ""COVID-19"" or ""SARS-CoV-2"", ""severity"", and ""electronic health records"" or ""EHR"" without date or language restrictions. Multiple studies explore factors associated with severity of COVID-19 infection, and model predictions of outcome for hospitalised patients. However, most work to date focused on isolated facets of the healthcare system, such as primary or secondary care only, was conducted in subpopulations (e.g. hospitalised patients) of limited sample size, and often utilized dichotomised outcomes (e.g. mortality or hospitalisation) ignoring the full spectrum of disease. We identified no studies which comprehensively detailed severity of infections while describing disease severity across pandemic waves, vaccination status, and patient trajectories. - -Added value of this studyTo our knowledge, this is the first study providing a comprehensive view of COVID-19 across pandemic waves using national data and focusing on severity, vaccination, and patient trajectories. Drawing on linked electronic health record (EHR) data on a national scale (56.6 million people alive and registered with GP in England), we describe key demographic factors, frequency of comorbidities, impact of the two main waves in England, and effect of full vaccination on COVID-19 severities. Additionally, we identify and describe patient trajectory networks which illustrate the main transition pathways of COVID-19 patients in the healthcare system. Finally, we provide reproducible COVID-19 phenotyping algorithms reflecting clinically relevant stages of disease severity i.e. positive tests, primary care diagnoses, hospitalisation, critical care treatments (e.g. ventilatory support) and mortality. - -Implications of all the available evidenceThe COVID-19 phenotypes and trajectory analysis framework outlined produce a reproducible, extensible and repurposable means to generate national-scale data to support critical policy decision making. By modelling patient trajectories as a series of interactions with healthcare systems, and linking these to demographic and outcome data, we provide a means to identify and prioritise care pathways associated with adverse outcomes and highlight healthcare system touch points which may act as tangible targets for intervention.",public and global health,exact,100,100 medRxiv,10.1101/2021.11.08.21265380,2021-11-08,https://medrxiv.org/cgi/content/short/2021.11.08.21265380,Describing the population experiencing COVID-19 vaccine breakthrough following second vaccination in England: A cohort study from OpenSAFELY,Amelia CA Green; Helen J Curtis; William J Hulme; Elizabeth J Williamson; Helen I McDonald; Krishnan Bhaskaran; Christopher T Rentsch; Anna Schultze; Brian MacKenna; Viyaasan Mahalingasivam; Laurie Tomlinson; Alex J Walker; Louis Fisher; Jon Massey; Colm D Andrews; Lisa E M Hopcroft; Caroline E Morton; Richard Croker; Jessica Morley; Amir Mehrkar; Sebastian CJ Bacon; David Evans; Peter Inglesby; George Hickman; Tom Ward; Simon Davy; Rohini Mathur; John Tazare; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; Christopher Bates; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Ian J Douglas; Stephen JW Evans; Liam Smeeth; Ben Goldacre,University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Bristol; TPP; TPP; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundWhile the vaccines against COVID-19 are considered to be highly effective, COVID-19 vaccine breakthrough is likely and a small number of people will still fall ill, be hospitalised, or die from COVID-19, despite being fully vaccinated. With the continued increase in numbers of positive SARS-CoV-2 tests, describing the characters of individuals who have experienced a COVID-19 vaccine breakthrough could be hugely important in helping to determine who may be at greatest risk. MethodWith the approval of NHS England we conducted a retrospective cohort study using routine clinical data from the OpenSAFELY TPP database of fully vaccinated individuals, linked to secondary care and death registry data, and described the characteristics of those experiencing a COVID-19 vaccine breakthrough. @@ -1249,6 +1236,7 @@ ResultsThe trial opened on April 2, 2020, with randomisation to colchicine start ConclusionsColchicine did not improve time to recovery in people at higher risk of complications with COVID-19 in the community. Trial registrationISRCTN86534580.",infectious diseases,exact,100,100 +medRxiv,10.1101/2021.09.13.21263487,2021-09-16,https://medrxiv.org/cgi/content/short/2021.09.13.21263487,SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population,Jia Wei; Koen B. Pouwels; Nicole Stoesser; Philippa C. Matthews; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John I Bell; John N Newton; Jeremy Farrar; Alison Howarth; Brian D. Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W. Crook; Tim E.A. Peto; A.Sarah Walker; David W. Eyre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.",infectious diseases,exact,100,100 medRxiv,10.1101/2021.09.09.21263026,2021-09-13,https://medrxiv.org/cgi/content/short/2021.09.09.21263026,The clinically extremely vulnerable to COVID: Identification and changes in health care while self-isolating (shielding) during the coronavirus pandemic,Jessica Erin Butler; Mintu Nath; Dimitra Blana; William P Ball; Nicola Beech; Corri Black; Graham Osler; Sebastien Peytrignet; Katie Wilde; Artur Wozniak; Simon Sawhney,University of Aberdeen; University of Aberdeen; University of Aberdeen; University of Aberdeen; NHS Grampian; NHS Grampian and University of Aberdeen; NHS Grampian; Health Foundation; University of Aberdeen; University of Aberdeen; NHS Grampian and University of Aberdeen,"BackgroundIn March 2020, the government of Scotland identified people deemed clinically extremely vulnerable to COVID due to their pre-existing health conditions. These people were advised to strictly self-isolate (shield) at the start of the pandemic, except for necessary healthcare. We examined who was identified as clinically extremely vulnerable, how their healthcare changed during isolation, and whether this process exacerbated healthcare inequalities. MethodsWe linked those on the shielding register in NHS Grampian, a health authority in Scotland, to healthcare records from 2015-2020. We described the source of identification, demographics, and clinical history of the cohort. We measured changes in out-patient, in-patient, and emergency healthcare during isolation in the shielding population and compared to the general non-shielding population. @@ -1558,6 +1546,9 @@ MethodsWorking on behalf of NHS England, we used OpenSAFELY data encompassing 96 ResultsLong COVID was recorded for 23,273 people. Coding was unevenly distributed amongst practices, with 26.7% of practices having not used the codes at all. Regional variation was high, ranging between 20.3 per 100,000 people for East of England (95% confidence interval 19.3-21.4) and 55.6 in London (95% CI 54.1-57.1). The rate was higher amongst women (52.1, 95% CI 51.3-52.9) compared to men (28.1, 95% CI 27.5-28.7), and higher amongst practices using EMIS software (53.7, 95% CI 52.9-54.4) compared to TPP software (20.9, 95% CI 20.3-21.4). ConclusionsLong COVID coding in primary care is low compared with early reports of long COVID prevalence. This may reflect under-coding, sub-optimal communication of clinical terms, under-diagnosis, a true low prevalence of long COVID diagnosed by clinicians, or a combination of factors. We recommend increased awareness of diagnostic codes, to facilitate research and planning of services; and surveys of clinicians experiences, to complement ongoing patient surveys.",epidemiology,exact,100,100 +medRxiv,10.1101/2021.05.05.21256668,2021-05-09,https://medrxiv.org/cgi/content/short/2021.05.05.21256668,COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland,Sofia de la Fuente Garcia; Fasih Haider; Saturnino Luz,The University of Edinburgh; The University of Edinburgh; The University of Edinburgh,"The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively. + +Clinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.",health informatics,exact,100,100 medRxiv,10.1101/2021.05.04.21256507,2021-05-06,https://medrxiv.org/cgi/content/short/2021.05.04.21256507,Describing the burden of the COVID-19 pandemic in people with psoriasis: findings from a global cross-sectional study,Satveer K Mahil; Mark Yates; Zenas Z Yiu; Sinead M Langan; Teresa Tsakok; Nick Dand; Kayleigh J Mason; Helen McAteer; Freya Meynall; Bolaji Coker; Alexandra Vincent; Dominic Urmston; Amber Vesty; Jade Kelly; Camille Lancelot; Lucy Moorhead; Herve Bachelez; Francesca Capon; Claudia R Contreras; Claudia De La Cruz; Paola Di Meglio; Paolo Gisondi; Denis Jullien; Jo Lambert; Luigi Naldi; Sam Norton; Luis Puig; Phyllis Spuls; Tiago Torres; Richard B Warren; Hoseah Waweru; John Weinman; Matt A Brown; James B Galloway; Christopher M Griffiths; Jonathan N Barker; Catherine H Smith,"St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Centre for Rheumatic Diseases, King's College London; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; Faculty of Epidemiology, and Population Health, London School of Hygiene and Tropical Medicine, London, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London, UK; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; The Psoriasis Association, Northampton, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; The Psoriasis Association, Northampton, UK; The Psoriasis Association, Northampton, UK; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; International Federation of Psoriasis Associations; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Department of Dermatology, AP-HP Hopital Saint-Louis, Paris, France; King's College London; Catedra de Dermatologia, Hospital de Clinicas, Facultad de Ciencias Medicas, Universidad Nacional de Asuncion, Paraguay; Clinica Dermacross, Santiago, Chile; King's College London; Section of Dermatology and Venereology, University of Verona, Verona, Italy; Department of Dermatology, Edouard Herriot Hospital, Hospices Civils de Lyon, University of Lyon, Lyon, France; Department of Dermatology, Ghent University, Ghent, Belgium; Centro Studi GISED, Bergamo, Italy; Psychology Department, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK; Department of Dermatology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Catalonia, Spain; Department of Dermatology, Amsterdam Public Health/Infection and Immunology, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands; Department of Dermatology, Centro Hospitalar do Porto, Portugal; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; International Federation of Psoriasis Associations; School of Cancer and Pharmaceutical Sciences, Kings College London, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK; 3Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Res; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK","BackgroundIndirect excess morbidity has emerged as a major concern in the COVID-19 pandemic. People with psoriasis may be particularly vulnerable to this because of prevalent anxiety and depression, multimorbidity and therapeutic use of immunosuppression. ObjectiveCharacterise the factors associated with worsening psoriasis in the COVID-19 pandemic, using mental health status (anxiety and depression) as the main exposure of interest. @@ -1589,6 +1580,13 @@ What this study addsO_LIIn 70,464 people with atrial fibrillation, at the thresh C_LIO_LIThis might be explained by OACs preventing severe COVID-19 outcomes, or more cautious behaviours and environmental factors reducing the risk of SARS-CoV-2 infection in those taking OACs. C_LIO_LIIn 372,746 people with non-valvular atrial fibrillation, there was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin compared with DOACs. C_LI",epidemiology,exact,100,100 +medRxiv,10.1101/2021.04.26.21255732,2021-04-28,https://medrxiv.org/cgi/content/short/2021.04.26.21255732,Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales,Sarah Beale; Isobel Braithwaite; Annalan MD Navaratnam; Pia Hardelid; Alison Rodger; Anna Aryee; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative,"University College London; University College London; University College London; University College London; University College London; Royal Free London NHS Foundation Trust,; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ","BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation. + +MethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period. + +ResultsRelative to participants in the least deprived areas, participants in the most deprived areas persistently exhibited elevated risk of exposure to vehicle sharing (aRR range across time points 1.73-8.52), public transport (aRR 3.13-5.73), work or education outside of the household (aRR 1.09-1.21), essential shops (aRR 1.09-1.13) and non-household contacts (aRR 1.15-1.19) across multiple survey periods. + +ConclusionDifferential exposure to essential public activities in deprived communities is likely to contribute to inequalities in infection risk and outcomes during the COVID-19 pandemic. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.",epidemiology,exact,100,100 medRxiv,10.1101/2021.04.21.21255807,2021-04-27,https://medrxiv.org/cgi/content/short/2021.04.21.21255807,A randomised clinical trial of azithromycin versus standard care in ambulatory COVID-19 - the ATOMIC2 trial,Timothy SC Hinks; Lucy Cureton; Ruth Knight; Ariel Wang; Jennifer L Cane; Vicki S Barber; Joanna Black; Susan J Dutton; James Melhorn; Maisha Jabeen; Phil Moss; Rajendar Garlapati; Tanya Baron; Graham Johnson; Fleur Cantle; David Clarke; Samer Elkhodair; Jonathan Underwood; Daniel Lasserson; Ian D Pavord; Sophie B Morgan; Duncan Richards,"University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; St George's Hospital, London; East Lancashire NHS Hospitals; Oxford University Hospitals NHS Trust; Royal Derby Hospital; Kings College Hospital, London; Royal Berkshire Hospital; University College London Hospital; Cardiff University; Oxford University Hospitals NHS Trust; University of Oxford; University of Oxford; University of Oxford","BackgroundThe antibacterial, anti-inflammatory and antiviral properties of azithromycin suggest therapeutic potential against COVID-19. Randomised data in mild-moderate disease are lacking. We assessed whether azithromycin is effective in reducing hospitalisation in patients with mild-moderate COVID-19. MethodsThis open-label, randomised superiority clinical trial at 19 centres in the United Kingdom enrolled adults, [≥]18 years, presenting to hospitals with clinically-diagnosed highly-probable or confirmed COVID-19 infection, with <14 days symptoms, considered suitable for initial ambulatory management. Patients were randomised (1:1) to azithromycin (500 mg daily orally for 14 days) or to standard care without macrolides. The primary outcome was the difference in proportion of participants with death or hospital admission from any cause over the 28 days from randomisation, assessed according to intention-to-treat (ITT). Trial registration: ClinicalTrials.gov, NCT04381962, Study closed. @@ -1690,23 +1688,6 @@ ResultsWe identified two models for prediction of mortality (referred to as Xie The performance of the models was variable. For prediction of mortality Xie had good discrimination at OUH with an area under the receiver-operating characteristic (AUROC) 0.87 [95 % confidence interval (CI) 0.79-0.95] and acceptable discrimination at KCH, AUROC 0.79 [0.76-0.82]. In prediction of severe disease, Allenbach had acceptable discrimination (OUH AUROC 0.81 [0.74-0.88] and KCH AUROC 0.72 [0.68-0.75]). The Zhang models had moderate to poor discrimination. Initial calibration was poor for all models but improved with recalibration. ConclusionsThe performance of the four prediction models was variable. The Xie model had the best discrimination for mortality, while the Allenbach model had acceptable results for prediction of severe disease.",infectious diseases,exact,100,100 -medRxiv,10.1101/2021.03.26.21254391,2021-03-26,https://medrxiv.org/cgi/content/short/2021.03.26.21254391,Vaccine effectiveness of the first dose of ChAdOx1 nCoV-19 and BNT162b2 against SARS-CoV-2 infection in residents of Long-Term Care Facilities (VIVALDI study),Madhumita Shrotri; Maria Krutikov; Tom Palmer; Rebecca Giddings; Borscha Azmi; Sathyavani Subbarao; Christopher Fuller; Aidan Irwin-Singer; Daniel Davies; Gokhan Tut; Jamie Lopez Bernal; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross,"University College London; University College London; University College London; University College London; University College London; Public Health England; University College London; Department of Health and Social Care, UK; Palantir Technologies UK Ltd; University of Birmingham; Public Health England; University of Birmingham; University College London; University College London; University College London","BackgroundThe effectiveness of SARS-CoV-2 vaccines in frail older adults living in Long-Term Care Facilities (LTCFs) is uncertain. We estimated protective effects of the first dose of ChAdOx1 and BNT162b2 vaccines against infection in this population. - -MethodsCohort study comparing vaccinated and unvaccinated LTCF residents in England, undergoing routine asymptomatic testing (8 December 2020 - 15 March 2021). We estimated the relative hazard of PCR-positive infection using Cox proportional hazards regression, adjusting for age, sex, prior infection, local SARS-CoV-2 incidence, LTCF bed capacity, and clustering by LTCF. - -ResultsOf 10,412 residents (median age 86 years) from 310 LTCFs, 9,160 were vaccinated with either ChAdOx1 (6,138; 67%) or BNT162b2 (3,022; 33%) vaccines. A total of 670,628 person days and 1,335 PCR-positive infections were included. Adjusted hazard ratios (aHRs) for PCR-positive infection relative to unvaccinated residents declined from 28 days following the first vaccine dose to 0{middle dot}44 (0{middle dot}24, 0{middle dot}81) at 28-34 days and 0{middle dot}38 (0{middle dot}19, 0{middle dot}77) at 35-48 days. Similar effect sizes were seen for ChAdOx1 (aHR 0{middle dot}32 [0{middle dot}15-0{middle dot}66] and BNT162b2 (aHR 0{middle dot}35 [0{middle dot}17, 0{middle dot}71]) vaccines at 35-48 days. Mean PCR cycle threshold values were higher, implying lower infectivity, for infections [≥]28 days post-vaccination compared with those prior to vaccination (31{middle dot}3 vs 26{middle dot}6, p<0{middle dot}001). - -InterpretationThe first dose of BNT162b2 and ChAdOx1 vaccines was associated with substantially reduced SARS-CoV-2 infection risk in LTCF residents from 4 weeks to at least 7 weeks. - -FundingUK Government Department of Health and Social Care. - -Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe conducted a systematic search for studies which evaluated SARS-CoV-2 vaccine effectiveness in residents of long-term care facilities (LTCFs) published between 01/01/2020 and 11/03/2021. We used variations of search terms for ""COVID-19"" AND ""vaccine effectiveness"" OR ""vaccine efficacy"" AND ""care homes"" OR ""long term care facilities"" OR ""older people"" on Ovid MEDLINE and MedRxiv. We identified one pre-print article regarding LTCFs in Denmark, which reported that a single dose of BNT162b was ineffective against SARS-CoV-2 infection in residents, however, participants received the second vaccine dose 24 days following the first dose on average, which is likely to be too soon to capture the protective effects of a single vaccine dose. Additionally, we identified two pre-print reports of studies evaluating vaccine effectiveness against symptomatic infection and hospitalisation amongst older adults in the community. The first of these found 81% vaccine effectiveness against COVID-19-related hospitalisation at 28-34 days following a single dose of BNT162b or ChAdOx1 in [≥]80-year-olds. The second of these found vaccine effectiveness against symptomatic infection of 60% at 28-34 days and 73% at 35+ days following a single dose of ChAdOx1 in [≥]70-year-olds. No studies were identified that focused on the effectiveness of a single vaccine dose against infection amongst LTCF residents at more than 4 weeks post-vaccination, a particularly important question in the context of the UK policy decision to extend the dose interval beyond 3 weeks. - -Added value of this studyWe conducted a prospective cohort study of 10,412 residents aged [≥]65 years, from 310 LTCFs across England, to investigate the protective effect of the first dose of the ChAdOx1 and BNT162b vaccines against SARS-CoV-2 infection in frail older adults. We retrieved results from routine monthly PCR testing, as well as outbreak and clinical testing for SARS-CoV-2, thereby capturing data on asymptomatic as well as symptomatic infections, which we linked to vaccination records. We estimated vaccine effectiveness to be 56% (19-76%) at 28-34 days, and 62% (23-81%) at 35-48 days following a single dose of ChAdOx1 or BNT162. Our findings suggest that the risk of SARS-CoV-2 infection is substantially reduced from 28 days following the first dose of either vaccine and that this effect is maintained for at least 7 weeks, with similar protection offered by both vaccine types. We also found that PCR cycle threshold (Ct) values, which are negatively associated with the ability to isolate virus, were significantly higher in infections occurring at [≥] 28days post vaccination compared to those occurring in the unvaccinated period, suggesting that vaccination may reduce onward transmission of SARS-CoV-2 in breakthrough infections. To the best of our knowledge, our findings constitute the first real-world evidence on vaccine effectiveness against infection for ChAdOx1, in any age group. We can also infer that both vaccines are effective against the B.1.1.7 variant, because our analysis period coincided with the rapid emergence of B.1.1.7 in England during the second wave of the pandemic. - -Implications of all the available evidenceOur findings add to the growing body of evidence on the protective effect of the BNT162b vaccines in residents of LTCFs and demonstrate the effectiveness of ChAdOx1 in this vulnerable population. Evaluating single-dose vaccine efficacy has become increasingly important in light of extended dosing intervals that have been implemented in order to maximise vaccine coverage across high-risk groups. Further work is required to evaluate the effectiveness of the first vaccine dose after 8-12 weeks, as well as following the second dose, and to evaluate the long-term impact of vaccination on SARS-CoV-2 infection, transmission and mortality in LTCFs. This will inform policy decisions regarding the ongoing need for disease control measures in LTCF such as visitor restrictions, which continue to have a detrimental impact on the wellbeing of residents, their relatives, and staff. - -Supplementary material attached.",infectious diseases,exact,100,100 medRxiv,10.1101/2021.03.19.21253940,2021-03-24,https://medrxiv.org/cgi/content/short/2021.03.19.21253940,"COVID-19 Infection Risk amongst 14,104 Vaccinated Care Home Residents: A national observational longitudinal cohort study in Wales, United Kingdom, December 2020 to March 2021",Joe Hollinghurst; Laura North; Malorie Perry; Ashley Akbari; Mike B Gravenor; Ronan A Lyons; Richard Fry,Swansea University; Swansea University; Public Health Wales; Swansea University; Swansea University; Swansea University; Swansea University,"BackgroundVaccinations for COVID-19 have been prioritised for older people living in care homes. However, vaccination trials included limited numbers of older people. AimWe aimed to study infection rates of SARS-CoV-2 for older care home residents following vaccination and identify factors associated with increased risk of infection. @@ -1843,21 +1824,6 @@ C_LIO_LIPupils were found to be at increased risk of testing positive, following C_LI C_TEXTBOX",health informatics,exact,100,100 -medRxiv,10.1101/2021.02.03.21251004,2021-02-05,https://medrxiv.org/cgi/content/short/2021.02.03.21251004,Ethnic differences in COVID-19 mortality during the first two waves of the Coronavirus Pandemic: a nationwide cohort study of 29 million adults in England,Vahe Nafilyan; Nazrul Islam; Rohini Mathur; Daniel Ayoubkhani; Amitava Banerjee; Myer Glickman; Ben Humberstone; Ian DIamond; Kamlesh Khunti,"Office for National Statistics; Nuffield Department of Population Health, Big Data Institute, University of Oxford; London School of Hygiene and Tropical Medicine; Office for National Statistics; University College London; Office for National Statistics; Office for National Statistics; Office for National Statistics; Diabetes Research Centre, University of Leicester","BackgroundEthnic minorities have experienced disproportionate COVID-19 mortality rates in the UK and many other countries. We compared the differences in the risk of COVID-19 related death between ethnic groups in the first and second waves the of COVID-19 pandemic in England. We also investigated whether the factors explaining differences in COVID-19 death between ethnic groups changed between the two waves. - -MethodsUsing data from the Office for National Statistics Public Health Data Asset on individuals aged 30-100 years living in private households, we conducted an observational cohort study to examine differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and second wave (from 1st September to 28th December 2020). We estimated age-standardised mortality rates (ASMR) in the two waves stratified by ethnic groups and sex. We also estimated hazard ratios (HRs) for ethnic-minority groups compared with the White British population, adjusted for geographical factors, socio-demographic characteristics, and pre-pandemic health conditions. - -ResultsThe study population included over 28.9 million individuals aged 30-100 years living in private households. In the first wave, all ethnic minority groups had a higher risk of COVID-19 related death compared to the White British population. In the second wave, the risk of COVID-19 death remained elevated for people from Pakistani (ASMR: 339.9 [95% CI: 303.7 - 376.2] and 166.8 [141.7 - 191.9] deaths per 100,000 population in men and women) and Bangladeshi (318.7 [247.4 - 390.1] and 127.1 [91.1 - 171.3] in men and women)background but not for people from Black ethnic groups. Adjustment for geographical factors explained a large proportion of the differences in COVID-19 mortality in the first wave but not in the second wave. Despite an attenuation of the elevated risk of COVID-19 mortality after adjusting for sociodemographic characteristics and health status, the risk was substantially higher in people from Bangladeshi and Pakistani background in both the first and the second waves. - -ConclusionBetween the first and second waves of the pandemic, the reduction in the difference in COVID-19 mortality between people from Black ethnic background and people from the White British group shows that ethnic inequalities in COVID-19 mortality can be addressed. The continued higher rate of mortality in people from Bangladeshi and Pakistani background is alarming and requires focused public health campaign and policy changes. - -*VN and NI contributed equally to this paper - -Research in contextO_ST_ABSEvidence before this studyC_ST_ABSA recent systematic review by Pan and colleagues demonstrated that people of ethnic minority background in the UK and the USA have been disproportionately affected by the Coronavirus (COVID-19) pandemic, compared to White populations. While several studies have investigated whether adjusting for socio-demographic and economic factors and medical history reduces the estimated difference in risk of mortality and hospitalisation, the reasons for the differences in the risk of experiencing harms from COVID-19 are still being explored during the course of the pandemic. Studies so far have analysed the ethnic differences in COVID-19 mortality in the first wave of the pandemic. The evidence on the temporal trend of ethnic inequalities in COVID-19 mortality, especially those from the second wave of the pandemic, is scarce. - -Added value of this studyUsing data from the Office for National Statistics (ONS) Public Health Data Asset on 29 million adults aged 30-100 years living in private households in England, we conducted an observational cohort study to examine the differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and second wave (from 1st September to 28th December 2020). We find that in the first wave all ethnic minority groups were at elevated risk of COVID-19 related death compared to the White British population. In the second wave, the differences in the risk of COVID-19 related death attenuated for Black African and Black Caribbean groups, remained substantially higher in people from Bangladeshi background, and worsened in people from Pakistani background. We also find that some of the factors explaining these differences in mortality have changed in the two waves. - -Implications of all the available evidenceThe risk of COVID-19 mortality during the first wave of the pandemic was elevated in people from ethnic minority background. An appreciable reduction in the difference in COVID-19 mortality in the second wave of the pandemic between people from Black ethnic background and people from the White British group is reassuring, but the continued higher rate of mortality in people from Bangladeshi and Pakistani background is alarming and requires focused public health campaign and policy response. Focusing on treating underlying conditions, although important, may not be enough in reducing the inequalities in COVID-19 mortality. Focused public health policy as well as community mobilisation and participatory public health campaign involving community leaders may help reduce the existing and widening inequalities in COVID-19 mortality.",epidemiology,exact,100,100 medRxiv,10.1101/2021.02.02.21250989,2021-02-03,https://medrxiv.org/cgi/content/short/2021.02.02.21250989,Short report: Ethnicity and COVID-19 death in the early part of the COVID-19 second wave in England: an analysis of OpenSAFELY data from 1st September to 9th November 2020,Krishnan Bhaskaran; Rohini Mathur; Christopher T Rentsch; Caroline E Morton; William J Hulme; Anna Schultze; Brian McKenna; Rosalind M Eggo; Angel YS Wong; Elizabeth J Williamson; Harriet J Forbes; Kevin Wing; Helen I McDonald; Chris J Bates; Sebastian CJ Bacon; Alex J Walker; David Evans; Peter Inglesby; Amir Mehrkar; Helen J Curtis; Nichola J DeVito; Richard Croker; Henry Drysdale; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Ian J Douglas; Laurie Tomlinson; Stephen JW Evans; Richard Grieve; Liam Smeeth; Ben Goldacre,"London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene and Tropical Medicine; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP, TPP House, Horsforth, Leeds; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford; TPP, TPP House, Horsforth, Leeds; TPP, TPP House, Horsforth, Leeds; TPP, TPP House, Horsforth, Leeds; TPP, TPP House, Horsforth, Leeds; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford","Black and minority ethnic groups were at raised risk of dying from COVID-19 during the first few months of the COVID-19 epidemic in England. We aimed to investigate whether ethnic inequalities in COVID-19 deaths were similar in the more recent ""second wave"" of the epidemic. Working on behalf of NHS England, we used primary care and linked ONS mortality data within the OpenSAFELY platform. All adults in the database at 1st September 2020 and with at least 1 year of prior follow-up and a record of ethnicity were included. The outcome was COVID-19-related death (death with COVID-19 listed as a cause of death on the death certificate). Follow-up was to 9th November 2020. Hazard ratios for ethnicity were calculated using Cox regression models adjusted for age and sex, and then further adjusted for deprivation. 13,223,154 people were included. During the study period, people of South Asian ethnicity were at higher risk of death due to COVID-19 than white people after adjusting for age and sex (HR = 3.47, 95% CI 2.99-4.03); the association attenuated somewhat on further adjustment for index of multiple deprivation (HR = 2.86, 2.46-3.33, Table 2). In contrast with the first wave of the epidemic, we found little evidence of a raised risk in black or other ethnic groups compared to white (HR for black vs white = 1.28, 0.87-1.88 adjusted for age and sex; and 1.01, 0.69-1.49 further adjusted for deprivation). Our findings suggest that ethnic inequalities in the risk of dying COVID-19-related death have changed between the first and early second wave of the epidemic in England. O_TBL View this table: @@ -1887,26 +1853,6 @@ We found evidence that all four devices have reduced sensitivity at lower antibo Our estimates of sensitivity and specificity are likely to be higher than would be observed in real use of these devices, as they were based on majority readings of three trained laboratory personnel. Implications of all the available evidenceWhen used in epidemiological studies of antibody prevalence, the estimates of sensitivity and specificity provided in this study can be used to adjust for test errors. Increased precision in error rates will translate to increased precision in seroprevalence estimates. If lateral flow devices were used for individual risk assessment, devices with maximum specificity would be preferable. However, if, for an example, 20% of the tested population had antibodies, we estimate that around 1 in 20 positive results on the most specific device would be incorrect.",epidemiology,exact,100,100 -medRxiv,10.1101/2021.01.25.21249942,2021-01-30,https://medrxiv.org/cgi/content/short/2021.01.25.21249942,Development and external validation of prognostic models for COVID-19 to support risk stratification in secondary care,Nicola J Adderley; Thomas Taverner; Malcolm Price; Christopher Sainsbury; David Greenwood; Joht Singh Chandan; Yemisi Takwoingi; Rashan Haniffa; Isaac Hosier; Carly Welch; Dhruv Parekh; Suzy Gallier; Krishna M Gokhale; Alastair K Denniston; Elizabeth Sapey; Krishnarajah Nirantharakumar,University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Oxford; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham,"ObjectivesExisting UK prognostic models for patients admitted to hospital with COVID-19 are limited by reliance on comorbidities, which are under-recorded in secondary care, and lack of imaging data among the candidate predictors. Our aims were to develop and externally validate novel prognostic models for adverse outcomes (death, intensive therapy unit (ITU) admission) in UK secondary care; and externally validate the existing 4C score. - -DesignCandidate predictors included demographic variables, symptoms, physiological measures, imaging, laboratory tests. Final models used logistic regression with stepwise selection. - -SettingModel development was performed in data from University Hospitals Birmingham (UHB). External validation was performed in the CovidCollab dataset. - -ParticipantsPatients with COVID-19 admitted to UHB January-August 2020 were included. - -Main outcome measuresDeath and ITU admission within 28 days of admission. - -Results1040 patients with COVID-19 were included in the derivation cohort; 288 (28%) died and 183 (18%) were admitted to ITU within 28 days of admission. Area under the receiver operating curve (AUROC) for mortality was 0.791 (95%CI 0.761-0.822) in UHB and 0.767 (95%CI 0.754-0.780) in CovidCollab; AUROC for ITU admission was 0.906 (95%CI 0.883-0.929) in UHB and 0.811 (95%CI 0.795-0.828) in CovidCollab. Models showed good calibration. Addition of comorbidities to candidate predictors did not improve model performance. AUROC for the 4C score in the UHB dataset was 0.754 (95%CI 0.721-0.786). - -ConclusionsThe novel prognostic models showed good discrimination and calibration in derivation and external validation datasets, and outperformed the existing 4C score. The models can be integrated into electronic medical records systems to calculate each individual patients probability of death or ITU admission at the time of hospital admission. Implementation of the models and clinical utility should be evaluated. - -Article SummaryO_ST_ABSStrengths and limitations of this studyC_ST_ABSO_LIWe developed novel prognostic models predicting mortality and ITU admission within 28 days of admission for patients hospitalised with COVID-19, using a large routinely collected dataset gathered at admission with a wide range of possible predictors (demographic variables, symptoms, physiological measures, imaging, laboratory test results). -C_LIO_LIThese novel models showed good discrimination and calibration in both derivation and external validation cohorts, and outperformed the existing ISARIC model and 4C score in the derivation dataset. We found that addition of comorbidities to the set of candidate predictors included in model derivation did not improve model performance. -C_LIO_LIIf integrated into hospital electronic medical records systems, the model algorithms will provide a predicted probability of mortality or ITU admission for each patient based on their individual data at, or close to, the time of admission, which will support clinicians decision making with regard to appropriate patient care pathways and triage. This information might also assist clinicians in explaining complex prognostic assessments and decisions to patients and their relatives. -C_LIO_LIA limitation of the study was that in the external validation cohort we were unable to examine all of the predictors included in the original full UHB model due to only a reduced set of candidate predictors being available in CovidCollab. Nevertheless, the reduced model performed well and the results suggest it may be applicable in a wide range of datasets where only a reduced set of predictor variables is available. -C_LIO_LIFurthermore, it was not possible to carry out stratified analysis by ethnicity as the UHB dataset contained too few patients in most of the strata, and no ethnicity data was available in the CovidCollab dataset. -C_LI",public and global health,exact,100,100 medRxiv,10.1101/2021.01.25.21250356,2021-01-26,https://medrxiv.org/cgi/content/short/2021.01.25.21250356,"Trends, regional variation, and clinical characteristics of COVID-19 vaccine recipients: a retrospective cohort study in 23.4 million patients using OpenSAFELY.",Helen J Curtis; Peter Inglesby; Caroline E Morton; Brian MacKenna; Alex J Walker; Jessica Morley; Amir Mehrkar; Sebastian CJ Bacon; George Hickman; Christopher Bates; Richard Croker; David Evans; Tom Ward; Jonathan Cockburn; Simon Davy; Krishnan Bhaskaran; Anna Schultze; Christopher T Rentsch; Elizabeth J Williamson; William J Hulme; Amelia Green; Anna Rowan; Louis Fisher; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Henry Drysdale; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; Ian J Douglas; John Parry; Frank Hester; Sam Harper; Shaun O'Hanlon; Alex Eavis; Richard Jarvis; Dima Avramov; Aaron Fowles; Nasreen Parkes; Paul Griffiths; Stephen JW Evans; Liam Smeeth; Ben Goldacre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; EMIS Group; EMIS Group; EMIS Group; EMIS Group; University of Oxford; EMIS Group; EMIS Group; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundOn December 8th 2020, NHS England administered the first COVID-19 vaccination as part of an ambitious vaccination programme during a global health emergency. AimsTo describe trends and variation in vaccine coverage by key clinical and demographic groups; to create a framework for near-real-time monitoring of vaccine coverage in key subgroups. @@ -2064,6 +2010,7 @@ C_LIO_LIOptimal symptom combinations maximise case capture considering available C_LIO_LIImplications for COVID-19 vaccine efficacy trials and wider public health C_LI",health informatics,exact,100,100 medRxiv,10.1101/2020.11.19.20234120,2020-11-23,https://medrxiv.org/cgi/content/short/2020.11.19.20234120,Actionable druggable genome-wide Mendelian randomization identifies repurposingopportunities for COVID-19,Liam Gaziano; Claudia Giambartolomei; Alexandre C Pereira; Anna Gaulton; Daniel C Posner; Sonja A Swanson; Yuk Lam Ho; Sudha K Iyengar; Nicole M Kosik; Marijana Vujkovic; David R Gagnon; A Patricia Bento; Pedro Beltrao; Inigo Barrio Hernandez; Lars Ronnblom; Niklas Hagberg; Christian Lundtoft; Claudia Langenberg; Maik Pietzner; Dennis Valentine; Elias Allara; Praveen Surendran; Stephen Burgess; Jing Hua Zhao; James E Peters; Bram P Prins; John Danesh; Poornima Devineni; Yunling Shi; Kristine E Lynch; Scott L DuVall; Helene Garcon; Lauren Thomann; Jin J Zhou; Bryan R Gorman; Jennifer E Huffman; Christopher J O'Donnell; Philip S Tsao; Jean C Beckham; Saiju Pyarajan; Sumitra Muralidhar; Grant D Huang; Rachel Ramoni; Adriana M Hung; Kyong-Mi Chang; Yan V Sun; Jacob Joseph; Andrew R Leach; Todd L Edwards; Kelly Cho; J Michael Gaziano; Adam S Butterworth; Juan P Casas,"VA Boston Healthcare System, University of Cambridge; Instituto Italiano di Tecnologia, University of California Los Angeles; University of Sao Paulo, Harvard University; European Molecular Biology Laboratory, European Bioinformatics Institute; VA Boston Healthcare System; Erasmus Medical Center; VA Boston Healthcare System; Case Western Reserve University and Louis Stoke Cleveland VAMC; VA Boston Healthcare System; The Corporal Michael J. Crescenz VA Medical Center, the University of Pennsylvania Perelman School of Medicine; Boston University, VA Boston Healthcare System; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; Uppsala University; Uppsala University; Uppsala University; Charite University Medicine Berlin, Universityof Cambridge; Universityof Cambridge; University College London; University of Cambridge; Wellcome Genome Campus and University of Cambridge; University of Cambridge; University of Cambridge; Imperial College London; Wellcome Genome Campus and University of Cambridge; University of Cambridge; VA Boston Healthcare System; VA Boston Healthcare System; VA Salt Lake City Health Care System, University of Utah; VA Salt Lake City Health Care System, University of Utah; VA Boston Healthcare System; VA Boston Healthcare System; University of Arizona, Phoenix VA Health Care System; VA Boston Healthcare System; VA Boston Healthcare System; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Palo Alto Health Care System, Stanford University School of Medicine; Durham VA Medical Center, Duke University School of Medicine; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs, Vanderbilt University; The Corporal Michael J. Crescenz VA Medical Center, University of Pennsylvania; Atlanta VA Health Care System, Emory University Rollins School of Public Health; VA Boston Healthcare System and Brigham & Women's Hospital; European Molecular Biology Laboratory, European Bioinformatics Institute; Department of Veterans Affairs Tennessee Valley Healthcare System, Vanderbilt Genetics Institute Vanderbilt University Medical Center; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; University of Cambridge, Wellcome Genome Campus and University of Cambridge; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School","Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization (MR) analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2: P=1.6x10-6, IFNAR2: P=9.8x10-11, and IL-10RB: P=1.9x10-14) using cis-eQTL genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared eQTL signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.",epidemiology,exact,100,100 +medRxiv,10.1101/2020.11.19.20234849,2020-11-22,https://medrxiv.org/cgi/content/short/2020.11.19.20234849,Community factors and excess mortality in first wave of the COVID-19 pandemic.,Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.",epidemiology,exact,100,100 medRxiv,10.1101/2020.11.06.20227108,2020-11-07,https://medrxiv.org/cgi/content/short/2020.11.06.20227108,Primary school staff reflections on school closures due to COVID-19 and recommendations for the future: a national qualitative survey,Emily Marchant; Charlotte Todd; Michaela James; Tom Crick; Russell Dwyer; Sinead Brophy,Swansea University; Swansea University; Swansea University; Swansea University; St Thomas Community Primary School; Swansea University,"School closures due to the COVID-19 global pandemic are likely to have a range of negative consequences spanning the domains of child development, education and health, in addition to the widening of inequalities and inequities. Research is required to improve understanding of the impact of school closures on the education, health and wellbeing of pupils and school staff, the challenges posed during reopening and importantly to identify how countries can return to in-school education and to inform policy. This qualitative study aimed to reflect on the perspectives and experiences of primary school staff (pupils aged 3-11) in Wales regarding school closures and the initial reopening of schools and to identify recommendations for the future. A total of 208 school staff completed a national online survey through the HAPPEN primary school network, consisting of questions about school closures (March to June 2020), the phased reopening of schools (June to July 2020) and a return to full-time education. Thematic analysis of survey responses highlighted that primary school staff perceive that gaps in learning, health and wellbeing have increased and inequalities have widened during school closures. Findings from this study identified five recommendations; (i) prioritise the health and wellbeing of pupils and staff; (ii) focus on enabling parental engagement and support; (iii) improve digital competence amongst pupils, teachers and parents; (iv) consider opportunities for smaller class sizes and additional staffing; and (v) improve the mechanism of communication between schools and families, and between government and schools.",public and global health,exact,100,100 medRxiv,10.1101/2020.11.03.20220699,2020-11-04,https://medrxiv.org/cgi/content/short/2020.11.03.20220699,A prospective study of risk factors associated with seroprevalence of SARS-CoV-2 antibodies in healthcare workers at a large UK teaching hospital,Daniel J Cooper; Sara Lear; Laura Watson; Ashley Shaw; Mark Ferris; Rainer Doffinger; Rachel Bousfield; Katherine Sharrocks; Michael Weekes; Ben Warne; Dominic Sparkes; Nick K Jones; Lucy Rivett; Matthew Routledge; Afzal Chaudhry; Katherine Dempsey; Montgomery Matson; Adil Lakha; George Gathercole; Olivia O'Connor; Emily Wilson; Orthi Shahzad; Kieran Toms; Rachel Thompson; Ian Halsall; David Halsall; Sally Houghton; Sofia Papadia; Nathalie Kingston; Kathleen Stirrups; Barbara Graves; Neil Walker; Hannah Stark; - The CITIID-NIHR BioResource COVID-19 Collaboration; Daniela De Angelis; Shaun Seaman; John Bradley; M Estée Török; Ian G. Goodfellow; Stephen Baker,"Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR Cambridge Clinical Research Facility; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR Cambridge Clinical Research Facility.; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust; ; MRC Biostatistics Unit, University of Cambridge; MRC Biostatistics Unit, University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Department of pathology, Division of virology, University of Cambridge; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK","BackgroundThe COVID-19 pandemic continues to grow at an unprecedented rate. Healthcare workers (HCWs) are at higher risk of SARS-CoV-2 infection than the general population but risk factors for HCW infection are not well described. @@ -2250,7 +2197,6 @@ MethodsRepeated cross-sectional surveys of random samples of the population aged ResultsOver the 9 days for which data are available, we find 363 positives from 84,610 samples giving a weighted prevalence to date of 0.55% (0.47%, 0.64%) in round 5. This implies that 411,000 (351,000, 478,000) people in England are virus-positive under the assumption that the swab assay is 75% sensitive. Using data from the most recent two rounds, we estimate a doubling time of 10.6 (9.4, 12.0) days covering the period 20th August to 26th September, corresponding to a reproduction number R of 1.47 (1.40, 1.53). Using data only from round 5 we estimate a reproduction number of 1.06 (0.74, 1.46) with probability of 63% that R is greater than 1. Between rounds 4 and 5 there was a marked increase in unweighted prevalence at all ages. In the most recent data, prevalence was highest in the 18 to 24 yrs age group at 0.96% (0.68%, 1.36%). At 65+ yrs prevalence increased [~]7-fold between rounds 4 and 5 from 0.04% (0.03%, 0.07%) to 0.29% (0.23%, 0.37%). Prevalence increased in all regions between rounds 4 and 5, giving the highest unweighted prevalence in round 5 in the North West at 0.86% (0.69%, 1.06%). In London, prevalence increased [~]5-fold from 0.10% (0.06%, 0.17%) to 0.49% (0.36%, 0.68%). Regional R values ranged from 1.32 (1.16,1.50) in Yorkshire and the Humber to 1.63 (1.42, 1.88) in the East Midlands over the same period. In the most recent data, there was extensive clustering in the North West, Midlands and in and around London with pockets of clustering in other regions including the South West, North East and East of England. Odds of swab-positivity were [~]2-fold higher in people of Asian and Black ethnicity compared with white participants. ConclusionRapid growth has led to high prevalence of SARS-CoV-2 virus in England among all regions and age groups, including those age groups at highest risk. Although there is evidence of a recent deceleration in the epidemic, current levels of prevalence will inevitably result in additional hospitalisations and mortality in coming weeks. A re-doubling of public health efforts is needed to return to a declining phase of the epidemic.",infectious diseases,exact,100,100 -medRxiv,10.1101/2020.09.28.20202929,2020-09-29,https://medrxiv.org/cgi/content/short/2020.09.28.20202929,T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses,Ane Ogbe; Barbara Kronsteiner; Donal T Skelly; Matthew Pace; Anthony Brown; Emily Adland; Kareena Adair; Hossain Delowar Akhter; Mohammad Ali; Serat-E Ali; Adrienn Angyal; M. Azim Ansari; Carolina V Arancibia-Carcamo; Helen Brown; Senthil Chinnakannan; Christopher P Conlon; Catherine de Lara; Thushan de Silva; Christina Dold; Tao Dong Dong; Timothy Donnison; David W Eyre; Amy Flaxman; Helen A Fletcher; Joshua Gardner; James T Grist; Carl-Philipp Hackstein; Kanoot Jaruthamsophon; Katie Jeffrey; Teresa Lambe; Lian Lee; Wenqin Li; Nicholas Lim; Philippa C Matthews; Alexander J Mentzer; Shona C Moore; Dean J Naisbitt; Monday Ogese; Graham Ogg; Peter Openshaw; Munir Pirmohamed; Andrew J Pollard; Narayan Ramamurthy; Patpong Rongkard; Sarah Rowland-Jones; Oliver L Sampson; Gavin Screaton; Alessandro Sette; Lizzie Stafford; Craig Thompson; Paul J Thomson; Ryan Thwaites; Vinicius Vieira; Daniela Weiskopf; Panagiota Zacharopoulou; - Oxford Immunology Network Covid-19 Response T cell Consortium; - Oxford Protective T cell Immunology for COVID-19 (OPTIC) Clinical team; Lance Turtle; Paul Klenerman; Philip Goulder; John Frater; Eleanor Barnes; Susanna Dunachie,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Liverpool; University of Liverpool; University of Oxford; Imperial College; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; La Jolla Institute for Immunology; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Liverpool; Imperial College; University of Oxford; La Jolla Institute for Immunology; University of Oxford; ; ; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"A major issue in identification of protective T cell responses against SARS-CoV-2 lies in distinguishing people infected with SARS-CoV-2 from those with cross-reactive immunity generated by exposure to other coronaviruses. We characterised SARS-CoV-2 T cell immune responses in 168 PCR-confirmed SARS-CoV-2 infected subjects and 118 seronegative subjects without known SARS-CoV-2 exposure using a range of T cell assays that differentially capture immune cell function. Strong ex vivo ELISpot and proliferation responses to multiple antigens (including M, NP and ORF3) were found in those who had been infected by SARS-CoV-2 but were rare in pre-pandemic and unexposed seronegative subjects. However, seronegative doctors with high occupational exposure and recent COVID-19 compatible illness showed patterns of T cell responses characteristic of infection, indicating that these readouts are highly sensitive. By contrast, over 90% of convalescent or unexposed people showed proliferation and cellular lactate responses to spike subunits S1/S2, indicating pre-existing cross-reactive T cell populations. The detection of T cell responses to SARS-CoV-2 is therefore critically dependent on the choice of assay and antigen. Memory responses to specific non-spike proteins provides a method to distinguish recent infection from pre-existing immunity in exposed populations.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.09.26.20202150,2020-09-28,https://medrxiv.org/cgi/content/short/2020.09.26.20202150,Comparison of mental health service activity before and shortly after UK social distancing responses to the COVID-19 pandemic: February-March 2020,Robert Stewart; Evangelia Martin; Ioannis Bakolis; Matthew Broadbent; Nicola Byrne; Sabine Landau,King's College London; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; South London and Maudsley NHS Foundation Trust; King's College London,"This study sought to provide an early description of mental health service activity before and after national implementation of social distancing for COVID-19. A time series analysis was carried out of daily service-level activity on data from a large mental healthcare provider in southeast London, from 01.02.2020 to 31.03.2020, comparing activity before and after 16.03.2020: i) inpatient admissions, discharges and numbers, ii) contact numbers and daily caseloads (Liaison, Home Treatment Teams, Community Mental Health Teams); iii) numbers of deaths for past and present patients. Daily face-to-face contact numbers fell for liaison, home treatment and community services with incomplete compensatory rises in non-face-to-face contacts. Daily caseloads fell for all services, apart from working age and child/adolescent community teams. Inpatient numbers fell 13.6% after 16th March, and daily numbers of deaths increased by 61.8%.",psychiatry and clinical psychology,exact,100,100 medRxiv,10.1101/2020.09.24.20200048,2020-09-25,https://medrxiv.org/cgi/content/short/2020.09.24.20200048,Genetic mechanisms of critical illness in Covid-19,Erola Pairo-Castineira; Sara Clohisey; Lucija Klaric; Andrew Bretherick; Konrad Rawlik; Nicholas Parkinson; Dorota Pasko; Susan Walker; Anne Richmond; Max Head Fourman; Andy Law; James Furniss; Elvina Gountouna; Nicola Wrobel; Clark D Russell; Loukas Moutsianas; Bo Wang; Alison Meynert; Zhijian Yang; Ranran Zhai; Chenqing Zheng; Fiona Griffith; Wilna Oosthuyzen; Barbara Shih; Seán Keating; Marie Zechner; Chris Haley; David J Porteous; Caroline Hayward; Julian Knight; Charlotte Summers; Manu Shankar-Hari; Lance Turtle; Antonia Ho; Charles Hinds; Peter Horby; Alistair Nichol; David Maslove; Lowell Ling; Paul Klenerman; Danny McAuley; Hugh Montgomery; Timothy Walsh; - The GenOMICC Investigators; - The ISARIC4C Investigators; - The Covid-19 Human Genetics Initiative; Xia Shen; Kathy Rowan; Angie Fawkes; Lee Murphy; Chris P Ponting; Albert Tenesa; Mark Caulfield; Richard Scott; Peter JM Openshaw; Malcolm G Semple; Veronique Vitart; James F Wilson; J Kenneth Baillie,"Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; The Roslin Institute; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England; Genomics England; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinb; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; University of Edinburgh Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh, UK; Genomics England; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.; Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.; Biostatistics Group, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Intenstive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinb; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinb; Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.; Department of Medicine, University of Cambridge, Cambridge, UK.; Department of Intensive Care Medicine, Guy's and St. Thomas NHS Foundation Trust, London, UK; School of Immunology and Microbial Sciences, King's College London; NIHR Health Protection Research Unit for Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences University of Liverpool, L; MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, Univer; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK.; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford, OX3 7FZ, UK.; Clinical Research Centre at St Vincent's University Hospital, University College Dublin, Dublin, Ireland; Australian and New Zealand Intensive Care Research Cen; Department of Critical Care Medicine, Queen's University and Kingston Health Sciences Centre, Kingston, ON, Canada.; Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China.; University of Oxford; Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK; Department of Intensive Care Medicine, Royal Vi; UCL Centre for Human Health and Performance, London, W1T 7HA, UK.; Intenstive Care Unit, Royal Infirmary of Edinburgh, 54 Little France Drive, Edinburgh, EH16 5SA, UK.; -; -; -; Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.; Intensive Care National Audit & Research Centre, London, UK.; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, EH4 2XU, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK.; Genomics England; William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK; Genomics England; National Heart & Lung Institute, Imperial College London (St Mary's Campus), Norfolk Place, Paddington, London W2 1PG, UK.; University of Liverpool, Liverpool, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK.; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK; Ce; Roslin Institute, University of Edinburgh","The subset of patients who develop critical illness in Covid-19 have extensive inflammation affecting the lungs1 and are strikingly different from other patients: immunosuppressive therapy benefits critically-ill patients, but may harm some non-critical cases.2 Since susceptibility to life-threatening infections and immune-mediated diseases are both strongly heritable traits, we reasoned that host genetic variation may identify mechanistic targets for therapeutic development in Covid-19.3 @@ -2316,6 +2262,15 @@ At the recommended threshold, PMEWS and the WHO criteria showed good sensitivity ConclusionCURB-65, PMEWS and NEWS2 provide good but not excellent prediction for adverse outcome in suspected COVID-19, and predicted death without organ support better than receipt of organ support. PMEWS, the WHO criteria and NEWS2 (using a lower threshold than usually recommended) provide good sensitivity at the expense of specificity. +RegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533",emergency medicine,exact,100,100 +medRxiv,10.1101/2020.09.01.20185793,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.01.20185793,Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study,Katie Biggs; Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Matthew Bursnall; Amanda Loban; Simon Waterhouse; Richard Simmonds; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter,University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust,"ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection. + +MethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome. + +ResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse outcome. C-statistics were 0.80 (95% confidence interval 0.73-0.87) for the WHO algorithm, 0.80 (0.71-0.90) for POPS, 0.76 (0.67-0.85) for COAST, and 0.71 (0.59-0.82) for SFHPC. Using pre-specified thresholds, the WHO algorithm had the highest sensitivity (0.85) and lowest specificity (0.75), but POPS and COAST could optimise sensitivity (0.96 and 0.92 respectively) at the expense of specificity (0.25 and 0.38 respectively) by using a threshold of any score above zero instead of the pre-specified threshold. + +ConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive. + RegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533",emergency medicine,exact,100,100 medRxiv,10.1101/2020.08.26.20182279,2020-09-01,https://medrxiv.org/cgi/content/short/2020.08.26.20182279,COVID-19 infection dynamics in care homes in the East of England: a retrospective genomic epidemiology study,William L Hamilton; Gerry Tonkin-Hill; Emily Smith; Dinesh Aggarwal; Charlotte Houldcroft; Ben Warne; Colin Brown; Luke Meredith; Myra Hosmillo; Aminu Jahun; Martin Curran; Surendra Parmar; Laura Caller; Sarah Caddy; Fahad Khokhar; Anna Yakovleva; Grant Hall; Theresa Feltwell; Malte Pinckert; Iliana Georgana; Yasmin Chaudhry; Nicholas Brown; Sonia Goncalves; Roberto Amato; Ewan Harrison; Mathew Beale; Michael Spencer Chapman; David Jackson; Ian Johnston; Alex Alderton; John Sillitoe; Cordelia Langford; Gordon Dougan; Sharon Peacock; Dominic Kwiatowski; Ian Goodfellow; M. Estee Torok; - COVID-19 Genomics Consortium UK,"University of Cambridge; Wellcome Sanger Institute; Cambridgeshire County Council, UK; Public Health England; University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; Public Health England; University of Cambridge; University of Cambridge; University of Cambridge; Public Health England; Public Health England; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; Public Health England; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; University of Cambridge; University of Cambridge; ","COVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people. Here, 1,167 residents from 337 care homes were identified from a dataset of 6,600 COVID-19 cases from the East of England. Older age and being a care home resident were associated with increased mortality. SARS-CoV-2 genomes were available for 700 residents from 292 care homes. By integrating genomic and temporal data, 409 viral clusters within the 292 homes were identified, indicating two different patterns - outbreaks among care home residents and independent introductions with limited onward transmission. Approximately 70% of residents in the genomic analysis were admitted to hospital during the study, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission within care homes should be a key target for infection control to reduce COVID-19 mortality in this population. @@ -2441,21 +2396,6 @@ Main outcomeHospitalisation with COVID-19 ResultsThe cohort comprised 158,445 healthcare workers, the majority being patient facing (90,733 / 158,445; 57.3%), and 229,905 household members. Of all COVID-19 hospitalisations in the working age population (18-65-year-old), 17.2% (360 / 2,097) were in healthcare workers or their households. Adjusting for age, sex, ethnicity, socio-economic deprivation and comorbidity, the risk of COVID-19 hospitalisation in non-patient facing healthcare workers and their households was similar to the risk in the general population (hazards ratio [HR] 0.81; 95%CI 0.52-1.26 and 0.86; 95%CI 0.49-1.51 respectively). In models adjusting for the same covariates however, patient facing healthcare workers, compared to non-patient facing healthcare workers, were at higher risk (HR 3.30; 95%CI 2.13-5.13); so too were household members of patient facing healthcare workers (HR 1.79; 95%CI 1.10-2.91). On sub-dividing patient-facing healthcare workers into those who worked in front-door, intensive care and non-intensive care aerosol generating settings and other, those in front door roles were at higher risk (HR 2.09; 95%CI 1.49-2.94). For most patient facing healthcare workers and their households, the estimated absolute risk of COVID-19 hospitalisation was less than 0.5% but was 1% and above in older men with comorbidity. ConclusionsHealthcare workers and their households contribute a sixth of hospitalised COVID-19 cases. Whilst the absolute risk of hospitalisation was low overall, patient facing healthcare workers and their households had 3- and 2-fold increased risks of COVID-19 hospitalisation.",epidemiology,exact,100,100 -medRxiv,10.1101/2020.08.03.20167122,2020-08-04,https://medrxiv.org/cgi/content/short/2020.08.03.20167122,Ethnic minority groups in England and Wales - factors affecting the size and timing of elevated COVID-19 mortality: a retrospective cohort study linking Census and death records,Daniel Ayoubkhani; Vahe Nafilyan; Chris White; Peter Goldblatt; Charlotte Gaughan; Louisa Blackwell; Nicky Rogers; Amitava Banerjee; Kamlesh Khunti; Myer Glickman; Ben Humberstone; Ian Diamond,"Office for National Statistics; Office for National Statistics; Office for National Statistics; UCL Institute for Health Equity; Office for National Statistics; Office for National Statistics; Office for National Statistics; Institute of Health Informatics, University College London; Diabetes Research Centre, University of Leicester; Office for National Statistics; Office for National Statistics; Office for National Statistics","ObjectivesTo estimate population-level associations between ethnicity and coronavirus disease 2019 (COVID-19) mortality, and to investigate how ethnicity-specific mortality risk evolved over the course of the pandemic. - -DesignRetrospective cohort study using linked administrative data. - -SettingEngland and Wales, deaths occurring 2 March to 15 May 2020. - -ParticipantsRespondents to the 2011 Census of England and Wales aged [≤]100 years and enumerated in private households, linked to death registrations and adjusted to account for emigration before the outcome period, who were alive on 1 March 2020 (n=47,872,412). - -Main outcome measureDeath related to COVID-19, registered by 29 May 2020. - -Statistical methodsWe estimated hazard ratios (HRs) for ethnic minority groups compared with the White population using Cox regression models, controlling for geographical, demographic, socio-economic, occupational, and self-reported health factors. HRs were estimated on the full outcome period and separately for pre- and post-lockdown periods in the UK. - -ResultsIn the age-adjusted models, people from all ethnic minority groups were at elevated risk of COVID-19 mortality; the HRs for Black males and females were 3.13 [95% confidence interval: 2.93 to 3.34] and 2.40 [2.20 to 2.61] respectively. However, in the fully adjusted model for females, the HRs were close to unity for all ethnic groups except Black (1.29 [1.18 to 1.42]). For males, COVID-19 mortality risk remained elevated for the Black (1.76 [1.63 to 1.90]), Bangladeshi/Pakistani (1.35 [1.21 to 1.49]) and Indian (1.30 [1.19 to 1.43]) groups. The HRs decreased after lockdown for all ethnic groups, particularly Black and Bangladeshi/Pakistani females. - -ConclusionsDifferences in COVID-19 mortality between ethnic groups were largely attenuated by geographical and socio-economic factors, although some residual differences remained. Lockdown was associated with reductions in excess mortality risk in ethnic minority populations, which has major implications for a second wave of infection or local spikes. Further research is needed to understand the causal mechanisms underpinning observed differences in COVID-19 mortality between ethnic groups.",epidemiology,exact,100,100 medRxiv,10.1101/2020.07.30.20165464,2020-08-02,https://medrxiv.org/cgi/content/short/2020.07.30.20165464,Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score,Stephen R Knight; Antonia Ho; Riinu Pius; Iain Buchan; Gail Carson; Thomas M Drake; Jake Dunning; Cameron J Fairfield; Carrol Gamble; Christopher A Green; Rishi K Gupta; Sophie Halpin; Hayley Hardwick; Karl Holden; Peter W Horby; Clare Jackson; Kenneth A McLean; Laura Merson; Jonathan S Nguyen-Van-Tam; Lisa Norman; Mahdad Noursadeghi; Piero L Olliaro; Mark G Pritchard; Clark D Russell; Catherine A Shaw; Aziz Sheikh; Tom Solomon; Cathie Sudlow; Olivia V Swann; Lance Turtle; Peter JM Openshaw; J Kenneth Baillie; Malcolm Gracie Semple; Annemarie B Docherty; Ewen M Harrison,"Centre for Medical Informatics, The Usher Institute, University of Edinburgh; Medical Research Council University of Glasgow Centre for Virus Research, Glasgow, UK; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; Institute of Population Health Sciences, University of Liverpool; University of Oxford; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; National Infection Service Public Health England; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK; Institute of Microbiology & Infection, University of Birmingham; University College London; Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections and Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and ; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections and Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and ; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; Division of Infection and Immunity, University College London, Gower Street, London, WC1E 6BT; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, United Kingdom; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, United Kingdom; Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK; Department of Clinical Surgery, University of Edinburgh; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections and Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and ; Health Data Research UK, Gibbs Building, 215 Euston Road, London, NW1 2BE; Department of Child Life and Health, University of Edinburgh, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections and Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and ; National Heart and Lung Institute, Imperial College London, London, UK; Roslin Institute, University of Edinburgh; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections and Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and ; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK","ObjectivesTo develop and validate a pragmatic risk score to predict mortality for patients admitted to hospital with covid-19. DesignProspective observational cohort study: ISARIC WHO CCP-UK study (ISARIC Coronavirus Clinical Characterisation Consortium [4C]). Model training was performed on a cohort of patients recruited between 6 February and 20 May 2020, with validation conducted on a second cohort of patients recruited between 21 May and 29 June 2020. @@ -2666,6 +2606,15 @@ MethodsWe investigated staff reports regarding the impact of the COVID-19 pandem Results2,180 staff from a range of sectors, professions and specialties participated. Immediate infection control concerns were highly salient for inpatient staff, new ways of working for community staff. Multiple rapid adaptations and innovations in response to the crisis were described, especially remote working. This was cautiously welcomed but found successful in only some clinical situations. Staff had specific concerns about many groups of service users, including people whose conditions are exacerbated by pandemic anxieties and social disruptions; people experiencing loneliness, domestic abuse and family conflict; those unable to understand and follow social distancing requirements; and those who cannot engage with remote care. ConclusionThis overview of staff concerns and experiences in the early COVID-19 pandemic suggests directions for further research and service development: we suggest that how to combine infection control and a therapeutic environment in hospital, and how to achieve effective and targeted tele-health implementation in the community, should be priorities. The limitations of our convenience sample must be noted.",psychiatry and clinical psychology,exact,100,100 +medRxiv,10.1101/2020.06.10.20127175,2020-06-11,https://medrxiv.org/cgi/content/short/2020.06.10.20127175,Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.,Amitava Banerjee; Suliang Chen; Laura Pasea; Alvina Lai; Michail Katsoulis; Spiros Denaxas; Vahe Nafilyan; Bryan Williams; Wai Keong Wong; Ameet Bakhai; Kamlesh Khunti; Deenan Pillay; Mahdad Noursadeghi; Honghan Wu; Nilesh Pareek; Daniel Bromage; Theresa Mcdonagh; Jonathan Byrne; James T Teo; Ajay Shah; Ben Humberstone; Liang V Tang; Anoop SV Shah; Andrea Rubboli; Yutao Guo; Yu Hu; Cathie LM Sudlow; Gregory YH Lip; Harry Hemingway,"University College London; University College London; University College London; University College London; UCL; University College London; Office for National Statistics; UCL; University College London Hospitals NHS Trust; Royal Free Hospitals NHS Trust; University of Leicester; UCL; UCL; UCL; King's College Hospital; Kings College London; Kings College London; Kings London NHS Trust; Kings College Hospital NHS Foundation Trust; King's College London; Office for National Statistics; Huazhong University of Science and Technology, Wuhan, China; University of Edinburgh; Ospedale S. Maria delle Croci, Ravenna, Italy; PLA General Hospital, Beijing, China.; Huazhong University of Science and Technology, Wuhan, China.; University of Edinburgh; University of Liverpool; UCL","BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both ""direct"", through infection, and ""indirect"", through changes in healthcare. + +MethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(""direct"" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For ""indirect"" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020. + +FindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths. + +InterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic. + +FundingNIHR, HDR UK, Astra Zeneca",cardiovascular medicine,exact,100,100 medRxiv,10.1101/2020.06.08.20120584,2020-06-09,https://medrxiv.org/cgi/content/short/2020.06.08.20120584,SARS-CoV-2 virus and antibodies in front-line Health Care Workers in an acute hospital in London: preliminary results from a longitudinal study,Catherine Houlihan; Nina Vora; Thomas Byrne; Dan Lewer; Judith Heaney; David A Moore; Rebecca Matthews; Sajida Adam; Louise Enfield; Abigail Severn; Angela McBride; Moira Jane Spyer; Rupert Beale; Peter Cherepanov; Kathleen Gaertner; Maryam Shahmanesh; - The SAFER Field Study Team; Kevin Ng; Georgina Cornish; Naomi Walker; Susan Michie; Ed Manley; Fabiana Lorencatto; - The Crick-COVID-Consortium; Richard Gilson; Sonia Gandhi; Steve Gamblin; George Kassiotis; Laura McCoy; Charles Swanton; Andrew Hayward; Eleni Nastouli,University College London Hospital; UCL; UCL; University College London; UCL; Francis Crick Institute; UCL; UCL; UCL; UCL; UCL; UCL; Francis Crick Institute; Francis Crick Institute; UCL; UCL; ; Francis Crick Institute; Francis Crick Institute; UCL; UCL; Leeds University; UCL; ; UCL; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; UCL; Francis Crick Institute; UCL; University College London,"BackgroundAlthough SARS-CoV-2 infection in Healthcare Workers (HCWs) is a public health concern, there is little description of their longitudinal antibody response in the presence or absence of SARS-CoV-2 and symptoms. We followed HCWs in an acute London hospital to measure seroconversion and RNA detection at the peak of the pandemic. MethodsWe enrolled 200 patient-facing HCWs between 26 March and 8 April 2020 and collected twice-weekly self-administered nose and throat swabs, symptom data and monthly blood samples. Swabs were tested for SARS-CoV-2 by PCR, and serum for antibodies to spike protein by ELISA and flow cytometry. diff --git a/data/covid/preprints.exact.json b/data/covid/preprints.exact.json index bd6b3529..69bf601e 100644 --- a/data/covid/preprints.exact.json +++ b/data/covid/preprints.exact.json @@ -1,4 +1,18 @@ [ + { + "site": "medRxiv", + "doi": "10.1101/2023.10.26.23297598", + "date": "2023-10-26", + "link": "https://medrxiv.org/cgi/content/short/2023.10.26.23297598", + "title": "Assessing the causal effect of air pollution on risk of SARS-CoV-2 infection", + "authors": "Annalan Mathew Dwight Navaratnam; Sarah Beale; Yamina Boukari; Vincent Nguyen; Wing Lam Erica Fong; Isobel Braithwaite; Thomas Edward Byrne; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Parth Patel; Madhumita Shrotri; Alexei Yavlinsky; Andrew Hayward; Haneen Khreis; Robert W Aldridge", + "affiliations": "University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCL; University College London; University College London; University College London; University College London; University College London; UCL; University of Cambridge; UCL", + "abstract": "Introduction Emerging evidence suggests association of air pollution exposure with risk of SARS-CoV-2 infection, but many of these findings are limited by study design, lack of individual-level covariate data or are specific to certain subpopulations. We aim to evaluate causal effects of air pollution on risk of infection, whilst overcoming these limitations. Methods Concentrations for black carbon(BC), particulate matter 10(PM10), particulate matter 2.5(PM2.5), nitrogen dioxide(NO2) and oxides of nitrogen(NOx) from the Department of Environment, Food and Rural Affairs (DEFRA) and Effect of Low-level Air Pollution: A Study in Europe (ELAPSE) were linked to postcodes of 53,683 Virus Watch study participants. The primary outcome was first SARS-CoV-2 infection, between 1st September 2020 and 30th April 2021. Regression analysis used modified Poisson with robust estimates, clustered by household, adjusting for individual (e.g., age, sex, ethnicity) and environmental covariates(e.g., population density, region) to estimate total and direct effects. Results Single pollutant analysis showed the direct effect of higher risk of SARS-CoV-2 infection with increased exposure to PM2.5(RR1.11,95%CI 1.08;1.15), PM10(RR1.06,95%CI 1.04;1.09), NO2(RR1.04,95%CI 1.04;1.05) and NOx(RR1.02,95%CI 1.02;1.02) per 1g/m3 increment with DEFRA 2015-19 data. Sensitivity analyses altering covariates, exposure window and modelled air pollution data source produced similar estimates. Higher risk of SARS-CoV-2 per 10-5m-1 increment of BC (RR1.86, 95%CI 1.62;2.14) was observed using ELAPSE data. Conclusion Long term exposure to higher concentrations of air pollutions increases the risk of SARS-CoV-2 infection, highlighting that adverse health effects of air pollution is not only limited to non-communicable diseases.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.10.11.23296866", @@ -83,20 +97,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.06.29.23292056", - "date": "2023-07-01", - "link": "https://medrxiv.org/cgi/content/short/2023.06.29.23292056", - "title": "Genome-wide Association Study of Long COVID", - "authors": "Vilma Lammi; Tomoko Nakanishi; Samuel E Jones; Shea J Andrews; Juha Karjalainen; Beatriz Cortes; Heath E O'Brien; Brian E Fulton-Howard; Hele H Haapaniemi; Axel Schmidt; Ruth E Mitchell; Abdou Mousas; Massimo Mangino; Alicia Huerta-Chagoya; Nasa Sinnott-Armstrong; Elizabeth T Cirulli; Marc Vaudel; Alex SF Kwong; Amit K Maiti; Minttu M Marttila; Chiara Batini; Francesca Minnai; Anna R Dearman; CA Robert Warmerdam; Celia B Sequeros; Thomas W Winkler; Daniel M Jordan; Lindsay Guare; Ekaterina Vergasova; Eirini Marouli; Pasquale Striano; Ummu Afeera Zainulabid; Ashutosh Kumar; Hajar Fauzan Ahmad; Ryuya Edahiro; Shuhei Azekawa; - Long COVID Host Genetics Initiative; - FinnGen; - DBDS Genomic Consortium; - GEN-COVID Multicenter Study; Joseph J Grzymski; Makoto Ishii; Yukinori Okada; Noam D Beckmann; Meena Kumari; Ralf Wagner; Iris M Heid; Catherine John; Patrick J Short; Per Magnus; Karina Banasik; Frank Geller; Lude H Franke; Alexander Rakitko; Emma L Duncan; Alessandra Renieri; Konstantinos K Tsilidis; Rafael de Cid; Ahmadreza Niavarani; Teresa Tusie-Luna; Shefali S Verma; George Davey Smith; Nicholas J Timpson; Mark J Daly; Andrea Ganna; Eva C Schulte; J Brent Richards; Kerstin U Ludwig; Michael Hultstrom; Hugo Zeberg; Hanna M Ollila", - "affiliations": "Institute for Molecular Medicine Finland (FIMM); Department of Human Genetics; Institute for Molecular Medicine Finland (FIMM); University of California San Francisco; Institute for Molecular Medicine Finland (FIMM); Genomes for Life-GCAT lab; Sano Genetics Limited; Genetics and Genomic Sciences; Institute for Molecular Medicine Finland (FIMM); Institute of Human Genetics; Centre for Clinical Brain Sciences; Department of Hygiene and Epidemiology; Department of Twin Research; Departamento de Medicina Genomica y Toxicologia Ambiental; Herbold Computational Biology Program; Helix; Mohn Center for Diabetes Precision Medicine; University of Bristol; Department of Genetics and Genomics; University of Helsinki; Department of Population Health Sciences; Institute for Biomedical Technologies - National Research Council; Institute for Social and Economic Research; Department of Genetics; Novo Nordisk Foundation Center for Protein Research; Department of Genetic Epidemiology; Charles Bronfman Institute for Personalized Medicine; Department of Pathology and Laboratory Medicine; Genotek Ltd.; William Harvey Research Institute; IRCCS G; Department of Internal Medicine; Department of Anatomy; Faculty of Industrial Sciences and Technology; Department of Statistical Genetics; Division of Pulmonary Medicine; ; ; ; ; Center for Genomic Medicine; Division of Pulmonary Medicine; Department of Statistical Genetics; Charles Bronfman Institute for Personalized Medicine; Institute for Social and Economic Research; Institute of Medical Microbiology & Hygiene; Department of Genetic Epidemiology; Department of Population Health Sciences; Sano Genetics Limited; Centre for Fertility and Health; Novo Nordisk Foundation Center for Protein Research; Statens Serum Institute; Department of Genetics; Genotek Ltd.; Department of Twin Research and Genetic Epidemiology; Medical Genetics; Department of Hygiene and Epidemiology; Genomes for Life-GCAT lab; Digestive Oncology Research Center; Instituto de Investigaciones Biomedicas Unam/ Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran; Department of Pathology and Laboratory Medicine; MRC Integrative Epidemiology Unit at the University of Bristol; MRC Integrative Epidemiology Unit at the University of Bristol; Institute for Molecular Medicine Finland (FIMM); Institute for Molecular Medicine Finland (FIMM); Institute of Psychiatric Phenomics & Genomics; Department of Human Genetics; Institute of Human Genetics; Anaesthesiology and Intensive Care Medicine; Department of Evolutionary Genetics; Institute for Molecular Medicine Finland (FIMM)", - "abstract": "Infections can lead to persistent or long-term symptoms and diseases such as shingles after varicella zoster, cancers after human papillomavirus, or rheumatic fever after streptococcal infections1, 2. Similarly, infection by SARS-CoV-2 can result in Long COVID, a condition characterized by symptoms of fatigue and pulmonary and cognitive dysfunction3-5. The biological mechanisms that contribute to the development of Long COVID remain to be clarified. We leveraged the COVID-19 Host Genetics Initiative6, 7 to perform a genome-wide association study for Long COVID including up to 6,450 Long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We identified the first genome-wide significant association for Long COVID at the FOXP4 locus. FOXP4 has been previously associated with COVID-19 severity6, lung function8, and cancers9, suggesting a broader role for lung function in the pathophysiology of Long COVID. While we identify COVID-19 severity as a causal risk factor for Long COVID, the impact of the genetic risk factor located in the FOXP4 locus could not be solely explained by its association to severe COVID-19. Our findings further support the role of pulmonary dysfunction and COVID-19 severity in the development of Long COVID.", - "category": "genetic and genomic medicine", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.06.30.23292079", @@ -1259,20 +1259,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.01.31.22269194", - "date": "2022-02-01", - "link": "https://medrxiv.org/cgi/content/short/2022.01.31.22269194", - "title": "An outbreak of SARS-CoV-2 in a public-facing office in England, 2021", - "authors": "Barry Atkinson; Karin van Veldhoven; Ian Nicholls; Matthew Coldwell; Adam Clarke; Gillian Frost; Christina J Atchison; Amber I Raja; Allan M Bennett; Derek Morgan; Neil Pearce; Tony Fletcher; Elizabeth B Brickley; Yiqun Chen", - "affiliations": "UK Health Security Agency; London School of Hygiene & Tropical Medicine; UK Health Security Agency; Health and Safety Executive; Health and Safety Executive; Health and Safety Executive; UK Health Security Agency; London School of Hygiene & Tropical Medicine; UK Health Security Agency; Health and Safety Executive; London School of Hygiene & Tropical Medicine; UK Health Security Agency; London School of Hygiene & Tropical Medicine; Health and Safety Executive", - "abstract": "Between August-September 2021, an outbreak of SARS-CoV-2, with an attack rate of 55% (22/40 workers), occurred in a public-facing office in England. To identify workplace and worker-related risk factors, a comprehensive investigation involving surface sampling, environmental assessment, molecular and serological testing, and worker questionnaires was performed in September - October 2021. The results affirm the utility of surface sampling to identify SARS-CoV-2 control deficiencies and the importance of evolving, site-specific risk assessments with layered COVID-19 mitigation strategies.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.01.26.22269901", @@ -1427,6 +1413,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "bioRxiv", + "doi": "10.1101/2021.12.17.473248", + "date": "2021-12-21", + "link": "https://biorxiv.org/cgi/content/short/2021.12.17.473248", + "title": "SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion", + "authors": "Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta", + "affiliations": "University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge", + "abstract": "The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.", + "category": "microbiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.12.20.21268098", @@ -1679,20 +1679,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.11.08.21265312", - "date": "2021-11-09", - "link": "https://medrxiv.org/cgi/content/short/2021.11.08.21265312", - "title": "Understanding COVID-19 trajectories from a nationwide linked electronic health record cohort of 56 million people: phenotypes, severity, waves & vaccination", - "authors": "Johan H Thygesen; Christopher R Tomlinson; Sam Hollings; Mehrdad A Mizani; Alex Handy; Ashley Akbari; Amitava Banerjee; Jennifer A Cooper; Alvina G Lai; Kezhi Li; Bilal A Mateen; Naveed Sattar; Reecha Sofat; Ana Torralbo; Honghan Wu; Angela Wood; Jonathan AC Sterne; Christina Pagel; William Whiteley; Cathie Sudlow; Harry Hemingway; Spiros Denaxas; - CVD-COVID-UK Consortium", - "affiliations": "Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; NHS Digital, Leeds, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Population Data Science and Health Data Research UK, Swansea University, Swansea, UK; Institute of Health Informatics, University College London, London, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; The Wellcome Trust, London, UK; Institute of Cardiovascular & Medical Sciences, University of Glasgow, Glasgow, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Clinical Operational Research Unit, University College London, London, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; ", - "abstract": "BackgroundUpdatable understanding of the onset and progression of individuals COVID-19 trajectories underpins pandemic mitigation efforts. In order to identify and characterize individual trajectories, we defined and validated ten COVID-19 phenotypes from linked electronic health records (EHR) on a nationwide scale using an extensible framework.\n\nMethodsCohort study of 56.6 million people in England alive on 23/01/2020, followed until 31/05/2021, using eight linked national datasets spanning COVID-19 testing, vaccination, primary & secondary care and death registrations data. We defined ten COVID-19 phenotypes reflecting clinically relevant stages of disease severity using a combination of international clinical terminologies (e.g. SNOMED-CT, ICD-10) and bespoke data fields; positive test, primary care diagnosis, hospitalisation, critical care (four phenotypes), and death (three phenotypes). Using these phenotypes, we constructed patient trajectories illustrating the transition frequency and duration between phenotypes. Analyses were stratified by pandemic waves and vaccination status.\n\nFindingsWe identified 3,469,528 infected individuals (6.1%) with 8,825,738 recorded COVID-19 phenotypes. Of these, 364,260 (11%) were hospitalised and 140,908 (4%) died. Of those hospitalised, 38,072 (10%) were admitted to intensive care (ICU), 54,026 (15%) received non-invasive ventilation and 21,404 (6%) invasive ventilation. Amongst hospitalised patients, first wave mortality (30%) was higher than the second (23%) in non-ICU settings, but remained unchanged for ICU patients. The highest mortality was for patients receiving critical care outside of ICU in wave 1 (51%). 13,083 (9%) COVID-19 related deaths occurred without diagnoses on the death certificate, but within 30 days of a positive test while 10,403 (7%) of cases were identified from mortality data alone with no prior phenotypes recorded. We observed longer patient trajectories in the second pandemic wave compared to the first.\n\nInterpretationOur analyses illustrate the wide spectrum of severity that COVID-19 displays and significant differences in incidence, survival and pathways across pandemic waves. We provide an adaptable framework to answer questions of clinical and policy relevance; new variant impact, booster dose efficacy and a way of maximising existing data to understand individuals progression through disease states.\n\nResearch in ContextO_ST_ABSEvidence before the studyC_ST_ABSWe searched PubMed on October 14, 2021, for publications with the terms \"COVID-19\" or \"SARS-CoV-2\", \"severity\", and \"electronic health records\" or \"EHR\" without date or language restrictions. Multiple studies explore factors associated with severity of COVID-19 infection, and model predictions of outcome for hospitalised patients. However, most work to date focused on isolated facets of the healthcare system, such as primary or secondary care only, was conducted in subpopulations (e.g. hospitalised patients) of limited sample size, and often utilized dichotomised outcomes (e.g. mortality or hospitalisation) ignoring the full spectrum of disease. We identified no studies which comprehensively detailed severity of infections while describing disease severity across pandemic waves, vaccination status, and patient trajectories.\n\nAdded value of this studyTo our knowledge, this is the first study providing a comprehensive view of COVID-19 across pandemic waves using national data and focusing on severity, vaccination, and patient trajectories. Drawing on linked electronic health record (EHR) data on a national scale (56.6 million people alive and registered with GP in England), we describe key demographic factors, frequency of comorbidities, impact of the two main waves in England, and effect of full vaccination on COVID-19 severities. Additionally, we identify and describe patient trajectory networks which illustrate the main transition pathways of COVID-19 patients in the healthcare system. Finally, we provide reproducible COVID-19 phenotyping algorithms reflecting clinically relevant stages of disease severity i.e. positive tests, primary care diagnoses, hospitalisation, critical care treatments (e.g. ventilatory support) and mortality.\n\nImplications of all the available evidenceThe COVID-19 phenotypes and trajectory analysis framework outlined produce a reproducible, extensible and repurposable means to generate national-scale data to support critical policy decision making. By modelling patient trajectories as a series of interactions with healthcare systems, and linking these to demographic and outcome data, we provide a means to identify and prioritise care pathways associated with adverse outcomes and highlight healthcare system touch points which may act as tangible targets for intervention.", - "category": "public and global health", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.11.08.21265380", @@ -1847,6 +1833,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.09.13.21263487", + "date": "2021-09-16", + "link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263487", + "title": "SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population", + "authors": "Jia Wei; Koen B. Pouwels; Nicole Stoesser; Philippa C. Matthews; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John I Bell; John N Newton; Jeremy Farrar; Alison Howarth; Brian D. Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W. Crook; Tim E.A. Peto; A.Sarah Walker; David W. Eyre", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford", + "abstract": "We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.09.09.21263026", @@ -2421,6 +2421,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.05.05.21256668", + "date": "2021-05-09", + "link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256668", + "title": "COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland", + "authors": "Sofia de la Fuente Garcia; Fasih Haider; Saturnino Luz", + "affiliations": "The University of Edinburgh; The University of Edinburgh; The University of Edinburgh", + "abstract": "The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively.\n\nClinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.", + "category": "health informatics", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.05.04.21256507", @@ -2449,6 +2463,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.04.26.21255732", + "date": "2021-04-28", + "link": "https://medrxiv.org/cgi/content/short/2021.04.26.21255732", + "title": "Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales", + "authors": "Sarah Beale; Isobel Braithwaite; Annalan MD Navaratnam; Pia Hardelid; Alison Rodger; Anna Aryee; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative", + "affiliations": "University College London; University College London; University College London; University College London; University College London; Royal Free London NHS Foundation Trust,; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ", + "abstract": "BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation.\n\nMethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period.\n\nResultsRelative to participants in the least deprived areas, participants in the most deprived areas persistently exhibited elevated risk of exposure to vehicle sharing (aRR range across time points 1.73-8.52), public transport (aRR 3.13-5.73), work or education outside of the household (aRR 1.09-1.21), essential shops (aRR 1.09-1.13) and non-household contacts (aRR 1.15-1.19) across multiple survey periods.\n\nConclusionDifferential exposure to essential public activities in deprived communities is likely to contribute to inequalities in infection risk and outcomes during the COVID-19 pandemic. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.04.21.21255807", @@ -2603,20 +2631,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.03.26.21254391", - "date": "2021-03-26", - "link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254391", - "title": "Vaccine effectiveness of the first dose of ChAdOx1 nCoV-19 and BNT162b2 against SARS-CoV-2 infection in residents of Long-Term Care Facilities (VIVALDI study)", - "authors": "Madhumita Shrotri; Maria Krutikov; Tom Palmer; Rebecca Giddings; Borscha Azmi; Sathyavani Subbarao; Christopher Fuller; Aidan Irwin-Singer; Daniel Davies; Gokhan Tut; Jamie Lopez Bernal; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross", - "affiliations": "University College London; University College London; University College London; University College London; University College London; Public Health England; University College London; Department of Health and Social Care, UK; Palantir Technologies UK Ltd; University of Birmingham; Public Health England; University of Birmingham; University College London; University College London; University College London", - "abstract": "BackgroundThe effectiveness of SARS-CoV-2 vaccines in frail older adults living in Long-Term Care Facilities (LTCFs) is uncertain. We estimated protective effects of the first dose of ChAdOx1 and BNT162b2 vaccines against infection in this population.\n\nMethodsCohort study comparing vaccinated and unvaccinated LTCF residents in England, undergoing routine asymptomatic testing (8 December 2020 - 15 March 2021). We estimated the relative hazard of PCR-positive infection using Cox proportional hazards regression, adjusting for age, sex, prior infection, local SARS-CoV-2 incidence, LTCF bed capacity, and clustering by LTCF.\n\nResultsOf 10,412 residents (median age 86 years) from 310 LTCFs, 9,160 were vaccinated with either ChAdOx1 (6,138; 67%) or BNT162b2 (3,022; 33%) vaccines. A total of 670,628 person days and 1,335 PCR-positive infections were included. Adjusted hazard ratios (aHRs) for PCR-positive infection relative to unvaccinated residents declined from 28 days following the first vaccine dose to 0{middle dot}44 (0{middle dot}24, 0{middle dot}81) at 28-34 days and 0{middle dot}38 (0{middle dot}19, 0{middle dot}77) at 35-48 days. Similar effect sizes were seen for ChAdOx1 (aHR 0{middle dot}32 [0{middle dot}15-0{middle dot}66] and BNT162b2 (aHR 0{middle dot}35 [0{middle dot}17, 0{middle dot}71]) vaccines at 35-48 days. Mean PCR cycle threshold values were higher, implying lower infectivity, for infections [≥]28 days post-vaccination compared with those prior to vaccination (31{middle dot}3 vs 26{middle dot}6, p<0{middle dot}001).\n\nInterpretationThe first dose of BNT162b2 and ChAdOx1 vaccines was associated with substantially reduced SARS-CoV-2 infection risk in LTCF residents from 4 weeks to at least 7 weeks.\n\nFundingUK Government Department of Health and Social Care.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe conducted a systematic search for studies which evaluated SARS-CoV-2 vaccine effectiveness in residents of long-term care facilities (LTCFs) published between 01/01/2020 and 11/03/2021. We used variations of search terms for \"COVID-19\" AND \"vaccine effectiveness\" OR \"vaccine efficacy\" AND \"care homes\" OR \"long term care facilities\" OR \"older people\" on Ovid MEDLINE and MedRxiv. We identified one pre-print article regarding LTCFs in Denmark, which reported that a single dose of BNT162b was ineffective against SARS-CoV-2 infection in residents, however, participants received the second vaccine dose 24 days following the first dose on average, which is likely to be too soon to capture the protective effects of a single vaccine dose. Additionally, we identified two pre-print reports of studies evaluating vaccine effectiveness against symptomatic infection and hospitalisation amongst older adults in the community. The first of these found 81% vaccine effectiveness against COVID-19-related hospitalisation at 28-34 days following a single dose of BNT162b or ChAdOx1 in [≥]80-year-olds. The second of these found vaccine effectiveness against symptomatic infection of 60% at 28-34 days and 73% at 35+ days following a single dose of ChAdOx1 in [≥]70-year-olds. No studies were identified that focused on the effectiveness of a single vaccine dose against infection amongst LTCF residents at more than 4 weeks post-vaccination, a particularly important question in the context of the UK policy decision to extend the dose interval beyond 3 weeks.\n\nAdded value of this studyWe conducted a prospective cohort study of 10,412 residents aged [≥]65 years, from 310 LTCFs across England, to investigate the protective effect of the first dose of the ChAdOx1 and BNT162b vaccines against SARS-CoV-2 infection in frail older adults. We retrieved results from routine monthly PCR testing, as well as outbreak and clinical testing for SARS-CoV-2, thereby capturing data on asymptomatic as well as symptomatic infections, which we linked to vaccination records. We estimated vaccine effectiveness to be 56% (19-76%) at 28-34 days, and 62% (23-81%) at 35-48 days following a single dose of ChAdOx1 or BNT162. Our findings suggest that the risk of SARS-CoV-2 infection is substantially reduced from 28 days following the first dose of either vaccine and that this effect is maintained for at least 7 weeks, with similar protection offered by both vaccine types. We also found that PCR cycle threshold (Ct) values, which are negatively associated with the ability to isolate virus, were significantly higher in infections occurring at [≥] 28days post vaccination compared to those occurring in the unvaccinated period, suggesting that vaccination may reduce onward transmission of SARS-CoV-2 in breakthrough infections. To the best of our knowledge, our findings constitute the first real-world evidence on vaccine effectiveness against infection for ChAdOx1, in any age group. We can also infer that both vaccines are effective against the B.1.1.7 variant, because our analysis period coincided with the rapid emergence of B.1.1.7 in England during the second wave of the pandemic.\n\nImplications of all the available evidenceOur findings add to the growing body of evidence on the protective effect of the BNT162b vaccines in residents of LTCFs and demonstrate the effectiveness of ChAdOx1 in this vulnerable population. Evaluating single-dose vaccine efficacy has become increasingly important in light of extended dosing intervals that have been implemented in order to maximise vaccine coverage across high-risk groups. Further work is required to evaluate the effectiveness of the first vaccine dose after 8-12 weeks, as well as following the second dose, and to evaluate the long-term impact of vaccination on SARS-CoV-2 infection, transmission and mortality in LTCFs. This will inform policy decisions regarding the ongoing need for disease control measures in LTCF such as visitor restrictions, which continue to have a detrimental impact on the wellbeing of residents, their relatives, and staff.\n\nSupplementary material attached.", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.03.19.21253940", @@ -2813,20 +2827,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.02.03.21251004", - "date": "2021-02-05", - "link": "https://medrxiv.org/cgi/content/short/2021.02.03.21251004", - "title": "Ethnic differences in COVID-19 mortality during the first two waves of the Coronavirus Pandemic: a nationwide cohort study of 29 million adults in England", - "authors": "Vahe Nafilyan; Nazrul Islam; Rohini Mathur; Daniel Ayoubkhani; Amitava Banerjee; Myer Glickman; Ben Humberstone; Ian DIamond; Kamlesh Khunti", - "affiliations": "Office for National Statistics; Nuffield Department of Population Health, Big Data Institute, University of Oxford; London School of Hygiene and Tropical Medicine; Office for National Statistics; University College London; Office for National Statistics; Office for National Statistics; Office for National Statistics; Diabetes Research Centre, University of Leicester", - "abstract": "BackgroundEthnic minorities have experienced disproportionate COVID-19 mortality rates in the UK and many other countries. We compared the differences in the risk of COVID-19 related death between ethnic groups in the first and second waves the of COVID-19 pandemic in England. We also investigated whether the factors explaining differences in COVID-19 death between ethnic groups changed between the two waves.\n\nMethodsUsing data from the Office for National Statistics Public Health Data Asset on individuals aged 30-100 years living in private households, we conducted an observational cohort study to examine differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and second wave (from 1st September to 28th December 2020). We estimated age-standardised mortality rates (ASMR) in the two waves stratified by ethnic groups and sex. We also estimated hazard ratios (HRs) for ethnic-minority groups compared with the White British population, adjusted for geographical factors, socio-demographic characteristics, and pre-pandemic health conditions.\n\nResultsThe study population included over 28.9 million individuals aged 30-100 years living in private households. In the first wave, all ethnic minority groups had a higher risk of COVID-19 related death compared to the White British population. In the second wave, the risk of COVID-19 death remained elevated for people from Pakistani (ASMR: 339.9 [95% CI: 303.7 - 376.2] and 166.8 [141.7 - 191.9] deaths per 100,000 population in men and women) and Bangladeshi (318.7 [247.4 - 390.1] and 127.1 [91.1 - 171.3] in men and women)background but not for people from Black ethnic groups. Adjustment for geographical factors explained a large proportion of the differences in COVID-19 mortality in the first wave but not in the second wave. Despite an attenuation of the elevated risk of COVID-19 mortality after adjusting for sociodemographic characteristics and health status, the risk was substantially higher in people from Bangladeshi and Pakistani background in both the first and the second waves.\n\nConclusionBetween the first and second waves of the pandemic, the reduction in the difference in COVID-19 mortality between people from Black ethnic background and people from the White British group shows that ethnic inequalities in COVID-19 mortality can be addressed. The continued higher rate of mortality in people from Bangladeshi and Pakistani background is alarming and requires focused public health campaign and policy changes.\n\n*VN and NI contributed equally to this paper\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSA recent systematic review by Pan and colleagues demonstrated that people of ethnic minority background in the UK and the USA have been disproportionately affected by the Coronavirus (COVID-19) pandemic, compared to White populations. While several studies have investigated whether adjusting for socio-demographic and economic factors and medical history reduces the estimated difference in risk of mortality and hospitalisation, the reasons for the differences in the risk of experiencing harms from COVID-19 are still being explored during the course of the pandemic. Studies so far have analysed the ethnic differences in COVID-19 mortality in the first wave of the pandemic. The evidence on the temporal trend of ethnic inequalities in COVID-19 mortality, especially those from the second wave of the pandemic, is scarce.\n\nAdded value of this studyUsing data from the Office for National Statistics (ONS) Public Health Data Asset on 29 million adults aged 30-100 years living in private households in England, we conducted an observational cohort study to examine the differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and second wave (from 1st September to 28th December 2020). We find that in the first wave all ethnic minority groups were at elevated risk of COVID-19 related death compared to the White British population. In the second wave, the differences in the risk of COVID-19 related death attenuated for Black African and Black Caribbean groups, remained substantially higher in people from Bangladeshi background, and worsened in people from Pakistani background. We also find that some of the factors explaining these differences in mortality have changed in the two waves.\n\nImplications of all the available evidenceThe risk of COVID-19 mortality during the first wave of the pandemic was elevated in people from ethnic minority background. An appreciable reduction in the difference in COVID-19 mortality in the second wave of the pandemic between people from Black ethnic background and people from the White British group is reassuring, but the continued higher rate of mortality in people from Bangladeshi and Pakistani background is alarming and requires focused public health campaign and policy response. Focusing on treating underlying conditions, although important, may not be enough in reducing the inequalities in COVID-19 mortality. Focused public health policy as well as community mobilisation and participatory public health campaign involving community leaders may help reduce the existing and widening inequalities in COVID-19 mortality.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.02.02.21250989", @@ -2855,20 +2855,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.01.25.21249942", - "date": "2021-01-30", - "link": "https://medrxiv.org/cgi/content/short/2021.01.25.21249942", - "title": "Development and external validation of prognostic models for COVID-19 to support risk stratification in secondary care", - "authors": "Nicola J Adderley; Thomas Taverner; Malcolm Price; Christopher Sainsbury; David Greenwood; Joht Singh Chandan; Yemisi Takwoingi; Rashan Haniffa; Isaac Hosier; Carly Welch; Dhruv Parekh; Suzy Gallier; Krishna M Gokhale; Alastair K Denniston; Elizabeth Sapey; Krishnarajah Nirantharakumar", - "affiliations": "University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Oxford; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham", - "abstract": "ObjectivesExisting UK prognostic models for patients admitted to hospital with COVID-19 are limited by reliance on comorbidities, which are under-recorded in secondary care, and lack of imaging data among the candidate predictors. Our aims were to develop and externally validate novel prognostic models for adverse outcomes (death, intensive therapy unit (ITU) admission) in UK secondary care; and externally validate the existing 4C score.\n\nDesignCandidate predictors included demographic variables, symptoms, physiological measures, imaging, laboratory tests. Final models used logistic regression with stepwise selection.\n\nSettingModel development was performed in data from University Hospitals Birmingham (UHB). External validation was performed in the CovidCollab dataset.\n\nParticipantsPatients with COVID-19 admitted to UHB January-August 2020 were included.\n\nMain outcome measuresDeath and ITU admission within 28 days of admission.\n\nResults1040 patients with COVID-19 were included in the derivation cohort; 288 (28%) died and 183 (18%) were admitted to ITU within 28 days of admission. Area under the receiver operating curve (AUROC) for mortality was 0.791 (95%CI 0.761-0.822) in UHB and 0.767 (95%CI 0.754-0.780) in CovidCollab; AUROC for ITU admission was 0.906 (95%CI 0.883-0.929) in UHB and 0.811 (95%CI 0.795-0.828) in CovidCollab. Models showed good calibration. Addition of comorbidities to candidate predictors did not improve model performance. AUROC for the 4C score in the UHB dataset was 0.754 (95%CI 0.721-0.786).\n\nConclusionsThe novel prognostic models showed good discrimination and calibration in derivation and external validation datasets, and outperformed the existing 4C score. The models can be integrated into electronic medical records systems to calculate each individual patients probability of death or ITU admission at the time of hospital admission. Implementation of the models and clinical utility should be evaluated.\n\nArticle SummaryO_ST_ABSStrengths and limitations of this studyC_ST_ABSO_LIWe developed novel prognostic models predicting mortality and ITU admission within 28 days of admission for patients hospitalised with COVID-19, using a large routinely collected dataset gathered at admission with a wide range of possible predictors (demographic variables, symptoms, physiological measures, imaging, laboratory test results).\nC_LIO_LIThese novel models showed good discrimination and calibration in both derivation and external validation cohorts, and outperformed the existing ISARIC model and 4C score in the derivation dataset. We found that addition of comorbidities to the set of candidate predictors included in model derivation did not improve model performance.\nC_LIO_LIIf integrated into hospital electronic medical records systems, the model algorithms will provide a predicted probability of mortality or ITU admission for each patient based on their individual data at, or close to, the time of admission, which will support clinicians decision making with regard to appropriate patient care pathways and triage. This information might also assist clinicians in explaining complex prognostic assessments and decisions to patients and their relatives.\nC_LIO_LIA limitation of the study was that in the external validation cohort we were unable to examine all of the predictors included in the original full UHB model due to only a reduced set of candidate predictors being available in CovidCollab. Nevertheless, the reduced model performed well and the results suggest it may be applicable in a wide range of datasets where only a reduced set of predictor variables is available.\nC_LIO_LIFurthermore, it was not possible to carry out stratified analysis by ethnicity as the UHB dataset contained too few patients in most of the strata, and no ethnicity data was available in the CovidCollab dataset.\nC_LI", - "category": "public and global health", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.01.25.21250356", @@ -3163,6 +3149,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.11.19.20234849", + "date": "2020-11-22", + "link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234849", + "title": "Community factors and excess mortality in first wave of the COVID-19 pandemic.", + "authors": "Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott", + "affiliations": "Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London", + "abstract": "Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.06.20227108", @@ -3443,20 +3443,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.09.28.20202929", - "date": "2020-09-29", - "link": "https://medrxiv.org/cgi/content/short/2020.09.28.20202929", - "title": "T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses", - "authors": "Ane Ogbe; Barbara Kronsteiner; Donal T Skelly; Matthew Pace; Anthony Brown; Emily Adland; Kareena Adair; Hossain Delowar Akhter; Mohammad Ali; Serat-E Ali; Adrienn Angyal; M. Azim Ansari; Carolina V Arancibia-Carcamo; Helen Brown; Senthil Chinnakannan; Christopher P Conlon; Catherine de Lara; Thushan de Silva; Christina Dold; Tao Dong Dong; Timothy Donnison; David W Eyre; Amy Flaxman; Helen A Fletcher; Joshua Gardner; James T Grist; Carl-Philipp Hackstein; Kanoot Jaruthamsophon; Katie Jeffrey; Teresa Lambe; Lian Lee; Wenqin Li; Nicholas Lim; Philippa C Matthews; Alexander J Mentzer; Shona C Moore; Dean J Naisbitt; Monday Ogese; Graham Ogg; Peter Openshaw; Munir Pirmohamed; Andrew J Pollard; Narayan Ramamurthy; Patpong Rongkard; Sarah Rowland-Jones; Oliver L Sampson; Gavin Screaton; Alessandro Sette; Lizzie Stafford; Craig Thompson; Paul J Thomson; Ryan Thwaites; Vinicius Vieira; Daniela Weiskopf; Panagiota Zacharopoulou; - Oxford Immunology Network Covid-19 Response T cell Consortium; - Oxford Protective T cell Immunology for COVID-19 (OPTIC) Clinical team; Lance Turtle; Paul Klenerman; Philip Goulder; John Frater; Eleanor Barnes; Susanna Dunachie", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Liverpool; University of Liverpool; University of Oxford; Imperial College; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; La Jolla Institute for Immunology; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Liverpool; Imperial College; University of Oxford; La Jolla Institute for Immunology; University of Oxford; ; ; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford", - "abstract": "A major issue in identification of protective T cell responses against SARS-CoV-2 lies in distinguishing people infected with SARS-CoV-2 from those with cross-reactive immunity generated by exposure to other coronaviruses. We characterised SARS-CoV-2 T cell immune responses in 168 PCR-confirmed SARS-CoV-2 infected subjects and 118 seronegative subjects without known SARS-CoV-2 exposure using a range of T cell assays that differentially capture immune cell function. Strong ex vivo ELISpot and proliferation responses to multiple antigens (including M, NP and ORF3) were found in those who had been infected by SARS-CoV-2 but were rare in pre-pandemic and unexposed seronegative subjects. However, seronegative doctors with high occupational exposure and recent COVID-19 compatible illness showed patterns of T cell responses characteristic of infection, indicating that these readouts are highly sensitive. By contrast, over 90% of convalescent or unexposed people showed proliferation and cellular lactate responses to spike subunits S1/S2, indicating pre-existing cross-reactive T cell populations. The detection of T cell responses to SARS-CoV-2 is therefore critically dependent on the choice of assay and antigen. Memory responses to specific non-spike proteins provides a method to distinguish recent infection from pre-existing immunity in exposed populations.", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.09.26.20202150", @@ -3625,6 +3611,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.09.01.20185793", + "date": "2020-09-03", + "link": "https://medrxiv.org/cgi/content/short/2020.09.01.20185793", + "title": "Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study", + "authors": "Katie Biggs; Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Matthew Bursnall; Amanda Loban; Simon Waterhouse; Richard Simmonds; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter", + "affiliations": "University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust", + "abstract": "ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection.\n\nMethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome.\n\nResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse outcome. C-statistics were 0.80 (95% confidence interval 0.73-0.87) for the WHO algorithm, 0.80 (0.71-0.90) for POPS, 0.76 (0.67-0.85) for COAST, and 0.71 (0.59-0.82) for SFHPC. Using pre-specified thresholds, the WHO algorithm had the highest sensitivity (0.85) and lowest specificity (0.75), but POPS and COAST could optimise sensitivity (0.96 and 0.92 respectively) at the expense of specificity (0.25 and 0.38 respectively) by using a threshold of any score above zero instead of the pre-specified threshold.\n\nConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive.\n\nRegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533", + "category": "emergency medicine", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.08.26.20182279", @@ -3821,20 +3821,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.08.03.20167122", - "date": "2020-08-04", - "link": "https://medrxiv.org/cgi/content/short/2020.08.03.20167122", - "title": "Ethnic minority groups in England and Wales - factors affecting the size and timing of elevated COVID-19 mortality: a retrospective cohort study linking Census and death records", - "authors": "Daniel Ayoubkhani; Vahe Nafilyan; Chris White; Peter Goldblatt; Charlotte Gaughan; Louisa Blackwell; Nicky Rogers; Amitava Banerjee; Kamlesh Khunti; Myer Glickman; Ben Humberstone; Ian Diamond", - "affiliations": "Office for National Statistics; Office for National Statistics; Office for National Statistics; UCL Institute for Health Equity; Office for National Statistics; Office for National Statistics; Office for National Statistics; Institute of Health Informatics, University College London; Diabetes Research Centre, University of Leicester; Office for National Statistics; Office for National Statistics; Office for National Statistics", - "abstract": "ObjectivesTo estimate population-level associations between ethnicity and coronavirus disease 2019 (COVID-19) mortality, and to investigate how ethnicity-specific mortality risk evolved over the course of the pandemic.\n\nDesignRetrospective cohort study using linked administrative data.\n\nSettingEngland and Wales, deaths occurring 2 March to 15 May 2020.\n\nParticipantsRespondents to the 2011 Census of England and Wales aged [≤]100 years and enumerated in private households, linked to death registrations and adjusted to account for emigration before the outcome period, who were alive on 1 March 2020 (n=47,872,412).\n\nMain outcome measureDeath related to COVID-19, registered by 29 May 2020.\n\nStatistical methodsWe estimated hazard ratios (HRs) for ethnic minority groups compared with the White population using Cox regression models, controlling for geographical, demographic, socio-economic, occupational, and self-reported health factors. HRs were estimated on the full outcome period and separately for pre- and post-lockdown periods in the UK.\n\nResultsIn the age-adjusted models, people from all ethnic minority groups were at elevated risk of COVID-19 mortality; the HRs for Black males and females were 3.13 [95% confidence interval: 2.93 to 3.34] and 2.40 [2.20 to 2.61] respectively. However, in the fully adjusted model for females, the HRs were close to unity for all ethnic groups except Black (1.29 [1.18 to 1.42]). For males, COVID-19 mortality risk remained elevated for the Black (1.76 [1.63 to 1.90]), Bangladeshi/Pakistani (1.35 [1.21 to 1.49]) and Indian (1.30 [1.19 to 1.43]) groups. The HRs decreased after lockdown for all ethnic groups, particularly Black and Bangladeshi/Pakistani females.\n\nConclusionsDifferences in COVID-19 mortality between ethnic groups were largely attenuated by geographical and socio-economic factors, although some residual differences remained. Lockdown was associated with reductions in excess mortality risk in ethnic minority populations, which has major implications for a second wave of infection or local spikes. Further research is needed to understand the causal mechanisms underpinning observed differences in COVID-19 mortality between ethnic groups.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.07.30.20165464", @@ -4199,6 +4185,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.06.10.20127175", + "date": "2020-06-11", + "link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127175", + "title": "Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.", + "authors": "Amitava Banerjee; Suliang Chen; Laura Pasea; Alvina Lai; Michail Katsoulis; Spiros Denaxas; Vahe Nafilyan; Bryan Williams; Wai Keong Wong; Ameet Bakhai; Kamlesh Khunti; Deenan Pillay; Mahdad Noursadeghi; Honghan Wu; Nilesh Pareek; Daniel Bromage; Theresa Mcdonagh; Jonathan Byrne; James T Teo; Ajay Shah; Ben Humberstone; Liang V Tang; Anoop SV Shah; Andrea Rubboli; Yutao Guo; Yu Hu; Cathie LM Sudlow; Gregory YH Lip; Harry Hemingway", + "affiliations": "University College London; University College London; University College London; University College London; UCL; University College London; Office for National Statistics; UCL; University College London Hospitals NHS Trust; Royal Free Hospitals NHS Trust; University of Leicester; UCL; UCL; UCL; King's College Hospital; Kings College London; Kings College London; Kings London NHS Trust; Kings College Hospital NHS Foundation Trust; King's College London; Office for National Statistics; Huazhong University of Science and Technology, Wuhan, China; University of Edinburgh; Ospedale S. Maria delle Croci, Ravenna, Italy; PLA General Hospital, Beijing, China.; Huazhong University of Science and Technology, Wuhan, China.; University of Edinburgh; University of Liverpool; UCL", + "abstract": "BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both \"direct\", through infection, and \"indirect\", through changes in healthcare.\n\nMethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(\"direct\" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For \"indirect\" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020.\n\nFindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths.\n\nInterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic.\n\nFundingNIHR, HDR UK, Astra Zeneca", + "category": "cardiovascular medicine", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.06.08.20120584", diff --git a/data/covid/preprints.json b/data/covid/preprints.json index 3c363202..5fd03da2 100644 --- a/data/covid/preprints.json +++ b/data/covid/preprints.json @@ -1,4 +1,18 @@ [ + { + "site": "medRxiv", + "doi": "10.1101/2023.10.26.23297598", + "date": "2023-10-26", + "link": "https://medrxiv.org/cgi/content/short/2023.10.26.23297598", + "title": "Assessing the causal effect of air pollution on risk of SARS-CoV-2 infection", + "authors": "Annalan Mathew Dwight Navaratnam; Sarah Beale; Yamina Boukari; Vincent Nguyen; Wing Lam Erica Fong; Isobel Braithwaite; Thomas Edward Byrne; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Parth Patel; Madhumita Shrotri; Alexei Yavlinsky; Andrew Hayward; Haneen Khreis; Robert W Aldridge", + "affiliations": "University College London; University College London; University College London; University College London; University College London; University College London; University College London; UCL; University College London; University College London; University College London; University College London; University College London; UCL; University of Cambridge; UCL", + "abstract": "Introduction Emerging evidence suggests association of air pollution exposure with risk of SARS-CoV-2 infection, but many of these findings are limited by study design, lack of individual-level covariate data or are specific to certain subpopulations. We aim to evaluate causal effects of air pollution on risk of infection, whilst overcoming these limitations. Methods Concentrations for black carbon(BC), particulate matter 10(PM10), particulate matter 2.5(PM2.5), nitrogen dioxide(NO2) and oxides of nitrogen(NOx) from the Department of Environment, Food and Rural Affairs (DEFRA) and Effect of Low-level Air Pollution: A Study in Europe (ELAPSE) were linked to postcodes of 53,683 Virus Watch study participants. The primary outcome was first SARS-CoV-2 infection, between 1st September 2020 and 30th April 2021. Regression analysis used modified Poisson with robust estimates, clustered by household, adjusting for individual (e.g., age, sex, ethnicity) and environmental covariates(e.g., population density, region) to estimate total and direct effects. Results Single pollutant analysis showed the direct effect of higher risk of SARS-CoV-2 infection with increased exposure to PM2.5(RR1.11,95%CI 1.08;1.15), PM10(RR1.06,95%CI 1.04;1.09), NO2(RR1.04,95%CI 1.04;1.05) and NOx(RR1.02,95%CI 1.02;1.02) per 1g/m3 increment with DEFRA 2015-19 data. Sensitivity analyses altering covariates, exposure window and modelled air pollution data source produced similar estimates. Higher risk of SARS-CoV-2 per 10-5m-1 increment of BC (RR1.86, 95%CI 1.62;2.14) was observed using ELAPSE data. Conclusion Long term exposure to higher concentrations of air pollutions increases the risk of SARS-CoV-2 infection, highlighting that adverse health effects of air pollution is not only limited to non-communicable diseases.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "bioRxiv", "doi": "10.1101/2023.10.22.563481", @@ -7,26 +21,12 @@ "title": "Microfluidic antibody profiling after repeated SARS-CoV-2 vaccination links antibody affinity and concentration to impaired immunity and variant escape in patients on anti-CD-20 therapy", "authors": "Ashley Priddey; Michael Xin Hua Chen-Xu; Daniel James Cooper; Serena MacMillan; Georg Meisl; Catherine K Xu; Myra Hosmillo; Ian G Goodfellow; Rafael Kollyfas; Rainer Doffinger; John R Bradley; Irina I Mohorianu; Rachel Jones; Tuomas P.J. Knowles; Rona Smith; Vasilis Kosmoliaptsis", "affiliations": "Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Department of Pathology, Division of Virology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK and Cambridge University Hospitals NHS Foundation Trust, Cambridge, U; Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK and NIHR Blood and Transplant Research Unit in Organ D", - "abstract": "Background: Patients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients. Methods: We performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30). Results: Rituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination. Discussion: Our results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.", + "abstract": "BackgroundPatients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients.\n\nMethodsWe performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30).\n\nResultsRituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination.\n\nDiscussionOur results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.", "category": "immunology", "match_type": "fuzzy", "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.10.12.23296948", - "date": "2023-10-13", - "link": "https://medrxiv.org/cgi/content/short/2023.10.12.23296948", - "title": "A nationwide study of 331 rare diseases among 58 million individuals: prevalence, demographics, and COVID-19 outcomes", - "authors": "Johan H Thygesen; HUAYU ZHANG; Hanane Issa; Jinge Wu; Tuankasfee Hama; Ana-Catarina Pinho-Gomes; Tudor Groza; Sara Khalid; Richard Lumbers; Mevhibe Hocaoglu; Kamlesh Khunti; Rouven Priedon; Amitava Banerjee; Nikolas Pontikos; Christopher Tomlinson; Ana Torralbo; Paul Taylor; Cathie Sudlow; Spiros Denaxas; Harry Hemingway; Honghan Wu", - "affiliations": "Institute of Health Informatics, University College London, London, UK; Advanced Care Research Centre, Usher Institute, University of Edinburgh, Edinburgh, UK.; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, UK; Institute of Health Informatics, University College London, London, UK; Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, Kings College London, London, UK; College of Life Sciences, University of Leicester, Leicester, UK; Health Data Research UK, London, UK; Institute of Health Informatics, University College London, London, UK; UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Health Data Research UK, London, UK; British Heart Foundation Data Science Centre, London, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edin; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK", - "abstract": "BackgroundThe Global Burden of Disease study has provided key evidence to inform clinicians, researchers, and policy makers across common diseases, but no similar effort with single study design exists for hundreds of rare diseases. Consequently, many rare conditions lack population-level evidence including prevalence and clinical vulnerability. This has led to the absence of evidence-based care for rare diseases, prominently in the COVID-19 pandemic.\n\nMethodThis study used electronic health records (EHRs) of more than 58 million people in England, linking nine National Health Service datasets spanning healthcare settings for people alive on Jan 23, 2020. Starting with all rare diseases listed in Orphanet, we quality assured and filtered down to analyse 331 conditions with ICD-10 or SNOMED-CT mappings clinically validated in our dataset. We report 1) population prevalence, clinical and demographic details of rare diseases, and 2) investigate differences in mortality with SARs-CoV-2.\n\nFindingsAmong 58,162,316 individuals, we identified 894,396 with at least one rare disease. Prevalence data in Orphanet originates from various sources with varying degrees of precision. Here we present reproducible age and gender-adjusted estimates for all 331 rare diseases, including first estimates for 186 (56.2%) without any reported prevalence estimate in Orphanet. We identified 49 rare diseases significantly more frequent in females and 62 in males. Similarly we identified 47 rare diseases more frequent in Asian as compared to White ethnicity and 22 with higher Black to white ratios as compared to similar ratios in population controls. 37 rare diseases were overrepresented in the white population as compared to both Black and Asian ethnicities. In total, 7,965 of 894,396 (0.9%) of rare-disease patients died from COVID-19, as compared to 141,287 of 58,162,316 (0.2%) in the full study population. Eight rare diseases had significantly increased risks for COVID-19-related mortality in fully vaccinated individuals, with bullous pemphigoid (8.07[3.01-21.62]) being worst affected.\n\nInterpretationOur study highlights that National-scale EHRs provide a unique resource to estimate detailed prevalence, clinical and demographic data for rare diseases. Using COVID-19-related mortality analysis, we showed the power of large-scale EHRs in providing insights to inform public health decision-making for these often neglected patient populations.\n\nFundingBritish Heart Foundation Data Science Centre, led by Health Data Research UK.\n\nResearch in contextO_ST_ABSEvidence before the studyC_ST_ABSWe have previously published the largest study looking at COVID-19 across rare diseases, but with a sample size of 158 COVID-19 infected rare disease patients and 125 unaffected relatives, from Genomics England, the power of that study was limited. We searched PubMed from database inception to Apr 21, 2023, for publications using the search terms \"COVID-19\" or \"SARS-CoV-2\" and \"rare disease\" or \"ORPHANET\", without language restrictions. There are many studies examining the severity of COVID-19 in rare disease patients. However, to date, most studies have focused on a single or a few rare diseases associated with severity of COVID-19, and not taken a comprehensive rare disease wide approach. So far no studies have examined the impact of vaccination on mortality in rare disease patients. Moreover, the sample size used to examine rare diseases is limited in most studies. The largest study we identified included 168,680 individuals but only focused on autoimmune rheumatic disease.\n\nAdded value of this studyIn this study we use national scale EHR data from England to report age and gender adjusted point prevalence for 331 rare diseases, with clinically-validated ICD-10 and/or SNOMED-CT code lists. Among these, 186 (56.2%) diseases did not have existing point prevalence data available in Orphanet. To our knowledge, this is the first time that rare diseases have been examined on a national scale, encompassing a population of over 58 million people. The large sample size provides sufficient statistical power to detect and describe enough carriers of even very rare conditions <1 case per million. Our analysis of COVID-related mortality has demonstrated the clinical relevance of national data for rare diseases. Specifically, we identified eight rare conditions that are associated with a significantly increased risk of mortality from COVID-19, even among fully vaccinated individuals.\n\nImplication of all the available evidenceThese findings provide robust reproducible prevalence, gender, and ethnicity estimates for disease that may often have been under prioritised, and where such information in most cases was not previously available. Our COVID-19 mortality findings highlight the need for targeted policy and support addressing the high level of vulnerability of these patients to COVID-19.", - "category": "health informatics", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.10.11.23296866", @@ -181,20 +181,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.07.25.23293143", - "date": "2023-07-27", - "link": "https://medrxiv.org/cgi/content/short/2023.07.25.23293143", - "title": "The Cost of Keeping Patients Waiting: Retrospective Treatment-Control Study of Additional Healthcare Utilisation for UK Patients Awaiting Elective Treatment Following COVID-19", - "authors": "Charlotte James; Rachel Denholm; Richard M Wood", - "affiliations": "University of Bristol; University of Bristol; UK National Health Service (BNSSG ICB)", - "abstract": "ObjectiveThe COVID-19 pandemic has led to increased waiting times for elective treatments in many countries. This study seeks to address a deficit in the literature concerning the effect of long waits on the wider consumption of healthcare resources.\n\nMethodsWe carried out a retrospective treatment-control study in a healthcare system in South West England from 15 June 2021 to 15 December 2021. We compared weekly contacts with health services of patients waiting over 18 weeks for treatment ( Treatments) and people not on a waiting list ( Controls). Controls were matched to Treatments based on age, sex, deprivation and multimorbidity. Treatments were stratified by the clinical specialty of the awaited treatment, with healthcare usage assessed over various healthcare settings. T-tests assessed whether there was an increase in healthcare utilisation and bootstrap resampling was used to estimate the magnitude of any differences.\n\nResultsA total of 44,616 patients were waiting over 18 weeks (the constitutional target in England) for treatment during the study period. Evidence suggests increases (p < 0.05) in healthcare utilisation for all specialties. Patients in the Cardiothoracic Surgery specialty had the largest increase, requiring 17.9 [4.3, 33.8] additional contacts with secondary care and 17.3 [-1.1, 34.1] additional prescriptions per year.\n\nConclusionPeople waiting for treatment consume higher levels of healthcare than comparable individuals not on a waiting list. These findings are relevant for clinicians and managers in better understanding patient need and reducing harm. Results also highlight the possible false economy in failing to promptly resolve long elective waits.\n\nHighlightsO_LILong waits for elective care can result in additional healthcare needs to manage symptoms up to the point of definitive treatment. While previous studies indicate some association, these mainly consider only a single elective specialty and are limited in the range of healthcare settings covered.\nC_LIO_LIThe large number of long-wait pathways produced as a consequence of COVID-19 disruption allows for a more holistic analysis, covering the full range of elective treatment specialties and wider healthcare impacts across primary, secondary, mental health, and community care, as well as emergency service calls and prescriptions.\nC_LIO_LIAnalysis of 44,616 elective care pathways reveals evidence of increases in wider healthcare consumption additional to that expected for similar patients not awaiting elective treatment. This suggests a false economy in failing to promptly resolve elective pathways, which should be reflected by healthcare providers in long-term resource allocation decisions.\nC_LI", - "category": "health systems and quality improvement", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.07.19.23292289", @@ -251,20 +237,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.06.29.23292056", - "date": "2023-07-01", - "link": "https://medrxiv.org/cgi/content/short/2023.06.29.23292056", - "title": "Genome-wide Association Study of Long COVID", - "authors": "Vilma Lammi; Tomoko Nakanishi; Samuel E Jones; Shea J Andrews; Juha Karjalainen; Beatriz Cortes; Heath E O'Brien; Brian E Fulton-Howard; Hele H Haapaniemi; Axel Schmidt; Ruth E Mitchell; Abdou Mousas; Massimo Mangino; Alicia Huerta-Chagoya; Nasa Sinnott-Armstrong; Elizabeth T Cirulli; Marc Vaudel; Alex SF Kwong; Amit K Maiti; Minttu M Marttila; Chiara Batini; Francesca Minnai; Anna R Dearman; CA Robert Warmerdam; Celia B Sequeros; Thomas W Winkler; Daniel M Jordan; Lindsay Guare; Ekaterina Vergasova; Eirini Marouli; Pasquale Striano; Ummu Afeera Zainulabid; Ashutosh Kumar; Hajar Fauzan Ahmad; Ryuya Edahiro; Shuhei Azekawa; - Long COVID Host Genetics Initiative; - FinnGen; - DBDS Genomic Consortium; - GEN-COVID Multicenter Study; Joseph J Grzymski; Makoto Ishii; Yukinori Okada; Noam D Beckmann; Meena Kumari; Ralf Wagner; Iris M Heid; Catherine John; Patrick J Short; Per Magnus; Karina Banasik; Frank Geller; Lude H Franke; Alexander Rakitko; Emma L Duncan; Alessandra Renieri; Konstantinos K Tsilidis; Rafael de Cid; Ahmadreza Niavarani; Teresa Tusie-Luna; Shefali S Verma; George Davey Smith; Nicholas J Timpson; Mark J Daly; Andrea Ganna; Eva C Schulte; J Brent Richards; Kerstin U Ludwig; Michael Hultstrom; Hugo Zeberg; Hanna M Ollila", - "affiliations": "Institute for Molecular Medicine Finland (FIMM); Department of Human Genetics; Institute for Molecular Medicine Finland (FIMM); University of California San Francisco; Institute for Molecular Medicine Finland (FIMM); Genomes for Life-GCAT lab; Sano Genetics Limited; Genetics and Genomic Sciences; Institute for Molecular Medicine Finland (FIMM); Institute of Human Genetics; Centre for Clinical Brain Sciences; Department of Hygiene and Epidemiology; Department of Twin Research; Departamento de Medicina Genomica y Toxicologia Ambiental; Herbold Computational Biology Program; Helix; Mohn Center for Diabetes Precision Medicine; University of Bristol; Department of Genetics and Genomics; University of Helsinki; Department of Population Health Sciences; Institute for Biomedical Technologies - National Research Council; Institute for Social and Economic Research; Department of Genetics; Novo Nordisk Foundation Center for Protein Research; Department of Genetic Epidemiology; Charles Bronfman Institute for Personalized Medicine; Department of Pathology and Laboratory Medicine; Genotek Ltd.; William Harvey Research Institute; IRCCS G; Department of Internal Medicine; Department of Anatomy; Faculty of Industrial Sciences and Technology; Department of Statistical Genetics; Division of Pulmonary Medicine; ; ; ; ; Center for Genomic Medicine; Division of Pulmonary Medicine; Department of Statistical Genetics; Charles Bronfman Institute for Personalized Medicine; Institute for Social and Economic Research; Institute of Medical Microbiology & Hygiene; Department of Genetic Epidemiology; Department of Population Health Sciences; Sano Genetics Limited; Centre for Fertility and Health; Novo Nordisk Foundation Center for Protein Research; Statens Serum Institute; Department of Genetics; Genotek Ltd.; Department of Twin Research and Genetic Epidemiology; Medical Genetics; Department of Hygiene and Epidemiology; Genomes for Life-GCAT lab; Digestive Oncology Research Center; Instituto de Investigaciones Biomedicas Unam/ Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran; Department of Pathology and Laboratory Medicine; MRC Integrative Epidemiology Unit at the University of Bristol; MRC Integrative Epidemiology Unit at the University of Bristol; Institute for Molecular Medicine Finland (FIMM); Institute for Molecular Medicine Finland (FIMM); Institute of Psychiatric Phenomics & Genomics; Department of Human Genetics; Institute of Human Genetics; Anaesthesiology and Intensive Care Medicine; Department of Evolutionary Genetics; Institute for Molecular Medicine Finland (FIMM)", - "abstract": "Infections can lead to persistent or long-term symptoms and diseases such as shingles after varicella zoster, cancers after human papillomavirus, or rheumatic fever after streptococcal infections1, 2. Similarly, infection by SARS-CoV-2 can result in Long COVID, a condition characterized by symptoms of fatigue and pulmonary and cognitive dysfunction3-5. The biological mechanisms that contribute to the development of Long COVID remain to be clarified. We leveraged the COVID-19 Host Genetics Initiative6, 7 to perform a genome-wide association study for Long COVID including up to 6,450 Long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We identified the first genome-wide significant association for Long COVID at the FOXP4 locus. FOXP4 has been previously associated with COVID-19 severity6, lung function8, and cancers9, suggesting a broader role for lung function in the pathophysiology of Long COVID. While we identify COVID-19 severity as a causal risk factor for Long COVID, the impact of the genetic risk factor located in the FOXP4 locus could not be solely explained by its association to severe COVID-19. Our findings further support the role of pulmonary dysfunction and COVID-19 severity in the development of Long COVID.", - "category": "genetic and genomic medicine", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.06.30.23292079", @@ -1609,20 +1581,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.06.14.22276391", - "date": "2022-06-16", - "link": "https://medrxiv.org/cgi/content/short/2022.06.14.22276391", - "title": "Factors associated with COVID-19 vaccine uptake in people with kidney disease: an OpenSAFELY cohort study", - "authors": "- The OpenSAFELY Collaborative; Edward PK Parker; John Tazare; William J Hulme; Christopher Bates; Rupert Beale; Edward J Carr; Jonathan Cockburn; Helen J Curtis; Louis Fisher; Amelia CA Green; Sam Harper; Frank Hester; Elsie MF Horne; Fiona Loud; Susan Lyon; Viyaasan Mahalingasivam; Amir Mehrkar; Linda Nab; John Parry; Shalini Santhakumaran; Retha Steenkamp; Jonathan AC Sterne; Alex J Walker; Elizabeth J Williamson; Michelle Willicombe; Bang Zheng; Ben Goldacre; Dorothea Nitsch; Laurie A Tomlinson", - "affiliations": "-; London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK; The Francis Crick Institute, London, NW1 1AT, UK; UCL Department of Renal Medicine, Royal Free Hospital, London, UK; The Francis Crick Institute, London, NW1 1AT, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK; Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK; NIHR Bristol Biomedical Research Centre, Bristol, UK; Kidney Care UK, Alton, UK; Patient Council, UK Kidney Association, Bristol, UK; London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK; UK Renal Registry, Bristol, UK; UK Renal Registry, Bristol, UK; Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK; NIHR Bristol Biomedical Research Centre, Bristol, UK; H; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, Du Cane Road London, W12 0NN, UK; London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK; London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; UK Renal Registry, Bristol, UK; London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK", - "abstract": "BackgroundKidney disease is a significant risk factor for COVID-19-related mortality. Achieving high COVID-19 vaccine coverage among people with kidney disease is therefore a public health priority.\n\nMethodsWith the approval of NHS England, we performed a retrospective cohort study using the OpenSAFELY-TPP platform. Individual-level routine clinical data from 24 million people in England were included. A cohort of individuals with stage 3-5 chronic kidney disease (CKD) or receiving renal replacement therapy (RRT) at the start of the COVID-19 vaccine roll-out was identified based on evidence of reduced estimated glomerular filtration rate or inclusion in the UK Renal Registry. Individual-level factors associated with vaccine uptake were explored via Cox proportional hazards models.\n\nResults948,845 people with stage 3-5 CKD or receiving RRT were included. Cumulative vaccine coverage as of 11th May 2022 was 97.5%, 97.0%, and 93.5% for doses 1, 2, and 3, respectively, and 61.1% among individuals with one or more indications for receipt of a fourth dose. Delayed 3-dose vaccine uptake was associated with non-White ethnicity, social deprivation, and severe mental illness - associations that were consistent across CKD stages and in RRT recipients. Similar associations were observed for 4-dose uptake, which was also delayed among care home residents.\n\nConclusionAlthough high primary and booster dose coverage has been achieved among people with kidney disease in England, key disparities in vaccine uptake remain across demographic groups. Identifying how to address these disparities remains a priority to reduce the risk of severe disease in this vulnerable patient group.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.06.09.22276232", @@ -2211,6 +2169,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.03.23.22272804", + "date": "2022-03-23", + "link": "https://medrxiv.org/cgi/content/short/2022.03.23.22272804", + "title": "Waning effectiveness of BNT162b2 and ChAdOx1 COVID-19 vaccines over six months since second dose: a cohort study using linked electronic health records", + "authors": "Elsie MF Horne; William J Hulme; Ruth H Keogh; Tom M Palmer; Elizabeth J Williamson; Edward PK Parker; Amelia Green; Venexia Walker; Alex J Walker; Helen Curtis; Louis Fisher; Brian MacKenna; Richard Croker; Lisa Hopcroft; Robin Y Park; Jon Massey; Jessica Morely; Amir Mehrkar; Sebastian Bacon; David Evans; Peter Inglesby; Caroline E Morton; George Hickman; Simon Davy; Tom Ward; Iain Dillingham; Ben Goldacre; Miguel A Hernan; Jonathan AC Sterne", + "affiliations": "University of Bristol; Univeristy of Oxford; London School of Hygiene and Tropical Medicine; University of Bristol; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Univeristy of Oxford; University of Bristol; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Harvard University; University of Bristol", + "abstract": "BackgroundThe rate at which COVID-19 vaccine effectiveness wanes over time is crucial for vaccination policies, but is incompletely understood with conflicting results from different studies.\n\nMethodsThis cohort study, using the OpenSAFELY-TPP database and approved by NHS England, included individuals without prior SARS-CoV-2 infection assigned to vaccines priority groups 2-12 defined by the UK Joint Committee on Vaccination and Immunisation. We compared individuals who had received two doses of BNT162b2 or ChAdOx1 with unvaccinated individuals during six 4-week comparison periods, separately for subgroups aged 65+ years; 16-64 years and clinically vulnerable; 40-64 years and 18-39 years. We used Cox regression, stratified by first dose eligibility and geographical region and controlled for calendar time, to estimate adjusted hazard ratios (aHRs) comparing vaccinated with unvaccinated individuals, and quantified waning vaccine effectiveness as ratios of aHRs per-4-week period. The outcomes were COVID-19 hospitalisation, COVID-19 death, positive SARS-CoV-2 test, and non-COVID-19 death.\n\nFindingsThe BNT162b2, ChAdOx1 and unvaccinated groups comprised 1,773,970, 2,961,011 and 2,433,988 individuals, respectively. Waning of vaccine effectiveness was similar across outcomes and vaccine brands: e.g. in the 65+ years subgroup ratios of aHRs versus unvaccinated for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test ranged from 1.23 (95% CI 1.15-1.32) to 1.27 (1.20-1.34) for BNT162b2 and 1.16 (0.98-1.37) to 1.20 (1.14-1.27) for ChAdOx1. Despite waning, rates of COVID-19 hospitalisation and COVID-19 death were substantially lower among vaccinated individuals compared to unvaccinated individuals up to 26 weeks after second dose, with estimated aHRs <0.20 (>80% vaccine effectiveness) for BNT162b2, and <0.26 (>74%) for ChAdOx1. By weeks 23-26, rates of SARS-CoV-2 infection in fully vaccinated individuals were similar to or higher than those in unvaccinated individuals: aHRs ranged from 0.85 (0.78-0.92) to 1.53 (1.07-2.18) for BNT162b2, and 1.21 (1.13-1.30) to 1.99 (1.94-2.05) for ChAdOx1.\n\nInterpretationThe rate at which estimated vaccine effectiveness waned was strikingly consistent for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test, and similar across subgroups defined by age and clinical vulnerability. If sustained to outcomes of infection with the Omicron variant and to booster vaccination, these findings will facilitate scheduling of booster vaccination doses.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.03.18.22272607", @@ -2561,20 +2533,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.01.31.22269194", - "date": "2022-02-01", - "link": "https://medrxiv.org/cgi/content/short/2022.01.31.22269194", - "title": "An outbreak of SARS-CoV-2 in a public-facing office in England, 2021", - "authors": "Barry Atkinson; Karin van Veldhoven; Ian Nicholls; Matthew Coldwell; Adam Clarke; Gillian Frost; Christina J Atchison; Amber I Raja; Allan M Bennett; Derek Morgan; Neil Pearce; Tony Fletcher; Elizabeth B Brickley; Yiqun Chen", - "affiliations": "UK Health Security Agency; London School of Hygiene & Tropical Medicine; UK Health Security Agency; Health and Safety Executive; Health and Safety Executive; Health and Safety Executive; UK Health Security Agency; London School of Hygiene & Tropical Medicine; UK Health Security Agency; Health and Safety Executive; London School of Hygiene & Tropical Medicine; UK Health Security Agency; London School of Hygiene & Tropical Medicine; Health and Safety Executive", - "abstract": "Between August-September 2021, an outbreak of SARS-CoV-2, with an attack rate of 55% (22/40 workers), occurred in a public-facing office in England. To identify workplace and worker-related risk factors, a comprehensive investigation involving surface sampling, environmental assessment, molecular and serological testing, and worker questionnaires was performed in September - October 2021. The results affirm the utility of surface sampling to identify SARS-CoV-2 control deficiencies and the importance of evolving, site-specific risk assessments with layered COVID-19 mitigation strategies.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.01.28.22270013", @@ -2617,20 +2575,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.01.26.22269877", - "date": "2022-01-27", - "link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269877", - "title": "The impacts of increased global vaccine sharing on the COVID-19 pandemic; a retrospective modelling study", - "authors": "Sam Moore; Edward M Hill; Louise J Dyson; Michael J Tildesley; Matt J Keeling", - "affiliations": "University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick", - "abstract": "BackgroundThe SARS-CoV-2 pandemic has generated considerable morbidity and mortality world-wide. While the protection offered by vaccines (and booster doses) offers a method of mitigating the worst effects, by the end of 2021 the distribution of vaccine was highly heterogeneous with some countries achieving over 90% coverage in adults by the end of 2021, while others have less than 2%. In part, this is due to the availability of sufficient vaccine, although vaccine hesitancy also plays a role.\n\nMethodsWe use an age-structured model of SARS-CoV-2 dynamics, matched to national data from 152 countries, to investigate the global impact of different vaccine sharing protocols during 2021. We assume a direct relationship between the emergence of variants with increased transmissibility and the cumulative amount of global infection, such that lower global prevalence leads to a lower reproductive number within each country. We compare five vaccine sharing scenarios, from the current situation, through sharing once a particular within-country threshold is reached (e.g. all over 40s have received 2 doses), to full sharing where all countries achieve equal age-dependent vaccine deployment.\n\nFindingsCompared to the observed distribution of vaccine uptake, we estimate full vaccine sharing would have generated a 1.5% (PI -0.1 - 4.5%) reduction in infections and a 11.3% (PI 0.6 - 23.2%) reduction in mortality globally by January 2022. The greatest benefit of vaccine sharing would have been experienced by low and middle income countries, who see an average 5.2% (PI 2.5% - 10.4%) infection reduction and 26.8% (PI 24.1% - 31.3%) mortality reduction. Many high income countries, that have had high vaccine uptake (most notably Canada, Chile, UK and USA), suffer increased infections and mortality under most of the sharing protocols investigated, assuming no other counter measures had been taken. However, if reductions in vaccine supply in these countries had been offset by prolonged use of non-pharmaceutical intervention measures, we predict far greater reductions in global infection and mortality of 64.5% (PI 62.6% - 65.4%) and 62.8% (PI 44.0% - 76.3%), respectively.\n\nInterpretationBy itself, our results suggest that although more equitable vaccine distribution would have had limited impact on overall infection numbers, vaccine sharing would have substantially reduced global mortality by providing earlier protection of the most vulnerable. If increased vaccine sharing from high income nations had been combined with slower easing of non pharmaceutical interventions to compensate for this, a large reduction in both infection and mortality globally would be expected, confounded by a lower risk of new variants arising.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.01.26.22269885", @@ -2855,6 +2799,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "bioRxiv", + "doi": "10.1101/2021.12.17.473248", + "date": "2021-12-21", + "link": "https://biorxiv.org/cgi/content/short/2021.12.17.473248", + "title": "SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion", + "authors": "Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta", + "affiliations": "University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge", + "abstract": "The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.", + "category": "microbiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.12.20.21268098", @@ -2981,6 +2939,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.12.13.21267368", + "date": "2021-12-15", + "link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267368", + "title": "Acute COVID-19 severity and 16-month mental morbidity trajectories in patient populations of six nations", + "authors": "Ingibjorg Magnusdottir; Aniko Lovik; Anna Bara Unnarsdottir; Daniel L. McCartney; Helga Ask; Kadri Koiv; Lea Arregui Nordahl Christoffersen; Sverre Urnes Johnson; Andrew M McIntosh; Anna K. Kahler; Archie Campbell; Arna Hauksdottir; Chloe Fawns-Ritchie; Christian Erikstrup; Dorte Helenius; Drew Altschul; Edda Bjork Thordardottir; Elias Eythorsson; Emma M. Frans; Gunnar Tomasson; Harpa Lind Jonsdottir; Harpa Runarsdottir; Henrik Hjalgrim; Hronn Hardardottir; Juan Gonzalez-Hijon; Karina Banasik; Khoa Manh Dinh; Li Lu; Lili Milani; Lill Trogstad; Maria Didriksen; Omid V. Ebrahimi; Patrick F. Sullivan; Per Minor Magnus; Qing Shen; Ragnar Nesvag; Reedik Magi; Runolfur Palsson; Sisse Rye Ostrowski; Thomas Werge; Asle Hoffart; David J. Porteous; Fang Fang; Johanna Jakobsdottir; Kelli Lehto; Ole A. Andreassen; Ole B.V. Pedersen; Thor Aspelund; Unnur Anna Valdimarsdottir", + "affiliations": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Division of Psychiatry, University of Edinburgh, Edinburgh, UK; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Edinburgh, Edinburgh, UK; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Faculty of Psychology, University of Iceland School of Health Sciences, Reykjavik, Iceland; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Danish Cancer Society Research Center, Copenhagen, Denmark; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA; Centre of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway.; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Clinical Immunology, Zealand University Hospital, Denmark; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland", + "abstract": "BACKGROUNDThe aim of this multinational study was to assess the development of adverse mental health symptoms among individuals diagnosed with COVID-19 in the general population by acute infection severity up to 16 months after diagnosis.\n\nMETHODSParticipants consisted of 247 249 individuals from seven cohorts across six countries (Denmark, Estonia, Iceland, Norway, Scotland, and Sweden) recruited from April 2020 through August 2021. We used multivariable Poisson regression to contrast symptom-prevalence of depression, anxiety, COVID-19 related distress, and poor sleep quality among individuals with and without a diagnosis of COVID-19 at entry to respective cohorts by time (0-16 months) from diagnosis. We also applied generalised estimating equations (GEE) analysis to test differences in repeated measures of mental health symptoms before and after COVID-19 diagnosis among individuals ever diagnosed with COVID-19 over time.\n\nFINDINGSA total of 9979 individuals (4%) were diagnosed with COVID-19 during the study period and presented overall with a higher symptom burden of depression (prevalence ratio [PR] 1{middle dot}18, 95% confidence interval [95% CI] 1{middle dot}03-1{middle dot}36) and poorer sleep quality (1{middle dot}13, 1{middle dot}03-1{middle dot}24) but not with higher levels of symptoms of anxiety or COVID-19 related distress compared with individuals without a COVID-19 diagnosis. While the prevalence of depression and COVID-19 related distress attenuated with time, the trajectories varied significantly by COVID-19 acute infection severity. Individuals diagnosed with COVID-19 but never bedridden due to their illness were consistently at lower risks of depression and anxiety (PR 0{middle dot}83, 95% CI 0{middle dot}75-0{middle dot}91 and 0{middle dot}77, 0{middle dot}63-0{middle dot}94, respectively), while patients bedridden for more than 7 days were persistently at higher risks of symptoms of depression and anxiety (PR 1{middle dot}61, 95% CI 1{middle dot}27-2{middle dot}05 and 1{middle dot}43, 1{middle dot}26-1{middle dot}63, respectively) throughout the 16-month study period.\n\nCONCLUSIONAcute infection severity is a key determinant of long-term mental morbidity among COVID-19 patients.", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 92 + }, { "site": "medRxiv", "doi": "10.1101/2021.12.14.21267460", @@ -3149,6 +3121,20 @@ "author_similarity": 94, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.11.22.21266692", + "date": "2021-11-24", + "link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266692", + "title": "Serological responses to COVID-19 booster vaccine in England", + "authors": "Georgina Ireland; Heather Whitaker; Shamez N Ladhani; Frances Baawuah; Vani Subbarao; Ezra Linley; Lenesha Warrener; Michelle O'Brien; Corrine Whillock; Paul Moss; Mary E Ramsay; Gayatri Amirthalingam; Kevin E Brown", + "affiliations": "UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; Brondesbury Medical Centre, Kilburn, London, United Kingdom; UK Health Security Agency; University of Birmingham; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency", + "abstract": "IntroductionThere are limited data on immune responses after COVID-19 vaccine boosters in individuals receiving primary immunisation with BNT162b2 (Pfizer-BioNTech) or AZD1222 (AstraZeneca).\n\nMethodsA prospective, cohort study to assess SARS-CoV-2 antibody responses before and after booster vaccination with BNT162b2 in adults receiving either (i) two BNT162b2 doses <30 days apart (BNT162b2-control), (ii) two BNT162b2 doses [≥]30 days apart (BNT162b2-extended) or (iii) two AZD1222 doses [≥]30 days apart (AZD1222-extended) in London, England. SARS-CoV-2 spike protein antibody geometric mean titres (GMTs) before and 2-4 weeks after booster were compared.\n\nResultsOf 750 participants, 626 provided serum samples for up to 38 weeks after their second vaccine dose. Antibody GMTs peaked at 2-4 weeks after the second dose, before declining by 68% at 36-38 weeks after dose 2 for BNT162b2-control participants, 85% at 24-29 weeks for BNT162b2-extended participants and 78% at 24-29 weeks for AZD1222-extended participants. Antibody GMTs was highest in BNT162b2-extended participants (942 [95%CI, 797-1113]) than AZD1222-extended (183 [124-268]) participants at 24-29 weeks or BNT162b2-control participants at 36-38 weeks (208; 95%CI, 150-289). At 2-4 weeks after booster, GMTs were significantly higher than after primary vaccination in all three groups: 18,104 (95%CI, 13,911-23,560; n=47) in BNT162b2-control (76.3-fold), 13,980 (11,902-16,421; n=118) in BNT162b2-extended (15.9-fold) and 10,799 (8,510-13,704; n=43) in AZD1222-extended (57.2-fold) participants. BNT162b2-control participants (median:262 days) had a longer interval between primary and booster doses than BNT162b2-extended or AZD1222-extended (both median:186 days) participants.\n\nConclusionsWe observed rapid serological responses to boosting with BNT162b2, irrespective of vaccine type or schedule used for primary immunisation, with higher post-booster responses with longer interval between primary immunisation and boosting. Boosters will not only provide additional protection for those at highest risk of severe COVID-19 but also prevent infection and, therefore, interrupt transmission, thereby reducing infections rates in the population. Ongoing surveillance will be important for monitoring the duration of protection after the booster.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.11.22.21266512", @@ -3275,20 +3261,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.11.08.21265312", - "date": "2021-11-09", - "link": "https://medrxiv.org/cgi/content/short/2021.11.08.21265312", - "title": "Understanding COVID-19 trajectories from a nationwide linked electronic health record cohort of 56 million people: phenotypes, severity, waves & vaccination", - "authors": "Johan H Thygesen; Christopher R Tomlinson; Sam Hollings; Mehrdad A Mizani; Alex Handy; Ashley Akbari; Amitava Banerjee; Jennifer A Cooper; Alvina G Lai; Kezhi Li; Bilal A Mateen; Naveed Sattar; Reecha Sofat; Ana Torralbo; Honghan Wu; Angela Wood; Jonathan AC Sterne; Christina Pagel; William Whiteley; Cathie Sudlow; Harry Hemingway; Spiros Denaxas; - CVD-COVID-UK Consortium", - "affiliations": "Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; NHS Digital, Leeds, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Population Data Science and Health Data Research UK, Swansea University, Swansea, UK; Institute of Health Informatics, University College London, London, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; The Wellcome Trust, London, UK; Institute of Cardiovascular & Medical Sciences, University of Glasgow, Glasgow, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Clinical Operational Research Unit, University College London, London, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK; Institute of Health Informatics, University College London, London, UK; Institute of Health Informatics, University College London, London, UK; ", - "abstract": "BackgroundUpdatable understanding of the onset and progression of individuals COVID-19 trajectories underpins pandemic mitigation efforts. In order to identify and characterize individual trajectories, we defined and validated ten COVID-19 phenotypes from linked electronic health records (EHR) on a nationwide scale using an extensible framework.\n\nMethodsCohort study of 56.6 million people in England alive on 23/01/2020, followed until 31/05/2021, using eight linked national datasets spanning COVID-19 testing, vaccination, primary & secondary care and death registrations data. We defined ten COVID-19 phenotypes reflecting clinically relevant stages of disease severity using a combination of international clinical terminologies (e.g. SNOMED-CT, ICD-10) and bespoke data fields; positive test, primary care diagnosis, hospitalisation, critical care (four phenotypes), and death (three phenotypes). Using these phenotypes, we constructed patient trajectories illustrating the transition frequency and duration between phenotypes. Analyses were stratified by pandemic waves and vaccination status.\n\nFindingsWe identified 3,469,528 infected individuals (6.1%) with 8,825,738 recorded COVID-19 phenotypes. Of these, 364,260 (11%) were hospitalised and 140,908 (4%) died. Of those hospitalised, 38,072 (10%) were admitted to intensive care (ICU), 54,026 (15%) received non-invasive ventilation and 21,404 (6%) invasive ventilation. Amongst hospitalised patients, first wave mortality (30%) was higher than the second (23%) in non-ICU settings, but remained unchanged for ICU patients. The highest mortality was for patients receiving critical care outside of ICU in wave 1 (51%). 13,083 (9%) COVID-19 related deaths occurred without diagnoses on the death certificate, but within 30 days of a positive test while 10,403 (7%) of cases were identified from mortality data alone with no prior phenotypes recorded. We observed longer patient trajectories in the second pandemic wave compared to the first.\n\nInterpretationOur analyses illustrate the wide spectrum of severity that COVID-19 displays and significant differences in incidence, survival and pathways across pandemic waves. We provide an adaptable framework to answer questions of clinical and policy relevance; new variant impact, booster dose efficacy and a way of maximising existing data to understand individuals progression through disease states.\n\nResearch in ContextO_ST_ABSEvidence before the studyC_ST_ABSWe searched PubMed on October 14, 2021, for publications with the terms \"COVID-19\" or \"SARS-CoV-2\", \"severity\", and \"electronic health records\" or \"EHR\" without date or language restrictions. Multiple studies explore factors associated with severity of COVID-19 infection, and model predictions of outcome for hospitalised patients. However, most work to date focused on isolated facets of the healthcare system, such as primary or secondary care only, was conducted in subpopulations (e.g. hospitalised patients) of limited sample size, and often utilized dichotomised outcomes (e.g. mortality or hospitalisation) ignoring the full spectrum of disease. We identified no studies which comprehensively detailed severity of infections while describing disease severity across pandemic waves, vaccination status, and patient trajectories.\n\nAdded value of this studyTo our knowledge, this is the first study providing a comprehensive view of COVID-19 across pandemic waves using national data and focusing on severity, vaccination, and patient trajectories. Drawing on linked electronic health record (EHR) data on a national scale (56.6 million people alive and registered with GP in England), we describe key demographic factors, frequency of comorbidities, impact of the two main waves in England, and effect of full vaccination on COVID-19 severities. Additionally, we identify and describe patient trajectory networks which illustrate the main transition pathways of COVID-19 patients in the healthcare system. Finally, we provide reproducible COVID-19 phenotyping algorithms reflecting clinically relevant stages of disease severity i.e. positive tests, primary care diagnoses, hospitalisation, critical care treatments (e.g. ventilatory support) and mortality.\n\nImplications of all the available evidenceThe COVID-19 phenotypes and trajectory analysis framework outlined produce a reproducible, extensible and repurposable means to generate national-scale data to support critical policy decision making. By modelling patient trajectories as a series of interactions with healthcare systems, and linking these to demographic and outcome data, we provide a means to identify and prioritise care pathways associated with adverse outcomes and highlight healthcare system touch points which may act as tangible targets for intervention.", - "category": "public and global health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.11.05.21265977", @@ -3653,6 +3625,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.09.13.21263487", + "date": "2021-09-16", + "link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263487", + "title": "SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population", + "authors": "Jia Wei; Koen B. Pouwels; Nicole Stoesser; Philippa C. Matthews; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John I Bell; John N Newton; Jeremy Farrar; Alison Howarth; Brian D. Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W. Crook; Tim E.A. Peto; A.Sarah Walker; David W. Eyre", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford", + "abstract": "We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.09.13.21262360", @@ -3751,20 +3737,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.09.03.21263083", - "date": "2021-09-07", - "link": "https://medrxiv.org/cgi/content/short/2021.09.03.21263083", - "title": "Suicide and self-harm in low- and middle- income countries during the COVID-19 pandemic: A systematic review", - "authors": "Duleeka Kniipe; Ann John; Prianka Padmanathan; Emily Eyles; Dana Dekel; Julian Higgins; Jason Bantjes; Rakhi Dandona; Catherine Macleod-Hall; Luke A McGuinness; Lena Schmidt; Roger Webb; David Gunnell", - "affiliations": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; South Asian Clinical Toxicology Research Collaboration, Faculty of Medic; Population Data Science, Swansea University Medical School, Swansea, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; Population Data Science, Swansea University Medical School, Swansea, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; National Institute of Health Research Biomedical Research Centre, Unive; Institute for Life Course Health Research, Department of Global Health, Faculty of medicine and Health Sciences, Stellenbosch University, South Africa.; Public Health Foundation of India, Gurugram, India; Institute for Health Metrics and Evaluation, University of Washington, Seattle, USA; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; Sciome LLC, Research Triangle Park, NC, United States.; Division of Psychology & Mental Health, University of Manchester, Manchester, UK; National Institute of Health Research Greater Manchester Patient Safety Transl; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; National Institute of Health Research Biomedical Research Centre, Unive", - "abstract": "There is widespread concern over the potential impact of the COVID-19 pandemic on suicide and self-harm globally, particularly in low- and middle-income countries (LMIC) where the burden of these behaviours is greatest. We synthesised the evidence from the published literature on the impact of the pandemic on suicide and self-harm in LMIC.\n\nThis review is nested within a living systematic review that continuously identifies published evidence (all languages) through a comprehensive automated search of multiple databases (PubMed; Scopus; medRxiv, PsyArXiv; SocArXiv; bioRxiv; the WHO COVID-19 database; and the COVID-19 Open Research Dataset by Semantic Scholar (up to 11/2020), including data from Microsoft Academic, Elsevier, arXiv and PubMed Central.) All articles identified by the 4th August 2021 were screened. Papers reporting on data from a LMIC and presenting evidence on the impact of the pandemic on suicide or self-harm were included.\n\nA total of 22 studies from LMIC were identified representing data from 12 countries. There was an absence of data from Africa. The reviewed studies mostly report on the early months of COVID-19 and were generally methodologically poor. Few studies directly assessed the impact of the pandemic. The most robust evidence, from time-series studies, indicate either a reduction or no change in suicide and self-harm behaviour.\n\nAs LMIC continue to experience repeated waves of the virus and increased associated mortality, against a backdrop of vaccine inaccessibility and limited welfare support, continued efforts are needed to track the indirect impact of the pandemic on suicide and self-harm in these countries.", - "category": "public and global health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.09.02.21263017", @@ -4045,6 +4017,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.07.20.21260558", + "date": "2021-07-22", + "link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260558", + "title": "Intentions to participate in cervical and colorectal cancer screening during the COVID-19 pandemic: a mixed-methods study", + "authors": "Rebecca Wilson; Harriet Quinn-Scoggins; Yvonne Moriarty; Jacqueline Hughes; Mark Goddard; Rebecca Cannings-John; Victoria Whitelock; Katriina L Whitaker; Detelina Grozeva; Julia Townson; Kirstie Osborne; Stephanie Smits; Michael Robling; Julie Hepburn; Graham Moore; Ardiana Gjini; Kate Brain; Jo Waller", + "affiliations": "Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cancer Research UK; University of Surrey; Cardiff University; Cardiff University; Cancer Research UK; Cardiff University; Cardiff University; Public Involvement Community, Health and Care Research Wales; Cardiff University; Public Health Wales; Cardiff University; Kings College London", + "abstract": "Worldwide, cancer screening faced significant disruption in 2020 due to the COVID-19 pandemic. If this has led to changes in public attitudes towards screening and reduced intention to participate, there is a risk of long-term adverse impact on cancer outcomes. In this study, we examined previous participation and future intentions to take part in cervical and colorectal cancer (CRC) screening following the first national lockdown in the UK.\n\nOverall, 7543 adults were recruited to a cross-sectional online survey in August-September 2020. Logistic regression analyses were used to identify correlates of strong screening intentions among 2,319 participants eligible for cervical screening and 2,502 eligible for home-based CRC screening. Qualitative interviews were conducted with a sub-sample of 30 participants. Verbatim transcripts were analysed thematically.\n\nOf those eligible, 74% of survey participants intended to attend cervical screening and 84% intended to complete home-based CRC screening when next invited. Thirty percent and 19% of the cervical and CRC samples respectively said they were less likely to attend a cancer screening appointment now than before the pandemic. Previous non-participation was the strongest predictor of low intentions for cervical (aOR 26.31, 95% CI: 17.61-39.30) and CRC (aOR 67.68, 95% CI: 33.91-135.06) screening. Interview participants expressed concerns about visiting healthcare settings but were keen to participate when screening programmes resumed.\n\nIntentions to participate in future screening were high and strongly associated with previous engagement in both programmes. As screening services recover, it will be important to monitor participation and to ensure people feel safe to attend.", + "category": "oncology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 98 + }, { "site": "medRxiv", "doi": "10.1101/2021.07.19.21260782", @@ -4241,20 +4227,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.07.07.21253295", - "date": "2021-07-08", - "link": "https://medrxiv.org/cgi/content/short/2021.07.07.21253295", - "title": "Mortality among Care Home Residents in England during the first and second waves of the COVID-19 pandemic: an analysis of 4.3 million adults over the age of 65", - "authors": "Anna Schultze; Emily Nightingale; David Evans; William J Hulme; Alicia Rosello; Chris Bates; Jonathan Cockburn; Brian MacKenna; Helen J Curtis; Caroline E Morton; Richard Croker; Seb Bacon; Helen I McDonald; Christopher T. Rentsch; Krishnan Bhaskaran; Rohini Mathur; Laurie A Tomlinson; Elizabeth J Williamson; Harriet Forbes; John Tazare; Daniel J Grint; Alex J Walker; Peter Inglesby; Nicholas J DeVito; Amir Mehrkar; George Hickman; Simon Davy; Tom Ward; Louis Fisher; Amelia CA Green; Kevin Wing; Angel YS Wong; Robert McManus; John Parry; Frank Hester; Sam Harper; Stephen JW Evans; Ian J Douglas; Liam Smeeth; Rosalind M Eggo; Ben Goldacre; David A Leon", - "affiliations": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT", - "abstract": "BackgroundResidents in care homes have been severely impacted by the COVID-19 pandemic. We describe trends in risk of mortality among care home residents compared to residents in private homes in England.\n\nMethodsOn behalf of NHS England, we used OpenSAFELY-TPP, an analytics platform running across the linked electronic health records of approximately a third of the English population, to calculate monthly age-standardised risks of death due to all causes and COVID-19 among adults aged >=65 years between 1/2/2019 and 31/03/2021. Care home residents were identified using linkage to the Care and Quality Commission.\n\nFindingsWe included 4,329,078 people aged 65 years or older on the 1st of February 2019, 2.2% of whom were classified as residing in a care or nursing home. Age-standardised mortality risks were approximately 10 times higher among care home residents compared to non-residents in February 2019 residents (CMF = 10.59, 95%CI = 9.51, 11.81 among women, CMF = 10.82, 95%CI = 9.89, 11.84 among men). This increased to more than 17 times in April 2020 (CMF = 17.52, 95%CI = 16.38, 18.74 among women, CMF = 18.12, 95%CI = 17.17 - 19.12 among men) before returning to pre-pandemic levels in June 2020. CMFs did not increase during the second wave, despite a rise in the absolute age-standardised COVID-19 mortality risks.\n\nInterpretationThe first COVID-19 wave had a disproportionate impact on care home residents in England compared to older private home residents. A degree of immunity, improved protective measures or changes in the underlying frailty of the populations may explain the lack of an increase in the relative mortality risks during the second wave. The care home population should be prioritised for measures aimed at controlling the spread of COVID-19.\n\nFundingMedical Research Council MR/V015737/1", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.07.07.21260137", @@ -4591,6 +4563,20 @@ "author_similarity": 95, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.06.08.21258533", + "date": "2021-06-12", + "link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258533", + "title": "The impact of co-circulating pathogens on SARS-CoV-2/COVID-19 surveillance. How concurrent epidemics may decrease true SARS-CoV-2 percent positivity.", + "authors": "Aleksandra Kovacevic; Rosalind M Eggo; Marc Baguelin; Matthieu Domenech de Cell\u00e8s; Lulla Opatowski", + "affiliations": "Institut Pasteur; London School of Hygiene & Tropical Medicine; Imperial College London; Max Planck Institute for Infection Biology; Univ Versailles Saint Quentin / Institut Pasteur / Inserm", + "abstract": "BackgroundCirculation of non-SARS-CoV-2 respiratory viruses during the COVID-19 pandemic may alter quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures. Here, we assess the impact of an increased circulation of other respiratory viruses on the monitoring of positivity rates of SARS-CoV-2 and interpretation of surveillance data.\n\nMethodsUsing a multi-pathogen Susceptible-Exposed-Infectious-Recovered (SEIR) transmission model formalizing co-circulation of SARS-CoV-2 and another respiratory we assess how an outbreak of secondary virus may inflate the number of SARS-CoV-2 tests and affect the interpretation of COVID-19 surveillance data. Using simulation, we assess to what extent the use of multiplex PCR tests on a subsample of symptomatic individuals can support correction of the observed SARS-CoV-2 percent positive during other virus outbreaks and improve surveillance quality.\n\nResultsModel simulations demonstrated that a non-SARS-CoV-2 epidemic creates an artificial decrease in the observed percent positivity of SARS-CoV-2, with stronger effect during the growth phase, until the peak is reached. We estimate that performing one multiplex test for every 1,000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percent positive.\n\nConclusionsThis study highlights that co-circulating respiratory viruses can disrupt SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex PCR, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.\n\nSummaryCOVID-19 surveillance indicators may be impacted by increased co-circulation of other respiratory viruses delaying control measure implementation. Continued surveillance through multiplex PCR testing in a subsample of the symptomatic population may play a role in fixing this problem.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.06.08.21258546", @@ -4801,6 +4787,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.05.18.21257267", + "date": "2021-05-18", + "link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257267", + "title": "Colchicine in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", + "authors": "Peter W Horby; Mark Campbell; Enti Spata; Jonathan R Emberson; Natalie Staplin; Guilherme Pessoa-Amorim; Leon Peto; Martin Wiselka; Laura Wiffen; Simon Tiberi; Ben Caplin; Caroline Wroe; Christopher Green; Paul Hine; Benjamin Prudon; Tina George; Andrew Wight; J Kenneth Baillie; Buddha Basnyat; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Faust; Raph L Hamers; Thomas Jaki; Edmund Juszczak; Katie Jeffery; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; Richard Haynes; Martin J Landray", + "affiliations": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and International Severe Acute Res; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and Nuffield Department of Populat; Department of Infectious Diseases, University Hospital Leicester, Leicester, United Kingdom; Portsmouth Hospitals University NHS Foundation Trust, Portsmouth, United Kingdom; Department of Infection, Barts Health NHS Trust, London, United Kingdom; Department of Renal Medicine, University College London, London, United Kingdom and Royal Free London NHS Trust, London, United Kingdom; James Cook University Hospital, Middlesbrough, United Kingdom; University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom; Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom; North Tees and Hartlepool NHS Foundation Trust, Hartlepool, United Kingdom; Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom; Wirral University Teaching Hospital NHS Foundation Trust, Birkenhead, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Oxford University Clinical Research Unit -Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Course Sciences, King?s College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia and Faculty of Medicine, University of Indonesia, Jakarta, Indonesia and Centre for Tropical Medicine ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom and MRC Biostatistics Unit, University of Cambridge, Cambridge, United; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom and Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Notting; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit & Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un", + "abstract": "BackgroundColchicine has been proposed as a treatment for COVID-19 on the basis of its anti-inflammatory actions.\n\nMethodsIn this randomised, controlled, open-label trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care alone or usual standard of care plus colchicine twice daily for 10 days or until discharge (or one of the other treatment arms) using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).\n\nFindingsBetween 27 November 2020 and 4 March 2021, 5610 patients were randomly allocated to receive colchicine and 5730 patients to receive usual care alone. Overall, 1173 (21%) patients allocated to colchicine and 1190 (21%) patients allocated to usual care died within 28 days (rate ratio 1.01; 95% confidence interval [CI] 0.93-1.10; p=0.77). Consistent results were seen in all pre-specified subgroups of patients. There was no significant difference in duration of hospitalisation (median 10 days vs. 10 days) or the proportion of patients discharged from hospital alive within 28 days (70% vs. 70%; rate ratio 0.98; 95% CI 0.94-1.03; p=0.44). Among those not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (25% vs. 25%; risk ratio 1.02; 95% CI 0.96-1.09; p=0.47).\n\nInterpretationIn adults hospitalised with COVID-19, colchicine was not associated with reductions in 28-day mortality, duration of hospital stay, or risk of progressing to invasive mechanical ventilation or death.\n\nFundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056). Wellcome Trust (Grant Ref: 222406/Z/20/Z) through the COVID-19 Therapeutics Accelerator.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.05.17.21256818", @@ -4969,6 +4969,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.05.05.21256668", + "date": "2021-05-09", + "link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256668", + "title": "COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland", + "authors": "Sofia de la Fuente Garcia; Fasih Haider; Saturnino Luz", + "affiliations": "The University of Edinburgh; The University of Edinburgh; The University of Edinburgh", + "abstract": "The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively.\n\nClinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.", + "category": "health informatics", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.05.05.21256649", @@ -5025,6 +5039,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.04.26.21255732", + "date": "2021-04-28", + "link": "https://medrxiv.org/cgi/content/short/2021.04.26.21255732", + "title": "Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales", + "authors": "Sarah Beale; Isobel Braithwaite; Annalan MD Navaratnam; Pia Hardelid; Alison Rodger; Anna Aryee; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative", + "affiliations": "University College London; University College London; University College London; University College London; University College London; Royal Free London NHS Foundation Trust,; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ", + "abstract": "BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation.\n\nMethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period.\n\nResultsRelative to participants in the least deprived areas, participants in the most deprived areas persistently exhibited elevated risk of exposure to vehicle sharing (aRR range across time points 1.73-8.52), public transport (aRR 3.13-5.73), work or education outside of the household (aRR 1.09-1.21), essential shops (aRR 1.09-1.13) and non-household contacts (aRR 1.15-1.19) across multiple survey periods.\n\nConclusionDifferential exposure to essential public activities in deprived communities is likely to contribute to inequalities in infection risk and outcomes during the COVID-19 pandemic. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.04.24.21255968", @@ -5361,20 +5389,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.03.26.21254391", - "date": "2021-03-26", - "link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254391", - "title": "Vaccine effectiveness of the first dose of ChAdOx1 nCoV-19 and BNT162b2 against SARS-CoV-2 infection in residents of Long-Term Care Facilities (VIVALDI study)", - "authors": "Madhumita Shrotri; Maria Krutikov; Tom Palmer; Rebecca Giddings; Borscha Azmi; Sathyavani Subbarao; Christopher Fuller; Aidan Irwin-Singer; Daniel Davies; Gokhan Tut; Jamie Lopez Bernal; Paul Moss; Andrew Hayward; Andrew Copas; Laura Shallcross", - "affiliations": "University College London; University College London; University College London; University College London; University College London; Public Health England; University College London; Department of Health and Social Care, UK; Palantir Technologies UK Ltd; University of Birmingham; Public Health England; University of Birmingham; University College London; University College London; University College London", - "abstract": "BackgroundThe effectiveness of SARS-CoV-2 vaccines in frail older adults living in Long-Term Care Facilities (LTCFs) is uncertain. We estimated protective effects of the first dose of ChAdOx1 and BNT162b2 vaccines against infection in this population.\n\nMethodsCohort study comparing vaccinated and unvaccinated LTCF residents in England, undergoing routine asymptomatic testing (8 December 2020 - 15 March 2021). We estimated the relative hazard of PCR-positive infection using Cox proportional hazards regression, adjusting for age, sex, prior infection, local SARS-CoV-2 incidence, LTCF bed capacity, and clustering by LTCF.\n\nResultsOf 10,412 residents (median age 86 years) from 310 LTCFs, 9,160 were vaccinated with either ChAdOx1 (6,138; 67%) or BNT162b2 (3,022; 33%) vaccines. A total of 670,628 person days and 1,335 PCR-positive infections were included. Adjusted hazard ratios (aHRs) for PCR-positive infection relative to unvaccinated residents declined from 28 days following the first vaccine dose to 0{middle dot}44 (0{middle dot}24, 0{middle dot}81) at 28-34 days and 0{middle dot}38 (0{middle dot}19, 0{middle dot}77) at 35-48 days. Similar effect sizes were seen for ChAdOx1 (aHR 0{middle dot}32 [0{middle dot}15-0{middle dot}66] and BNT162b2 (aHR 0{middle dot}35 [0{middle dot}17, 0{middle dot}71]) vaccines at 35-48 days. Mean PCR cycle threshold values were higher, implying lower infectivity, for infections [≥]28 days post-vaccination compared with those prior to vaccination (31{middle dot}3 vs 26{middle dot}6, p<0{middle dot}001).\n\nInterpretationThe first dose of BNT162b2 and ChAdOx1 vaccines was associated with substantially reduced SARS-CoV-2 infection risk in LTCF residents from 4 weeks to at least 7 weeks.\n\nFundingUK Government Department of Health and Social Care.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe conducted a systematic search for studies which evaluated SARS-CoV-2 vaccine effectiveness in residents of long-term care facilities (LTCFs) published between 01/01/2020 and 11/03/2021. We used variations of search terms for \"COVID-19\" AND \"vaccine effectiveness\" OR \"vaccine efficacy\" AND \"care homes\" OR \"long term care facilities\" OR \"older people\" on Ovid MEDLINE and MedRxiv. We identified one pre-print article regarding LTCFs in Denmark, which reported that a single dose of BNT162b was ineffective against SARS-CoV-2 infection in residents, however, participants received the second vaccine dose 24 days following the first dose on average, which is likely to be too soon to capture the protective effects of a single vaccine dose. Additionally, we identified two pre-print reports of studies evaluating vaccine effectiveness against symptomatic infection and hospitalisation amongst older adults in the community. The first of these found 81% vaccine effectiveness against COVID-19-related hospitalisation at 28-34 days following a single dose of BNT162b or ChAdOx1 in [≥]80-year-olds. The second of these found vaccine effectiveness against symptomatic infection of 60% at 28-34 days and 73% at 35+ days following a single dose of ChAdOx1 in [≥]70-year-olds. No studies were identified that focused on the effectiveness of a single vaccine dose against infection amongst LTCF residents at more than 4 weeks post-vaccination, a particularly important question in the context of the UK policy decision to extend the dose interval beyond 3 weeks.\n\nAdded value of this studyWe conducted a prospective cohort study of 10,412 residents aged [≥]65 years, from 310 LTCFs across England, to investigate the protective effect of the first dose of the ChAdOx1 and BNT162b vaccines against SARS-CoV-2 infection in frail older adults. We retrieved results from routine monthly PCR testing, as well as outbreak and clinical testing for SARS-CoV-2, thereby capturing data on asymptomatic as well as symptomatic infections, which we linked to vaccination records. We estimated vaccine effectiveness to be 56% (19-76%) at 28-34 days, and 62% (23-81%) at 35-48 days following a single dose of ChAdOx1 or BNT162. Our findings suggest that the risk of SARS-CoV-2 infection is substantially reduced from 28 days following the first dose of either vaccine and that this effect is maintained for at least 7 weeks, with similar protection offered by both vaccine types. We also found that PCR cycle threshold (Ct) values, which are negatively associated with the ability to isolate virus, were significantly higher in infections occurring at [≥] 28days post vaccination compared to those occurring in the unvaccinated period, suggesting that vaccination may reduce onward transmission of SARS-CoV-2 in breakthrough infections. To the best of our knowledge, our findings constitute the first real-world evidence on vaccine effectiveness against infection for ChAdOx1, in any age group. We can also infer that both vaccines are effective against the B.1.1.7 variant, because our analysis period coincided with the rapid emergence of B.1.1.7 in England during the second wave of the pandemic.\n\nImplications of all the available evidenceOur findings add to the growing body of evidence on the protective effect of the BNT162b vaccines in residents of LTCFs and demonstrate the effectiveness of ChAdOx1 in this vulnerable population. Evaluating single-dose vaccine efficacy has become increasingly important in light of extended dosing intervals that have been implemented in order to maximise vaccine coverage across high-risk groups. Further work is required to evaluate the effectiveness of the first vaccine dose after 8-12 weeks, as well as following the second dose, and to evaluate the long-term impact of vaccination on SARS-CoV-2 infection, transmission and mortality in LTCFs. This will inform policy decisions regarding the ongoing need for disease control measures in LTCF such as visitor restrictions, which continue to have a detrimental impact on the wellbeing of residents, their relatives, and staff.\n\nSupplementary material attached.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.03.22.21254057", @@ -5445,20 +5459,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.03.18.21253888", - "date": "2021-03-23", - "link": "https://medrxiv.org/cgi/content/short/2021.03.18.21253888", - "title": "Long Covid in adults discharged from UK hospitals after Covid-19: A prospective, multicentre cohort study using the ISARIC WHO Clinical Characterisation Protocol.", - "authors": "Louise Sigfrid; Tom M Drake; Ellen Pauley; Edwin C Jesudason; Piero Olliaro; Wei Shen Lim; Annelise Gillesen; Colin Berry; David Lowe; Joanne McPeake; Nazir Lone; Muge Cevik; Daniel Munblit; Anna Casey; Peter Bannister; Clark D Russell; Lynsey Goodwin; Antonia Ho; Lance Turtle; Margret E O'Hara; Claire Hastie; Chloe Donohue; Rebecca Spencer; Cara Donegan; Alison Gummery; Janet Harrison; Hayley Hardwick; Claire E Hastie; Gail Carson; Laura Merson; John Kenneth Baillie; Peter Openshaw; Ewen M Harrison; Annemarie Docherty; Malcolm G Semple; Janet T Scott", - "affiliations": "ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK; Centre for Medical Informatics, University of Edinburgh, Edinburgh, UK; University of Edinburgh Medical School, Edinburgh, UK.; NHS Lothian, Edinburgh, UK,; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, UK.; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK; NHS Greater Glasgow and Clyde, Emergency Department, Glasgow, UK; School of Medicine, Dentistry and Nursing, University of Glasgow, UK; Usher Institute, University of Edinburgh, Edinburgh, UK; University of St Andrews; Sechenov First Moscow State Medical University, Imperial College London, Imperial College London, RSMU; Medical Student, Brighton and Sussex Medical School, UK; Brighton & Sussex Medical School, Brighton, UK; Centre for Inflammation Research, University of Edinburgh, UK; Institute of Infection, Veterinary and Ecological Studies, Univeristy of Liverpool. Tropical and Infectious Diseases Unit, North Manchester General Hospital, De; University of Glasgow, Glasgow, UK; NIHR Health Protection Research Unit in emerging and zoonotic infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L; Long COVID Support, Birmingham, UK; Long COVID Support, Birmingham, UK; Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK; Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK.; Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK.; Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK.; National Institute of Health Research (NIHR) Health Protection research Unit in Emerging and Zoonotic Infections, Liverpool, UK. 2. Institute of Infection and G; National Institute of Health Research (NIHR) Health Protection research Unit in Emerging and Zoonotic Infections, Liverpool, UK. 2. Institute of Infection and G; Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK.; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK; Roslin Institute, University of Edinburgh, Edinburgh, UK; National Heart and Lung Institute, Imperial College, London UK.; Director Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK.; Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK. 2. Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK; Health Protection Research Unit In Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK 2. ; MRC-University of Glasgow Center for Virus research", - "abstract": "Structured AbstractO_ST_ABSObjectivesC_ST_ABSThe long-term consequences of severe Covid-19 requiring hospital admission are not well characterised. The objective of this study was to establish the long-term effects of Covid-19 following hospitalisation and the impact these may have on patient reported outcome measures.\n\nDesignA multicentre, prospective cohort study with at least 3 months follow-up of participants admitted to hospital between 5th February 2020 and 5th October 2020.\n\nSetting31 hospitals in the United Kingdom.\n\nParticipants327 hospitalised participants discharged alive from hospital with confirmed/high likelihood SARS-CoV-2 infection.\n\nMain outcome measures and comparisonsThe primary outcome was self-reported recovery at least ninety days after initial Covid-19 symptom onset. Secondary outcomes included new symptoms, new or increased disability (Washington group short scale), breathlessness (MRC Dyspnoea scale) and quality of life (EQ5D-5L). We compared these outcome measures across age, comorbidity status and in-hospital Covid-19 severity to identify groups at highest risk of developing long-term difficulties. Multilevel logistic and linear regression models were built to adjust for the effects of patient and centre level risk factors on these outcomes.\n\nResultsIn total 53.7% (443/824) contacted participants responded, yielding 73.8% (327/443) responses with follow-up of 90 days or more from symptom onset. The median time between symptom onset of initial illness and completing the participant questionnaire was 222 days (Interquartile range (IQR) 189 to 269 days). In total, 54.7% (179/327) of participants reported they did not feel fully recovered. Persistent symptoms were reported by 93.3% (305/325) of participants, with fatigue the most common (82.8%, 255/308), followed by breathlessness (53.5%, 175/327). 46.8% (153/327) reported an increase in MRC dyspnoea scale of at least one grade. New or worse disability was reported by 24.2% (79/327) of participants. Overall (EQ5D-5L) summary index was significantly worse at the time of follow-up (median difference 0.1 points on a scale of 0 to 1, IQR: -0.2 to 0.0). Females under the age of 50 years were five times less likely to report feeling recovered (adjusted OR 5.09, 95% CI 1.64 to 15.74), were more likely to have greater disability (adjusted OR 4.22, 95% CI 1.12 to 15.94), twice as likely to report worse fatigue (adjusted OR 2.06, 95% CI 0.81 to 3.31) and seven times more likely to become more breathless (adjusted OR 7.15, 95% CI 2.24 to 22.83) than men of the same age.\n\nConclusionsSurvivors of Covid-19 experienced long-term symptoms, new disability, increased breathlessness, and reduced quality of life. These findings were present even in young, previously healthy working age adults, and were most common in younger females. Policymakers should fund further research to identify effective treatments for long-Covid and ensure healthcare, social care and welfare support is available for individuals with long-Covid.\n\nSection 1: What is already known on this topicO_LILong-term symptoms after hospitalisation for Covid-19 have been reported, but it is not clear what impact this has on quality of life.\nC_LIO_LIIt is not known which patient groups are most likely to have long-term persistent symptoms following hospitalisation for Covid-19, or if this differs by disease severity.\nC_LI\n\nSection 2: What this study addsO_LIMore than half of patients reported not being fully recovered 7 months after onset of Covid-19 symptoms.\nC_LIO_LIPreviously healthy participants and those under the age of 50 had higher odds of worse long-term outcomes compared to older participants and those with comorbidities.\nC_LIO_LIYounger women and those with more severe acute disease in-hospital had the worst long-term outcomes.\nC_LIO_LIPolicy makers need to ensure there is long-term support for people experiencing long-Covid and should plan for lasting long-term population morbidity. Funding for research to understand mechanisms underlying long-Covid and identify potential interventions for testing in randomised trials is urgently required.\nC_LI", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.03.20.21254010", @@ -5571,6 +5571,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.12.21253484", + "date": "2021-03-13", + "link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253484", + "title": "Limits of lockdown: characterising essential contacts during strict physical distancing", + "authors": "Amy C Thomas; Leon Danon; Hannah Christensen; Kate Northstone; Daniel Smith; Emily J Nixon; Adam Trickey; Gibran Hemani; Sarah Sauchelli; Adam Finn; Nicholas J Timpson; Ellen Brooks-Pollock", + "affiliations": "University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; NIHR Bristol Biomedical Research Centre, University of Bristol; University of Bristol; University of Bristol; University of Bristol", + "abstract": "COVID-19 has exposed health inequalities within countries and globally. The fundamental determining factor behind an individuals risk of infection is the number of social contacts they make. In many countries, physical distancing measures have been implemented to control transmission of SARS-CoV-2, reducing social contacts to a minimum. Characterising unavoidable social contacts is key for understanding the inequalities behind differential risks and planning vaccination programmes. We utilised an existing English longitudinal birth cohort, which is broadly representative of the wider population (n=6807), to explore social contact patterns and behaviours when strict physical distancing measures were in place during the UKs first lockdown in March-May 2020. Essential workers, specifically those in healthcare, had 4.5 times as many contacts as non-essential workers [incident rate ratio = 4.42 (CI95%: 3.88-5.04)], whilst essential workers in other sectors, mainly teaching and the police force had three times as many contacts [IRR = 2.84 (2.58-3.13)]. The number of individuals in a household, which is conflated by number of children, increases essential social contacts by 40%. Self-isolation effectively reduces numbers of contacts outside of the home, but not entirely. Together, these findings will aid the interpretation of epidemiological data and impact the design of effective SARS-CoV-2 control strategies, such as vaccination, testing and contact tracing.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.10.21253173", @@ -5949,20 +5963,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.02.10.21251480", - "date": "2021-02-12", - "link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251480", - "title": "Symptom reporting in over 1 million people: community detection of COVID-19", - "authors": "Joshua Elliott; Matthew Whitaker; Barbara Bodinier; Steven Riley; Helen Ward; Graham Cooke; Ara Darzi; Marc Chadeau-Hyam; Paul Elliott", - "affiliations": "Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College; Imperial College London; Imperial College London; Imperial College London", - "abstract": "", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 96, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.02.11.21251587", @@ -6063,14 +6063,14 @@ }, { "site": "medRxiv", - "doi": "10.1101/2021.02.03.21251004", + "doi": "10.1101/2021.02.02.21251043", "date": "2021-02-05", - "link": "https://medrxiv.org/cgi/content/short/2021.02.03.21251004", - "title": "Ethnic differences in COVID-19 mortality during the first two waves of the Coronavirus Pandemic: a nationwide cohort study of 29 million adults in England", - "authors": "Vahe Nafilyan; Nazrul Islam; Rohini Mathur; Daniel Ayoubkhani; Amitava Banerjee; Myer Glickman; Ben Humberstone; Ian DIamond; Kamlesh Khunti", - "affiliations": "Office for National Statistics; Nuffield Department of Population Health, Big Data Institute, University of Oxford; London School of Hygiene and Tropical Medicine; Office for National Statistics; University College London; Office for National Statistics; Office for National Statistics; Office for National Statistics; Diabetes Research Centre, University of Leicester", - "abstract": "BackgroundEthnic minorities have experienced disproportionate COVID-19 mortality rates in the UK and many other countries. We compared the differences in the risk of COVID-19 related death between ethnic groups in the first and second waves the of COVID-19 pandemic in England. We also investigated whether the factors explaining differences in COVID-19 death between ethnic groups changed between the two waves.\n\nMethodsUsing data from the Office for National Statistics Public Health Data Asset on individuals aged 30-100 years living in private households, we conducted an observational cohort study to examine differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and second wave (from 1st September to 28th December 2020). We estimated age-standardised mortality rates (ASMR) in the two waves stratified by ethnic groups and sex. We also estimated hazard ratios (HRs) for ethnic-minority groups compared with the White British population, adjusted for geographical factors, socio-demographic characteristics, and pre-pandemic health conditions.\n\nResultsThe study population included over 28.9 million individuals aged 30-100 years living in private households. In the first wave, all ethnic minority groups had a higher risk of COVID-19 related death compared to the White British population. In the second wave, the risk of COVID-19 death remained elevated for people from Pakistani (ASMR: 339.9 [95% CI: 303.7 - 376.2] and 166.8 [141.7 - 191.9] deaths per 100,000 population in men and women) and Bangladeshi (318.7 [247.4 - 390.1] and 127.1 [91.1 - 171.3] in men and women)background but not for people from Black ethnic groups. Adjustment for geographical factors explained a large proportion of the differences in COVID-19 mortality in the first wave but not in the second wave. Despite an attenuation of the elevated risk of COVID-19 mortality after adjusting for sociodemographic characteristics and health status, the risk was substantially higher in people from Bangladeshi and Pakistani background in both the first and the second waves.\n\nConclusionBetween the first and second waves of the pandemic, the reduction in the difference in COVID-19 mortality between people from Black ethnic background and people from the White British group shows that ethnic inequalities in COVID-19 mortality can be addressed. The continued higher rate of mortality in people from Bangladeshi and Pakistani background is alarming and requires focused public health campaign and policy changes.\n\n*VN and NI contributed equally to this paper\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSA recent systematic review by Pan and colleagues demonstrated that people of ethnic minority background in the UK and the USA have been disproportionately affected by the Coronavirus (COVID-19) pandemic, compared to White populations. While several studies have investigated whether adjusting for socio-demographic and economic factors and medical history reduces the estimated difference in risk of mortality and hospitalisation, the reasons for the differences in the risk of experiencing harms from COVID-19 are still being explored during the course of the pandemic. Studies so far have analysed the ethnic differences in COVID-19 mortality in the first wave of the pandemic. The evidence on the temporal trend of ethnic inequalities in COVID-19 mortality, especially those from the second wave of the pandemic, is scarce.\n\nAdded value of this studyUsing data from the Office for National Statistics (ONS) Public Health Data Asset on 29 million adults aged 30-100 years living in private households in England, we conducted an observational cohort study to examine the differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and second wave (from 1st September to 28th December 2020). We find that in the first wave all ethnic minority groups were at elevated risk of COVID-19 related death compared to the White British population. In the second wave, the differences in the risk of COVID-19 related death attenuated for Black African and Black Caribbean groups, remained substantially higher in people from Bangladeshi background, and worsened in people from Pakistani background. We also find that some of the factors explaining these differences in mortality have changed in the two waves.\n\nImplications of all the available evidenceThe risk of COVID-19 mortality during the first wave of the pandemic was elevated in people from ethnic minority background. An appreciable reduction in the difference in COVID-19 mortality in the second wave of the pandemic between people from Black ethnic background and people from the White British group is reassuring, but the continued higher rate of mortality in people from Bangladeshi and Pakistani background is alarming and requires focused public health campaign and policy response. Focusing on treating underlying conditions, although important, may not be enough in reducing the inequalities in COVID-19 mortality. Focused public health policy as well as community mobilisation and participatory public health campaign involving community leaders may help reduce the existing and widening inequalities in COVID-19 mortality.", - "category": "epidemiology", + "link": "https://medrxiv.org/cgi/content/short/2021.02.02.21251043", + "title": "COVID-19 infection and subsequent thromboembolism: A self-controlled case series analysis of a population cohort", + "authors": "Frederick Ho; Kenneth Man; Mark Toshner; Colin Church; Carlos Celis-Morales; Ian Wong; Colin Berry; Naveed Sattar; Jill Pell", + "affiliations": "University of Glasgow; UCL; University of Cambridge; NHS Greater Glasgow and Clyde; University of Glasgow; UCL; University of Glasgow; University of Glasgow; University of Glasgow", + "abstract": "ObjectiveAn unexpectedly large number of people infected with Covid-19 had experienced a thrombotic event. This study aims to assess the associations between Covid-19 infection and thromboembolism including myocardial infarction (MI), ischaemic stroke, deep-vein thrombosis (DVT), and pulmonary embolism (PE).\n\nPatients and MethodsA self-controlled case-series study was conducted covering the whole of Scotlands general population. The study population comprised individuals with confirmed (positive test) Covid-19 and at least one thromboembolic event between March 2018 and October 2020. Their incidence rates during the risk interval (5 days before to 56 days after the positive test) and the control interval (the remaining periods) were compared intra-personally.\n\nResultsAcross Scotland, 1,449 individuals tested positive for Covid-19 and experienced a thromboembolic event. The risk of thromboembolism was significantly elevated over the whole risk period but highest in the 7 days following the positive test (IRR 12.01, 95% CI 9.91-14.56) in all included individuals. The association was also present in individuals not originally hospitalised for Covid-19 (IRR 4.07, 95% CI 2.83-5.85). Risk of MI, stroke, PE and DVT were all significantly higher in the week following a positive test. The risk of PE and DVT was particularly high and remained significantly elevated even 56 days following the test.\n\nConclusionConfirmed Covid-19 infection was associated with early elevations in risk with MI, ischaemic stroke, and substantially stronger and prolonged elevations with DVT and PE both in hospital and community settings. Clinicians should consider thromboembolism, especially PE, among people with Covid-19 in the community.", + "category": "cardiovascular medicine", "match_type": "fuzzy", "author_similarity": 100, "affiliation_similarity": 100 @@ -6145,20 +6145,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.01.25.21249942", - "date": "2021-01-30", - "link": "https://medrxiv.org/cgi/content/short/2021.01.25.21249942", - "title": "Development and external validation of prognostic models for COVID-19 to support risk stratification in secondary care", - "authors": "Nicola J Adderley; Thomas Taverner; Malcolm Price; Christopher Sainsbury; David Greenwood; Joht Singh Chandan; Yemisi Takwoingi; Rashan Haniffa; Isaac Hosier; Carly Welch; Dhruv Parekh; Suzy Gallier; Krishna M Gokhale; Alastair K Denniston; Elizabeth Sapey; Krishnarajah Nirantharakumar", - "affiliations": "University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Oxford; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham", - "abstract": "ObjectivesExisting UK prognostic models for patients admitted to hospital with COVID-19 are limited by reliance on comorbidities, which are under-recorded in secondary care, and lack of imaging data among the candidate predictors. Our aims were to develop and externally validate novel prognostic models for adverse outcomes (death, intensive therapy unit (ITU) admission) in UK secondary care; and externally validate the existing 4C score.\n\nDesignCandidate predictors included demographic variables, symptoms, physiological measures, imaging, laboratory tests. Final models used logistic regression with stepwise selection.\n\nSettingModel development was performed in data from University Hospitals Birmingham (UHB). External validation was performed in the CovidCollab dataset.\n\nParticipantsPatients with COVID-19 admitted to UHB January-August 2020 were included.\n\nMain outcome measuresDeath and ITU admission within 28 days of admission.\n\nResults1040 patients with COVID-19 were included in the derivation cohort; 288 (28%) died and 183 (18%) were admitted to ITU within 28 days of admission. Area under the receiver operating curve (AUROC) for mortality was 0.791 (95%CI 0.761-0.822) in UHB and 0.767 (95%CI 0.754-0.780) in CovidCollab; AUROC for ITU admission was 0.906 (95%CI 0.883-0.929) in UHB and 0.811 (95%CI 0.795-0.828) in CovidCollab. Models showed good calibration. Addition of comorbidities to candidate predictors did not improve model performance. AUROC for the 4C score in the UHB dataset was 0.754 (95%CI 0.721-0.786).\n\nConclusionsThe novel prognostic models showed good discrimination and calibration in derivation and external validation datasets, and outperformed the existing 4C score. The models can be integrated into electronic medical records systems to calculate each individual patients probability of death or ITU admission at the time of hospital admission. Implementation of the models and clinical utility should be evaluated.\n\nArticle SummaryO_ST_ABSStrengths and limitations of this studyC_ST_ABSO_LIWe developed novel prognostic models predicting mortality and ITU admission within 28 days of admission for patients hospitalised with COVID-19, using a large routinely collected dataset gathered at admission with a wide range of possible predictors (demographic variables, symptoms, physiological measures, imaging, laboratory test results).\nC_LIO_LIThese novel models showed good discrimination and calibration in both derivation and external validation cohorts, and outperformed the existing ISARIC model and 4C score in the derivation dataset. We found that addition of comorbidities to the set of candidate predictors included in model derivation did not improve model performance.\nC_LIO_LIIf integrated into hospital electronic medical records systems, the model algorithms will provide a predicted probability of mortality or ITU admission for each patient based on their individual data at, or close to, the time of admission, which will support clinicians decision making with regard to appropriate patient care pathways and triage. This information might also assist clinicians in explaining complex prognostic assessments and decisions to patients and their relatives.\nC_LIO_LIA limitation of the study was that in the external validation cohort we were unable to examine all of the predictors included in the original full UHB model due to only a reduced set of candidate predictors being available in CovidCollab. Nevertheless, the reduced model performed well and the results suggest it may be applicable in a wide range of datasets where only a reduced set of predictor variables is available.\nC_LIO_LIFurthermore, it was not possible to carry out stratified analysis by ethnicity as the UHB dataset contained too few patients in most of the strata, and no ethnicity data was available in the CovidCollab dataset.\nC_LI", - "category": "public and global health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.01.28.21250680", @@ -6243,6 +6229,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "bioRxiv", + "doi": "10.1101/2021.01.25.428136", + "date": "2021-01-25", + "link": "https://biorxiv.org/cgi/content/short/2021.01.25.428136", + "title": "mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge", + "authors": "Michelle Meyer; Yuan Wang; Darin Edwards; Gregory R Smith; Aliza B Rubenstein; Palaniappan Ramanathan; Chad E Mire; Colette Pietzsch; Xi Chen; Yongchao Ge; Wan Sze Cheng; Carole Henry; Angela Woods; LingZhi Ma; Guillaume B. E. Stewart-Jones; Kevin W Bock; Minai Mahnaz; Bianca M Nagata; Sivakumar Periasamy; Pei-Yong Shi; Barney S Graham; Ian N Moore; Irene Ramos; Olga G. Troyanskaya; Elena Zaslavsky; Andrea Carfi; Stuart C Sealfon; Alexander Bukreyev", + "affiliations": "University of Texas Medical Branch; Princeton University; Moderna Inc; Icahn School of Medicine at Mount Sinai; Icahn School of Medicine at Mount Sinai; University of Texas Medical Branch; University of Texas Medical Branch; University of Texas Medical Branch; Flatiron Institute, Simons Foundation; Icahn School of Medicine at Mount Sinai; Icahn School of Medicine at Mount Sinai; Moderna Inc; Moderna Inc; Moderna Inc; Moderna Inc; National Institute of Health; National Institutes of Health; National Institutes of Health; University of Texas Medical Branch; University of Texas Medical Branch; National Institutes of Health; National Institutes of Health; Icahn School of Medicine at Mount Sinai; Princeton University; Icahn School of Medicine at Mount Sinai; Moderna Inc; Icahn School of Medicine at Mount Sinai; University of Texas Medical Branch at Galveston", + "abstract": "The mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase 3 results. Human studies, however, cannot provide the controlled response to infection and complex immunological insight that are only possible with preclinical studies. Hamsters are the only model that reliably exhibit more severe SARS-CoV-2 disease similar to hospitalized patients, making them pertinent for vaccine evaluation. We demonstrate that prime or prime-boost administration of mRNA-1273 in hamsters elicited robust neutralizing antibodies, ameliorated weight loss, suppressed SARS-CoV-2 replication in the airways, and better protected against disease at the highest prime-boost dose. Unlike in mice and non-human primates, mRNA-1273- mediated immunity was non-sterilizing and coincided with an anamnestic response. Single-cell RNA sequencing of lung tissue permitted high resolution analysis which is not possible in vaccinated humans. mRNA-1273 prevented inflammatory cell infiltration and the reduction of lymphocyte proportions, but enabled antiviral responses conducive to lung homeostasis. Surprisingly, infection triggered transcriptome programs in some types of immune cells from vaccinated hamsters that were shared, albeit attenuated, with mock-vaccinated hamsters. Our results support the use of mRNA-1273 in a two-dose schedule and provides insight into the potential responses within the lungs of vaccinated humans who are exposed to SARS-CoV-2.", + "category": "immunology", + "match_type": "fuzzy", + "author_similarity": 96, + "affiliation_similarity": 94 + }, { "site": "medRxiv", "doi": "10.1101/2021.01.21.20240887", @@ -6593,20 +6593,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.12.11.20247742", - "date": "2020-12-14", - "link": "https://medrxiv.org/cgi/content/short/2020.12.11.20247742", - "title": "Changes in cardiovascular disease monitoring in English primary care during the COVID-19 pandemic: an observational cohort study", - "authors": "Clare R Bankhead; Sarah Lay-Flurrie; Brian D Nicholson; James P Sheppard; Chris P Gale; Harshana Liyanage; Dylan McGagh; Mark Minchin; Rafael Perera; Julian Sherlock; Margaret Smith; Nicholas PB Thomas; Cynthia Wright Drakesmith; Simon D de Lusignan; Richard Hobbs", - "affiliations": "University of Oxford; University of Oxford; Nuffield Department of Primary Care Health Sciences; University of Oxford; University of Leeds; University of Oxford; University of Oxford; National Institute for Health and Care Excellence; University of Oxford; University of Oxford; University of Oxford; Royal College of General Practitioners; University of Oxford; University of Oxford; University of Oxford", - "abstract": "ObjectiveTo quantify the impact and recovery in cardiovascular disease monitoring in primary care associated with the first COVID-19 lockdown.\n\nDesignRetrospective nationwide primary care cohort study, utilising data from 1st January 2018 to 27th September 2020.\n\nSettingWe extracted primary care electronic health records data from 514 primary care practices in England contributing to the Oxford Royal College of General Practitioners Clinical Informatics Digital Hub (ORCHID). These practices were representative of English primary care across urban and non-urban practices.\n\nParticipantsThe ORCHID database included 6,157,327 active patients during the study period, and 13,938,390 patient years of observation (final date of follow-up 27th September 2020). The mean (SD) age was 38{+/-}24 years, 49.4% were male and the majority were of white ethnicity (65% [21.9% had unknown ethnicity])\n\nExposureThe primary exposure was the first national lockdown in the UK, starting on 23rd March 2020.\n\nMain outcome measuresRecords of cholesterol, blood pressure, HbA1c and International Normalised Ratio (INR) measurement derived from coded entries in the primary care electronic health record.\n\nResultsRates of cholesterol, blood pressure, HbA1c and INR recording dropped by 23-87% in the week following the first UK national lockdown, compared with the previous week. The largest decline was seen in cholesterol (IRR 0.13, 95% CI 0.11 to 0.15) and smallest for INR (IRR 0.77, 95% CI 0.72 to 0.81).\n\nFollowing the immediate drop, rates of recorded tests increased on average by 5-9% per week until 27th September 2020. However, the number of recorded measures remained below that expected for the time of year, reaching 51.8% (95% CI 51.8 to 51.9%) for blood pressure, 63.7%, (95% CI 63.7% to 63.8%) for cholesterol measurement and 70.3% (95% CI 70.2% to 70.4%) for HbA1c. Rates of INR recording declined throughout the previous two years, a trend that continued after lockdown. There were no differences in the times series trends based on sex, age, ethnicity or deprivation.\n\nConclusionsCardiovascular disease monitoring in English primary care declined substantially from the time of the first UK lockdown. Despite a consistent recovery in activity, there is still a substantial shortfall in the numbers of recorded measurements to those expected. Strategies are required to ensure cardiovascular disease monitoring is maintained during the COVID-19 pandemic.", - "category": "primary care research", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.12.10.20247155", @@ -6817,6 +6803,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.11.19.20234849", + "date": "2020-11-22", + "link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234849", + "title": "Community factors and excess mortality in first wave of the COVID-19 pandemic.", + "authors": "Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott", + "affiliations": "Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London", + "abstract": "Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.18.20233932", @@ -6847,13 +6847,13 @@ }, { "site": "medRxiv", - "doi": "10.1101/2020.11.18.20234369", - "date": "2020-11-19", - "link": "https://medrxiv.org/cgi/content/short/2020.11.18.20234369", - "title": "Antibodies to SARS-CoV-2 are associated with protection against reinfection", - "authors": "Sheila F Lumley; Nicole E Stoesser; Philippa C Matthews; Alison Howarth; Stephanie B Hatch; Brian D Marsden; Stuart Cox; Tim James; Fiona Warren; Liam J Peck; Thomas G Ritter; Zoe de Toledo; Laura Warren; David Axten; Richard J Cornall; E Yvonne Jones; David I Stuart; Gavin Screaton; Daniel Ebner; Sarah Hoosdally; Meera Chand; - Oxford University Hospitals Staff Testing Group; Derrick W Crook; Christopher P Conlon; Koen B Pouwels; A Sarah Walker; Tim EA Peto; Susan Hopkins; Tim M Walker; Katie Jeffery; David W Eyre", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; Oxford University Hospitals; Oxford University Hospitals; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; Oxford University Hospitals; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Public Health England; ; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Public Health England; University of Oxford; University of Oxford; University of Oxford", - "abstract": "BackgroundIt is critical to understand whether infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) protects from subsequent reinfection.\n\nMethodsWe investigated the incidence of SARS-CoV-2 PCR-positive results in seropositive and seronegative healthcare workers (HCWs) attending asymptomatic and symptomatic staff testing at Oxford University Hospitals, UK. Baseline antibody status was determined using anti-spike and/or anti-nucleocapsid IgG assays and staff followed for up to 30 weeks. We used Poisson regression to estimate the relative incidence of PCR-positive results and new symptomatic infection by antibody status, accounting for age, gender and changes in incidence over time.\n\nResultsA total of 12219 HCWs participated and had anti-spike IgG measured, 11052 were followed up after negative and 1246 after positive antibody results including 79 who seroconverted during follow up. 89 PCR-confirmed symptomatic infections occurred in seronegative individuals (0.46 cases per 10,000 days at risk) and no symptomatic infections in those with anti-spike antibodies. Additionally, 76 (0.40/10,000 days at risk) anti-spike IgG seronegative individuals had PCR-positive tests in asymptomatic screening, compared to 3 (0.21/10,000 days at risk) seropositive individuals. Overall, positive baseline anti-spike antibodies were associated with lower rates of PCR-positivity (with or without symptoms) (adjusted rate ratio 0.24 [95%CI 0.08-0.76, p=0.015]). Rate ratios were similar using anti-nucleocapsid IgG alone or combined with anti-spike IgG to determine baseline status.\n\nConclusionsPrior SARS-CoV-2 infection that generated antibody responses offered protection from reinfection for most people in the six months following infection. Further work is required to determine the long-term duration and correlates of post-infection immunity.", + "doi": "10.1101/2020.11.18.20225029", + "date": "2020-11-20", + "link": "https://medrxiv.org/cgi/content/short/2020.11.18.20225029", + "title": "The Invasive Respiratory Infection Surveillance (IRIS) Initiative reveals significant reductions in invasive bacterial infections during the COVID-19 pandemic", + "authors": "Angela B Brueggemann; Melissa J Jansen van Rensburg; David Shaw; Noel D McCarthy; Keith A Jolley; Martin CJ Maiden; Mark PG van der Linden", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Warwick; University of Oxford; University of Oxford; University Hospital RWTH Aachen", + "abstract": "BackgroundStreptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis are leading causes of invasive diseases including bacteraemic pneumonia and meningitis, and of secondary infections post-viral respiratory disease. They are typically transmitted via respiratory droplets. We investigated rates of invasive disease due to these pathogens during the early phase of the COVID-19 pandemic.\n\nMethodsLaboratories in 26 countries across six continents submitted data on cases of invasive disease due to S pneumoniae, H influenzae and N meningitidis from 1 January 2018 to 31 May 2020. Weekly cases in 2020 vs 2018-2019 were compared. Streptococcus agalactiae data were collected from nine laboratories for comparison to a non-respiratory pathogen. The stringency of COVID-19 containment measures was quantified by the Oxford COVID-19 Government Response Tracker. Changes in population movements were assessed by Google COVID-19 Community Mobility Reports. Interrupted time series modelling quantified changes in rates of invasive disease in 2020 relative to when containment measures were imposed.\n\nFindingsAll countries experienced a significant, sustained reduction in invasive diseases due to S pneumoniae, H influenzae and N meningitidis, but not S agalactiae, in early 2020, which coincided with the introduction of COVID-19 containment measures in each country. Similar impacts were observed across most countries despite differing stringency in COVID-19 control policies. There was no evidence of a specific effect due to enforced school closures.\n\nInterpretationThe introduction of COVID-19 containment policies and public information campaigns likely reduced transmission of these bacterial respiratory pathogens, leading to a significant reduction in life-threatening invasive diseases in many countries worldwide.", "category": "infectious diseases", "match_type": "fuzzy", "author_similarity": 100, @@ -6887,20 +6887,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.11.11.20229500", - "date": "2020-11-13", - "link": "https://medrxiv.org/cgi/content/short/2020.11.11.20229500", - "title": "Association of social distancing and masking with risk of COVID-19", - "authors": "Sohee Kwon; Amit D. Joshi; Chun-Han Lo; David Alden Drew; Long Nguyen; Chuan-Guo Guo; Wenjie Ma; Raaj S. Mehta; Erica T. Warner; Christina M. Astley; Jordi Merino; Benjamin Murray; Jonathan Wolf; Sebastien Ourselin; Claire Steves; Timothy Spector; Jaime E. Hart; Mingyang Song; Trang VoPham; Andrew T. Chan", - "affiliations": "Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Boston Children's Hospital; Massachusetts General Hospital; King's College London; Zoe Global Limited; King's College London; King's College London; King's College London; Harvard T.H. Chan School of Public Health; Massachusetts General Hospital; Fred Hutchinson Cancer Research Center; Massachusetts General Hospital", - "abstract": "Given the continued burden of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) disease (COVID-19) across the U.S., there is a high unmet need for data to inform decision-making regarding social distancing and universal masking. We examined the association of community-level social distancing measures and individual masking with risk of predicted COVID-19 in a large prospective U.S. cohort study of 198,077 participants. Individuals living in communities with the greatest social distancing had a 31% lower risk of predicted COVID-19 compared with those living in communities with poor social distancing. Self-reported masking was associated with a 63% reduced risk of predicted COVID-19 even among individuals living in a community with poor social distancing. These findings provide support for the efficacy of mask-wearing even in settings of poor social distancing in reducing COVID-19 transmission. In the current environment of relaxed social distancing mandates and practices, universal masking may be particularly important in mitigating risk of infection.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 94, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.11.10.20229278", @@ -6971,20 +6957,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.11.05.20223289", - "date": "2020-11-06", - "link": "https://medrxiv.org/cgi/content/short/2020.11.05.20223289", - "title": "Longitudinal proteomic profiling of high-risk patients with COVID-19 reveals markers of severity and predictors of fatal disease", - "authors": "Jack Gisby; Candice L Clarke; Nicholas Medjeral-Thomas; Talat H Malik; Artemis Papadaki; Paige M Mortimer; Norzawani B Buang; Shanice Lewis; Marie Pereira; Frederic Toulza; Ester Fagnano; Marie-Anne Mawhin; Emma E Dutton; Lunnathaya Tapeng; Arianne C Richard; Paul Kirk; Jacques Behmoaras; Eleanor Sandhu; Stephen P McAdoo; Maria F Prendecki; Matthew C Pickering; Marina Botto; Michelle Willicombe; David C Thomas; James E. Peters", - "affiliations": "Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; University of Cambridge; MRC Biostatistics Unit University of Cambridge; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London", - "abstract": "End-stage kidney disease (ESKD) patients are at high risk of severe COVID-19. We measured 436 circulating proteins in serial blood samples from hospitalised and non-hospitalised ESKD patients with COVID-19 (n=256 samples from 55 patients). Comparison to 51 non-infected patients revealed 221 differentially expressed proteins, with consistent results in a separate subcohort of 46 COVID-19 patients. 203 proteins were associated with clinical severity, including IL6, markers of monocyte recruitment (e.g. CCL2, CCL7), neutrophil activation (e.g. proteinase-3) and epithelial injury (e.g. KRT19). Machine learning identified predictors of severity including IL18BP, CTSD, GDF15, and KRT19. Survival analysis with joint models revealed 69 predictors of death. Longitudinal modelling with linear mixed models uncovered 32 proteins displaying different temporal profiles in severe versus non-severe disease, including integrins and adhesion molecules. These data implicate epithelial damage, innate immune activation, and leucocyte-endothelial interactions in the pathology of severe COVID-19 and provide a resource for identifying drug targets.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "bioRxiv", "doi": "10.1101/2020.11.06.369439", @@ -7545,20 +7517,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.09.28.20202929", - "date": "2020-09-29", - "link": "https://medrxiv.org/cgi/content/short/2020.09.28.20202929", - "title": "T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses", - "authors": "Ane Ogbe; Barbara Kronsteiner; Donal T Skelly; Matthew Pace; Anthony Brown; Emily Adland; Kareena Adair; Hossain Delowar Akhter; Mohammad Ali; Serat-E Ali; Adrienn Angyal; M. Azim Ansari; Carolina V Arancibia-Carcamo; Helen Brown; Senthil Chinnakannan; Christopher P Conlon; Catherine de Lara; Thushan de Silva; Christina Dold; Tao Dong Dong; Timothy Donnison; David W Eyre; Amy Flaxman; Helen A Fletcher; Joshua Gardner; James T Grist; Carl-Philipp Hackstein; Kanoot Jaruthamsophon; Katie Jeffrey; Teresa Lambe; Lian Lee; Wenqin Li; Nicholas Lim; Philippa C Matthews; Alexander J Mentzer; Shona C Moore; Dean J Naisbitt; Monday Ogese; Graham Ogg; Peter Openshaw; Munir Pirmohamed; Andrew J Pollard; Narayan Ramamurthy; Patpong Rongkard; Sarah Rowland-Jones; Oliver L Sampson; Gavin Screaton; Alessandro Sette; Lizzie Stafford; Craig Thompson; Paul J Thomson; Ryan Thwaites; Vinicius Vieira; Daniela Weiskopf; Panagiota Zacharopoulou; - Oxford Immunology Network Covid-19 Response T cell Consortium; - Oxford Protective T cell Immunology for COVID-19 (OPTIC) Clinical team; Lance Turtle; Paul Klenerman; Philip Goulder; John Frater; Eleanor Barnes; Susanna Dunachie", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Sheffield; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Liverpool; University of Oxford; University of Oxford; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Liverpool; University of Liverpool; University of Liverpool; University of Oxford; Imperial College; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; La Jolla Institute for Immunology; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Liverpool; Imperial College; University of Oxford; La Jolla Institute for Immunology; University of Oxford; ; ; University of Liverpool; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford", - "abstract": "A major issue in identification of protective T cell responses against SARS-CoV-2 lies in distinguishing people infected with SARS-CoV-2 from those with cross-reactive immunity generated by exposure to other coronaviruses. We characterised SARS-CoV-2 T cell immune responses in 168 PCR-confirmed SARS-CoV-2 infected subjects and 118 seronegative subjects without known SARS-CoV-2 exposure using a range of T cell assays that differentially capture immune cell function. Strong ex vivo ELISpot and proliferation responses to multiple antigens (including M, NP and ORF3) were found in those who had been infected by SARS-CoV-2 but were rare in pre-pandemic and unexposed seronegative subjects. However, seronegative doctors with high occupational exposure and recent COVID-19 compatible illness showed patterns of T cell responses characteristic of infection, indicating that these readouts are highly sensitive. By contrast, over 90% of convalescent or unexposed people showed proliferation and cellular lactate responses to spike subunits S1/S2, indicating pre-existing cross-reactive T cell populations. The detection of T cell responses to SARS-CoV-2 is therefore critically dependent on the choice of assay and antigen. Memory responses to specific non-spike proteins provides a method to distinguish recent infection from pre-existing immunity in exposed populations.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.09.26.20202150", @@ -7839,6 +7797,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.09.01.20185793", + "date": "2020-09-03", + "link": "https://medrxiv.org/cgi/content/short/2020.09.01.20185793", + "title": "Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study", + "authors": "Katie Biggs; Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Matthew Bursnall; Amanda Loban; Simon Waterhouse; Richard Simmonds; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter", + "affiliations": "University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust", + "abstract": "ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection.\n\nMethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome.\n\nResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse outcome. C-statistics were 0.80 (95% confidence interval 0.73-0.87) for the WHO algorithm, 0.80 (0.71-0.90) for POPS, 0.76 (0.67-0.85) for COAST, and 0.71 (0.59-0.82) for SFHPC. Using pre-specified thresholds, the WHO algorithm had the highest sensitivity (0.85) and lowest specificity (0.75), but POPS and COAST could optimise sensitivity (0.96 and 0.92 respectively) at the expense of specificity (0.25 and 0.38 respectively) by using a threshold of any score above zero instead of the pre-specified threshold.\n\nConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive.\n\nRegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533", + "category": "emergency medicine", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.09.02.20186502", @@ -8217,20 +8189,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.08.03.20167122", - "date": "2020-08-04", - "link": "https://medrxiv.org/cgi/content/short/2020.08.03.20167122", - "title": "Ethnic minority groups in England and Wales - factors affecting the size and timing of elevated COVID-19 mortality: a retrospective cohort study linking Census and death records", - "authors": "Daniel Ayoubkhani; Vahe Nafilyan; Chris White; Peter Goldblatt; Charlotte Gaughan; Louisa Blackwell; Nicky Rogers; Amitava Banerjee; Kamlesh Khunti; Myer Glickman; Ben Humberstone; Ian Diamond", - "affiliations": "Office for National Statistics; Office for National Statistics; Office for National Statistics; UCL Institute for Health Equity; Office for National Statistics; Office for National Statistics; Office for National Statistics; Institute of Health Informatics, University College London; Diabetes Research Centre, University of Leicester; Office for National Statistics; Office for National Statistics; Office for National Statistics", - "abstract": "ObjectivesTo estimate population-level associations between ethnicity and coronavirus disease 2019 (COVID-19) mortality, and to investigate how ethnicity-specific mortality risk evolved over the course of the pandemic.\n\nDesignRetrospective cohort study using linked administrative data.\n\nSettingEngland and Wales, deaths occurring 2 March to 15 May 2020.\n\nParticipantsRespondents to the 2011 Census of England and Wales aged [≤]100 years and enumerated in private households, linked to death registrations and adjusted to account for emigration before the outcome period, who were alive on 1 March 2020 (n=47,872,412).\n\nMain outcome measureDeath related to COVID-19, registered by 29 May 2020.\n\nStatistical methodsWe estimated hazard ratios (HRs) for ethnic minority groups compared with the White population using Cox regression models, controlling for geographical, demographic, socio-economic, occupational, and self-reported health factors. HRs were estimated on the full outcome period and separately for pre- and post-lockdown periods in the UK.\n\nResultsIn the age-adjusted models, people from all ethnic minority groups were at elevated risk of COVID-19 mortality; the HRs for Black males and females were 3.13 [95% confidence interval: 2.93 to 3.34] and 2.40 [2.20 to 2.61] respectively. However, in the fully adjusted model for females, the HRs were close to unity for all ethnic groups except Black (1.29 [1.18 to 1.42]). For males, COVID-19 mortality risk remained elevated for the Black (1.76 [1.63 to 1.90]), Bangladeshi/Pakistani (1.35 [1.21 to 1.49]) and Indian (1.30 [1.19 to 1.43]) groups. The HRs decreased after lockdown for all ethnic groups, particularly Black and Bangladeshi/Pakistani females.\n\nConclusionsDifferences in COVID-19 mortality between ethnic groups were largely attenuated by geographical and socio-economic factors, although some residual differences remained. Lockdown was associated with reductions in excess mortality risk in ethnic minority populations, which has major implications for a second wave of infection or local spikes. Further research is needed to understand the causal mechanisms underpinning observed differences in COVID-19 mortality between ethnic groups.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.08.04.20163782", @@ -8259,20 +8217,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.07.30.20164921", - "date": "2020-08-01", - "link": "https://medrxiv.org/cgi/content/short/2020.07.30.20164921", - "title": "Estrogen and COVID-19 symptoms: associations in women from the COVID Symptom Study", - "authors": "Ricardo Costeira; Karla A Lee; Benjamin Murray; Colette Christiansen; Juan Castillo-Fernandez; Mary Ni Lochlainn; Joan Capdevila Pujol; Iain Buchan; Louise C Kenny; Jonathan Wolf; Janice Rymer; Sebastien Ourselin; Claire Steves; Timothy Spector; Louise Newson; Jordana Bell", - "affiliations": "King's College London; Department of Twin Research and Genetic Epidemiology; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; University of Liverpool; University of Liverpool; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London; Newson HealthMenopause & Wellbeing Centre; King's College London", - "abstract": "BackgroundMen and older women have been shown to be at higher risk of adverse COVID-19 outcomes. Animal model studies of SARS-CoV and MERS suggest that the age and sex difference in COVID-19 symptom severity may be due to a protective effect of the female sex hormone estrogen. Females have shown an ability to mount a stronger immune response to a variety of viral infections because of more robust humoral and cellular immune responses.\n\nObjectivesWe sought to determine whether COVID-19 positivity increases in women entering menopause. We also aimed to identify whether premenopausal women taking exogenous hormones in the form of the combined oral contraceptive pill (COCP) and post-menopausal women taking hormone replacement therapy (HRT) have lower predicted rates of COVID-19, using our published symptom-based model.\n\nDesignThe COVID Symptom Study developed by Kings College London and Zoe Global Limited was launched in the UK on 24th March 2020. It captured self-reported information related to COVID-19 symptoms. Data used for this study included records collected between 7th May - 15th June 2020.\n\nMain outcome measuresWe investigated links between COVID-19 rates and 1) menopausal status, 2) COCP use and 3) HRT use, using symptom-based predicted COVID-19, tested COVID-19, and disease severity based on requirement for hospital attendance or respiratory support.\n\nParticipantsFemale users of the COVID Symptom Tracker Application in the UK, including 152,637 women for menopause status, 295,689 for COCP use, and 151,193 for HRT use. Analyses were adjusted for age, smoking and BMI.\n\nResultsPost-menopausal women aged 40-60 years had a higher rate of predicted COVID (P=0.003) and a corresponding range of symptoms, with consistent, but not significant trends observed for tested COVID-19 and disease severity. Women aged 18-45 years taking COCP had a significantly lower predicted COVID-19 (P=8.03E-05), with a reduction in hospital attendance (P=0.023). Post-menopausal women using HRT or hormonal therapies did not exhibit consistent associations, including increased rates of predicted COVID-19 (P=2.22E-05) for HRT users alone.\n\nConclusionsOur findings support a protective effect of estrogen on COVID-19, based on positive association between predicted COVID-19 and menopausal status, and a negative association with COCP use. HRT use was positively associated with COVID-19 symptoms; however, the results should be considered with caution due to lack of data on HRT type, route of administration, duration of treatment, and potential comorbidities.\n\nTrial registrationThe App Ethics has been approved by KCL ethics Committee REMAS ID 18210, review reference LRs-19/20-18210", - "category": "obstetrics and gynecology", - "match_type": "fuzzy", - "author_similarity": 94, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.07.30.20165134", @@ -8399,20 +8343,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.07.19.20156869", - "date": "2020-07-25", - "link": "https://medrxiv.org/cgi/content/short/2020.07.19.20156869", - "title": "Paired nasopharyngeal and deep lung testing for SARS-CoV2 reveals a viral gradient in critically ill patients: a multi-centre study", - "authors": "Islam Hamed; Nesreen Shaban; Marwan Nassar; Sam Love; Martin D Curran; Stephen Webb; Huina Yang; Anthony Rostron; Katherine Watson; Vilas Navapurkar; Razeenn Mahroof; Andrew Conway Morris", - "affiliations": "John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK; John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK; John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK; John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK; Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge, United Kingdom; Royal Papworth Hospital, Cambridge, UK; Royal Papworth Hospital, Cambridge, UK; Sunderland Royal Hospital, South Tyneside and Sunderland NHS Foundation Trust, UK; Sunderland Royal Hospital, South Tyneside and Sunderland NHS Foundation Trust, UK; John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK; John Farman Intensive Care Unit, Addenbrooke's Hospital, Cambridge, UK; University of Cambridge", - "abstract": "Samples for diagnostic tests for SARS-CoV-2 can be obtained from the upper (nasopharyngeal/oropharyngeal swabs) or lower respiratory tract (sputum or tracheal aspirate or broncho-alveolar lavage - BAL). Data from different testing sites indicates different rates of positivity. Reverse-transcriptase polymerase chain reaction (RT-PCR) allows for semi-quantitative estimates of viral load as time to crossing threshold (Ct) is inversely related to viral load.\n\nObjectivesThe objective of our study was to evaluate SARS-CoV2 RNA loads between paired nasopharyngeal (NP) and deep lung (endotracheal aspirate or BAL) samples from critically ill patients.\n\nMethodsSARS-CoV-2 RT-PCR results were retrospectively reviewed for 51 critically ill patients from 5 intensive care units in 3 hospitals ; Addenbrookes Hospital Cambridge (3 units), Royal Papworth Cambridge (1 unit), and Royal Sunderland Hospital (1 unit). At the times when paired NP and deep lung samples were obtained, one patient had been on oxygen only, 6 patients on non-invasive ventilation, 18 patients on ECMO, and 26 patients mechanically ventilated.\n\nResultsResults collected showed significant gradient between NP and deep lung viral loads. Median Ct value was 29 for NP samples and 24 for deep lung samples. Of 51 paired samples, 16 were negative (below limit of detection) on NP swabs but positive (above limit of detection) on deep lung sample, whilst 2 were negative on deep sample but positive on NP (both patients were on ECMO).\n\nConclusionsIt has been suggested that whilst SARS-CoV1 tends to replicate in the lower respiratory tract, SARS-CoV2 replicates more vigorously in the upper respiratory tract. These data challenge that assumption. These data suggest that viral migration to, and proliferation in, the lower respiratory tract may be a key factor in the progression to critical illness and the development of severe acute respiratory syndrome (SARS). Factors which promote this migration should be examined for association with severe COVID-19. From a practical point of view, patients with suspected severe COVID-19 should have virological samples obtained from the lower respiratory tract where-ever possible, as upper respiratory samples have a significant negative rate.", - "category": "intensive care and critical care medicine", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.07.22.20159632", @@ -8903,20 +8833,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.06.12.20129056", - "date": "2020-06-16", - "link": "https://medrxiv.org/cgi/content/short/2020.06.12.20129056", - "title": "Symptom clusters in Covid19: A potential clinical prediction tool from the COVID Symptom study app", - "authors": "Carole H Sudre; Karla Lee; Mary Ni Lochlainn; Thomas Varsavsky; Benjamin Murray; Mark S. Graham; Cristina Menni; Marc Modat; Ruth C.E. Bowyer; Long H Nguyen; David Alden Drew; Amit D Joshi; Wenjie Ma; Chuan Guo Guo; Chun Han Lo; Sajaysurya Ganesh; Abubakar Buwe; Joan Capdevila Pujol; Julien Lavigne du Cadet; Alessia Visconti; Maxim Freydin; Julia S. El Sayed Moustafa; Mario Falchi; Richard Davies; Maria F. Gomez; Tove Fall; M. Jorge Cardoso; Jonathan Wolf; Paul W Franks; Andrew T Chan; Timothy D Spector; Claire J Steves; Sebastien Ourselin", - "affiliations": "King's College London; Department of Twin Research and Genetic Epidemiology; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; Lund University; Lund University; King's College London; Zoe Global Limited; Lund University; Massachusetts General Hospital; King's College London; King's College London; King's College London", - "abstract": "As no one symptom can predict disease severity or the need for dedicated medical support in COVID-19, we asked if documenting symptom time series over the first few days informs outcome. Unsupervised time series clustering over symptom presentation was performed on data collected from a training dataset of completed cases enlisted early from the COVID Symptom Study Smartphone application, yielding six distinct symptom presentations. Clustering was validated on an independent replication dataset between May 1-May 28th, 2020. Using the first 5 days of symptom logging, the ROC-AUC of need for respiratory support was 78.8%, substantially outperforming personal characteristics alone (ROC-AUC 69.5%). Such an approach could be used to monitor at-risk patients and predict medical resource requirements days before they are required.\n\nOne sentence summaryLongitudinal clustering of symptoms can predict the need for respiratory support in severe COVID-19.", - "category": "health informatics", - "match_type": "fuzzy", - "author_similarity": 94, - "affiliation_similarity": 100 - }, { "site": "bioRxiv", "doi": "10.1101/2020.06.16.153817", @@ -8973,6 +8889,20 @@ "author_similarity": 100, "affiliation_similarity": 91 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.06.10.20127175", + "date": "2020-06-11", + "link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127175", + "title": "Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.", + "authors": "Amitava Banerjee; Suliang Chen; Laura Pasea; Alvina Lai; Michail Katsoulis; Spiros Denaxas; Vahe Nafilyan; Bryan Williams; Wai Keong Wong; Ameet Bakhai; Kamlesh Khunti; Deenan Pillay; Mahdad Noursadeghi; Honghan Wu; Nilesh Pareek; Daniel Bromage; Theresa Mcdonagh; Jonathan Byrne; James T Teo; Ajay Shah; Ben Humberstone; Liang V Tang; Anoop SV Shah; Andrea Rubboli; Yutao Guo; Yu Hu; Cathie LM Sudlow; Gregory YH Lip; Harry Hemingway", + "affiliations": "University College London; University College London; University College London; University College London; UCL; University College London; Office for National Statistics; UCL; University College London Hospitals NHS Trust; Royal Free Hospitals NHS Trust; University of Leicester; UCL; UCL; UCL; King's College Hospital; Kings College London; Kings College London; Kings London NHS Trust; Kings College Hospital NHS Foundation Trust; King's College London; Office for National Statistics; Huazhong University of Science and Technology, Wuhan, China; University of Edinburgh; Ospedale S. Maria delle Croci, Ravenna, Italy; PLA General Hospital, Beijing, China.; Huazhong University of Science and Technology, Wuhan, China.; University of Edinburgh; University of Liverpool; UCL", + "abstract": "BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both \"direct\", through infection, and \"indirect\", through changes in healthcare.\n\nMethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(\"direct\" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For \"indirect\" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020.\n\nFindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths.\n\nInterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic.\n\nFundingNIHR, HDR UK, Astra Zeneca", + "category": "cardiovascular medicine", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "bioRxiv", "doi": "10.1101/2020.06.11.145920", @@ -9183,20 +9113,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.05.27.20114447", - "date": "2020-05-28", - "link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114447", - "title": "Automated and partially-automated contact tracing: a rapid systematic review to inform the control of COVID-19", - "authors": "Isobel Braithwaite; Tom Callender; Miriam Bullock; Robert W Aldridge", - "affiliations": "UCL Public Health Data Science Research Group, Institute of Health Informatics, University College London, London, UK; Department of Applied Health Research, University College London, London, UK; UCL Collaborative Centre for Inclusion Health, University College London, London UK; UCL Public Health Data Science Group, Institute of Health Informatics, University College London, London UK", - "abstract": "BackgroundAutomated or partially-automated contact tracing tools are being deployed by many countries to contain SARS-CoV-2; however, the evidence base for their use is not well-established.\n\nMethodsWe undertook a rapid systematic review of automated or partially-automated contact tracing, registered with PROSPERO (CRD42020179822). We searched PubMed, EMBASE, OVID Global Health, EBSCO COVID Portal, Cochrane Library, medRxiv, bioRxiv, arXiv and Google Advanced for articles relevant to COVID-19, SARS, MERS, influenza or Ebola from 1/1/200014/4/2020. Two authors reviewed all full-text manuscripts. One reviewer extracted data using a pre-piloted form; a second independently verified extracted data. Primary outcomes were the number or proportion of contacts (and/or subsequent cases) identified; secondary outcomes were indicators of outbreak control, app/tool uptake, resource use, cost-effectiveness and lessons learnt. The Effective Public Health Practice Project tool or CHEERS checklist were used in quality assessment.\n\nFindings4,033 citations were identified and 15 were included. No empirical evidence of automated contact tracings effectiveness (regarding contacts identified or transmission reduction) was identified. Four of seven included modelling studies suggested that controlling COVID-19 requires high population uptake of automated contact-tracing apps (estimates from 56% to 95%), typically alongside other control measures. Studies of partially-automated contact tracing generally reported more complete contact identification and follow-up, and greater intervention timeliness (0.5-5 hours faster), than previous systems. No meta-analyses were possible.\n\nInterpretationAutomated contact tracing has potential to reduce transmission with sufficient population uptake and usage. However, there is an urgent need for well-designed prospective evaluations as no studies provided empirical evidence of its effectiveness.", - "category": "public and global health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.05.19.20105460", @@ -9337,6 +9253,20 @@ "author_similarity": 94, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.05.14.20101824", + "date": "2020-05-19", + "link": "https://medrxiv.org/cgi/content/short/2020.05.14.20101824", + "title": "Changing travel patterns in China during the early stages of the COVID-19 pandemic", + "authors": "Hamish Gibbs; Yang Liu; Carl AB Pearson; Christopher I Jarvis; Chris Grundy; Billy J Quilty; Charlie Diamond; Rosalind M Eggo", + "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine", + "abstract": "Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigated the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020 and discussed their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower access to care. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and have not yet led to structural reorganisation of the transportation network at the time of this study.\n\nOne sentence summaryUnderstanding travel before, during, and after the introduction of travel restrictions in China in response to the COVID-19 Pandemic.", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.05.11.20098269", @@ -9785,20 +9715,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.04.19.20071639", - "date": "2020-04-22", - "link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071639", - "title": "How best to use limited tests? Improving COVID-19 surveillance in long-term care", - "authors": "David RM Smith; Audrey Duval; Koen B Pouwels; Didier Guillemot; Jerome Fernandes; Bich-Tram Huynh; Laura Temime; Lulla Opatowski", - "affiliations": "Institut Pasteur; Institut Pasteur; University of Oxford; Institut Pasteur; Clinique de soins de suite et readaptation, Choisy-Le-Roi; Institut Pasteur; Conservatoire national des arts et metiers; Institut Pasteur", - "abstract": "BackgroundLong-term care facilities (LTCFs) are vulnerable to COVID-19 outbreaks. Timely epidemiological surveillance is essential for outbreak response, but is complicated by a high proportion of silent (non-symptomatic) infections and limited testing resources.\n\nMethodsWe used a stochastic, individual-based model to simulate SARS-CoV-2 transmission along detailed inter-individual contact networks describing patient-staff interactions in real LTCF settings. We distributed nasopharyngeal swabs and RT-PCR tests using clinical and demographic indications, and evaluated the efficacy and resource-efficiency of a range of surveillance strategies, including group testing (sample pooling) and testing cascades, which couple (i) testing for multiple indications (symptoms, admission) with (ii) random daily testing.\n\nResultsIn the baseline scenario, randomly introducing SARS-CoV-2 into a 170-bed LTCF led to large outbreaks, with a cumulative 86 (6-224) infections after three weeks of unmitigated transmission. Efficacy of symptom-based screening was limited by (i) lags between infection and symptom onset, and (ii) silent transmission from asymptomatic and pre-symptomatic infections. Testing upon admission detected up to 66% of patients silently infected upon LTCF entry, but missed potential introductions from staff. Random daily testing was more effective when targeting patients than staff, but was overall an inefficient use of limited resources. At high testing capacity (>1 test/10 beds/day), cascades were most effective, with a 22-52% probability of detecting outbreaks prior to any nosocomial transmission, and 38-63% prior to first onset of COVID-19 symptoms. Conversely, at low capacity (<1 test/85 beds/day), pooling randomly selected patients in a daily group test was most effective (9-15% probability of detecting outbreaks prior to transmission; 30-44% prior to symptoms). The most efficient strategy compared to the reference was to pool individuals with any COVID-like symptoms, requiring only 5-7 additional tests and 17-24 additional swabs to detect outbreaks 5-6 days earlier, prior to an additional 14-18 infections.\n\nConclusionsGroup testing is an effective and efficient COVID-19 surveillance strategy for resource-limited LTCFs. Cascades are even more effective given ample testing resources. Increasing testing capacity and updating surveillance protocols accordingly could facilitate earlier detection of emerging outbreaks, informing a need for urgent intervention in settings with ongoing nosocomial transmission.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.04.16.20067504", @@ -9897,20 +9813,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.04.02.20051334", - "date": "2020-04-06", - "link": "https://medrxiv.org/cgi/content/short/2020.04.02.20051334", - "title": "Rapid implementation of mobile technology for real-time epidemiology of COVID-19", - "authors": "David A. Drew; Long H. Nguyen; Claire J. Steves; Jonathan Wolf; Tim D. Spector; Andrew T. Chan; COPE Consortium", - "affiliations": "Massachusetts General Hospital; Massachusetts General Hospital; King's College London; Zoe Global Limited; King's College London; Massachusetts General Hospital; ", - "abstract": "The rapid pace of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic (COVID-19) presents challenges to the robust collection of population-scale data to address this global health crisis. We established the COronavirus Pandemic Epidemiology (COPE) consortium to bring together scientists with expertise in big data research and epidemiology to develop a COVID-19 Symptom Tracker mobile application that we launched in the UK on March 24, 2020 and the US on March 29, 2020 garnering more than 2.25 million users to date. This mobile application offers data on risk factors, herald symptoms, clinical outcomes, and geographical hot spots. This initiative offers critical proof-of-concept for the repurposing of existing approaches to enable rapidly scalable epidemiologic data collection and analysis which is critical for a data-driven response to this public health challenge.\n\nOne Sentence SummaryCOVID-19 symptom tracker for smartphones", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.04.02.20051284", @@ -10148,5 +10050,19 @@ "match_type": "fuzzy", "author_similarity": 100, "affiliation_similarity": 100 + }, + { + "site": "medRxiv", + "doi": "10.1101/2020.01.31.20019901", + "date": "2020-02-02", + "link": "https://medrxiv.org/cgi/content/short/2020.01.31.20019901", + "title": "Early dynamics of transmission and control of 2019-nCoV: a mathematical modelling study", + "authors": "Adam J Kucharski; Timothy W Russell; Charlie Diamond; Yang Liu; CMMID nCoV working group; John Edmunds; Sebastian Funk; Rosalind M Eggo", + "affiliations": "London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine", + "abstract": "BackgroundAn outbreak of the novel coronavirus SARS-CoV-2 has led to 46,997 confirmed cases as of 13th February 2020. Understanding the early transmission dynamics of the infection and evaluating the effectiveness of control measures is crucial for assessing the potential for sustained transmission to occur in new areas.\n\nMethodsWe combined a stochastic transmission model with data on cases of novel coronavirus disease (COVID-19) in Wuhan and international cases that originated in Wuhan to estimate how transmission had varied over time during January and February 2020. Based on these estimates, we then calculated the probability that newly introduced cases might generate outbreaks in other areas.\n\nFindingsWe estimated that the median daily reproduction number, Rt, declined from 2.35 (95% CI: 1.15-4.77) one week before travel restrictions were introduced on 23rd January to 1.05 (95% CI: 0.413-2.39) one week after. Based on our estimates of Rt,we calculated that in locations with similar transmission potential as Wuhan in early January, once there are at least four independently introduced cases, there is a more than 50% chance the infection will establish within that population.\n\nInterpretationOur results show that COVID-19 transmission likely declined in Wuhan during late January 2020, coinciding with the introduction of control measures. As more cases arrive in international locations with similar transmission potential to Wuhan pre-control, it is likely many chains of transmission will fail to establish initially, but may still cause new outbreaks eventually.\n\nFundingWellcome Trust (206250/Z/17/Z, 210758/Z/18/Z), HDR UK (MR/S003975/1), Gates Foundation (INV-003174), NIHR (16/137/109)", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 } ] \ No newline at end of file diff --git a/data/covid/raw-preprints.json b/data/covid/raw-preprints.json index b62f5cf1..c2cfec45 100644 --- a/data/covid/raw-preprints.json +++ b/data/covid/raw-preprints.json @@ -1,4 +1,1219 @@ [ + { + "rel_doi": "10.1101/2023.10.26.23297613", + "rel_title": "Cost-effectiveness analysis of COVID-19 booster doses and oral antivirals in the Indo-Pacific", + "rel_date": "2023-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.26.23297613", + "rel_abs": "Background: Decision-makers in middle-income countries need evidence on the cost-effectiveness of COVID-19 booster doses and oral antivirals to appropriately prioritise these healthcare interventions. Methods: We used a dynamic transmission model to assess the cost-effectiveness of COVID-19 booster doses and oral antivirals in Fiji, Indonesia, Papua New Guinea, and Timor-Leste. We conducted cost-effectiveness analysis from both healthcare and societal perspectives using 3% discounting for ongoing costs and health benefits. We developed an interactive R Shiny which allows the user to vary key model assumptions, such as the choice of discounting rate, and view how these assumptions affect model results. Findings: Booster doses were cost saving and therefore cost-effective in all four middle-income settings from both healthcare and societal perspectives using 3% discounting. Providing oral antivirals was cost-effective from a healthcare perspective if procured at a low generic ($25 United States Dollars) or middle-income reference price ($250 United States Dollars); however, their cost-effectiveness was strongly influenced by rates of wastage or misuse, and the ongoing costs of care for patients hospitalised with COVID-19. Interestingly, the cost or wastage of rapid antigen tests did not appear strongly influential over the cost-effectiveness of oral antivirals in any of the four study settings. Conclusions: Our results support that government funded COVID-19 booster programs continue to be cost-effective in middle-income settings. Oral antivirals demonstrate the potential to be cost-effective if procured at or below a middle-income reference price of $250 USD per schedule. Further research should quantify the rates of wastage or misuse of oral COVID-19 antivirals in middle-income settings.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Gizem Mayis Bilgin", + "author_inst": "Australian National University" + }, + { + "author_name": "Syarifah Liza Munira", + "author_inst": "Universitas Indonesia" + }, + { + "author_name": "Kamalini Lokuge", + "author_inst": "Australian National University" + }, + { + "author_name": "Kathryn Glass", + "author_inst": "Australian National University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, + { + "rel_doi": "10.1101/2023.10.26.564184", + "rel_title": "Immune Epitopes of SARS-CoV-2 Spike Protein and Considerations for Universal Vaccine Development", + "rel_date": "2023-10-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.26.564184", + "rel_abs": "Despite the success of global vaccination programs in slowing the spread of COVID-19, these efforts have been hindered by the emergence of new SARS-CoV-2 strains capable of evading prior immunity. The mutation and evolution of SARS-CoV-2 have created a demand for persistent efforts in vaccine development. SARS-CoV-2 Spike protein has been the primary target for COVID-19 vaccine development, but it is also the hotspot of mutations directly involved in host susceptibility and immune evasion. Our ability to predict emerging mutants and select conserved epitopes is critical for the development of a broadly neutralizing therapy or a universal vaccine. In this article, we review the general paradigm of immune responses to COVID-19 vaccines, highlighting the immunological epitopes of Spike protein that are likely associated with eliciting protective immunity resulting from vaccination. Specifically, we analyze the structural and evolutionary characteristics of the SARS-CoV-2 Spike protein related to immune activation and function via the toll-like receptors (TLRs), B cells, and T cells. We aim to provide a comprehensive analysis of immune epitopes of Spike protein, thereby contributing to the development of new strategies for broad neutralization or universal vaccination.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nicholas Magazine", + "author_inst": "Louisiana State University" + }, + { + "author_name": "Tianyi Zhang", + "author_inst": "Louisiana State University" + }, + { + "author_name": "Anang D. Bungwon", + "author_inst": "Louisiana State University" + }, + { + "author_name": "Michael C. McGee", + "author_inst": "Louisiana State University" + }, + { + "author_name": "Yingying Wu", + "author_inst": "University of Houston" + }, + { + "author_name": "Gianluca Veggiani", + "author_inst": "Louisiana State University" + }, + { + "author_name": "Weishan Huang", + "author_inst": "Louisiana State University" + } + ], + "version": "1", + "license": "cc_by", + "type": "confirmatory results", + "category": "immunology" + }, + { + "rel_doi": "10.1101/2023.10.26.564289", + "rel_title": "Overcoming antibody-resistant SARS-CoV-2 variants with bispecific antibodies constructed using non-neutralizing antibodies", + "rel_date": "2023-10-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.26.564289", + "rel_abs": "A current challenge is the emergence of SARS-CoV-2 variants, such as BQ.1.1 and XBB.1.5, that can evade immune defenses, thereby limiting antibody drug effectiveness. Emergency-use antibody drugs, including the widely effective bebtelovimab, are losing their benefits. One potential approach to address this issue are bispecific antibodies which combine the targeting abilities of two antibodies with distinct epitopes. We engineered neutralizing bispecific antibodies in the IgG-scFv format from two initially non-neutralizing antibodies, CvMab-6 (which binds to the receptor-binding domain [RBD]) and CvMab-62 (targeting a spike protein S2 subunit epitope adjacent to the known anti-S2 antibody epitope). Furthermore, we created a bispecific antibody by incorporating the scFv of bebtelovimab with our anti-S2 antibody, demonstrating significant restoration of effectiveness against bebtelovimab-resistant BQ.1.1 variants. This study highlights the potential of neutralizing bispecific antibodies, which combine existing less effective anti-RBD antibodies with anti-S2 antibodies, to revive the effectiveness of antibody therapeutics compromised by immune-evading variants.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Tetsuya Inoue", + "author_inst": "Tokyo University of Science" + }, + { + "author_name": "Yuichiro Yamamoto", + "author_inst": "Tokyo University of Science" + }, + { + "author_name": "Kaoru Sato", + "author_inst": "Tokyo University of Science" + }, + { + "author_name": "Yuko Nakamura", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Yoshimi Shimizu", + "author_inst": "Teikyo Heisei University" + }, + { + "author_name": "Motohiko Ogawa", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Taishi Onodera", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Yoshimasa Takahashi", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Takaji Wakita", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Mika K Kaneko", + "author_inst": "Tohoku University Graduate School of Medicine" + }, + { + "author_name": "Masayoshi Fukasawa", + "author_inst": "National Institute of Infectious Diseases" + }, + { + "author_name": "Yukinari Kato", + "author_inst": "Tohoku University Graduate School of Medicine" + }, + { + "author_name": "Kohji Noguchi", + "author_inst": "Tokyo University of Science" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, + { + "rel_doi": "10.1101/2023.10.25.23297561", + "rel_title": "Changes in emergency department utilization in vulnerable populations after COVID-19 shelter in place orders", + "rel_date": "2023-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.25.23297561", + "rel_abs": "Purpose: To compare emergency department (ED) utilization and admission rates for patients with a history of mental health (MH), substance use disorder (SUD) and social determinants of health (SDOH) before and after implementing COVID-19's shelter-inplace (SIP) orders. Methods: This was a retrospective, multicenter study leveraging electronic medical record data from 20 EDs across a large Midwest integrated healthcare system from 5/2/2019 to 12/31/2019 (pre-SIP) and from 5/2/2020 to 12/31/2020 (post-SIP). Diagnoses were documented in the patient's medical records. Poisson and logistic regression models were used to evaluate ED utilization and admission rate changes. Results: 871,020 total ED encounters from 487,028 unique patients were captured. 2,572 (0.53%) patients had a documented Z code for SDOH. Patients with previously diagnosed MH or SUDs were more likely to seek ED care after the SIP orders were implemented (RR: 1.20, 95% CI: 1.18 - 1.22, p<0.001), as were patients with SDOH (RR: 2.37, 95% CI: 2.19 - 2.55, p<0.001). Patients with both previously diagnosed MH or SUD and a documented SDOH had even higher ED utilization (RR: 3.31, 95% CI: 2.83 - 3.88, p<0.001) than those with either condition alone. Patients with MH and SUDs (OR: 0.89, 95% CI: 0.86 - 0.92, p<0.001) or SDOH (OR: 0.67, 95% CI: 0.54, 0.83, p<0.001) were less likely to be admitted post-SIP orders while patients with a history of diseases of physiologic systems were more likely to be admitted. Conclusions: Vulnerable populations with a history of MH, SUD, and SDOH experienced increased ED utilization but a lower rate of hospital admissions after the implementation of SIP orders. The findings highlight the importance of addressing these needs to mitigate the impact of public health crises on these populations.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Philip Wang", + "author_inst": "Cleveland Clinic Lerner College of Medicine at Case Western Reserve University, EC-10 Cleveland Clinic, Cleveland, OH, USA" + }, + { + "author_name": "Akhil Anand", + "author_inst": "Department of Psychiatry and Psychology, Center for Behavioral Health, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA" + }, + { + "author_name": "James Bena", + "author_inst": "Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio" + }, + { + "author_name": "Shannon Morrison", + "author_inst": "Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio" + }, + { + "author_name": "Jeremy Weleff", + "author_inst": "Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, + { + "rel_doi": "10.1101/2023.10.25.23297548", + "rel_title": "The experiences and impact of the COVID-19 pandemic on Young Carers: practice implications and planning for future health emergencies", + "rel_date": "2023-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.25.23297548", + "rel_abs": "Background: Young Carers faced significant challenges brought on by the COVID-19 pandemic. We explored the impact of the pandemic and associated restrictions on mental health, wellbeing and access to support in Young Carers in the United Kingdom (UK) to understand how to improve services, as well as support this population in future health emergencies. Method: We conducted 22 qualitative semi-structured interviews from May to November 2021, with 14 Young Carers and 8 staff working in organisations that supported them. Interviews took place remotely over video or telephone call, discussing topics such as experiences of the pandemic on their health, wellbeing and caring responsibilities. We used reflexive thematic analysis to analyse interview transcripts. Results: We identified 4 overarching themes pertaining to the impact of the pandemic and associated restrictions on mental health, wellbeing, and access to support in Young Carers in the UK: 1) challenges to following the guidelines, 2) changes to and loss of routine, 3) changes in provision of informal and formal support and 4) better understanding of inner resilience and goals. Many participants struggled with their mental health and wellbeing as a result of pandemic related restrictions, impacting on support structures for themselves, as well as the individual cared for. However, positive impacts pertained to additional support from local authority and third sector organisations. Conclusions: Our findings highlight some of the changes that affected Young Carers during the COVID-19 pandemic. The impact of changes to routine and a reduction in pre-pandemic support were the greatest concerns reported by participants in this study. The additional support provided by local authority and third sector organisations during social restrictions suggests such organisations could play a greater role in supporting this population going forward, and that schools and Governments may wish to put in additional strategies and provisions to protect this population in the future.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Dan Hayes", + "author_inst": "University College London" + }, + { + "author_name": "Daisy Fancourt", + "author_inst": "University College London" + }, + { + "author_name": "Alexandra Burton", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, + { + "rel_doi": "10.1101/2023.10.25.563967", + "rel_title": "Discovery of a novel inhibitor of macropinocytosis with antiviral activity", + "rel_date": "2023-10-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.25.563967", + "rel_abs": "Several viruses hijack various forms of endocytosis in order to infect host cells. Here, we report the discovery of a new molecule with antiviral properties that we named virapinib, which limits viral entry by macropinocytosis. The identification of virapinib derives from a chemical screen using High-Throughput Microscopy, where we identified new chemical entities capable of preventing infection with a pseudotype virus expressing the spike (S) protein from SARS-CoV-2. Subsequent experiments confirmed the capacity of virapinib to inhibit infection by SARS-CoV-2, as well as by additional viruses, such as Monkeypox virus and TBEV. Mechanistic analyses revealed that the compound inhibited macropinocytosis, limiting this entry route for the viruses. Importantly, virapinib has no significant toxicity to host cells. In summary, we present a new molecule that inhibits viral entry via the endocytic route, offering a new alternative to prevent viral infection.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Bartlomiej Porebski", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Wanda Christ", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Alba Corman", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Martin Haraldsson", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Myriam Barz", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Louise Lidemalm", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Maria Haggblad", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Juliana Illmain", + "author_inst": "NYU" + }, + { + "author_name": "Shane Wright", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Matilde Murga", + "author_inst": "CNIO" + }, + { + "author_name": "Jan Schlegel", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Erdinc Sezgin", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Gira Bhabha", + "author_inst": "NYU" + }, + { + "author_name": "Volker M Lauschke", + "author_inst": "Karolinska Instituet" + }, + { + "author_name": "Miguel Lafarga", + "author_inst": "University of Cantabria" + }, + { + "author_name": "Jonas Klingstrom", + "author_inst": "Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden" + }, + { + "author_name": "Daniela Huhn", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Oscar Fernandez-Capetillo", + "author_inst": "CNIO/KI" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pharmacology and toxicology" + }, + { + "rel_doi": "10.1101/2023.10.25.564014", + "rel_title": "Early antiviral CD4 and CD8 T cell responses are associated with upper respiratory tract clearance of SARS-CoV-2", + "rel_date": "2023-10-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.25.564014", + "rel_abs": "T cells are involved in protective immunity against numerous viral infections. Limited data have been available regarding roles of human T cell responses controlling SARS-CoV-2 viral clearance in primary COVID-19. Here, we examined longitudinal SARS-CoV-2 upper respiratory tract viral RNA levels and early adaptive immune responses from 95 unvaccinated individuals with acute COVID-19. Acute SARS-CoV-2-specific CD4 and CD8 T cell responses were evaluated in addition to antibody responses. Most individuals with acute COVID-19 developed rapid SARS-CoV-2-specific T cell responses during infection, and both early CD4 T cell and CD8 T cell responses correlated with reduced upper respiratory tract SARS-CoV-2 viral RNA, independent of neutralizing antibody titers. Overall, our findings indicate a distinct protective role for SARS-CoV-2-specific T cells during acute COVID-19.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Sydney I Ramirez", + "author_inst": "La Jolla Institute for Immunology (LJI), University of California San Diego (UCSD)" + }, + { + "author_name": "Paul G Lopez", + "author_inst": "La Jolla Institute for Immunology (LJI)" + }, + { + "author_name": "Farhoud Faraji", + "author_inst": "University of California San Diego (UCSD)" + }, + { + "author_name": "Urvi M Parikh", + "author_inst": "University of Pittsburgh School of Medicine" + }, + { + "author_name": "Amy Heaps", + "author_inst": "University of Pittsburgh School of Medicine" + }, + { + "author_name": "Justin Ritz", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Carlee Moser", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Joseph J Eron", + "author_inst": "University of North Carolina at Chapel Hill School of Medicine" + }, + { + "author_name": "David A Wohl", + "author_inst": "University of North Carolina at Chapel Hill School of Medicine" + }, + { + "author_name": "Judith S Currier", + "author_inst": "David Geffen School of Medicine at University of California Los Angeles" + }, + { + "author_name": "Eric S Daar", + "author_inst": "8Lundquist Institute at Harbor-UCLA Medical Center" + }, + { + "author_name": "Alex L Greninger", + "author_inst": "University of Washington Medical Center" + }, + { + "author_name": "Paul Klekotka", + "author_inst": "Eli Lilly and Company" + }, + { + "author_name": "Alba Grifoni", + "author_inst": "La Jolla Institute for Immunology (LJI)" + }, + { + "author_name": "Daniela Weiskopf", + "author_inst": "La Jolla Institute for Immunology (LJI), University of California San Diego (UCSD)" + }, + { + "author_name": "Alessandro Sette", + "author_inst": "La Jolla Institute for Immunology (LJI), University of California San Diego (UCSD)" + }, + { + "author_name": "Bjoern Peters", + "author_inst": "La Jolla Institute for Immunology (LJI), University of California San Diego (UCSD)" + }, + { + "author_name": "Michael D Hughes", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Kara W Chew", + "author_inst": "David Geffen School of Medicine at University of California Los Angeles" + }, + { + "author_name": "Davey M Smith", + "author_inst": "University of California San Diego (UCSD)" + }, + { + "author_name": "Shane Crotty", + "author_inst": "La Jolla Institute For Immunology (LJI)" + }, + { + "author_name": "- ACTIV-2/A5401 Study Team", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, + { + "rel_doi": "10.1101/2023.10.24.563847", + "rel_title": "A deep learning framework for predicting the neutralizing activity of COVID-19 therapeutics and vaccines against evolving SARS-CoV-2 variants", + "rel_date": "2023-10-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.24.563847", + "rel_abs": "Understanding how viral variants evade neutralization is crucial for improving antibody-based treatments, especially with rapidly evolving viruses like SARS-CoV-2. Yet, conventional assays are limited in the face of rapid viral evolution, relying on a narrow set of viral isolates, and falling short in capturing the full spectrum of variants. To address this, we have developed a deep learning approach to predict changes in neutralizing antibody activity of COVID-19 therapeutics and vaccines against emerging viral variants. First, we trained a variational autoencoder (VAE) using all 67,885 unique SARS-CoV-2 spike protein sequences from the NCBI virus (up to October 31, 2022) database to encode spike protein variants into a latent space. Using this VAE and a curated dataset of 7,069 in vitro assay data points from the NCATS OpenData Portal, we trained a neural network regression model to predict fold changes in neutralizing activity of 40 COVID-19 therapeutics and vaccines against spike protein sequence variants, relative to their neutralizing activity against the ancestral strain (Wuhan-Hu-1). Our model also employs Bayesian inference to quantify prediction uncertainty, providing more nuanced and informative estimates. To validate the model's predictive capacity, we assessed its performance on a test set of in vitro assay data collected up to eight months after the data included in the model training (N = 980). The model accurately predicted fold changes in neutralizing activity for this prospective dataset, with an R2 of 0.77. Expanding our methodology to include all available data from NCBI virus and NCATS OpenData Portal up to date, we assessed predicted changes in activity for current COVID-19 monoclonal antibodies and vaccines against newly identified SARS-CoV-2 lineages. Our predictions suggest that current therapeutic and vaccine-induced antibodies will have significantly reduced activity against newer XBB descendants, notably EG.5, FL.1.5.1, and XBB.1.16. Using the model, we were able to primarily attribute the observed predicted loss in activity to the F456L spike mutation found in EG.5 and FL.1.5.1 sequences. Conversely, mRNA-bivalent vaccines are predicted to be less susceptible to the recent BA.2.86 variant compared to new XBB descendants. These findings align closely with recent research, underscoring the potential of deep learning in shaping therapeutic and vaccine strategies for emerging viral variants.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Robert P Matson", + "author_inst": "nference, inc." + }, + { + "author_name": "Isin Y Comba", + "author_inst": "nference, inc." + }, + { + "author_name": "Eli Silvert", + "author_inst": "nference, inc." + }, + { + "author_name": "Michiel JM Niesen", + "author_inst": "nference, inc." + }, + { + "author_name": "Karthik Murugadoss", + "author_inst": "nference, inc." + }, + { + "author_name": "Dhruti Padwardhan", + "author_inst": "nference labs" + }, + { + "author_name": "Rohit Suratekar", + "author_inst": "nference labs" + }, + { + "author_name": "Elizabeth-Grace Goel", + "author_inst": "nference, inc." + }, + { + "author_name": "Brittany J Poelaert", + "author_inst": "NIH" + }, + { + "author_name": "Kanny Wan", + "author_inst": "NIH" + }, + { + "author_name": "Kyle R Brimacombe", + "author_inst": "NIH" + }, + { + "author_name": "AJ Venkatakrishnan", + "author_inst": "nference, inc." + }, + { + "author_name": "Venky Soundararajan", + "author_inst": "nference, inc." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, + { + "rel_doi": "10.1101/2023.10.25.563806", + "rel_title": "Reduced Monocyte Proportions and Responsiveness in Convalescent COVID-19 Patients", + "rel_date": "2023-10-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.25.563806", + "rel_abs": "The clinical manifestations of acute severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection and COVID-19 suggest a dysregulation of the host immune response that leads to inflammation, thrombosis, and organ dysfunction. It is less clear whether these dysregulated processes persist during the convalescent phase of disease or during long COVID. We investigated the effects of SARS-CoV-2 infection on the proportions of classical, intermediate, and non-classical monocytes, their activation status, and their functional properties in convalescent COVID-19 patients and uninfected control subjects. We found that the percentage of total monocytes was decreased in convalescent COVID-19 patients compared to uninfected controls. This was due to decreased intermediate and non-classical monocytes. Classical monocytes from convalescent COVID-19 patients demonstrated a decrease in activation markers, such as CD56, in response to stimulation with bacterial lipopolysaccharide (LPS). In addition, classical monocytes from convalescent COVID-19 patients showed decreased expression of CD142 (tissue factor), which can initiate the extrinsic coagulation cascade, in response to LPS stimulation. Finally, we found that monocytes from convalescent COVID-19 patients produced less TNF- and IL-6 in response to LPS stimulation, than those from uninfected controls. In conclusion, SARS-CoV-2 infection exhibits a clear effect on the relative proportions of monocyte subsets, the activation status of classical monocytes, and proinflammatory cytokine production that persists during the convalescent phase of disease.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Eugene Ravkov", + "author_inst": "ARUP Laboratories" + }, + { + "author_name": "Elizabth S C P Williams", + "author_inst": "University of Utah" + }, + { + "author_name": "Marc Elgort", + "author_inst": "ARUP Laboratories" + }, + { + "author_name": "Adam Spivak", + "author_inst": "University of Utah" + }, + { + "author_name": "Adam P Barker", + "author_inst": "University of Utah and ARUP Laboratories" + }, + { + "author_name": "Vicente Planelles", + "author_inst": "University of Utah" + }, + { + "author_name": "Julio Delgado", + "author_inst": "ARUP Laboratories" + }, + { + "author_name": "Leo Lin", + "author_inst": "University of Utah" + }, + { + "author_name": "Timothy Hanley", + "author_inst": "University of Utah" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, + { + "rel_doi": "10.1101/2023.10.25.564079", + "rel_title": "Integrating population-level and cell-based signatures for drug repositioning", + "rel_date": "2023-10-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.25.564079", + "rel_abs": "Drug repositioning presents a streamlined and cost-efficient way to expand the range of therapeutic possibilities. Furthermore, drugs with genetic evidence are more likely to progress successfully through clinical trials towards FDA approval. Exploiting these developments, single gene-based drug repositioning methods have been implemented, but approaches leveraging the entire spectrum of molecular signatures are critically underexplored. Most multi-gene-based approaches rely on differential gene expression (DGE) analysis, which is prone to identify the molecular consequence of disease and renders causal inference challenging. We propose a framework TReD (Transcriptome-informed Reversal Distance) that integrates population-level disease signatures robust to reverse causality and cell-based drug-induced transcriptome response profiles. TReD embeds the disease signature and drug profile in a high-dimensional normed space, quantifying the reversal potential of candidate drugs in a disease-related cell screen assay. The robustness is ensured by evaluation in additional cell screens. For an application, we implement the framework to identify potential drugs against COVID-19. Taking transcriptome-wide association study (TWAS) results from four relevant tissues and three DGE results as disease features, we identify 37 drugs showing potential reversal roles in at least four of the seven disease signatures. Notably, over 70% (27/37) of the drugs have been linked to COVID-19 from other studies, and among them, eight drugs are supported by ongoing/completed clinical trials. For example, TReD identifies the well-studied JAK1/JAK2 inhibitor baricitinib, the first FDA-approved immunomodulatory treatment for COVID-19. Novel potential candidates, including enzastaurin, a selective inhibitor of PKC-beta which can be activated by SARS-CoV-2, are also identified. In summary, we propose a comprehensive genetics-anchored framework integrating population-level signatures and cell-based screens that can accelerate the search for new therapeutic strategies.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Chunfeng He", + "author_inst": "School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China;The Key Laboratory of Intelligent Preventive" + }, + { + "author_name": "Yue Xu", + "author_inst": "School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; The Key Laboratory of Intelligent Preventiv" + }, + { + "author_name": "Yuan Zhou", + "author_inst": "Department of Biostatistics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, USA;" + }, + { + "author_name": "Jiayao Fan", + "author_inst": "School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; The Key Laboratory of Intelligent Preventiv" + }, + { + "author_name": "Chunxiao Cheng", + "author_inst": "School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China" + }, + { + "author_name": "Ran Meng", + "author_inst": "School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China" + }, + { + "author_name": "Eric R. Gamazon", + "author_inst": "Vanderbit Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA; Data Science Institute, Vanderbilt University Medical Center, Nashville," + }, + { + "author_name": "Dan Zhou", + "author_inst": "School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China; The Key Laboratory of Intelligent Preventiv" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, + { + "rel_doi": "10.1101/2023.10.26.23297635", + "rel_title": "Online trend estimation and detection of trend deviations in sub-sewershed time series of SARS-CoV-2 RNA measured in wastewater.", + "rel_date": "2023-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.26.23297635", + "rel_abs": "Wastewater surveillance has proven a key public health tool to understand a wide range of community health diseases and has proven to be especially critical to health departments throughout the SARS CoV-2 pandemic. The size of the population served by a wastewater treatment plant (WWTP) may limit the targeted insight about community disease dynamics. To investigate this concern, samples of wastewater were obtained at lift stations upstream of WWTPs within the sewer network. First, an online, semi-automatic time series model is fitted to the weekly measurements of WWTP samples to estimate the viral trend for the community and compared to the time series observations from the lift stations. Second, deviations from the WWTP trend are identified using an Exponentially Weighted Moving Average (EWMA) control chart. The analysis reveals that the lift stations display slightly different dynamics than the larger WWTP, highlighting the more granular insight gleaned from sampling sites which represent smaller populations. Discussion focuses on the use of our methods to support rapid public health decision-making based on additional, targeted samples in times of concern.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Katherine B Ensor", + "author_inst": "Rice University" + }, + { + "author_name": "Julia C Schedler", + "author_inst": "Rice University" + }, + { + "author_name": "Thomas Sun", + "author_inst": "Rice University" + }, + { + "author_name": "Rebecca Schneider", + "author_inst": "Houston Health Department" + }, + { + "author_name": "Anthony Mulenga", + "author_inst": "Houston Health Department" + }, + { + "author_name": "Jingjing Wu", + "author_inst": "Rice University" + }, + { + "author_name": "Lauren Stadler", + "author_inst": "Rice University" + }, + { + "author_name": "Loren Hopkins", + "author_inst": "Rice University and Houston Health Department" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, + { + "rel_doi": "10.1101/2023.10.26.23297626", + "rel_title": "Comparative Organ Disease Burden and Sequelae of Influenza and SARS-CoV-2 Infection: An Observational Study Using Real-World Data", + "rel_date": "2023-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.26.23297626", + "rel_abs": "Infections with SARS-CoV-2 and influenza are associated with acute and post-acute complications and sequelae of many organ systems (i.e., disease burden). It is important to understand the global disease burden that associates with and follows acute infection in order to establish preventive and therapeutic strategies and to reduce the use of health resources and improve patient health outcomes. To address these questions, we utilized the National Covid Cohort Collaborative, which is an integrated and harmonized data repository of electronic health record data in the USA. From this database, we included in analysis 346,493 eligible SARS-CoV-2-infected patients, 75,829 eligible influenza infected patients, and 199,963 uninfected controls. We describe the disease burden that extends over 2-3 months following infection, and we quantify the reduction of disease burden by treatment. We identify a burden of disease following medically attended influenza that is comparable to that of medically attended SARS-CoV-2 infection. However, in contrast to SARS-CoV-2, influenza acute infection and disease burden are not responsive to antiviral treatment and thus remain as an unmet medical need. Focusing therapeutic strategies solely on the short-term management of acute infection may also underestimate the extended health benefits of antiviral treatment.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Istvan Bartha", + "author_inst": "Vir Biotechnology, Inc." + }, + { + "author_name": "M. Cyrus Maher", + "author_inst": "Vir Biotechnology, Inc." + }, + { + "author_name": "Victor Lavrenko", + "author_inst": "Vir Biotechnology, Inc." + }, + { + "author_name": "Keith Boundy", + "author_inst": "Vir Biotechnology, Inc." + }, + { + "author_name": "Elizabeth Kinter", + "author_inst": "Vir Biotechnology, Inc." + }, + { + "author_name": "Wendy Yeh", + "author_inst": "Vir Biotechnology, Inc." + }, + { + "author_name": "Davide Corti", + "author_inst": "Vir Biotechnology" + }, + { + "author_name": "Amalio Telenti", + "author_inst": "Vir Biotechnology, Inc." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, + { + "rel_doi": "10.1101/2023.10.26.23297607", + "rel_title": "Medical tourism's vulnerability to COVID-19 and its path to recovery: a 10-year data analysis of international patient visits", + "rel_date": "2023-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.26.23297607", + "rel_abs": "Background This study seeks to assess the trends in international patient intake over the past decade, with a specific focus on the impact of the COVID-19 pandemic. Methods This is a retrospective study on the data obtained from SUPREME (CDW Research Search System) of Information Center from a single university hospital. Patient demographics on the gender, age, nationality, and diagnosis visiting International Healthcare Center from January 2013 to June 2023 were collected, and the impact and recovery rates from COVID-19 were calculated in terms of the number of foreign patients. The patient number was further analyzed based on gender, age, nationality, and diagnosis. Results The impact and recovery rates of COVID-19 on the number of foreign patients was 57% and 71%, respectively. The patients from USA, the old adult group (age 40-64), and patients with cancer were least affected by COVID-19, whereas the patients from the UAE, the young adult group (age 19-39), and patients for medical screening were most affected by COVID-19. Conclusions The number of international patients steadily was steadily rising since 2013 with a drop in number more than half with the advent of COVID-19 in 2019. However, recent data suggests a revival of this trend, signaling a gradual return to pre-pandemic levels. Despite the overall recovery, future trends are not entirely predictable due to potential factors. Future pandemics, international conflicts, or economic instability could potentially affect the influx of foreign patients. To revive medical tourism, a joint effort from the government and hospital is necessary.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Gihyun Myung", + "author_inst": "Seoul National University Hospital" + }, + { + "author_name": "Juwon Lim", + "author_inst": "Seoul National University Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, + { + "rel_doi": "10.1101/2023.10.25.23297469", + "rel_title": "Peripheral Transcriptomics in Acute and Long-Term Kidney Dysfunction in SARS-CoV2 Infection", + "rel_date": "2023-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.25.23297469", + "rel_abs": "Background. Acute kidney injury (AKI) is common in hospitalized patients with SARS-CoV2 infection despite vaccination and leads to long-term kidney dysfunction. However, peripheral blood molecular signatures in AKI from COVID-19 and their association with long-term kidney dysfunction are yet unexplored. Methods. In patients hospitalized with SARS-CoV2, we performed bulk RNA sequencing using peripheral blood mononuclear cells (PBMCs). We applied linear models accounting for technical and biological variability on RNA-Seq data accounting for false discovery rate (FDR) and compared the functional enrichment and pathway results to a historical sepsis-AKI cohort. Finally, we evaluated the association of these signatures with long-term trends in kidney function. Results. Of 283 patients, 106 had AKI. After adjustment for sex, age, mechanical ventilation, and chronic kidney disease (CKD), we identified 2635 significant differential gene expressions at FDR<0.05. Top canonical pathways were EIF2 signaling, oxidative phosphorylation, mTOR signaling, and Th17 signaling, indicating mitochondrial dysfunction and endoplasmic reticulum (ER) stress. Comparison with sepsis associated AKI showed considerable overlap of key pathways (48.14%). Using follow-up estimated glomerular filtration rate (eGFR) measurements from 115 patients, we found that 164/2635 (6.2%) of the significantly differentiated genes were associated with overall decrease in long-term kidney function. The strongest associations were autophagy, renal impairment via fibrosis and cardiac structure/function. Conclusions. We show that AKI in SARS-CoV2 is a multifactorial process with mitochondrial dysfunction driven by ER stress whereas long-term kidney function decline is associated with cardiac structure and function, and immune dysregulation. Functional overlap with sepsis-AKI also highlights common signatures indicating generalizability in therapeutic approaches.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Pushkala Jayaraman MS", + "author_inst": "The Charles Bronfman Institute for Personalized Medicine (CBIPM) , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Madhumitha Rajagopal MD", + "author_inst": "Samuel Bronfman Department of Medicine The Barbara T Murphy Division of Nephrology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ishan Paranjpe MD", + "author_inst": "Department of Medicine , Stanford University" + }, + { + "author_name": "Lora Liharska BS", + "author_inst": "Department of Genetics and Genomic Sciences , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Mayte Suarez-Farinas PhD", + "author_inst": "Department of Population Health Science and Policy , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ryan Thompson PhD", + "author_inst": "The Charles Bronfman Institute for Personalized Medicine (CBIPM) , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Diane Marie Del Valle BS", + "author_inst": "Department of Immunology and Immunotherapy The Charles Bronfman Institute for Personalized Medicine (CBIPM) , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Noam Beckmann PhD", + "author_inst": "The Charles Bronfman Institute for Personalized Medicine (CBIPM) , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Wonsuk Oh PhD", + "author_inst": "The Charles Bronfman Institute for Personalized Medicine (CBIPM) , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Faris F Gulamali BS", + "author_inst": "The Charles Bronfman Institute for Personalized Medicine (CBIPM) , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Justin Kauffman BS", + "author_inst": "The Charles Bronfman Institute for Personalized Medicine (CBIPM) , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Edgar Gonzalez-Kozlova PhD", + "author_inst": "Department of Genetics and Genomic Sciences , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sergio Dellepiane MD PhD", + "author_inst": "The Barbara T Murphy Division of Nephrology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "George Vasquez-Rios MD", + "author_inst": "The Barbara T Murphy Division of Nephrology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Akhil Vaid", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Joy Jiang", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Annie Chen", + "author_inst": "Samuel Bronfman Department of Medicine , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ankit Sakhuja MD", + "author_inst": "The Charles Bronfman Institute for Personalized Medicine (CBIPM) , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Steven Chen PhD", + "author_inst": "The Precision Immunology Institute , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ephraim Kenigsberg PhD", + "author_inst": "Department of Genetics and Genomic Sciences , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "John Cijiang He MD PhD", + "author_inst": "The Barbara T Murphy Division of Nephrology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Steven G Coca MD", + "author_inst": "The Barbara T Murphy Division of Nephrology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Lili Chan MD", + "author_inst": "The Barbara T Murphy Division of Nephrology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Eric Schadt PhD", + "author_inst": "Department of Genetics and Genomic Sciences , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Miram Merad MD", + "author_inst": "Department of Immunology and Immunotherapy, The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Seunghee Kim-Schulze PhD", + "author_inst": "Department of Immunology and Immunotherapy The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sacha Gnjatic MD", + "author_inst": "The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ephraim Tsalik MD PhD", + "author_inst": "Center for Applied Genomics and Precision Medicine Division of Infectious Diseases, Duke University School of Medicine" + }, + { + "author_name": "Raymond Langley PhD", + "author_inst": "Department of Pharmacology , University of South Alabama" + }, + { + "author_name": "Alexander W Charney MD", + "author_inst": "The Charles Bronfman Institute for Personalized Medicine (CBIPM) , Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Girish N Nadkarni MD MPH", + "author_inst": "The Charles Bronfman Institute for Personalized Medicine (CBIPM) , Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, + { + "rel_doi": "10.1101/2023.10.25.23297554", + "rel_title": "Safety and Efficacy of Disulfiram in Hospitalized Patients with Moderate COVID-19: A Randomized, Double-Blind, Placebo-Controlled Trial.", + "rel_date": "2023-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.25.23297554", + "rel_abs": "OBJECTIVES: Disulfiram, a low-cost generic drug used for alcohol dependence, holds the potential to mitigate disease progression in patients with moderate COVID-19 by targeting inflammasomes. This study aimed to evaluate the clinical efficacy and safety of disulfiram when administered alongside standard of care for the treatment of hospitalized individuals with moderate COVID-19. DESIGN: A randomized, double-blind, placebo-controlled trial. SETTING: Conducted at four clinical sites in Brazil between December 2020 and August 2021. PARTICIPANTS: 140 participants aged 35 and older with laboratory-confirmed SARS-CoV-2 infection, hospitalized for [≤]5 days with moderate symptoms of COVID-19 were enrolled, 137 were randomized. INTERVENTION: Participants were randomized in a 1:1 ratio to receive a daily dose of 500 mg of disulfiram (N=68) or placebo (N=69) for 14 days while receiving the current standard of care. Randomization was stratified by age and comorbidities (hypertension, diabetes, and BMI [≥]35). MEASUREMENTS AND MAIN RESULTS The primary outcome, median time to clinical improvement [95% CI] did not significantly differ between groups (disulfiram: 3.5 [3.00, 4.00] days; placebo: 4 [3.00, 5.00] days; P=.73). Key secondary outcomes, such as mean days (SD) on supplemental oxygen [disulfiram: 4.4 (6.61) days; placebo: 3.7 (5.80) days, P=.34], median (95% CI) time to hospital discharge [disulfiram: 6.0 (5.00, 8.00) days, placebo: 5.0 (4.00, 7.00)], proportion of participants discharged by day 8 [disulfiram (68%), placebo (63%), odds ratio: 0.801], and proportion of participants who clinically worsened [disulfiram (21%), placebo (19%), P=.79], did not reveal significant differences. While the incidence of adverse events was higher in the disulfiram group, serious adverse events and 28-day mortality were comparable between the two groups. CONCLUSIONS Although disulfiram was found to be safe in hospitalized patients with moderate COVID-19, it did not shorten the time to clinical improvement. These findings do not support the use of disulfiram alongside standard of care in this patient population. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT04594343", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Augusto Cesar Mota", + "author_inst": "AMO Clinic / ETICA, Salvador, Brazil." + }, + { + "author_name": "Valdir C. Sant'Ana Filho", + "author_inst": "BAHIANA/School of Medicine and Public Health, Salvador, Brazil; Feira de Santana Municipal Secretary of Health, Brazil" + }, + { + "author_name": "Carolyn M. Hendrickson", + "author_inst": "University of California San Francisco; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Zuckerberg San Francisco General Hospital and " + }, + { + "author_name": "Rachel M DeVay", + "author_inst": "Spring Discovery Inc., San Carlos, CA, United States" + }, + { + "author_name": "Matt Donne", + "author_inst": "Spring Discovery Inc., San Carlos, CA, United States; Spring Research Foundation, San Francisco, CA." + }, + { + "author_name": "An M Nguyen", + "author_inst": "Spring Discovery Inc., San Carlos, CA, United States; Spring Research Foundation, San Carlos, CA" + }, + { + "author_name": "Caroline Junqueira", + "author_inst": "Instituto Ren\u00e9 Rachou/ FIOCRUZ; Centro de Tecnologia de Vacinas (CT Vacinas), Belo Horizonte, MG, Brazil." + }, + { + "author_name": "Mark Marino", + "author_inst": "Mark T. Marino Consulting LLC" + }, + { + "author_name": "Munish Mehra", + "author_inst": "Tigermed" + }, + { + "author_name": "Ransi Somaratne", + "author_inst": "Spring Discovery Inc., San Carlos, CA, United States" + }, + { + "author_name": "Christian ELABD", + "author_inst": "Spring Discovery Inc., San Carlos, CA, United States" + }, + { + "author_name": "Ben Kamens", + "author_inst": "Spring Discovery Inc., San Carlos, CA, United States; Spring Research Foundation, San Carlos, CA." + }, + { + "author_name": "Wendy Cousin", + "author_inst": "Spring Discovery Inc., 1121 industrial rd., Suite 500, San Carlos, CA 94070 CA, United States; Spring Research Foundation, 1121 industrial rd., Suite 500, San C" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, + { + "rel_doi": "10.1101/2023.10.26.23297581", + "rel_title": "Potential impact of annual vaccination with reformulated COVID-19 vaccines: lessons from the U.S. COVID-19 Scenario Modeling Hub", + "rel_date": "2023-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.26.23297581", + "rel_abs": "Importance: COVID-19 continues to cause significant hospitalizations and deaths in the United States. Its continued burden and the impact of annually reformulated vaccines remain unclear. Objective: To project COVID-19 hospitalizations and deaths from April 2023-April 2025 under two plausible assumptions about immune escape (20% per year and 50% per year) and three possible CDC recommendations for the use of annually reformulated vaccines (no vaccine recommendation, vaccination for those aged 65+, vaccination for all eligible groups). Design: The COVID-19 Scenario Modeling Hub solicited projections of COVID-19 hospitalization and deaths between April 15, 2023-April 15, 2025 under six scenarios representing the intersection of considered levels of immune escape and vaccination. State and national projections from eight modeling teams were ensembled to produce projections for each scenario. Setting: The entire United States. Participants: None. Exposure: Annually reformulated vaccines assumed to be 65% effective against strains circulating on June 15 of each year and to become available on September 1. Age and state specific coverage in recommended groups was assumed to match that seen for the first (fall 2021) COVID-19 booster. Main outcomes and measures: Ensemble estimates of weekly and cumulative COVID-19 hospitalizations and deaths. Expected relative and absolute reductions in hospitalizations and deaths due to vaccination over the projection period. Results: From April 15, 2023-April 15, 2025, COVID-19 is projected to cause annual epidemics peaking November-January. In the most pessimistic scenario (high immune escape, no vaccination recommendation), we project 2.1 million (90% PI: 1,438,000-4,270,000) hospitalizations and 209,000 (90% PI: 139,000-461,000) deaths, exceeding pre-pandemic mortality of influenza and pneumonia. In high immune escape scenarios, vaccination of those aged 65+ results in 230,000 (95% CI: 104,000-355,000) fewer hospitalizations and 33,000 (95% CI: 12,000-54,000) fewer deaths, while vaccination of all eligible individuals results in 431,000 (95% CI: 264,000-598,000) fewer hospitalizations and 49,000 (95% CI: 29,000-69,000) fewer deaths. Conclusion and Relevance: COVID-19 is projected to be a significant public health threat over the coming two years. Broad vaccination has the potential to substantially reduce the burden of this disease.", + "rel_num_authors": 60, + "rel_authors": [ + { + "author_name": "Sung-mok Jung", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Sara L Loo", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Emily Howerton", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Lucie Contamin", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Claire P Smith", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Erica C Carcel\u00e9n", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Katie Yan", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Samantha J Bents", + "author_inst": "National Institutes of Health Fogarty International Center" + }, + { + "author_name": "Jessi Espino", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "John Levander", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Nicholas G Reich", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Joseph C Lemaitre", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Koji Sato", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Clifton D McKee", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Alison L Hill", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Matteo Chinazzi", + "author_inst": "Northeastern University" + }, + { + "author_name": "Jessica T Davis", + "author_inst": "Northeastern University" + }, + { + "author_name": "Kunpeng Mu", + "author_inst": "Northeastern University" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Northeastern University" + }, + { + "author_name": "Erik T Rosenstrom", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Sebastian A Rodriguez-Cartes", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Julie S Ivy", + "author_inst": "North Carolina State University and University of Michigan" + }, + { + "author_name": "Maria E Mayorga", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Julie L Swann", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Guido Espa\u00f1a", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Sean Cavany", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Sean M Moore", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Alex Perkins", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Shi Chen", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Rajib Paul", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Daniel Janies", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Jean-Claude Thill", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Ajitesh Srivastava", + "author_inst": "University of Southern California" + }, + { + "author_name": "Majd Al Aawar", + "author_inst": "University of Southern California" + }, + { + "author_name": "Kaiming Bi", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Shraddha Ramdas Bandekar", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Anass Bouchnita", + "author_inst": "University of Texas at El Paso" + }, + { + "author_name": "Spencer J Fox", + "author_inst": "University of Georgia" + }, + { + "author_name": "Lauren Ancel Meyers", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Przemyslaw Porebski", + "author_inst": "University of Virginia" + }, + { + "author_name": "Srinivasan Venkatramanan", + "author_inst": "University of Virginia" + }, + { + "author_name": "Aniruddha Adiga", + "author_inst": "University of Virginia" + }, + { + "author_name": "Bryan Lewis", + "author_inst": "University of Virginia" + }, + { + "author_name": "Brian Klahn", + "author_inst": "University of Virginia" + }, + { + "author_name": "Benjamin Hurt", + "author_inst": "University of Virginia" + }, + { + "author_name": "Jiangzhuo Chen", + "author_inst": "University of Virginia" + }, + { + "author_name": "Amanda Wilson", + "author_inst": "University of Virginia" + }, + { + "author_name": "Stefan Hoops", + "author_inst": "University of Virginia" + }, + { + "author_name": "Parantapa Bhattacharya", + "author_inst": "University of Virginia" + }, + { + "author_name": "Dustin Machi", + "author_inst": "University of Virginia" + }, + { + "author_name": "Joseph Outten", + "author_inst": "University of Virginia" + }, + { + "author_name": "Henning Mortveit", + "author_inst": "University of Virginia" + }, + { + "author_name": "Anil Vullikanti", + "author_inst": "University of Virginia" + }, + { + "author_name": "Madhav Marathe", + "author_inst": "University of Virginia" + }, + { + "author_name": "Harry Hochheiser", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Michael C Runge", + "author_inst": "U.S. Geological Survey Eastern Ecological Science Center" + }, + { + "author_name": "Katriona Shea", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Shaun Truelove", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "C\u00e9cile Viboud", + "author_inst": "National Institutes of Health Fogarty International Center" + }, + { + "author_name": "Justin Lessler", + "author_inst": "University of North Carolina at Chapel Hill" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, + { + "rel_doi": "10.1101/2023.10.26.23297598", + "rel_title": "Assessing the causal effect of air pollution on risk of SARS-CoV-2 infection", + "rel_date": "2023-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.26.23297598", + "rel_abs": "Introduction Emerging evidence suggests association of air pollution exposure with risk of SARS-CoV-2 infection, but many of these findings are limited by study design, lack of individual-level covariate data or are specific to certain subpopulations. We aim to evaluate causal effects of air pollution on risk of infection, whilst overcoming these limitations. Methods Concentrations for black carbon(BC), particulate matter 10(PM10), particulate matter 2.5(PM2.5), nitrogen dioxide(NO2) and oxides of nitrogen(NOx) from the Department of Environment, Food and Rural Affairs (DEFRA) and Effect of Low-level Air Pollution: A Study in Europe (ELAPSE) were linked to postcodes of 53,683 Virus Watch study participants. The primary outcome was first SARS-CoV-2 infection, between 1st September 2020 and 30th April 2021. Regression analysis used modified Poisson with robust estimates, clustered by household, adjusting for individual (e.g., age, sex, ethnicity) and environmental covariates(e.g., population density, region) to estimate total and direct effects. Results Single pollutant analysis showed the direct effect of higher risk of SARS-CoV-2 infection with increased exposure to PM2.5(RR1.11,95%CI 1.08;1.15), PM10(RR1.06,95%CI 1.04;1.09), NO2(RR1.04,95%CI 1.04;1.05) and NOx(RR1.02,95%CI 1.02;1.02) per 1g/m3 increment with DEFRA 2015-19 data. Sensitivity analyses altering covariates, exposure window and modelled air pollution data source produced similar estimates. Higher risk of SARS-CoV-2 per 10-5m-1 increment of BC (RR1.86, 95%CI 1.62;2.14) was observed using ELAPSE data. Conclusion Long term exposure to higher concentrations of air pollutions increases the risk of SARS-CoV-2 infection, highlighting that adverse health effects of air pollution is not only limited to non-communicable diseases.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Annalan Mathew Dwight Navaratnam", + "author_inst": "University College London" + }, + { + "author_name": "Sarah Beale", + "author_inst": "University College London" + }, + { + "author_name": "Yamina Boukari", + "author_inst": "University College London" + }, + { + "author_name": "Vincent Nguyen", + "author_inst": "University College London" + }, + { + "author_name": "Wing Lam Erica Fong", + "author_inst": "University College London" + }, + { + "author_name": "Isobel Braithwaite", + "author_inst": "University College London" + }, + { + "author_name": "Thomas Edward Byrne", + "author_inst": "University College London" + }, + { + "author_name": "Ellen Fragaszy", + "author_inst": "UCL" + }, + { + "author_name": "Cyril Geismar", + "author_inst": "University College London" + }, + { + "author_name": "Jana Kovar", + "author_inst": "University College London" + }, + { + "author_name": "Parth Patel", + "author_inst": "University College London" + }, + { + "author_name": "Madhumita Shrotri", + "author_inst": "University College London" + }, + { + "author_name": "Alexei Yavlinsky", + "author_inst": "University College London" + }, + { + "author_name": "Andrew Hayward", + "author_inst": "UCL" + }, + { + "author_name": "Haneen Khreis", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Robert W Aldridge", + "author_inst": "UCL" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.10.24.561010", "rel_title": "VIPERA: Viral Intra-Patient Evolution Reporting and Analysis", @@ -323,13 +1538,564 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.10.25.23297539", + "rel_title": "Estimated transmission dynamics of SARS-CoV-2 variants from wastewater are robust to differential shedding", + "rel_date": "2023-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.25.23297539", + "rel_abs": "The COVID-19 pandemic has accelerated the development and adoption of wastewater-based epidemiology. Wastewater samples can provide genomic information for detecting and assessing the spread of SARS-CoV-2 variants in communities and for estimating important epidemiological parameters such as the growth advantage of the variant. However, despite demonstrated successes, epidemiological data derived from wastewater suffers from potential biases. Of particular concern are differential shedding profiles that different variants of concern exhibit, because they can shift the relationship between viral loads in wastewater and prevalence estimates derived from clinical cases. Using mathematical modeling, simulations, and Swiss surveillance data, we demonstrate that this bias does not affect estimation of the growth advantage of the variant and has only a limited and transient impact on estimates of the effective reproduction number. Thus, population-level epidemiological parameters derived from wastewater maintain their advantages over traditional clinical-derived estimates, even in the presence of differential shedding among variants.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "David Dreifuss", + "author_inst": "ETHZ" + }, + { + "author_name": "Jana S Huisman", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Johannes C. Rusch", + "author_inst": "Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dubendorf, Switzerland" + }, + { + "author_name": "Lea Caduff", + "author_inst": "Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dubendorf, Switzerland" + }, + { + "author_name": "Pravin Ganesanandamoorthy", + "author_inst": "Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dubendorf, Switzerland" + }, + { + "author_name": "Alexander J. Devaux", + "author_inst": "Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dubendorf, Switzerland" + }, + { + "author_name": "Charles Gan", + "author_inst": "Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dubendorf, Switzerland" + }, + { + "author_name": "Tanja Stadler", + "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland" + }, + { + "author_name": "Tamar Kohn", + "author_inst": "Laboratory of Environmental Chemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Federale de Lausanne (EPFL), CH-1015 Lau" + }, + { + "author_name": "Christoph Ort", + "author_inst": "Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dubendorf, Switzerland" + }, + { + "author_name": "Niko Beerenwinkel", + "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland; SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland" + }, + { + "author_name": "Timothy R. Julian", + "author_inst": "Eawag, Swiss Federal Institute of Aquatic Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, + { + "rel_doi": "10.1101/2023.10.25.23297544", + "rel_title": "The Influence Of Covid-19 On Patient Mobilization And Injury Attributes In The ICU: A Retrospective Analysis Of A Level II Trauma Center", + "rel_date": "2023-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.25.23297544", + "rel_abs": "The objectives of this study were to determine the effect of COVID-19 on physical therapy (PT) mobilization of traumatically-injured patients and to determine if mobilization affected patient course in the ICU. This retrospective study included patients who were admitted to the ICU of a level II trauma center. The patients were divided into two groups, i.e., those admitted before (n=378) and after (n=499) April 1, 2020 when Georgia's COVID-19 Shelter-in-place order was mandated. The two groups were contrasted on nominal and ratio variables using Chi-square and Student's t-tests. A secondary analysis focused specifically on the after COVID patients examined the extent to which mobilization (n=328) or lack of mobilization (n=171) influenced ICU outcomes (e.g., mortality, readmission). The two groups were contrasted on nominal and ratio variables using Chi-square and Student's -tests. The after COVID patients had higher injury severity as a greater proportion was classified as severely injured (i.e., >15 on Injury Severity Score) compared to the before COVID patients. After COVID patients also had greater cumulative number of comorbidities and experienced greater complications in the ICU. Despite this, there was no difference between patients in receiving a PT consultation or day-to-mobilization. Within the after COVID cohort, those that were mobilized were older, a higher proportion were female, they had greater Glasgow Coma Scale scores, had longer total hospital days, and a lesser mortality rate. Despite shifting patient injury attributes post-COVID-19, a communicable disease, mobilization care remained consistent and effective.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Yelissa Navarro", + "author_inst": "Medical College of Georgia" + }, + { + "author_name": "Elizabeth Huang", + "author_inst": "Medical College of Georgia" + }, + { + "author_name": "Chandler Johnson", + "author_inst": "Medical College of Georgia" + }, + { + "author_name": "Forrest Clark", + "author_inst": "Medical College of Georgia" + }, + { + "author_name": "Samuel Coppola", + "author_inst": "Medical College of Georgia" + }, + { + "author_name": "Suraj Modi", + "author_inst": "Medical College of Georgia" + }, + { + "author_name": "Gordon L Warren", + "author_inst": "Georgia State University" + }, + { + "author_name": "Jarrod Call", + "author_inst": "University of Georgia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "rehabilitation medicine and physical therapy" + }, + { + "rel_doi": "10.1101/2023.10.25.23289986", + "rel_title": "'We are not the virus - Experiences of racism among East & Southeast Asian heritage young people in London during the height of the COVID-19 pandemic", + "rel_date": "2023-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.25.23289986", + "rel_abs": "The spread of COVID-19 was accompanied by news reports of surging racism, xenophobia, and hate crime all over the Global North targeting individuals of East and Southeast Asian (ESEA) descent. However, little empirical research has documented the impacts of COVID-19 on child and adolescent ESEAs. We describe and analyse the mental health experiences of young ESEA Londoners during the height of the COVID-19 pandemic. We purposively recruited 23 young people (aged 9-20) of ESEA heritage through social media and existing ESEA networks and analysed transcripts using thematic analysis. Participants experienced distress from being exposed to multiple forms of racism ranging from strangers on the street avoiding or harassing them to classmates at school or university making racist jokes, comments or banter. Participants worried about hate crimes reported in news media and experienced anxiety from seeing pervasive racist content in online social media. Some participants responded by physically isolating themselves at home for long periods, whilst others chose to participate in activism, providing a sense of agency. Action by parents and school authorities was reported to help prevent further bullying, but respondents did not always feel able to approach these for help. Our findings put into focus the strain on young ESEA Londoners mental health caused by COVID-related racism and jar against simplified depictions of metropolitan places, such as London, as centres of cosmopolitanism and tolerance. To promote the emotional wellbeing of young ESEAs, future policy should facilitate action by schools and universities against anti-ESEA racism and support ESEA community-building efforts to enhance resilience in the face of racism.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Lu Gram", + "author_inst": "University College London" + }, + { + "author_name": "Ada Mau", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, + { + "rel_doi": "10.1101/2023.10.25.23297531", + "rel_title": "Changes in sleep duration during the long-lasting COVID-19 pandemic: individual and regional disparities", + "rel_date": "2023-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.25.23297531", + "rel_abs": "The adequate quality and quantity of sleep are related to maintaining the immune system and mental well-being; therefore, it is necessary to evaluate sleep duration during COVID-19. This study aimed to investigate the changes in sleep duration during the long-lasting COVID-19 period (2020 and 2021) in South Korea, and to examine the individual and regional disparities. The study population comprised 1,143,460 adults aged [≥]19 years who participated in the 2017-2021 Korea Community Health Survey excluding those who did not respond to the daily sleep duration questionnaire. For statistical analysis, we first conducted a multiple regression model for 229 districts to estimate the district-specific changes in sleep duration. We then applied a meta-analysis to pool the 229 estimates and a meta-regression to examine the association between changes in sleep duration and regional characteristics. The sleep duration increased by 9.66 (95% CI: 8.53, 10.80) min in 2020 and 3.66 (95% CI: 2.09, 5.22) min in 2021 compared to the pre-pandemic period (2017-2019). The increase was more prominent in males, younger adults, employed individuals, and those with a high socioeconomic status compared to the general population. Communities with a higher proportion of apartments, lower normalized difference vegetation index in summer, and lower practice rate of moderate exercise were associated with a higher increase in sleep duration during the pandemic. The sleep duration increased during the COVID-19 pandemic, and the increase decreased as the COVID-19 lasted longer. The findings of our study highlight that preventive measures to manage sleep health during a pandemic should be framed in consideration of individual and regional characteristics.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jieun Min", + "author_inst": "Ewha Womans University" + }, + { + "author_name": "Jieun Oh", + "author_inst": "Seoul National University Graduate School of Public Health" + }, + { + "author_name": "Whanhee Lee", + "author_inst": "Pusan National University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, + { + "rel_doi": "10.1101/2023.10.25.23297530", + "rel_title": "Viral and host factors associated with SARS-CoV-2 disease severity in Georgia, USA", + "rel_date": "2023-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.25.23297530", + "rel_abs": "While SARS-CoV-2 vaccines have shown strong efficacy, their suboptimal uptake combined with the continued emergence of new viral variants raises concerns about the ongoing and future public health impact of COVID-19. We investigated viral and host factors, including vaccination status, that were associated with SARS-CoV-2 disease severity in a setting with low vaccination rates. We analyzed clinical and demographic data from 1,957 individuals in the state of Georgia, USA, coupled with viral genome sequencing from 1,185 samples. We found no difference in disease severity between individuals infected with Delta and Omicron variants among the participants in this study, after controlling for other factors, and we found no specific mutations associated with disease severity. Compared to those who were unvaccinated, vaccinated individuals experienced less severe SARS-CoV-2 disease, and the effect was similar for both variants. Vaccination within 270 days before infection was associated with decreased odds of moderate and severe outcomes, with the strongest association observed at 91-270 days post-vaccination. Older age and underlying health conditions, especially immunosuppression and renal disease, were associated with increased disease severity. Overall, this study provides insights into the impact of vaccination status, variants/mutations, and clinical factors on disease severity in SARS-CoV-2 infection when vaccination rates are low. Understanding these associations will help refine and reinforce messaging around the crucial importance of vaccination in mitigating the severity of SARS-CoV-2 disease.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Ludy R. Carmola", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Allison Dorothy Roebling", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Dara Khosravi", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Rose M. Langsjoen", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Andrei Bombin", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Bri Bixler", + "author_inst": "Emory University" + }, + { + "author_name": "Alex Reid", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Cara Chen", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Ethan Wang", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Yang Lu", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Ziduo Zheng", + "author_inst": "Emory University" + }, + { + "author_name": "Rebecca Zhang", + "author_inst": "Emory University" + }, + { + "author_name": "Phuong-Vi Nguyen", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Robert A. Arthur", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Eric Fitts", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Dalia Arafat Gulick", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Dustin Higginbotham", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Azmain Taz", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Alaa Ahmed", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "John Hunter Crumpler", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Colleen Kraft", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Wilbur A. Lam", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Ahmed Babiker", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Jesse J. Waggoner", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Kyle P. Openo", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Laura M. Johnson", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Adrianna Westbrook", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Anne Piantadosi", + "author_inst": "Emory University School of Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, + { + "rel_doi": "10.1101/2023.10.25.23297503", + "rel_title": "Fc-dependent functional activity of ChAdOx1-S and CoronaVac vaccine-induced antibodies to the SARS-CoV-2 spike protein", + "rel_date": "2023-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.25.23297503", + "rel_abs": "Ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission and COVID-19 disease severity is influenced by immunity acquired by natural exposure and/or vaccination, whereby most vaccines are formulated on the Ancestral strain. However, population-level immunity is complicated by the emergence of variants of concern (VOCs), such as Omicron that is the dominant variant currently in circulation. Antibody Fc-dependent effector functions are being increasingly recognised as important mediators in immunity, especially against VOCs. However, induction of these functions in populations with diverse infection and/or vaccination histories, remains poorly defined. Here, we evaluated Fc-dependent functional antibodies following vaccination with two widely used vaccines: AstraZeneca (AZ; ChAdOx1-S) and Sinovac (SV). We quantified Fc{gamma}R-binding and C1q-fixing antibodies against Ancestral and variant spike (S) proteins in Brazilian adults vaccinated with AZ or SV (n=222), some of which were previously exposed to SARS-CoV-2. AZ induced greater Fc{gamma}R-binding responses to Ancestral S than the SV vaccine. Previously exposed individuals had significantly greater vaccine-induced responses compared to their naive counterparts, with notably high C1q-fixation levels, irrespective of vaccine type. Fc{gamma}R-binding was highest among AZ vaccinated individuals with a prior exposure, and these responses were well retained against the Omicron S protein. Overall, these findings contribute to our understanding of vaccine-induced immunity and its effectiveness against evolving variants.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Alexander W Harris", + "author_inst": "Burnet Institute, Melbourne, Australia" + }, + { + "author_name": "Liriye Kurtovic", + "author_inst": "Burnet Institute, Melbourne, Australia" + }, + { + "author_name": "Jeane Nogueira", + "author_inst": "Rio de Janeiro State University, Rio de Janeiro, Brazil." + }, + { + "author_name": "Isabel Bouzas", + "author_inst": "Rio de Janeiro State University, Rio de Janeiro, Brazil." + }, + { + "author_name": "Herbert D Opi", + "author_inst": "Burnet Institute, Melbourne, Australia." + }, + { + "author_name": "Bruce D Wines", + "author_inst": "Burnet Institute, Melbourne, Australia." + }, + { + "author_name": "Mark P Hogarth", + "author_inst": "Burnet Institute, Melbourne, Australia." + }, + { + "author_name": "Pantelis Poumbourios", + "author_inst": "Burnet Institute, Melbourne, Australia." + }, + { + "author_name": "Heidi E Drummer", + "author_inst": "Burnet Institute, Melbourne, Australia." + }, + { + "author_name": "Clarissa Valim", + "author_inst": "Boston University, Boston, USA." + }, + { + "author_name": "Lu\u00eds Crist\u00f3v\u00e3o E. Porto", + "author_inst": "Rio de Janeiro State University" + }, + { + "author_name": "James G Beeson", + "author_inst": "Burnet Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, + { + "rel_doi": "10.1101/2023.10.24.23297114", + "rel_title": "Plasma-based antigen persistence in the post-acute phase of SARS-CoV-2 infection", + "rel_date": "2023-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.24.23297114", + "rel_abs": "BACKGROUND: Although RNA viruses like SARS-CoV-2 are generally thought to be transient, the persistence of viral components beyond the acute phase can be driven by a variety of virologic and immunologic factors. Recent studies have suggested that SARS-CoV-2 antigens may persist following COVID-19 but were limited by a lack of comparison to a large number of true negative control samples. METHODS: Using single molecule array (Simoa) assays for SARS-CoV-2 spike, S1, and nucleocapsid antigen in plasma from 171 pandemic-era individuals in the post-acute phase of SARS-CoV-2 infection and 250 pre-pandemic control samples, we compared prevalence of antigen detection. We used logistic regression models and prevalence ratios (PRs) to assess the relationship between demographic and disease factors and antigen persistence. RESULTS: Compared to the proportion of antigen positivity in the pre-pandemic controls (2%), detection of any SARS-CoV-2 antigen was more frequent across all post-acute COVID-19 time bins (3-6 months: 12.6%, p<0.001; 6-10 months, 10.7%, p=0.0002; 10-14 months, 7.5%, p=0.017). These differences were driven by spike protein for up to 14 months and nucleocapsid in the first 6 months after infection. The co-occurrence of multiple antigens at a single timepoint was uncommon. Hospitalization for acute COVID-19 (versus not hospitalized) and worse self-reported health during acute COVID-19 among those not hospitalized (versus more benign illness) were associated with higher prevalence of post-acute antigen detection (PR 1.86, p=0.03; PR 3.5, p=0.07, respectively) in the pandemic era. CONCLUSIONS: Our findings provide strong evidence that SARS-CoV-2 antigens can persist beyond the period of acute illness. The observation that more than 10% of plasma samples for over a year following initial SARS-CoV-2 infection contain detectable viral antigen, which are potentially immunogenic, has significant implications given the sheer number of people infected with SARS-CoV-2 to date. More work will be needed to determine whether these antigens have a causal role in post-acute sequelae of SARS-CoV-2 infection (PASC).", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Michael J. Peluso", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Zoe N. Swank", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Sarah A. Goldberg", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Scott Lu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Thomas Dalhuisen", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Ella Borberg", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Yasmeen Senussi", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Michael A. Luna", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Celina Chang Song", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alexus Clark", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Andhy Zamora", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Megan Lew", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Badri Viswanathan", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Beatrice Huang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Khamal Anglin", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Rebecca Hoh", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Priscilla Y. Hsue", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Matthew S. Durstenfeld", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Matthew A. Spinelli", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "David V. Glidden", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Timothy J. Henrich", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "J. D. Kelly", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Steven G. Deeks", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "David R. Walt", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Jeffrey N. Martin", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, + { + "rel_doi": "10.1101/2023.10.24.23297192", + "rel_title": "COVID-19 vaccination-induced antibody responses and waning by age and comorbidity status in a large population-based prospective cohort study", + "rel_date": "2023-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.24.23297192", + "rel_abs": "Background Information on the magnitude and duration of antibody levels after COVID-19 vaccination in different groups may be useful for prioritizing of additional vaccinations. Methods Serum samples were collected every six months in a prospective cohort study among adults in the Netherlands. Geometric mean concentrations (GMCs) of antibodies against the receptor binding domain of the SARS-CoV-2 spike protein were calculated after the primary series, first, and second booster vaccinations. Effects of age (18-59 vs 60-85 years) and medical risk conditions on GMC 2-6 weeks and 21-25 weeks after each vaccination, and on waning during 3-25 weeks after each vaccination, were estimated by linear regression. Results We included 20,816, 16,820 and 5,879 samples collected after primary, first and second booster vaccination, respectively. GMCs at 2-6 and 21-25 weeks after primary series were lower in participants with older age or medical risk conditions. After the first booster, older age was associated with lower GMC at 2-6 weeks, higher GMC at 21-25 weeks, and slower waning. GMCs or waning after the first and second boosters (only 60-85) were not associated with medical risk conditions. Conclusions Since antibody differences by age and medical risk groups have become small with increasing number of doses, other factors such as disease severity rather than antibody levels are useful for prioritization of additional vaccinations.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Christina E Hoeve", + "author_inst": "National Institute for Public Health and Environment" + }, + { + "author_name": "Anne J. Huiberts", + "author_inst": "National Institute for Public Health and Environment" + }, + { + "author_name": "Brechje de Gier", + "author_inst": "National Institute for Public Health and Environment" + }, + { + "author_name": "Stijn P Andeweg", + "author_inst": "National Institute for Public Health and Environment" + }, + { + "author_name": "Gerco den Hartog", + "author_inst": "National Institute for Public Health and Environment" + }, + { + "author_name": "Hester E de Melker", + "author_inst": "National Institute for Public Health and Environment" + }, + { + "author_name": "Susan JM Hahne", + "author_inst": "National Institute for Public Health and Environment" + }, + { + "author_name": "Janneke HHM van de Wijgert", + "author_inst": "National Institute for Public Health and Environment" + }, + { + "author_name": "Susan van den Hof", + "author_inst": "National Institute for Public Health and Environment" + }, + { + "author_name": "Mirjam Knol", + "author_inst": "National Institute for Public Health and the Environment" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, + { + "rel_doi": "10.1101/2023.10.24.23297475", + "rel_title": "Projections of the incidence of COVID-19 in Japan and the potential impact of a Fall 2023 COVID-19 Vaccine", + "rel_date": "2023-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.24.23297475", + "rel_abs": "Background: The study objective was to estimate the incidence of COVID-19 infection, hospitalization, and deaths in Japan from September 2023 to August 2024 and potential impact of a Fall 2023 COVID-19 vaccine for adults 18 years and older on these outcomes. Methods: A previously developed Susceptible Exposed Infected Recovered model for the United States (US) was adapted to Japan. The numbers of symptomatic infections, COVID-19 related hospitalizations, and deaths were calculated. Given differences in vaccination coverage, masking practices and social mixing patterns between the US and Japan, all inputs were updated to reflect the Japanese context. Vaccine effectiveness (VE) values are hypothetical, but predicted based on existing VE values of bivalent BA.4/BA.5 boosters against BA.4/BA.5 in Japan, from the VERSUS test-negative case-control study. Sensitivity analyses were performed. Results: The base case model predicts overall that there will be approximately 35.2 million symptomatic COVID-19 infections, 690,000 hospitalizations, and 62,000 deaths in Japan between September 2023 and August 2024. If an updated COVID-19 vaccine is offered to all adults aged 18 years and older in Fall 2023, the model predicts that 7.3 million infections, 275,000 hospitalizations and 26,000 deaths will be prevented. If vaccines are only given to those aged 65 years and older, only 2.9 million infections, 180,000 hospitalizations and 19,000 deaths will be prevented. Sensitivity analysis results suggest that hospitalizations and deaths prevented are most sensitive to initial vaccine effectiveness (VE) against infection and hospitalizations, and the waning rate associated with VE against infection. Symptomatic infections prevented was most sensitive to initial VE against infection and VE waning. Conclusions: Results suggest that a Fall 2023 COVID-19 vaccine would reduce total numbers of COVID-19 related infections, hospitalizations, and deaths.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Michele Kohli", + "author_inst": "Quadrant Health Economics Inc." + }, + { + "author_name": "Michael Maschio", + "author_inst": "Quadrant Health Economics Inc." + }, + { + "author_name": "Amy Lee", + "author_inst": "Quadrant Health Economics Inc." + }, + { + "author_name": "Ataru Igarashi", + "author_inst": "Yokohama City University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.10.22.563156", "rel_title": "A 50-gene high-risk profile predictive of COVID-19 and Idiopathic Pulmonary Fibrosis mortality originates from a molecular imbalance in monocyte and T-cell subsets that reverses in survivors with post-COVID-19 Interstitial Lung Disease", "rel_date": "2023-10-24", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.22.563156", - "rel_abs": "Background: We aim to study the source of circulating immune cells expressing a 50-gene signature predictive of COVID-19 and IPF mortality. Methods: Whole blood and Peripheral Blood Mononuclear cells (PBMC) were obtained from 231 subjects with COVID-19, post-COVID-19-ILD, IPF and controls. We measured the 50-gene signature (nCounter, Nanostring), interleukin 6 (IL6), interferon gamma;-induced protein (IP10), secreted phosphoprotein 1 (SPP1) and transforming growth factor beta (TGF-beta) by Luminex. PCR was used to validate COVID-19 endotypes. For single-cell RNA sequencing (scRNA-seq) we used Chromium Controller (10X Genomics). For analysis we used the Scoring Algorithm of Molecular Subphenotypes (SAMS), Cell Ranger, Seurat, Propeller, Kaplan-Meier curves, CoxPH models, Two-way ANOVA, T-test, and Fisher exact. Results: We identified three genomic risk profiles based on the 50-gene signature, and a subset of seven genes, associated with low, intermediate, or high-risk of mortality in COVID-19 with significant differences in IL6, IP10, SPP1 and TGF{beta}-1. scRNA-seq identified Monocytic-Myeloid-Derived Suppressive cells (M-MDSCs) expressing CD14+HLA DRlowCD163+ and high levels of the 7-gene signature (7Gene-M-MDSC) in COVID-19. These cells were not observed in post-COVID-19-ILD or IPF. The 43-gene signature was mostly expressed in CD4 T and CD8 T cell subsets. Increased expression of the 43 gene signature was seen in T cell subsets from survivors with post-COVID-19-ILD. The expression of these genes remained low in IPF. Conclusion: A 50-gene, high-risk profile in COVID-19 is characterized by a genomic imbalance in monocyte and T-cell subsets that reverses in survivors with post-COVID-19 Interstitial Lung Disease.", + "rel_abs": "BackgroundWe aim to study the source of circulating immune cells expressing a 50-gene signature predictive of COVID-19 and IPF mortality.\n\nMethodsWhole blood and Peripheral Blood Mononuclear cells (PBMC) were obtained from 231 subjects with COVID-19, post-COVID-19-ILD, IPF and controls. We measured the 50-gene signature (nCounter, Nanostring), interleukin 6 (IL6), interferon {gamma}-induced protein (IP10), secreted phosphoprotein 1 (SPP1) and transforming growth factor beta (TGF-{beta}) by Luminex. PCR was used to validate COVID-19 endotypes. For single-cell RNA sequencing (scRNA-seq) we used Chromium Controller (10X Genomics). For analysis we used the Scoring Algorithm of Molecular Subphenotypes (SAMS), Cell Ranger, Seurat, Propeller, Kaplan-Meier curves, CoxPH models, Two-way ANOVA, T-test, and Fishers exact.\n\nResultsWe identified three genomic risk profiles based on the 50-gene signature, and a subset of seven genes, associated with low, intermediate, or high-risk of mortality in COVID-19 with significant differences in IL6, IP10, SPP1 and TGF{beta}-1. scRNA-seq identified Monocytic-Myeloid-Derived Suppressive cells (M-MDSCs) expressing CD14+HLA DRlowCD163+ and high levels of the 7-gene signature (7Gene-M-MDSC) in COVID-19. These cells were not observed in post-COVID-19-ILD or IPF. The 43-gene signature was mostly expressed in CD4 T and CD8 T cell subsets. Increased expression of the 43 gene signature was seen in T cell subsets from survivors with post-COVID-19-ILD. The expression of these genes remained low in IPF.\n\nConclusionA 50-gene, high-risk profile in COVID-19 is characterized by a genomic imbalance in monocyte and T-cell subsets that reverses in survivors with post-COVID-19 Interstitial Lung Disease", "rel_num_authors": 20, "rel_authors": [ { @@ -424,7 +2190,7 @@ "rel_date": "2023-10-24", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.23.563139", - "rel_abs": "Monoclonal antibodies (mAbs) administered intranasally as dry powders can be potentially applied for the treatment or pre-exposure prevention of viral infections in the upper respiratory tract. However, a method to transform the mAbs from liquid to dry powders suitable for intranasal administration and a device that can spray the dry powders to the desired region of the nasal cavity are needed to fully realize the potentials of the mAbs. Herein, we report that thin-film freeze-drying can be applied to prepare aerosolizable mAb dry powders and that the dry powders can be sprayed into the posterior nasal cavity using the Unidose (UDS) Powder Nasal Spray System from Aptar Pharma. AUG-3387, a human-derived mAb that neutralizes the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was used in the present study. First, we prepared AUG-3387 thin-film freeze-dried powders (i.e., TFF AUG-3387 powders) from liquid formulations containing different levels of mAbs. The TFF AUG-3387 powder with the highest solid content (i.e., TFF AUG-3387C powder) was then chosen for further characterization, including the evaluation of the plume geometry, spray pattern, and particle size distribution after the powder was sprayed using the UDS Powder device. Finally, the deposition patterns of the TFF AUG-3387C powder sprayed using the UDS Powder device were studied using 3D-printed nasal replica casts based on an adult model and a child model. It is concluded that it is feasible to intranasally deliver mAbs as dry powders by transforming the mAbs into dry powders using thin-film freeze-drying and then spray the powder using the UDS Powder device.", + "rel_abs": "Monoclonal antibodies (mAbs) administered intranasally as dry powders can be potentially applied for the treatment or pre-exposure prevention of viral infections in the upper respiratory tract. However, a method to transform the mAbs from liquid to dry powders suitable for intranasal administration and a device that can spray the dry powders to the desired region of the nasal cavity are needed to fully realize the potentials of the mAbs. Herein, we report that thin-film freeze-drying can be applied to prepare aerosolizable mAb dry powders and that the dry powders can be sprayed into the posterior nasal cavity using Aptar Pharmas Unidose (UDS) Powder Nasal Spray System. AUG-3387, a human-derived mAb that neutralizes the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was used in the present study. First, we prepared AUG-3387 thin-film freeze-dried powders (i.e., TFF AUG-3387 powders) from liquid formulations containing different levels of mAbs. The TFF AUG-3387 powder with the highest solid content (i.e., TFF AUG-3387C powder) was then chosen for further characterization, including the evaluation of the plume geometry, spray pattern, and particle size distribution after the powder was sprayed using the UDS Powder device. Finally, the deposition patterns of the TFF AUG-3387C powder sprayed using the UDS Powder device were studied using 3D-printed nasal replica casts based on an adult model and a child model. It is concluded that it is feasible to intranasally deliver mAbs as dry powders by transforming the mAbs into dry powders using thin-film freeze-drying and then spray the powder using the UDS Powder device.", "rel_num_authors": 11, "rel_authors": [ { @@ -593,7 +2359,7 @@ "rel_date": "2023-10-24", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.22.563481", - "rel_abs": "Background: Patients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients. Methods: We performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30). Results: Rituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination. Discussion: Our results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.", + "rel_abs": "BackgroundPatients with autoimmune/inflammatory conditions on anti-CD20 therapies, such as Rituximab, have suboptimal humoral responses to vaccination and are vulnerable to poorer clinical outcomes following SARS-CoV-2 infection. We aimed to examine how the fundamental parameters of antibody responses, namely affinity and concentration, shape the quality of humoral immunity after vaccination in these patients.\n\nMethodsWe performed in depth antibody characterisation in sera collected four to six weeks after each of three vaccine doses to wild-type (WT) SARS-CoV-2 in Rituximab-treated primary vasculitis patients (n=14) using Luminex and pseudovirus neutralisation assays, whereas a novel microfluidic-based immunoassay was used to quantify polyclonal antibody affinity and concentration against both WT and Omicron (B.1.1.529) variants. Comparative antibody profiling was performed at equivalent time points in healthy individuals after three antigenic exposures to WT SARS-CoV-2 (one infection and two vaccinations; n=15) and in convalescent patients after WT SARS-CoV-2 infection (n=30).\n\nResultsRituximab-treated patients had lower antibody levels and neutralisation titres against both WT and Omicron SARS-CoV-2 variants compared to healthy individuals. Neutralisation capacity was weaker against Omicron versus WT both in Rituximab-treated patients and in healthy individuals. In the Rituximab cohort, this was driven by lower antibody affinity against Omicron versus WT (median [range] KD: 21.6 [9.7-38.8] nM vs 4.6 [2.3-44.8] nM, p=0.0004). By contrast, healthy individuals with hybrid immunity produced a broader antibody response, a subset of which recognised Omicron with higher affinity than antibodies in Rituximab-treated patients (median [range] KD: 1.05 [0.45-1.84] nM vs 20.25 [13.2-38.8] nM, p=0.0002), underpinning the stronger serum neutralisation capacity against Omicron in the former group. Rituximab-treated patients had similar anti-WT antibody levels and neutralisation titres to unvaccinated convalescent individuals, despite two more exposures to SARS-CoV-2 antigen. Temporal profiling of the antibody response showed evidence of affinity maturation in healthy convalescent patients after a single SARS-CoV-2 infection which was not observed in Rituximab-treated patients, despite repeated vaccination.\n\nDiscussionOur results enrich previous observations of impaired humoral immune responses to SARS-CoV-2 in Rituximab-treated patients and highlight the significance of quantitative assessment of serum antibody affinity and concentration in monitoring anti-viral immunity, viral escape, and the evolution of the humoral response.", "rel_num_authors": 16, "rel_authors": [ { @@ -672,7 +2438,7 @@ "rel_date": "2023-10-24", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.23.563088", - "rel_abs": "Since it was proposed as a potential host-directed antiviral agent for SARS-CoV-2, the antiparasitic drug ivermectin has been investigated thoroughly in clinical trials, which have provided insufficient support for its clinical efficacy. To examine the potential for ivermectin to be repurposed as an antiviral agent, we therefore undertook a series of preclinical studies. Consistent with early reports, ivermectin decreased SARS-CoV-2 viral burden in in vitro models at low micromolar concentrations, five- to ten-fold higher than the reported toxic clinical concentration. At similar concentrations, ivermectin also decreased cell viability and increased biomarkers of cytotoxicity and apoptosis. Further mechanistic and profiling studies revealed that ivermectin nonspecifically perturbs membrane bilayers at the same concentrations where it decreases the SARS-CoV-2 viral burden, resulting in nonspecific modulation of membrane-based targets such as G-protein coupled receptors and ion channels. These results suggest that a primary molecular mechanism for the in vitro antiviral activity of ivermectin may be nonspecific membrane perturbation, indicating that ivermectin is unlikely to be translatable into a safe and effective antiviral agent. These results and experimental workflow provide a useful paradigm for performing preclinical studies on (pandemic-related) drug repurposing candidates.", + "rel_abs": "Since it was proposed as a potential host-directed antiviral agent for SARS-CoV-2, the antiparasitic drug ivermectin has been investigated thoroughly in clinical trials, which have provided insufficient support for its clinical efficacy. To examine the potential for ivermectin to be repurposed as an antiviral agent, we therefore undertook a series of preclinical studies. Consistent with early reports, ivermectin decreased SARS-CoV-2 viral burden in in vitro models at low micromolar concentrations, five-to ten-fold higher than the reported toxic clinical concentration. At similar concentrations, ivermectin also decreased cell viability and increased biomarkers of cytotoxicity and apoptosis. Further mechanistic and profiling studies revealed that ivermectin nonspecifically perturbs membrane bilayers at the same concentrations where it decreases the SARS-CoV-2 viral burden, resulting in nonspecific modulation of membrane-based targets such as G-protein coupled receptors and ion channels. These results suggest that a primary molecular mechanism for the in vitro antiviral activity of ivermectin may be nonspecific membrane perturbation, indicating that ivermectin is unlikely to be translatable into a safe and effective antiviral agent. These results and experimental workflow provide a useful paradigm for performing preclinical studies on (pandemic-related) drug repurposing candidates.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC=\"FIGDIR/small/563088v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@2900aaorg.highwire.dtl.DTLVardef@1eab7c1org.highwire.dtl.DTLVardef@c5f460org.highwire.dtl.DTLVardef@2edc75_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG", "rel_num_authors": 14, "rel_authors": [ { @@ -743,7 +2509,7 @@ "rel_date": "2023-10-24", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.24.563721", - "rel_abs": "The COVID-19 pandemic exemplified the need for a rapid, effective genomic-based surveillance system to predict emerging SARS-CoV-2 variants and lineages. Traditional molecular epidemiology methods, which leverage public health surveillance or integrated sequence data repositories, are able to characterize the evolutionary history of infection waves and genetic evolution but fall short in predicting future outlooks in promptly anticipating viral genetic alterations. To bridge this gap, we introduce a novel Deep learning, autoencoder-based method for anomaly detection in SARS-CoV-2 (DeepAutoCov). Trained and updated on the public global SARS-CoV-2 GISAID database. DeepAutoCov identifies Future Dominant Lineages (FDLs), defined as lineages comprising at least 25% of SARS-CoV-2 genomes added on a given week, on a weekly basis, using the Spike (S) protein. Our algorithm is grounded on anomaly detection via an unsupervised approach, which is necessary given that FDLs can be known only a posteriori (i.e., after they have become dominant). We developed two concurrent approaches (a linear unsupervised and a posteriori supervised) to evaluate DeepAutoCoV performance. DeepAutoCoV identifies FDL, using the spike (S) protein, with a median lead time of 31 weeks on global data and achieves a positive predictive value ~7x better and 23% higher than the other approaches. Furthermore, it predicts vaccine related FDLs up to 17 months in advance. Finally, DeepAutoCoV is not only predictive but also interpretable, since it can pinpoint specific mutations within FDLs, generating hypotheses on the potential increases in virulence or transmissibility of a lineage. By integrating genomic surveillance with artificial intelligence, our work marks a transformative step that may provide valuable insights for the optimization of public health prevention and intervention strategies.", + "rel_abs": "The COVID-19 pandemic exemplified the need for a rapid, effective genomic-based surveillance system to predict emerging SARS-CoV-2 variants and lineages. Traditional molecular epidemiology methods, which leverage public health surveillance or integrated sequence data repositories, are able to characterize the evolutionary history of infection waves and genetic evolution but fall short in predicting future outlooks in promptly anticipating viral genetic alterations. To bridge this gap, we introduce a novel Deep learning, autoencoder-based method for anomaly detection in SARS-CoV-2 (DeepAutoCov). Trained and updated on the public global SARS-CoV-2 GISAID database. DeepAutoCov identifies Future Dominant Lineages (FDLs), defined as lineages comprising at least 25% of SARS-CoV-2 genomes added on a given week, on a weekly basis, using the Spike (S) protein. Our algorithm is grounded on anomaly detection via an unsupervised approach, which is necessary given that FDLs can be known only a posteriori (i.e., after they have become dominant). We developed two concurrent approaches (a linear unsupervised and a posteriori supervised) to evaluate DeepAutoCoV performance. DeepAutoCoV identifies FDL, using the spike (S) protein, with a median lead time of 31 weeks on global data and achieves a positive predictive value [~]7x better and 23% higher than the other approaches. Furthermore, it predicts vaccine related FDLs up to 17 months in advance. Finally, DeepAutoCoV is not only predictive but also interpretable, since it can pinpoint specific mutations within FDLs, generating hypotheses on the potential increases in virulence or transmissibility of a lineage. By integrating genomic surveillance with artificial intelligence, our work marks a transformative step that may provide valuable insights for the optimization of public health prevention and intervention strategies.", "rel_num_authors": 6, "rel_authors": [ { @@ -782,7 +2548,7 @@ "rel_date": "2023-10-24", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.16.23297124", - "rel_abs": "Background: The WHO and the US. CDC documented that facemask-wearing in public situations is one of the most important prevention measures that can limit the acquisition and spread of COVID-19. Considering this, WHO and US. CDC developed guidelines for using facemasks in public settings. This study aimed to determine correlates and prevalence of facemask wearing during COVID-19 pandemic among adult population of Northern Uganda. Methods. We conducted a cross-sectional study on five hundred and eighty-seven adult population of northern Uganda. A single stage stratified, and systematic sampling methods were used to select respondents from twenty-four Acholi subregions health facilities. Data was collected in a face-to-face questionnaire interview with an internal validity of Cronbach's =0.72. A local IRB approved the study, and Stata 18 was used for data analysis at multivariable Poisson regression with a p-value set at [≤]0.05. Results: The most substantial findings from this study were the high prevalence of face mask-wearing in public among respondents [88.7%,95%CI:86%-91%]. At a multivariable Poisson regression analysis, we found that obese respondents were 1.12 times more likely to wear facemasks than those who were not, [adjusted Interval Rates Ratios, aIRR=1.12,95%CI:1.04-1.19;p<0.01], and respondent who agreed to the lockdown measures were 1.23 times more likely to wear facemasks during COVID-19 pandemic than those who did not, [aIRR=1.23, 95%CI:1.07-1.41;p<0.01]. Other sociodemographic characteristics such as sex, age, occupation, level of education, religion, tribes, marital status, nationality, race, and comorbidities were not statistically significant at 95% Confidence Intervals. Conclusion: The most significant findings from this study were the high prevalence of face mask-wearing among adult community members in northern Uganda. The correlates of facemask wearing in public were the obese and respondents who agreed with the presidential directives on the lockdown measures. Although this was within acceptable prevalence rates, the strict enforcement of face mask-wearing by security forces raised concerns among many community members and human rights advocates. We recommend more studies on communities' perspectives on the challenges and benefits of facemask-wearing during the COVID-19 pandemic.", + "rel_abs": "BackgroundThe WHO and the US. CDC documented that facemask-wearing in public situations is one of the most important prevention measures that can limit the acquisition and spread of COVID-19. Considering this, WHO and US. CDC developed guidelines for using facemasks in public settings. This study aimed to determine correlates and prevalence of facemask wearing during COVID-19 pandemic among adult population of Northern Uganda.\n\nMethodsWe conducted a cross-sectional study on five hundred and eighty-seven adult population of northern Uganda. A single stage stratified, and systematic sampling methods were used to select respondents from twenty-four Acholi subregions health facilities. Data was collected in a face-to-face questionnaire interview with an internal validity of Cronbachs =0.72. A local IRB approved the study, and Stata 18 was used for data analysis at multivariable Poisson regression with a p-value set at [≤]0.05.\n\nResultsThe most substantial findings from this study were the high prevalence of face mask-wearing in public among respondents [88.7%,95%CI:86%-91%]. At a multivariable Poisson regression analysis, we found that obese respondents were 1.12 times more likely to wear facemasks than those who were not, [adjusted Interval Rates Ratios, aIRR=1.12,95%CI:1.04-1.19;p<0.01], and respondent who agreed to the lockdown measures were 1.23 times more likely to wear facemasks during COVID-19 pandemic than those who did not, [aIRR=1.23, 95%CI:1.07-1.41;p<0.01]. Other sociodemographic characteristics such as sex, age, occupation, level of education, religion, tribes, marital status, nationality, race, and comorbidities were not statistically significant at 95% Confidence Intervals.\n\nConclusionThe most significant findings from this study were the high prevalence of face mask-wearing among adult community members in northern Uganda. The correlates of facemask wearing in public were the obese and respondents who agreed with the presidential directives on the lockdown measures. Although this was within acceptable prevalence rates, the strict enforcement of face mask-wearing by security forces raised concerns among many community members and human rights advocates. We recommend more studies on communities perspectives on the challenges and benefits of facemask-wearing during the COVID-19 pandemic.", "rel_num_authors": 15, "rel_authors": [ { @@ -947,7 +2713,7 @@ "rel_date": "2023-10-23", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.21.563433", - "rel_abs": "Motivation: Charged amino acid residues on the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been shown to influence its binding to different cell surface receptors, its non-specific electrostatic interactions with the environment, and its structural stability and conformation. It is therefore important to obtain a good understanding of amino acid mutations that affect the total charge on the spike protein which have arisen across different SARS-CoV-2 lineages during the course of the virus' evolution. Results: We analyse the change in the number of ionizable amino acids and the corresponding total charge on the spike proteins of almost 2000 SARS-CoV-2 lineages that have emerged over the span of the pandemic. Our results show that the previously observed trend toward an increase in the positive charge on the spike protein of SARS-CoV-2 variants of concern has essentially stopped with the emergence of the early omicron variants. Furthermore, recently emerged lineages show a greater diversity in terms of their composition of ionizable amino acids. We also demonstrate that the patterns of change in the number of ionizable amino acids on the spike protein are characteristic of related lineages within the broader clade division of the SARS-CoV-2 phylogenetic tree. Due to the ubiquity of electrostatic interactions in the biological environment, our findings are relevant for a broad range of studies dealing with the structural stability of SARS-CoV-2 and its interactions with the environment. Availability: The data underlying the article are available in the online Supplementary Material.", + "rel_abs": "MotivationCharged amino acid residues on the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been shown to influence its binding to different cell surface receptors, its non-specific electrostatic interactions with the environment, and its structural stability and conformation. It is therefore important to obtain a good understanding of amino acid mutations that affect the total charge on the spike protein which have arisen across different SARS-CoV-2 lineages during the course of the virus evolution.\n\nResultsWe analyse the change in the number of ionizable amino acids and the corresponding total charge on the spike proteins of almost 2000 SARS-CoV-2 lineages that have emerged over the span of the pandemic. Our results show that the previously observed trend toward an increase in the positive charge on the spike protein of SARS-CoV-2 variants of concern has essentially stopped with the emergence of the early omicron variants. Furthermore, recently emerged lineages show a greater diversity in terms of their composition of ionizable amino acids. We also demonstrate that the patterns of change in the number of ionizable amino acids on the spike protein are characteristic of related lineages within the broader clade division of the SARS-CoV-2 phylogenetic tree. Due to the ubiquity of electrostatic interactions in the biological environment, our findings are relevant for a broad range of studies dealing with the structural stability of SARS-CoV-2 and its interactions with the environment.\n\nAvailabilityThe data underlying the article are available in the online Supplementary Material.", "rel_num_authors": 2, "rel_authors": [ { @@ -1155,7 +2921,7 @@ "rel_date": "2023-10-23", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.23.23297388", - "rel_abs": "ABSTRACT \"Purpose/ Introduction: Recent Evidences reveal that COVID-19 pandemic caused MCH services interruption world-wide. In Timor-Leste, MCH services is one of service priorities and delivers through 3 tiers of health structures consists of hospitals, CHCs, and HPs. The Country (Timor-Leste) identified its first case of COVID-19 in March and by April 2020, it was lockdown and stringent actions were enforced. Nuring the pandemic COVID-19, the MOH health structures and facilities continued delivers essential health services. However, the strict lockdown and mandatory stay home order had negatively impacted the health system capacities. This study to thoroughly assess the disruption of System Components of MCH Services by interviewed frontline HCWs from Comoro -CHC, in Dili-Timor-Leste. Patients and Methods: The cross-sectional approach with quantitative descriptive method was employed for this study. We employed a modified who six building blocks (service delivery, human resources, drugs and consumables, ICT, Financing, Stewardship) to assess system disruption of MCH services in Comoro CHC due to COVID-19 Pandemic. Sample of 99 participants consisted of medical doctors, midwives, nurses who work at MCH unit pharmacy technicians, unit laboratory technicians, a structured questionnaire was utilized and data analysis was used SPSS. Result: The findings reveal the disruption of all 6 system blocks from MCH services in Comoro-CHC, Dili, Timor-Leste due to COVID-19 Pandemic. Except leadership, statistical tests reveal statistically significant association between interruption of five blocks from MCH services. The service delivery, human resources, drugs and consumables, ICT, Financing, Stewardship. Conclusion: COVID-19 Pandemic Caused disruption of all six health system blocks of MCH Services in Comoro, CHC. For future pandemic preparation plan, the attention must be given to all six-health system blocks to guarantee continue delivery of MCH care in CHC Comoro, Dili, Timor-Leste and a primary health care facility and other similar settings.Keywords: Performance, Maternal, Child, Health, System, COVID-19\"", + "rel_abs": "Purpose/ IntroductionRecent Evidences reveal that COVID-19 pandemic caused MCH services interruption world-wide. In Timor-Leste, MCH services is one of service priorities and delivers through 3 tiers of health structures consists of hospitals, CHCs, and HPs. The Country (Timor-Leste) identified its first case of COVID-19 in March and by April 2020, it was lockdown and stringent actions were enforced. During the pandemic COVID-19, the MOH health structures and facilities continued delivers essential health services. However, the strict lockdown and mandatory stay home order had negatively impacted the health system capacities. This study to thoroughly assess the disruption of System Components of MCH Services by interviewed frontline HCWs from Comoro -CHC, in Dili-Timor-Leste.\n\nPatients and MethodsThe cross-sectional approach with quantitative descriptive method was employed for this study. We employed a modified who six building blocks (service delivery, human resources, drugs and consumables, ICT, Financing, Stewardship) to assess system disruption of MCH services in Comoro CHC due to COVID-19 Pandemic. Sample of 99 participants consisted of medical doctors, midwives, nurses who work at MCH unit pharmacy technicians, unit laboratory technicians, a structured questionnaire was utilized and data analysis was used SPSS.\n\nResultThe findings reveal the disruption of all 6 system blocks from MCH services in Comoro-CHC, Dili, Timor-Leste due to COVID-19 Pandemic. Except leadership, statistical tests reveal statistically significant association between interruption of five blocks from MCH services. The service delivery, human resources, drugs and consumables, ICT, Financing, Stewardship.\n\nConclusionCOVID-19 Pandemic Caused disruption of all six health system blocks of MCH Services in Comoro, CHC. For future pandemic preparation plan, the attention must be given to all six-health system blocks to guarantee continue delivery of MCH care in CHC Comoro, Dili, Timor-Leste and a primary health care facility and other similar settings.", "rel_num_authors": 5, "rel_authors": [ { @@ -1190,7 +2956,7 @@ "rel_date": "2023-10-23", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.22.23297358", - "rel_abs": "OBJECTIVE: To estimate the fraction of cancer cases and deaths attributable to potentially modifiable risk factors in Peru in 2018, prior to the COVID-19 pandemic. MATERIAL AND METHODS: An ecological study was carried out using the prevalence of exposure of the Peruvian population to modifiable risk factors for cancer, relative risk of each risk factor, and number of cancer cases and deaths in 2018 as inputs. We used the Parkin formula with a Montecarlo statistical simulation model to calculate the population attributable fraction (PAF) and confidence intervals. The number of new cancer cases and deaths attributable to each risk factor was calculated by multiplying the number of cases and deaths in each sex by the PAF of each risk factor. RESULTS: 38.4% of new cases (34.4% in men and 41.8% in women) and 43.2% of deaths by cancer in Peru (43.1% in men and 43.2% in women) were attributable to modifiable risk factors. The number of cancers attributable was 25,591 (10,616 in men and 14,975 in women) and the number of deaths attributable to cancer was 14,922 (6,996 in men and 7,926 in women). The modifiable risk factors that caused a greater number of cases and deaths were HPV infection (4563 cases, 2410 deaths), current tobacco use (3387 cases, 2198 deaths), and Helicobacter pylori infection (2686 cases, 1874 deaths). The oncogenic infections made up the group of risk factors that presented a greater PAF (16.6% for cases, 19.1% for deaths) followed by other unhealthy lifestyle factors (14.1% for cases, 16.5% for deaths), tobacco (7.2% for cases, 7.3% for deaths) and ultraviolet radiation (0.5% for cases, 0.3% for deaths). CONCLUSION: Prior to the COVID-19 pandemic, a proportion of 38.4% of cancer cases and 43.2% of cancer deaths in Peru during 2018 were attributable to modifiable risk factors. Most preventable cancer cases and deaths are linked to oncogenic infections, primarily caused by HPV and Helicobacter pylori.", + "rel_abs": "OBJECTIVETo estimate the fraction of cancer cases and deaths attributable to potentially modifiable risk factors in Peru in 2018, prior to the COVID-19 pandemic.\n\nMATERIAL AND METHODSAn ecological study was carried out using the prevalence of exposure of the Peruvian population to modifiable risk factors for cancer, relative risk of each risk factor, and number of cancer cases and deaths in 2018 as inputs. We used the Parkin formula with a Montecarlo statistical simulation model to calculate the population attributable fraction (PAF) and confidence intervals. The number of new cancer cases and deaths attributable to each risk factor was calculated by multiplying the number of cases and deaths in each sex by the PAF of each risk factor.\n\nRESULTS38.4% of new cases (34.4% in men and 41.8% in women) and 43.2% of deaths by cancer in Peru (43.1% in men and 43.2% in women) were attributable to modifiable risk factors. The number of cancers attributable was 25,591 (10,616 in men and 14,975 in women) and the number of deaths attributable to cancer was 14,922 (6,996 in men and 7,926 in women). The modifiable risk factors that caused a greater number of cases and deaths were HPV infection (4563 cases, 2410 deaths), current tobacco use (3387 cases, 2198 deaths), and Helicobacter pylori infection (2686 cases, 1874 deaths). The oncogenic infections made up the group of risk factors that presented a greater PAF (16.6% for cases, 19.1% for deaths) followed by other unhealthy lifestyle factors (14.1% for cases, 16.5% for deaths), tobacco (7.2% for cases, 7.3% for deaths) and ultraviolet radiation (0.5% for cases, 0.3% for deaths).\n\nCONCLUSIONPrior to the COVID-19 pandemic, a proportion of 38.4% of cancer cases and 43.2% of cancer deaths in Peru during 2018 were attributable to modifiable risk factors. Most preventable cancer cases and deaths are linked to oncogenic infections, primarily caused by HPV and Helicobacter pylori.", "rel_num_authors": 8, "rel_authors": [ { @@ -1237,7 +3003,7 @@ "rel_date": "2023-10-23", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.22.23297069", - "rel_abs": "Background Limited data about chronic post-COVID neuropsychiatric complaints exist in the literature. Aim: Our study aims to delineate the phenotypes of chronic neuropsychiatric symptoms among adult subjects recovering from their first COVID that occurred more than one year ago. We also aim to explore the clinical and socioeconomic risk factors of having a high loading of chronic neuropsychiatric symptoms. Methods We recruited a post-COVID group who suffered from their first pre-Omicron COVID more than a year ago, and a control group who had never had COVID. The subjects completed app-based questionnaires on demographic, socioeconomic and health status, a COVID symptoms checklist, mental and sleep health measures, and neurocognitive tests. Results The post-COVID group has a statistically significantly higher level of fatigue compared to the control group (p<0.001). Among the post-COVID group, the lack of any COVID vaccination before the first COVID and a higher level of material deprivation before the COVID pandemic predicts a higher load of chronic post-COVID neuropsychiatric symptoms. Partial correlation network analysis suggests that the chronic post-COVID neuropsychiatric symptoms can be clustered into two major (cognitive complaints -fatigue and anxiety-depression) and one minor (headache-dizziness) cluster. A higher level of material deprivation predicts a higher number of symptoms in both major clusters, but the lack of any COVID vaccination before the first COVID only predicts a higher number of symptoms in the cognitive complaints-fatigue cluster. Conclusions Our result suggests heterogeneity among chronic post-COVID neuropsychiatric symptoms, which are associated with the complex interplay of biological and socioeconomic factors.", + "rel_abs": "BackgroundLimited data about chronic post-COVID neuropsychiatric complaints exist in the literature.\n\nAimOur study aims to delineate the phenotypes of chronic neuropsychiatric symptoms among adult subjects recovering from their first COVID that occurred more than one year ago. We also aim to explore the clinical and socioeconomic risk factors of having a high loading of chronic neuropsychiatric symptoms.\n\nMethodsWe recruited a post-COVID group who suffered from their first pre-Omicron COVID more than a year ago, and a control group who had never had COVID. The subjects completed app-based questionnaires on demographic, socioeconomic and health status, a COVID symptoms checklist, mental and sleep health measures, and neurocognitive tests.\n\nResultsThe post-COVID group has a statistically significantly higher level of fatigue compared to the control group (p<0.001). Among the post-COVID group, the lack of any COVID vaccination before the first COVID and a higher level of material deprivation before the COVID pandemic predicts a higher load of chronic post-COVID neuropsychiatric symptoms. Partial correlation network analysis suggests that the chronic post-COVID neuropsychiatric symptoms can be clustered into two major (cognitive complaints -fatigue and anxiety-depression) and one minor (headache-dizziness) cluster. A higher level of material deprivation predicts a higher number of symptoms in both major clusters, but the lack of any COVID vaccination before the first COVID only predicts a higher number of symptoms in the cognitive complaints-fatigue cluster.\n\nConclusionsOur result suggests heterogeneity among chronic post-COVID neuropsychiatric symptoms, which are associated with the complex interplay of biological and socioeconomic factors.", "rel_num_authors": 12, "rel_authors": [ { @@ -2129,6 +3895,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.10.19.563117", + "rel_title": "Neuroinflammation in post-acute sequelae of COVID-19 (PASC) as assessed by PBR28 PET correlates with vascular disease measures", + "rel_date": "2023-10-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.19.563117", + "rel_abs": "The COVID-19 pandemic caused by SARS-CoV-2 has triggered a consequential public health crisis of post-acute sequelae of COVID-19 (PASC), sometimes referred to as long COVID. The mechanisms of the heterogeneous persistent symptoms and signs that comprise PASC are under investigation, and several studies have pointed to the central nervous and vascular systems as being potential sites of dysfunction. In the current study, we recruited individuals with PASC with diverse symptoms, and examined the relationship between neuroinflammation and circulating markers of vascular dysfunction. We used [11C]PBR28 PET neuroimaging, a marker of neuroinflammation, to compare 12 PASC individuals versus 43 normative healthy controls. We found significantly increased neuroinflammation in PASC versus controls across a wide swath of brain regions including midcingulate and anterior cingulate cortex, corpus callosum, thalamus, basal ganglia, and at the boundaries of ventricles. We also collected and analyzed peripheral blood plasma from the PASC individuals and found significant positive correlations between neuroinflammation and several circulating analytes related to vascular dysfunction. These results suggest that an interaction between neuroinflammation and vascular health may contribute to common symptoms of PASC.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Michael B VanElzakker", + "author_inst": "Massachusetts General Hospital / Harvard Medical School" + }, + { + "author_name": "Hannah F Bues", + "author_inst": "Massachusetts General Hospital / Harvard Medical School" + }, + { + "author_name": "Ludovica Brusaferri", + "author_inst": "London South Bank University, Massachusetts General Hospital / Harvard Medical School" + }, + { + "author_name": "Minhae Kim", + "author_inst": "Massachusetts General Hospital / Harvard Medical School" + }, + { + "author_name": "Deena Saadi", + "author_inst": "Massachusetts General Hospital / Harvard Medical School" + }, + { + "author_name": "Eva-Maria Ratai", + "author_inst": "Massachusetts General Hospital / Harvard Medical School" + }, + { + "author_name": "Darin D Dougherty", + "author_inst": "Massachusetts General Hospital / Harvard Medical School" + }, + { + "author_name": "Marco L Loggia", + "author_inst": "Massachusetts General Hospital / Harvard Medical School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2023.10.19.563051", "rel_title": "FAKHRAVAC and BBIBP-CorV vaccine seeds' binding to angiotensin-converting enzyme 2: A comparative molecular dynamics study", @@ -2250,41 +4063,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.10.18.563024", - "rel_title": "Caveolin-1 mediates neuroinflammation and cognitive impairment in SARS-CoV-2 infection", - "rel_date": "2023-10-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.18.563024", - "rel_abs": "Leukocyte infiltration of the CNS can contribute to neuroinflammation and cognitive impairment. Brain endothelial cells regulate adhesion, activation, and diapedesis of T cells across the blood-brain barrier (BBB) in inflammatory diseases. The integral membrane protein Caveolin-1 (Cav-1) critically regulates BBB permeability, but its influence on T cell CNS infiltration in respiratory viral infections is unknown. In this study, we sought to determine the role of Cav-1 at the BBB in neuroinflammation in a COVID-19 mouse model. We used mice genetically deficient in Cav-1 to test the role of this protein in T cell infiltration and cognitive impairment. We found that SARS-CoV-2 infection upregulated brain endothelial Cav-1. Moreover, SARS-CoV-2 infection increased brain endothelial cell vascular cell adhesion molecule-1 (VCAM-1) and CD3+ T cell infiltration of the hippocampus, a region important for short term learning and memory. Concordantly, we observed learning and memory deficits. Importantly, genetic deficiency in Cav-1 attenuated brain endothelial VCAM-1 expression and T cell infiltration in the hippocampus of mice with SARS-CoV-2 infection. Moreover, Cav-1 KO mice were protected from the learning and memory deficits caused by SARS-CoV-2 infection. These results indicate the importance of BBB permeability in COVID-19 neuroinflammation and suggest potential therapeutic value of targeting Cav-1 to improve disease outcomes.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Troy Nolan Trevino", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Avital B Fogel", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Richard Minshall", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Justin M Richner", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Sarah E Lutz", - "author_inst": "University of Illinois at Chicago" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2023.10.18.563016", "rel_title": "Th2 and Th17-Associated Immunopathology Following SARS-CoV-2 Breakthrough Infection in Spike-vaccinated ACE2-humanized Mice", @@ -2882,7 +4660,7 @@ "rel_date": "2023-10-16", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.13.562198", - "rel_abs": "This research offers a bioinformatics approach to forecasting both domestic and wild animals likelihood of being susceptible to SARS-CoV-2 infection. Genomic sequencing can resolve phylogenetic relationships between the virus and the susceptible host. The genome sequence of SARS-CoV-2 is highly interactive with the specific sequence region of the ACE2 receptor of the host species. We further evaluate this concept to identify the most important SARS-CoV-2 binding amino acid sites in the ACE2 receptor sequence through the common similarity of the last common amino acid sites (LCAS) in known susceptible host species. Therefore, the SARS-CoV-2 viral genomic interacting key amino acid region in the ACE2 receptor sequence of known susceptible human host was summarized and compared with other reported known SARS-CoV-2 susceptible host species. We identified the 10 most significant amino acid sites for interaction with SARS-CoV-2 infection from the ACE2 receptor sequence region based on the LCAS similarity pattern in known sensitive SARS-CoV-2 hosts. The most significant 10 LCAS were further compared with ACE2 receptor sequences of unknown species to evaluate the similarity of the last common amino acid pattern (LCAP). We predicted the probability of SARS-CoV-2 infection risk in unknown species through the LCAS similarity pattern. This method can be used as a screening tool to assess the risk of SARS-CoV-2 infection in domestic and wild animals to prevent outbreaks of infection.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC=\"FIGDIR/small/562198v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (25K):\norg.highwire.dtl.DTLVardef@e272d7org.highwire.dtl.DTLVardef@e188e3org.highwire.dtl.DTLVardef@e20a34org.highwire.dtl.DTLVardef@bfe3a_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "This research offers a bioinformatics approach to forecasting both domestic and wild animals likelihood of being susceptible to SARS-CoV-2 infection. Genomic sequencing can resolve phylogenetic relationships between the virus and the susceptible host. The genome sequence of SARS-CoV-2 is highly interactive with the specific sequence region of the ACE2 receptor of the host species. We further evaluate this concept to identify the most important SARS-CoV-2 binding amino acid sites in the ACE2 receptor sequence through the common similarity of the last common amino acid sites (LCAS) in known susceptible host species. Therefore, the SARS-CoV-2 viral genomic interacting key amino acid region in the ACE2 receptor sequence of known susceptible human host was summarized and compared with other reported known SARS-CoV-2 susceptible host species. We identified the 10 most significant amino acid sites for interaction with SARS-CoV-2 infection from the ACE2 receptor sequence region based on the LCAS similarity pattern in known sensitive SARS-CoV-2 hosts. The most significant 10 LCAS were further compared with ACE2 receptor sequences of unknown species to evaluate the similarity of the last common amino acid pattern (LCAP). We predicted the probability of SARS-CoV-2 infection risk in unknown species through the LCAS similarity pattern. This method can be used as a screening tool to assess the risk of SARS-CoV-2 infection in domestic and wild animals to prevent outbreaks of infection.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC=\"FIGDIR/small/562198v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (25K):\norg.highwire.dtl.DTLVardef@1c77e4corg.highwire.dtl.DTLVardef@34cf43org.highwire.dtl.DTLVardef@113734forg.highwire.dtl.DTLVardef@1f763c8_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 8, "rel_authors": [ { @@ -3719,6 +5497,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.10.12.561995", + "rel_title": "Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein driving the genesis of Omicron variants", + "rel_date": "2023-10-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.12.561995", + "rel_abs": "Continued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants has long been suggested but its molecular basis remains poorly understood. Here, we identify a class of SARS-CoV-2 neutralising public antibodies defined by their shared usage of VL6-57 light chains. Although heavy chains of diverse genotypes are utilized, convergent HCDR3 rearrangements have been observed among these public antibodies to cooperate with germline VL6-57 LCDRs to target a convergent epitope defined by RBD residues S371-S373-S375. Antibody repertoire analysis identifies that this class of VL6-57 antibodies is present in SARS-CoV-2-naive individuals and is clonally expanded in most COVID-19 patients. We confirm that Omicron specific substitutions at S371, S373 and S375 mediate escape of antibodies of the VL6-57 class. These findings support that this class of public antibodies constitutes immune pressure promoting the introduction of S371L/F-S373P-S375F in Omicron variants. The results provide further molecular evidences to support that antigenic evolution of SARS-CoV-2 is driven by antibody mediated population immunity.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Qihong Yan", + "author_inst": "The First Affiliated Hospital of Guangzhou Medical University" + }, + { + "author_name": "Xijie Gao", + "author_inst": "The Fifth Affiliated Hospital of Guangzhou Medical University" + }, + { + "author_name": "Banghui Liu", + "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" + }, + { + "author_name": "Ruitian Hou", + "author_inst": "Guangzhou Eighth People's Hospital, Guangzhou Medical University" + }, + { + "author_name": "Ping He", + "author_inst": "Guangzhou National Laboratory" + }, + { + "author_name": "Yong Ma", + "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" + }, + { + "author_name": "Yudi Zhang", + "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" + }, + { + "author_name": "Yanjun Zhang", + "author_inst": "The First Affiliated Hospital of Guangzhou Medical University" + }, + { + "author_name": "Zimu Li", + "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" + }, + { + "author_name": "Qiuluan Chen", + "author_inst": "Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory)" + }, + { + "author_name": "Jingjing Wang", + "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" + }, + { + "author_name": "Xiaohan Huang", + "author_inst": "The First Affiliated Hospital of Guangzhou Medical University" + }, + { + "author_name": "Huan Liang", + "author_inst": "The First Affiliated Hospital of Guangzhou Medical University" + }, + { + "author_name": "Xianying Chen", + "author_inst": "The First Affiliated Hospital of Guangzhou Medical University" + }, + { + "author_name": "Xuefeng Niu", + "author_inst": "The First Affiliated Hospital of Guangzhou Medical University" + }, + { + "author_name": "Jun He", + "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" + }, + { + "author_name": "Ling Chen", + "author_inst": "Guangzhou National Laboratory" + }, + { + "author_name": "Jincun Zhao", + "author_inst": "The First Affiliated Hospital of Guangzhou Medical University" + }, + { + "author_name": "Xiaoli Xiong", + "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2023.10.12.561935", "rel_title": "Hidden evolutionary constraints dictate the retention of coronavirus accessory genes", @@ -3884,105 +5753,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.10.12.23296948", - "rel_title": "A nationwide study of 331 rare diseases among 58 million individuals: prevalence, demographics, and COVID-19 outcomes", - "rel_date": "2023-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.12.23296948", - "rel_abs": "BackgroundThe Global Burden of Disease study has provided key evidence to inform clinicians, researchers, and policy makers across common diseases, but no similar effort with single study design exists for hundreds of rare diseases. Consequently, many rare conditions lack population-level evidence including prevalence and clinical vulnerability. This has led to the absence of evidence-based care for rare diseases, prominently in the COVID-19 pandemic.\n\nMethodThis study used electronic health records (EHRs) of more than 58 million people in England, linking nine National Health Service datasets spanning healthcare settings for people alive on Jan 23, 2020. Starting with all rare diseases listed in Orphanet, we quality assured and filtered down to analyse 331 conditions with ICD-10 or SNOMED-CT mappings clinically validated in our dataset. We report 1) population prevalence, clinical and demographic details of rare diseases, and 2) investigate differences in mortality with SARs-CoV-2.\n\nFindingsAmong 58,162,316 individuals, we identified 894,396 with at least one rare disease. Prevalence data in Orphanet originates from various sources with varying degrees of precision. Here we present reproducible age and gender-adjusted estimates for all 331 rare diseases, including first estimates for 186 (56.2%) without any reported prevalence estimate in Orphanet. We identified 49 rare diseases significantly more frequent in females and 62 in males. Similarly we identified 47 rare diseases more frequent in Asian as compared to White ethnicity and 22 with higher Black to white ratios as compared to similar ratios in population controls. 37 rare diseases were overrepresented in the white population as compared to both Black and Asian ethnicities. In total, 7,965 of 894,396 (0.9%) of rare-disease patients died from COVID-19, as compared to 141,287 of 58,162,316 (0.2%) in the full study population. Eight rare diseases had significantly increased risks for COVID-19-related mortality in fully vaccinated individuals, with bullous pemphigoid (8.07[3.01-21.62]) being worst affected.\n\nInterpretationOur study highlights that National-scale EHRs provide a unique resource to estimate detailed prevalence, clinical and demographic data for rare diseases. Using COVID-19-related mortality analysis, we showed the power of large-scale EHRs in providing insights to inform public health decision-making for these often neglected patient populations.\n\nFundingBritish Heart Foundation Data Science Centre, led by Health Data Research UK.\n\nResearch in contextO_ST_ABSEvidence before the studyC_ST_ABSWe have previously published the largest study looking at COVID-19 across rare diseases, but with a sample size of 158 COVID-19 infected rare disease patients and 125 unaffected relatives, from Genomics England, the power of that study was limited. We searched PubMed from database inception to Apr 21, 2023, for publications using the search terms \"COVID-19\" or \"SARS-CoV-2\" and \"rare disease\" or \"ORPHANET\", without language restrictions. There are many studies examining the severity of COVID-19 in rare disease patients. However, to date, most studies have focused on a single or a few rare diseases associated with severity of COVID-19, and not taken a comprehensive rare disease wide approach. So far no studies have examined the impact of vaccination on mortality in rare disease patients. Moreover, the sample size used to examine rare diseases is limited in most studies. The largest study we identified included 168,680 individuals but only focused on autoimmune rheumatic disease.\n\nAdded value of this studyIn this study we use national scale EHR data from England to report age and gender adjusted point prevalence for 331 rare diseases, with clinically-validated ICD-10 and/or SNOMED-CT code lists. Among these, 186 (56.2%) diseases did not have existing point prevalence data available in Orphanet. To our knowledge, this is the first time that rare diseases have been examined on a national scale, encompassing a population of over 58 million people. The large sample size provides sufficient statistical power to detect and describe enough carriers of even very rare conditions <1 case per million. Our analysis of COVID-related mortality has demonstrated the clinical relevance of national data for rare diseases. Specifically, we identified eight rare conditions that are associated with a significantly increased risk of mortality from COVID-19, even among fully vaccinated individuals.\n\nImplication of all the available evidenceThese findings provide robust reproducible prevalence, gender, and ethnicity estimates for disease that may often have been under prioritised, and where such information in most cases was not previously available. Our COVID-19 mortality findings highlight the need for targeted policy and support addressing the high level of vulnerability of these patients to COVID-19.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Johan H Thygesen", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "HUAYU ZHANG", - "author_inst": "Advanced Care Research Centre, Usher Institute, University of Edinburgh, Edinburgh, UK." - }, - { - "author_name": "Hanane Issa", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Jinge Wu", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Tuankasfee Hama", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Ana-Catarina Pinho-Gomes", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Tudor Groza", - "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK" - }, - { - "author_name": "Sara Khalid", - "author_inst": "Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, Oxford, UK" - }, - { - "author_name": "Richard Lumbers", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Mevhibe Hocaoglu", - "author_inst": "Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, Kings College London, London, UK" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "College of Life Sciences, University of Leicester, Leicester, UK" - }, - { - "author_name": "Rouven Priedon", - "author_inst": "Health Data Research UK, London, UK" - }, - { - "author_name": "Amitava Banerjee", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Nikolas Pontikos", - "author_inst": "UCL Institute of Ophthalmology, University College London, London EC1V 9EL, UK" - }, - { - "author_name": "Christopher Tomlinson", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Ana Torralbo", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Paul Taylor", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Cathie Sudlow", - "author_inst": "Health Data Research UK, London, UK; British Heart Foundation Data Science Centre, London, UK; Centre for Clinical Brain Sciences, University of Edinburgh, Edin" - }, - { - "author_name": "Spiros Denaxas", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Harry Hemingway", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Honghan Wu", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2023.10.12.561993", "rel_title": "Akaluc bioluminescence offers superior sensitivity to track in vivo dynamics of SARS-CoV-2 infection", @@ -5745,6 +7515,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.10.09.23296732", + "rel_title": "Unravelling Causal Associations between Population Mobility and COVID-19 Cases in Spain: a Transfer Entropy Analysis", + "rel_date": "2023-10-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.09.23296732", + "rel_abs": "Human mobility is a well-known factor in the spread of infectious diseases. During the COVID-19 pandemic, the rapid spread of the SARS-CoV-2 virus led to healthcare systems collapsing in numerous countries, such as Spain and Italy, resulting in a significant number of deaths. To avoid such disastrous outcomes in the future, it is vital to understand how population mobility is linked to the spread of infectious diseases. To assess that, we applied an information theoretic approach called transfer entropy (TE) to measure the influence of the number of infected people travelling between two localities on the future number of infected people in the destination. We first validated our approach using simulated data from a SIR epidemiological model and found that the mobility-based TE was effective in filtering out non-causal influences that could otherwise arise, thereby successfully recovering the epidemics spreading patterns and the mobility network topology. We then applied the mobility-based TE to analyse the COVID-19 pandemic in Spain. We identified which regions acted as the main drivers of the pandemic at different periods, both globally and locally. Our results unravelled significant epidemiological events such as the outbreak in Lleida during the Summer of 2020, caused by the influx of temporary workers. We also analysed the effects of a non-pharmaceutical intervention in Catalunya, using mobility- based TE to compare the infection dynamics with a control region. These results help clarify how human mobility influences the dynamic spread of infectious diseases and could be used to inform future non-pharmaceutical interventions.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Miguel Ponce de Leon", + "author_inst": "Barcelona Supercomputing Center" + }, + { + "author_name": "Camila Pontes", + "author_inst": "Barcelona Supercomputing Center" + }, + { + "author_name": "Alex Arenas", + "author_inst": "Universitat Rovira i Virgili" + }, + { + "author_name": "Alfonso Valencia", + "author_inst": "Barcelona supercomputing Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.10.09.23296737", "rel_title": "Covid-19 vaccine safety in pregnancy, a nested case-control study in births from April 2021 to March 2022, England", @@ -5942,81 +7743,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, - { - "rel_doi": "10.1101/2023.10.08.23296717", - "rel_title": "Immunomodulators and risk for breakthrough infection after third COVID-19 mRNA vaccine among patients with rheumatoid arthritis: A cohort study", - "rel_date": "2023-10-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.08.23296717", - "rel_abs": "ObjectivesTo investigate COVID-19 breakthrough infection after third mRNA vaccine dose among patients with RA by immunomodulator drug class, and we hypothesized that CD20 inhibitors (CD20i) would have higher risk for breakthrough COVID-19 vs. TNF inhibitors (TNFi).\n\nMethodsWe performed a retrospective cohort study investigating breakthrough COVID-19 among RA patients at Mass General Brigham in Boston, MA, USA. Patients were followed from the date of 3rd vaccine dose until breakthrough COVID-19, death, or end of follow-up (18/Jan/2023). Covariates included demographics, lifestyle, comorbidities, and prior COVID-19. We used Cox proportional hazards models to estimate breakthrough COVID-19 risk by immunomodulator drug class. We used propensity score (PS) overlap-weighting to compare users of CD20i vs. TNFi.\n\nResultsWe analyzed 5781 patients with RA that received 3 mRNA vaccine doses (78.8% female, mean age 64.2 years). During mean follow-up of 12.8 months, 1173 (20.2%) had breakthrough COVID_19. Use of CD20i (adjusted HR 1.74, 95%CI 1.30-2.33) and glucocorticoid monotherapy (adjusted HR 1.47, 95%CI 1.09-1.98) were each associated with breakthrough COVID-19 compared to TNFi use. In the PS overlap-weighted analysis, CD20i users also had higher breakthrough COVID-19 risk than TNFi users (HR 1.62, 95%CI 1.02-2.56). A sensitivity analysis excluding patients with cancer or interstitial lung disease yielded similar findings.\n\nConclusionsWe identified CD20i and glucocorticoid monotherapy as risk factors for breakthrough COVID-19 among patients with RA after a 3rd vaccine dose. This contemporary study highlights the real-world impact of blunted immune responses in these subgroups and the need for effective risk mitigation strategies.\n\nWhat is already known about this topicO_LIPatients with RA are at increased risk for COVID-19 breakthrough infection after two vaccine doses so a third dose is recommended to complete the initial series.\nC_LIO_LISome immunomodulator medications, particularly CD20 inhibitors, can impact vaccine immunogenicity and waning.\nC_LI\n\nWhat this study addsO_LICD20 inhibitor use was associated with increased risk of COVID-19 breakthrough infection in people with RA who received 3 vaccine doses compared to TNF inhibitor use.\nC_LIO_LIGlucocorticoid monotherapy was also associated with increased risk of COVID-19 breakthrough infection.\nC_LI\n\nHow this study might affect research, practice or policyO_LIPatients with RA who are using CD20 inhibitors or glucocorticoid monotherapy should be prioritized for risk mitigation strategies after the initial vaccine series of 3 mRNA doses.\nC_LIO_LIThe impact of additional vaccine doses, timing of medication dosing, and other protective measures will need further study.\nC_LI", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Abigail E. Schiff", - "author_inst": "Brigham and Women's Hospital and Harvard Medical School" - }, - { - "author_name": "Xiaosong Wang", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Naomi J. Patel", - "author_inst": "Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Yumeko Kawano", - "author_inst": "Brigham and Women's Hospital and Harvard Medical School" - }, - { - "author_name": "Emily N. Kowalski", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Claire E. Cook", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Kathleen M.M. Vanni", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Grace Qian", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Katarina J. Bade", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Alene A. Saavedra", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Shruthi Srivatsan", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Zachary K. Williams", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Rathnam K. Venkat", - "author_inst": "Tufts University School of Medicine" - }, - { - "author_name": "Zachary S. Wallace", - "author_inst": "Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Jeffrey A. Sparks", - "author_inst": "Brigham and Women's Hospital and Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "rheumatology" - }, { "rel_doi": "10.1101/2023.10.07.23296694", "rel_title": "Non-pharmacological interventions aimed at promoting the mental health of children and adolescents during the COVID-19 pandemic", @@ -7547,6 +9273,73 @@ "type": "new results", "category": "ecology" }, + { + "rel_doi": "10.1101/2023.09.29.23296142", + "rel_title": "Seroincidence of SARS-CoV-2 infection prior to and during the rollout of vaccines in a community-based prospective cohort of U.S. adults", + "rel_date": "2023-10-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.29.23296142", + "rel_abs": "LONG ABSTRACTO_ST_ABSBackgroundC_ST_ABSInfectious disease surveillance systems, which largely rely on diagnosed cases, underestimate the true incidence of SARS-CoV-2 infection, due to under-ascertainment and underreporting. We used repeat serologic testing to measure N-protein seroconversion in a well-characterized cohort of U.S. adults with no serologic evidence of SARS-CoV-2 infection to estimate the incidence of SARS-CoV-2 infection and characterize risk factors, with comparisons before and after the start of the SARS-CoV-2 vaccine and variant eras.\n\nMethodsWe assessed the incidence rate of infection and risk factors in two sub-groups (cohorts) that were SARS-CoV-2 N-protein seronegative at the start of each follow-up period: 1) the pre-vaccine/wild-type era cohort (n=3,421), followed from April to November 2020; and 2) the vaccine/variant era cohort (n=2,735), followed from November 2020 to June 2022. Both cohorts underwent repeat serologic testing with an assay for antibodies to the SARS-CoV-2 N protein (Bio-Rad Platelia SARS-CoV-2 total Ab). We estimated crude incidence and sociodemographic/epidemiologic risk factors in both cohorts. We used multivariate Poisson models to compare the risk of SARS-CoV-2 infection in the pre-vaccine/wild-type era cohort (referent group) to that in the vaccine/variant era cohort, within strata of vaccination status and epidemiologic risk factors (essential worker status, child in the household, case in the household, social distancing).\n\nFindingsIn the pre-vaccine/wild-type era cohort, only 18 of the 3,421 participants (0.53%) had >1 vaccine dose by the end of follow-up, compared with 2,497/2,735 (91.3%) in the vaccine/variant era cohort. We observed 323 and 815 seroconversions in the pre-vaccine/wild-type era and the vaccine/variant era and cohorts, respectively, with corresponding incidence rates of 9.6 (95% CI: 8.3-11.5) and 25.7 (95% CI: 24.2-27.3) per 100 person-years. Associations of sociodemographic and epidemiologic risk factors with SARS-CoV-2 incidence were largely similar in the pre-vaccine/wild-type and vaccine/variant era cohorts. However, some new epidemiologic risk factors emerged in the vaccine/variant era cohort, including having a child in the household, and never wearing a mask while using public transit. Adjusted incidence rate ratios (aIRR), with the entire pre-vaccine/wild-type era cohort as the referent group, showed markedly higher incidence in the vaccine/variant era cohort, but with more vaccine doses associated with lower incidence: aIRRun/undervaccinated=5.3 (95% CI: 4.2-6.7); aIRRprimary series only=5.1 (95% CI: 4.2-7.3); aIRRboosted once=2.5 (95% CI: 2.1-3.0), and aIRRboosted twice=1.65 (95% CI: 1.3-2.1). These associations were essentially unchanged in risk factor-stratified models.\n\nInterpretationIn SARS-CoV-2 N protein seronegative individuals, large increases in incidence and newly emerging epidemiologic risk factors in the vaccine/variant era likely resulted from multiple co-occurring factors, including policy changes, behavior changes, surges in transmission, and changes in SARS-CoV-2 variant properties. While SARS-CoV-2 incidence increased markedly in most groups in the vaccine/variant era, being up to date on vaccines and the use of non-pharmaceutical interventions (NPIs), such as masking and social distancing, remained reliable strategies to mitigate the risk of SARS-CoV-2 infection, even through major surges due to immune evasive variants. Repeat serologic testing in cohort studies is a useful and complementary strategy to characterize SARS-CoV-2 incidence and risk factors.\n\nSHORT ABSTRACTThis study used repeat serologic testing to estimate infection rates and risk factors in two overlapping cohorts of SARS-CoV-2 N protein seronegative U.S. adults. One mostly unvaccinated sub-cohort was tracked from April to November 2020 (pre-vaccine/wild-type era, n=3,421), and the other, mostly vaccinated cohort, from November 2020 to June 2022 (vaccine/variant era, n=2,735). Vaccine uptake was from 0.53% and 91.3% in the pre-vaccine and vaccine/variant cohorts, respectively. Corresponding seroconversion rates were 9.6 and 25.7 per 100 person-years. In both cohorts, sociodemographic and epidemiologic risk factors for infection were similar, though new risks emerged in the vaccine/variant era, such as having a child in the household. Despite higher incidence rates in the vaccine/variant cohort, vaccine boosters, masking, and distancing likely reduced infection risk, even through major variant surges. Repeat serologic testing in cohorts is a useful and complementary strategy to characterize incidence and risk factors.\n\nFundingThe work was supported by the CUNY Institute for Implementation Science in Population Health, the U.S. National Institutes of Allergy and Infectious Diseases (NIAID), Pfizer, Inc., and the U.S. National Institute of Mental Health (NIMH).", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Denis Nash", + "author_inst": "City University of New York School of Public Health" + }, + { + "author_name": "Avantika Srivastava", + "author_inst": "CUNY Institute for Implementation Science in Population Health" + }, + { + "author_name": "Yanhan Shen", + "author_inst": "City University of New York School of Public Health" + }, + { + "author_name": "Kate Penrose", + "author_inst": "CUNY Institute for Implementation Science in Population Health" + }, + { + "author_name": "Sarah Kulkarni", + "author_inst": "CUNY Institute for Implementation Science in Population Health" + }, + { + "author_name": "Rebecca Zimba", + "author_inst": "CUNY Graduate School of Public Health and Health Policy" + }, + { + "author_name": "William You", + "author_inst": "The CUNY Institute for Implementation Science in Population Health" + }, + { + "author_name": "Amanda Berry", + "author_inst": "CUNY Institute for Implementation Science in Population Health" + }, + { + "author_name": "Chloe Mirzayi", + "author_inst": "CUNY Institute for Implementation Science in Population Health" + }, + { + "author_name": "Andrew R Maroko", + "author_inst": "CUNY Graduate School of Public Health and Health Policy" + }, + { + "author_name": "Angela Parcesepe", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Christian Grov", + "author_inst": "CUNY Graduate School of Public Health" + }, + { + "author_name": "McKaylee Robertson", + "author_inst": "CUNY ISPH" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.09.30.560318", "rel_title": "Synthesis, Insertion and Characterization of SARS-CoV-2 Membrane Protein Within Lipid Bilayers", @@ -7776,45 +9569,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2023.09.29.23296359", - "rel_title": "Dynamic Contact Networks of Residents of an Urban Jail in the Era of SARS-CoV-2", - "rel_date": "2023-10-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.29.23296359", - "rel_abs": "BackgroundIn custodial settings such as jails and prisons, infectious disease transmission is heightened by factors such as overcrowding and limited healthcare access. Specific features of social contact networks within these settings have not been sufficiently characterized, especially in the context of a large-scale respiratory infectious disease outbreak. The study aims to quantify contact network dynamics within the Fulton County Jail in Atlanta, Georgia, to improve our understanding respiratory disease spread to informs public health interventions.\n\nMethodsAs part of the Surveillance by Wastewater and Nasal Self-collection of Specimens (SWANSS) study, jail roster data were utilized to construct social contact networks. Rosters included resident details, cell locations, and demographic information. This analysis involved 6,702 residents over 140,901 person days. Network statistics, including degree, mixing, and turnover rates, were assessed across age groups, race/ethnicities, and jail floors. We compared outcomes for two distinct periods (January 2022 and April 2022) to understand potential responses in network structures during and after the SARS-CoV-2 Omicron variant peak.\n\nResultsWe found high cross-sectional network degree at both cell and block levels, indicative of substantial daily contacts. While mean degree increased with age, older residents exhibited lower degree during the Omicron peak, suggesting potential quarantine measures. Block-level networks demonstrated higher mean degrees than cell-level networks. Cumulative degree distributions for both levels increased from January to April, indicating heightened contacts after the outbreak. Assortative age mixing was strong, especially for residents aged 20-29. Dynamic network statistics illustrated increased degrees over time, emphasizing the potential for disease spread, albeit with a lower growth rate during the Omicron peak.\n\nConclusionsThe contact networks within the Fulton County Jail presented ideal conditions for infectious disease transmission. Despite some reduction in network characteristics during the Omicron peak, the potential for disease spread remained high. Age-specific mixing patterns suggested unintentional age segregation, potentially limiting disease spread to older residents. The study underscores the need for ongoing monitoring of contact networks in carceral settings and provides valuable insights for epidemic modeling and intervention strategies, including quarantine, depopulation, and vaccination. This network analysis offers a foundation for understanding disease dynamics in carceral environments.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Samuel M Jenness", - "author_inst": "Emory University" - }, - { - "author_name": "Karina Wallrafen-Sam", - "author_inst": "Emory University" - }, - { - "author_name": "Isaac Schneider", - "author_inst": "Emory University" - }, - { - "author_name": "Shanika M Kennedy", - "author_inst": "Emory University" - }, - { - "author_name": "Matthew J Akiyama", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Anne C Spaulding", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.09.29.23296176", "rel_title": "Trends in Healthcare Service Disruptions and Associations with COVID-19 Outcomes among Patients with SMI vs. Non-SMI during COVID-19", @@ -8554,7 +10308,7 @@ "rel_date": "2023-09-29", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.28.560070", - "rel_abs": "Turmeric extract (TE) with curcumin as its main active ingredient has been studied as a potential COVID-19 therapeutic. Curcumin has been studied in silico and in vitro against a naive SARS-CoV-2 virus, yet little is known about TEs impact on SARS-CoV-2 infection. Moreover, no study reveals the potentials of both curcumin and TE on the inhibition of SARS-CoV-2 cell-to-cell transmission. Here, we investigated the effects of both curcumin and TE on the inhibition of SARS-CoV-2 entry and cell-to-cell transmission using pseudovirus (PSV) and syncytia models. We performed PSV entry assay in 293T or 293 cells expressing hACE2. The cells were pretreated with curcumin or TE, then treated with PSV with or without the test samples. Next, we carried out syncytia assay by co-transfecting 293T cells with plasmids encoding Spike, hACE2, and TMPRSS2 to be treated with the test samples. The results showed that in PSV entry assay on 293T/hACE/TMPRSS2 cells, both curcumin and TE inhibited PSV entry at concentrations of 1 {micro}M and 10 {micro}M for curcumin and 1 {micro}g/ml and 10 {micro}g/ml for TE. Moreover, both curcumin and TE also reduced syncytia formation compared to control cells. Based on our study, both TE and curcumin are potential inhibitors of SARS-CoV-2 infection at entry points, either by direct or indirect infection models.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC=\"FIGDIR/small/560070v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@6fe60corg.highwire.dtl.DTLVardef@682227org.highwire.dtl.DTLVardef@9a6504org.highwire.dtl.DTLVardef@5e1814_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "Turmeric extract (TE) with curcumin as its main active ingredient has been studied as a potential COVID-19 therapeutic. Curcumin has been studied in silico and in vitro against a naive SARS-CoV-2 virus, yet little is known about TEs impact on SARS-CoV-2 infection. Moreover, no study reveals the potentials of both curcumin and TE on the inhibition of SARS-CoV-2 cell-to-cell transmission. Here, we investigated the effects of both curcumin and TE on the inhibition of SARS-CoV-2 entry and cell-to-cell transmission using pseudovirus (PSV) and syncytia models. We performed PSV entry assay in 293T or 293 cells expressing hACE2. The cells were pretreated with curcumin or TE, then treated with PSV with or without the test samples. Next, we carried out syncytia assay by co-transfecting 293T cells with plasmids encoding Spike, hACE2, and TMPRSS2 to be treated with the test samples. The results showed that in PSV entry assay on 293T/hACE/TMPRSS2 cells, both curcumin and TE inhibited PSV entry at concentrations of 1 {micro}M and 10 {micro}M for curcumin and 1 {micro}g/ml and 10 {micro}g/ml for TE. Moreover, both curcumin and TE also reduced syncytia formation compared to control cells. Based on our study, both TE and curcumin are potential inhibitors of SARS-CoV-2 infection at entry points, either by direct or indirect infection models.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=165 SRC=\"FIGDIR/small/560070v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@1457792org.highwire.dtl.DTLVardef@1ad3f01org.highwire.dtl.DTLVardef@10363b8org.highwire.dtl.DTLVardef@187c79a_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 7, "rel_authors": [ { @@ -9033,6 +10787,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.09.26.559580", + "rel_title": "SARS-CoV-2 Omicron BA.2.86: less neutralization evasion compared to XBB sub-variants", + "rel_date": "2023-09-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.26.559580", + "rel_abs": "The continual emergence and circulation of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have caused a great challenge for the coronavirus disease 2019 (COVID-19) pandemic control. Recently, Omicron BA.2.86 was identified with more than 30 amino acid changes on the spike (S) protein, compared to Omicron BA.2 or XBB.1.5. The immune evasion potential of BA.2.86 is of great concern. In this study, we evaluated the neutralizing activities of sera collected from participants and mice. Participants were divided into five groups according to their vaccination (inactivated vaccine, protein subunit vaccine ZF2001 or ZF2202-A) and infection (Omicron BF.7/BA.5.2) status. ZF2202-A is ZF2001 vaccines next-generation COVID-19 vaccine with updated bivalent Delta-BA.5 RBD-heterodimer immunogen. BALB/c mice were immunized with XBB.1.5 RBD-homodimer, BA.5-BA.2, Delta-XBB.1.5 or BQ.1.1-XBB.1.5 RBD-heterodimers protein vaccine candidates for evaluating the neutralizing responses. We found that Omicron BA.2.86 shows stronger immune evasion than BA.2 due to >30 additional mutations on S protein. Compared to XBB sub-variants, BA.2.86 does not display more resistance to the neutralizing responses induced by ZF2001-vaccination, BF.7/BA.5.2 breakthrough infection or a booster dose of ZF2202-A-vaccination. In addition, the mouse experiment results showed that BQ.1.1-XBB.1.5 RBD-heterodimer and XBB.1.5 RBD-homodimer induced high neutralizing responses against XBB sub-variants and BA.2.86, indicating that next-generation COVID-19 vaccine should be developed to enhance the protection efficacy against the circulating strains in the future.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yaling An", + "author_inst": "Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Xuemei Zhou", + "author_inst": "Hebei University" + }, + { + "author_name": "Lifeng Tao", + "author_inst": "Anhui Zhifei Longcom Biopharmaceutical Co. Ltd" + }, + { + "author_name": "Haitang Xie", + "author_inst": "Yijishan Hospital of Wannan Medical College" + }, + { + "author_name": "Dedong Li", + "author_inst": "Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Ruyue Wang", + "author_inst": "Anhui Zhifei Longcom Biopharmaceutical Co. Ltd" + }, + { + "author_name": "Hua Hu", + "author_inst": "Yijishan Hospital of Wannan Medical College" + }, + { + "author_name": "Zepeng Xu", + "author_inst": "Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Lianpan Dai", + "author_inst": "Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Kun Xu", + "author_inst": "Beijing Institutes of Life Science, Chinese Academy of Sciences" + }, + { + "author_name": "George F. Gao", + "author_inst": "Institute of Microbiology, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.09.26.559550", "rel_title": "Development of a mutant aerosolized ACE2 that neutralizes SARS-CoV-2 in vivo", @@ -9150,205 +10963,6 @@ "type": "confirmatory results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.09.27.559689", - "rel_title": "Comparative Analysis of SARS-CoV-2 Antigenicity across Assays and in Human and Animal Model Sera", - "rel_date": "2023-09-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.27.559689", - "rel_abs": "The antigenic evolution of SARS-CoV-2 requires ongoing monitoring to judge the immune escape of newly arising variants. A surveillance system necessitates an understanding of differences in neutralization titers measured in different assays and using human and animal sera. We compared 18 datasets generated using human, hamster, and mouse sera, and six different neutralization assays. Titer magnitude was lowest in human, intermediate in hamster, and highest in mouse sera. Fold change, immunodominance patterns and antigenic maps were similar among sera. Most assays yielded similar results, except for differences in fold change in cytopathic effect assays. Not enough data was available for conclusively judging mouse sera, but hamster sera were a consistent surrogate for human first-infection sera.", - "rel_num_authors": 46, - "rel_authors": [ - { - "author_name": "Barbara M\u00fchlemann", - "author_inst": "Institute of Virology, Charit\u00e9 - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Samuel Hedley Wilks", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Lauren Baracco", - "author_inst": "Center for Pathogen Research, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA" - }, - { - "author_name": "Meriem Bekliz", - "author_inst": "Department of Medicine, Faculty of Medicine, University of Geneva, Switzerland" - }, - { - "author_name": "Juan Manuel Carreno", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Victor M Corman", - "author_inst": "Charite - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Meredith E Davis-Gardner", - "author_inst": "Emory University" - }, - { - "author_name": "Wanwisa Dejnirattisai", - "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK" - }, - { - "author_name": "Michael Diamond", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Danny Doueck", - "author_inst": "NIH Vaccine Research Center" - }, - { - "author_name": "Christian Drosten", - "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin" - }, - { - "author_name": "Isabella Eckerle", - "author_inst": "University of Geneva, Switzerland" - }, - { - "author_name": "Venkata Vishwanadh Edara", - "author_inst": "Emory University" - }, - { - "author_name": "Madison Ellis", - "author_inst": "Emory University" - }, - { - "author_name": "Ron AM Fouchier", - "author_inst": "Erasmus Medical Centre" - }, - { - "author_name": "Matthew Frieman", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Sucheta Godbole", - "author_inst": "National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Bart Haagmans", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Peter Halfmann", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Amy R Henry", - "author_inst": "National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Terry C Jones", - "author_inst": "Charit\u00e9 Universit\u00e4tsmedizin" - }, - { - "author_name": "Leah Katzelnick", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Janine Kimpel", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Lilin Lai", - "author_inst": "Emory University" - }, - { - "author_name": "Chang Liu", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sabrina Lusvarghi", - "author_inst": "U.S. Food and Drug Administration" - }, - { - "author_name": "Benjamin Meyer", - "author_inst": "Faculty of Medicine, University of Geneva" - }, - { - "author_name": "Juthathip Mongkolsapaya", - "author_inst": "Oxford University: University of Oxford" - }, - { - "author_name": "David Montefiori", - "author_inst": "Duke University" - }, - { - "author_name": "Anna Z Mykytyn", - "author_inst": "Erasmus Medical Centre" - }, - { - "author_name": "Antonia Netzl", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Simon Pollett", - "author_inst": "Uniformed Services University of the Health Sciences" - }, - { - "author_name": "Annika R\u00f6ssler", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Gavin Screaton", - "author_inst": "John Radcliffe Hospital" - }, - { - "author_name": "Xiaoying Shen", - "author_inst": "Duke University" - }, - { - "author_name": "Alex Sigal", - "author_inst": "Africa Health Research Institute, University of KwaZulu-Natal" - }, - { - "author_name": "Viviana Simon", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Rahul Subramanian", - "author_inst": "National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda" - }, - { - "author_name": "Piyada Supasa", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mehul Suthar", - "author_inst": "Emory University" - }, - { - "author_name": "Sina Tureli", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Wei Wang", - "author_inst": "FDA" - }, - { - "author_name": "Carol D. Weiss", - "author_inst": "US Food and Drug Administration" - }, - { - "author_name": "Derek J Smith", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.09.24.558921", "rel_title": "Genomic evolution of SARS-CoV-2 variants of concern under in vitro neutralising selection pressure following two doses of the Pfizer-BioNTech BNT162b2 COVID-19 vaccine", @@ -10858,7 +12472,7 @@ "rel_date": "2023-09-25", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.22.23295541", - "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@214226org.highwire.dtl.DTLVardef@17df8f7org.highwire.dtl.DTLVardef@164314eorg.highwire.dtl.DTLVardef@e123ae_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@89cf8org.highwire.dtl.DTLVardef@179680eorg.highwire.dtl.DTLVardef@19e90b7org.highwire.dtl.DTLVardef@12ee350_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 22, "rel_authors": [ { @@ -10955,6 +12569,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2023.09.21.23295891", + "rel_title": "Simulation-based validation of a method to detect changes in SARS-CoV-2 reinfection risk", + "rel_date": "2023-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.21.23295891", + "rel_abs": "BackgroundGiven the high global seroprevalence of SARS-CoV-2, understanding the risk of reinfection becomes increasingly important. Models developed to track trends in reinfection risk should be robust against possible biases arising from imperfect data observation processes.\n\nObjectivesWe performed simulation-based validation of an existing catalytic model designed to detect changes in the risk of reinfection by SARS-CoV-2.\n\nMethodsThe catalytic model assumes the risk of reinfection is proportional to observed infections. Validation involved using simulated primary infections, consistent with the number of observed infections in South Africa. We then simulated reinfection datasets that incorporated different processes that may bias inference, including imperfect observation and mortality, to assess the performance of the catalytic model. A Bayesian approach was used to fit the model to simulated data, assuming a negative binomial distribution around the expected number of reinfections, and model projections were compared to the simulated data generated using different magnitudes of change in reinfection risk. We assessed the approachs ability to accurately detect changes in reinfection risk when included in the simulations, as well as the occurrence of false positives when reinfection risk remained constant.\n\nKey FindingsThe model parameters converged in most scenarios leading to model outputs aligning with anticipated outcomes. The model successfully detected changes in the risk of reinfection when such a change was introduced to the data. Low observation probabilities (10%) of both primary- and re-infections resulted in low numbers of observed cases from the simulated data and poor convergence.\n\nLimitationsThe models performance was assessed on simulated data representative of the South African SARS-CoV-2 epidemic, reflecting its timing of waves and outbreak magnitude. Model performance under similar scenarios may be different in settings with smaller epidemics (and therefore smaller numbers of reinfections).\n\nConclusionsEnsuring model parameter convergence is essential to avoid false-positive detection of shifts in reinfection risk. While the model is robust in most scenarios of imperfect observation and mortality, further simulation-based validation for regions experiencing smaller outbreaks is recommended. Caution must be exercised in directly extrapolating results across different epidemiological contexts without additional validation efforts.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Belinda Lombard", + "author_inst": "SACEMA, Stellenbosch University" + }, + { + "author_name": "Harry Moultrie", + "author_inst": "National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa" + }, + { + "author_name": "Juliet RC Pulliam", + "author_inst": "SACEMA, Stellenbosch University" + }, + { + "author_name": "Cari Van Schalkwyk", + "author_inst": "SACEMA, Stellenbosch University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.09.21.23295905", "rel_title": "Liver abnormalities following SARS-CoV-2 infection in children under 10 years of age", @@ -11212,65 +12857,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2023.09.21.23295904", - "rel_title": "Impact of bivalent BA.4/5 BNT162b2 COVID-19 vaccine on acute symptoms, quality of life, work productivity and activity levels among symptomatic US adults testing positive for SARS-CoV-2 at a national retail pharmacy", - "rel_date": "2023-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.21.23295904", - "rel_abs": "BackgroundEvidence on the impact of COVID-19 vaccination on symptoms, Health-Related Quality of Life (HRQoL), Work Productivity and Activity Impairment (WPAI) is scarce. We analyzed associations between bivalent BA.4/5 BNT162b2 and these patient-reported outcomes (PROs).\n\nMethodsSymptomatic US adults who tested positive for SARS-CoV-2 were recruited between 03/02-05/18/2023. PROs were assessed using a CDC-based symptom questionnaire, EQ-5D-5L, WPAI-GH, and PROMIS Fatigue, from pre-COVID to Week 4 following infection. Multivariable analysis using mixed models for repeated measures was conducted, adjusting for several covariates.\n\nResultsThe study included 641 participants: 314 vaccinated with bivalent BA.4/5 BNT162b2 and 327 unvaccinated/not up-to-date. Mean (SD) age was 46.5 years (15.9), 71.2% were female, 44.2% reported prior infection, 25.7% had [≥]1 comorbidity. The BA.4/5 BNT162b2 cohort reported fewer acute symptoms through Week 4, especially systemic and respiratory symptoms. All PROs were adversely affected, especially at Week 1; however, at that time point, the bivalent BA.4/5 BNT162b2 cohort reported better work performance, driven by less absenteeism, and fewer work hours lost. No significant differences were observed for HRQoL.\n\nConclusionsCOVID-19 negatively impacted patient outcomes. Compared with unvaccinated/not up-to-date participants, those vaccinated with bivalent BA.4/5 BNT162b2 reported fewer and less persistent symptoms and improved work performance.\n\nClinicaltrials.gov NCT05160636", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Manuela Di Fusco", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Xiaowu Sun", - "author_inst": "CVS Health" - }, - { - "author_name": "Laura Anatale-Tardiff", - "author_inst": "CVS Health" - }, - { - "author_name": "Alon Yehoshua", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Henriette Coetzer", - "author_inst": "CVS Health" - }, - { - "author_name": "Mary B. Alvarez", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Kristen Emily Allen", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Thomas M. Porter", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Laura Puzniak", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Santiago M. C. Lopez", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Joseph C. Cappelleri", - "author_inst": "Pfizer Inc." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.09.21.23295927", "rel_title": "Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution", @@ -12853,6 +14439,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.09.14.557827", + "rel_title": "Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics", + "rel_date": "2023-09-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.14.557827", + "rel_abs": "We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 Spike (S) protein. With this approach, we first identified Candidate Adaptive Polymorphisms (CAPs) of the SARS-CoV-2 Spike protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of S protein compared to the closed form. In particular, the CAP sites control the dynamics binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly compensatory variants. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nicholas James Ose", + "author_inst": "Arizona State University" + }, + { + "author_name": "Paul James Campitelli", + "author_inst": "Arizona State University" + }, + { + "author_name": "Tushar Modi", + "author_inst": "Arizona State University" + }, + { + "author_name": "I. Can Kazan", + "author_inst": "Arizona State University" + }, + { + "author_name": "Sudhir Kumar", + "author_inst": "Temple University" + }, + { + "author_name": "S. Banu Ozkan", + "author_inst": "Arizona State University - Tempe Campus: Arizona State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2023.09.14.557682", "rel_title": "Enhanced neutralization of SARS-CoV-2 XBB sub-lineages and BA.2.86 by a tetravalent COVID-19 vaccine booster", @@ -13082,33 +14707,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2023.09.14.557558", - "rel_title": "MixOmics Integration of Biological Datasets Identifies Highly Correlated Key Variables of COVID-19 severity.", - "rel_date": "2023-09-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.14.557558", - "rel_abs": "BackgroundDespite several years since the COVID-19 pandemic was declared, challenges remain in understanding the factors that can predict the severity of COVID-19 disease and complications of SARS-CoV-2 infection. While many large-scale Multiomic datasets have been published, integration of these datasets has the potential to substantially increase the biological insight gained allowing a more complex comprehension of the disease pathogenesis. Such insight may improve our ability to predict disease progression, detect severe cases more rapidly and develop effective therapeutics.\n\nMethodsIn this study we have applied an innovative machine learning algorithm to delineate COVID-severity based on integration of paired samples of proteomic and transcriptomic data from a small cohort of patients testing positive for SARS-CoV-2 infection with differential disease severity. Targeted plasma proteomics and an onco-immune targeted transcriptomic panel was performed on sequential samples from a cohort of 23 severe, 21 moderate and 10 mild COVID-19 patients. We applied DIABLO, a new integrative method, to identify multi- omics biomarker panels that can discriminate between multiple phenotypic groups, such as the varied severity of disease in COVID-19 patients.\n\nResultsAs COVID-19 severity is known among our sample group, we can train models using this as the outcome variable and calculate features that are important predictors of severe disease. In this study, we detect highly correlated key variables of severe COVID-19 using transcriptomic discriminant analysis and multi-omics integration methods.\n\nConclusionsThis approach highlights the power of data integration from a small cohort of patients offering a better biological understanding of the molecular mechanisms driving COVID-19 severity and an opportunity to improve prediction of disease trajectories and targeted therapeutics.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Noa C Harriott", - "author_inst": "University of Iowa" - }, - { - "author_name": "Michael S Chimenti", - "author_inst": "University of Iowa" - }, - { - "author_name": "Amy L Ryan", - "author_inst": "University of Iowa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2023.09.15.23295560", "rel_title": "Clinical Performance of SARS-CoV-2 Rapid Antigen Tests: A Systematic Review and Meta-Analysis", @@ -14347,6 +15945,49 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.09.12.557347", + "rel_title": "Concurrent administration of COVID-19 and influenza vaccines enhances Spike-specific antibody responses", + "rel_date": "2023-09-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.12.557347", + "rel_abs": "The bivalent COVID-19 mRNA boosters became available in fall 2022 and were recommended alongside the seasonal influenza vaccine. However, the immunogenicity of concurrent versus separate administration of these vaccines remains unclear. Here, we analyzed antibody responses in healthcare workers who received the bivalent COVID-19 booster and the influenza vaccine on the same day or different days. IgG1 responses to SARS-CoV-2 Spike were higher at peak immunogenicity and 6 months following concurrent administration compared with separate administration of the COVID-19 and influenza vaccines. These data suggest that concurrent administration of these vaccines may yield higher and more durable SARS-CoV-2 antibody responses.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Susanna E Barouch", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Taras M Chicz", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Ross Blanc", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Domenic R Barbati", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Lily J Parker", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Xin Tong", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Ryan P McNamara", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.09.11.557219", "rel_title": "Dual inhibition of coronavirus Mpro and PLpro enzymes by phenothiazines and their antiviral activity", @@ -14536,37 +16177,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.09.11.557292", - "rel_title": "WELPCR: Low-cost polymerase chain reaction (PCR) thermal cycler for nucleic acid amplification and sensing", - "rel_date": "2023-09-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.11.557292", - "rel_abs": "The COVID-19 pandemic highlighted the need for sensitive and cost-effective diagnostics. The gold standard test to diagnose infectious diseases such as COVID-19 is quantitative polymerase chain reaction (qPCR). Although there have been multiple advances in nucleic acid testing, PCR thermocyclers are expensive and typically not affordable for offering hands-on training to PCR in instructional laboratory courses in undergraduate colleges. We introduce a low-cost, portable, and automated real-time PCR device designed at the Wadhwani Electronics Lab (WEL) at IIT Bombay, christened WELPCR. WELPCR is an open-source design, and capable of reverse transcription PCR (RT-PCR) for complementary DNA synthesis, as well as end-point PCR of small amount of DNA in a test sample. The WELPCR design enables ramp rate up to 2 {degrees}C/s, weighs less than 2 kg, and is easy to assemble. The built-in LED display and keypad provides an intuitive and seamless user interface to configure and set up WELPCR. With bill of materials (BOM) cost less than INR Rs. 10 000, WELPCR is an attractive solution for bringing PCR technology to instructional and research laboratories in a cost-effective manner.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Poulami Mandal", - "author_inst": "IIT Bombay" - }, - { - "author_name": "Vivekanand Dhakane", - "author_inst": "IIT Bombay" - }, - { - "author_name": "Avani Kulkarni", - "author_inst": "IIT Bombay" - }, - { - "author_name": "Siddharth Tallur", - "author_inst": "IIT Bombay" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2023.09.11.557205", "rel_title": "Examining Functional Linkages Between Conformational Dynamics, Protein Stability and Evolution of Cryptic Binding Pockets in the SARS-CoV-2 Omicron Spike Complexes with the ACE2 Host Receptor: Recombinant Omicron Variants Mediate Variability of Conserved Allosteric Sites and Binding Epitopes", @@ -16249,6 +17859,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.09.08.23295246", + "rel_title": "Change in body weight of older adults before and during the COVID-19 pandemic: Longitudinal results from the Berlin Aging Study II", + "rel_date": "2023-09-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.08.23295246", + "rel_abs": "BackgroundChange in body weight during the COVID-19 pandemic as an unintended side effect of lockdown measures has been predominantly reported for younger and middle-aged adults. However, information on older adults for which weight loss is known to result in adverse outcomes, is scarce.\n\nAimsDescribe body weight change in older adults before, during, and after the COVID-19 lockdown measures and explore putative associated factors with a focus on the period that includes the first six months of the COVID-19 containment measures.\n\nMethodsIn this study, we analyzed the longitudinal weight change of 472 participants of the Berlin Aging Study II (mean age of 67.5 years at baseline, average follow-up time 10 years). Additionally, differences between subgroups characterized by socio-economic, cognitive, and psychosocial variables as well as morbidity burden, biological age markers (epigenetic clocks, telomere length), and frailty were compared.\n\nResultsOn average, women and men lost 0.87% (n=227) and 0.5% (n=245) of their body weight per year in the study period covering the first six months of the COVID-19 pandemic. Weight loss among men was particularly pronounced among groups characterized by change in physical activity due to COVID-19 lockdown, low positive affect, premature epigenetic age (7-CpG clock), diagnosed metabolic syndrome, and a more masculine gender score (all variables: p<0.05, n=245).\n\nConclusionsOlder participants lost weight with a 2.5-times (women) and 2-times (men) higher rate than what is expected in this age.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Valentin Max Vetter", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Johanna Drewelies", + "author_inst": "Max Planck Institute for Human Development" + }, + { + "author_name": "Sandra Duezel", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Jan Homann", + "author_inst": "University of Muenster" + }, + { + "author_name": "Lil Meyer-Arndt", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Julian Braun", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Anne Pohrt", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Friederike Kendel", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Gert G Wagner", + "author_inst": "German Institute for Economic Research (DIW)" + }, + { + "author_name": "Andreas Thiel", + "author_inst": "Si-M Charite Universitaetsmedizin Berlin" + }, + { + "author_name": "Lars Bertram", + "author_inst": "Luebeck Interdisciplinary Platform for Genome Analytics (LIGA), University of Luebeck" + }, + { + "author_name": "Vera Regitz-Zagrosek", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Denis Gerstorf", + "author_inst": "Humboldt University Berlin" + }, + { + "author_name": "Ilja Demuth", + "author_inst": "Charite - Universitaetsmedizin Berlin" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.09.08.23295136", "rel_title": "Pre-dominance of dengue non-cross-reacting SARS-CoV-2 spike antibodies during the Omicron era and their role in the ADE-mediated surge of Dengue virus serotype 3", @@ -16406,69 +18087,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.09.08.556788", - "rel_title": "SARS-CoV-2 ORF8 modulates lung inflammation and clinical disease progression", - "rel_date": "2023-09-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.08.556788", - "rel_abs": "The virus severe acute respiratory syndrome coronavirus 2, SARS-CoV-2, is the causative agent of the current COVID-19 pandemic. It possesses a large 30 kilobase (kb) genome that encodes structural, non-structural, and accessory proteins. Although not necessary to cause disease, these accessory proteins are known to influence viral replication and pathogenesis. Through the synthesis of novel infectious clones of SARS-CoV-2 that lack one or more of the accessory proteins of the virus, we have found that one of these accessory proteins, ORF8, is critical for the modulation of the host inflammatory response. Mice infected with a SARS-CoV-2 virus lacking ORF8 exhibit increased weight loss and exacerbated macrophage infiltration into the lungs. Additionally, infection of mice with recombinant SARS-CoV-2 viruses encoding ORF8 mutations found in variants of concern reveal that naturally occurring mutations in this protein influence disease severity. Our studies with a virus lacking this ORF8 protein and viruses possessing naturally occurring point mutations in this protein demonstrate that this protein impacts pathogenesis.\n\nSignificanceSince its emergence in 2019, SARS-CoV-2 has accrued mutations throughout its 30kb genome. Of particular interest are the mutations present in the ORF8 protein, which occur in every major variant. The precise function and impact of this protein on disease severity and pathogenesis remains understudies. Our studies reveal that the ORF8 protein modulates the immune response by impacting macrophage infiltration into the lungs. Additionally, we have shown that the ORF8 protein of SARS-CoV-2 has accrued mutations throughout its evolution that lead to a loss of function phenotype in this protein. Our work reveals that the ORF8 protein of SARS-CoV-2 contributes significantly to disease progression through modulation of the inflammatory response.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Matthew Frieman", - "author_inst": "University of Maryland Baltimore" - }, - { - "author_name": "Marisa E. McGrath", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Yong Xue", - "author_inst": "JCVI: J Craig Venter Institute" - }, - { - "author_name": "Louis Taylor", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Carly Dillen", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Jeremy Ardanuy", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Norberto Gonzalez-Juarbe", - "author_inst": "J Craig Venter Institute" - }, - { - "author_name": "Lauren Baracco", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Raymond Kim", - "author_inst": "J Craig Venter Institute" - }, - { - "author_name": "Rebecca Hart", - "author_inst": "J Craig Venter Institute" - }, - { - "author_name": "Nacyra Assad-Garcia", - "author_inst": "J Craig Venter Institute" - }, - { - "author_name": "Sanjay Vashee", - "author_inst": "J Craig Venter Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.09.07.23295202", "rel_title": "Early combination with remdesivir, nirmatrelvir/ritonavir and sotrovimab for the treatment of COVID-19 in immunocompromised hosts", @@ -18239,6 +19857,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.09.04.23295014", + "rel_title": "Individual and spatial determinants of mortality during the Covid-19 pandemic: The case of Belgium in 2020", + "rel_date": "2023-09-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.04.23295014", + "rel_abs": "ContextThe year 2020 was marked by the Covid-19 pandemic. In Belgium, it led to a doubling in deaths, mainly grouped into two periods. This article aims to compare the relative importance of predictors and individual and spatial determinants of mortality during these two waves to an equivalent non-pandemic period and to identify whether and to what extent the pandemic has altered the sociodemographic patterns of conventional mortality.\n\nMethodsThe analyses relate to all-cause mortality during the two waves of Covid-19 and their equivalent in 2019. They are based on matching individual and exhaustive data from the Belgian National Register with tax and population census data. A multi-level approach was adopted combining individual and spatial determinants.\n\nResultsMortality patterns during the pandemic are very similar to those observed outside the pandemic. As in 2019, age, sex, and household composition significantly determine the individual risk of dying, with a higher risk of death among the oldest people, men, and residents of collective households. However, their risk of death increases during the Covid period, especially in the 65-79 age group. Spatial information is no more significant in 2020 than in 2019. However, a higher risk of death is observed when the local excess mortality index or the proportions of isolated or disadvantaged people increase.\n\nConclusionsWhile the Covid pandemic did not fundamentally alter conventional mortality patterns, it did amplify some of the pre-existing differences in mortality.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Melanie Bourguignon", + "author_inst": "UCLouvain, Centre de recherche en demographie" + }, + { + "author_name": "Aurelie Bertrand", + "author_inst": "UCLouvain" + }, + { + "author_name": "Joan Damiens", + "author_inst": "UCLouvain, Centre de recherche en demographie" + }, + { + "author_name": "Yoann Doignon", + "author_inst": "CNRS" + }, + { + "author_name": "Thierry Eggerickx", + "author_inst": "UCLouvain, Centre de recherche en demographie" + }, + { + "author_name": "Audrey Plavsic", + "author_inst": "UCLouvain, Centre de recherche en demographie" + }, + { + "author_name": "Jean-Paul Sanderson", + "author_inst": "UCLouvain, Centre de recherche en demographie" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.09.05.23295025", "rel_title": "Bivalent mRNA vaccine effectiveness against COVID-19 infections, hospitalisations and deaths in Portugal: a cohort study based on electronic health records, September 2022 to May 2023", @@ -18360,81 +20021,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.08.28.555008", - "rel_title": "Reference materials for SARS-CoV-2 molecular diagnostic: validation of encapsulated synthetic RNAs for room temperature storage and shipping", - "rel_date": "2023-09-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.28.555008", - "rel_abs": "The Coronavirus pandemic unveiled the unprecedented need for diagnostic tests to rapidly detect the presence of pathogens in the population. Real-time RT-PCR and other nucleic acid amplification techniques are accurate and sensitive molecular techniques that necessitate positive controls. To meet this need, Twist Bioscience has developed and released synthetic RNA controls. However, RNA is an inherently unstable molecule needing cold storage, costly shipping, and resource-intensive logistics. Imagene provides a solution to this problem by encapsulating dehydrated RNA inside metallic capsules filled with anhydrous argon, allowing room temperature and eco-friendly storage and shipping. Here, RNA controls produced by Twist were encapsulated (RNAshells) and distributed to several laboratories that used them for COVID-19 detection tests by amplification. One RT-LAMP procedure, four different RT-PCR devices and 6 different PCR kits were used. The amplification targets were genes E, N; RdRp, Sarbeco-E and Orf1a/b. RNA retrieval was satisfactory, and the detection was reproducible. RNA stability was checked by accelerated aging. The results for a 10-year equivalent storage time at 25 {degrees}C were not significantly different from those for unaged samples. This room temperature RNA stability allows the preparation and distribution of large strategic batches which can be stored for a long time and used for standardization processes between detection sites. Moreover, it makes it also possible to use these controls for single use and in the field where large differences in temperature can occur. Consequently, this type of encapsulated RNA controls, processed at room temperature, can be used as reference materials for the SARS-Cov-2 virus as well as for other pathogens detection.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Marthe Colotte", - "author_inst": "Imagene Company, Gradignan France" - }, - { - "author_name": "Aur\u00e9lie Luis", - "author_inst": "Imagene Company, Gradignan France" - }, - { - "author_name": "Delphine Coudy", - "author_inst": "Imagene Company, Gradignan France" - }, - { - "author_name": "Sophie Tuffet", - "author_inst": "Imagene Company, Gradignan France" - }, - { - "author_name": "Isabelle Robene", - "author_inst": "CIRAD Pole de Protection des Plantes, Saint-Pierre, La Reunion, France" - }, - { - "author_name": "Babbitha Fenelon", - "author_inst": "CIRAD Pole de Protection des Plantes, Saint-Pierre, La Reunion, France" - }, - { - "author_name": "Emmanuel Jouen", - "author_inst": "CIRAD Pole de Protection des Plantes, Saint-Pierre, La Reunion, France" - }, - { - "author_name": "Nicolas Leveque", - "author_inst": "CHU de Poitiers, Poitiers, France" - }, - { - "author_name": "Luc Deroche", - "author_inst": "CHU de Poitiers, Poitiers, France;" - }, - { - "author_name": "Laurent Busson", - "author_inst": "CHU de Bordeaux, Laboratoire de Virologie, UMR 5234, Universite de Bordeaux, Bordeaux, France" - }, - { - "author_name": "Sophie Alain", - "author_inst": "CHU de Poitiers, Poitiers, France" - }, - { - "author_name": "Dorian Plumelle", - "author_inst": "Laboratoire d'Analyses Medicales, Laboratoire Plumelle, Salon De Provence, France" - }, - { - "author_name": "Camille Tumiotto", - "author_inst": "CHU de Bordeaux, Laboratoire de Virologie, UMR 5234, Universite de Bordeaux, Bordeaux, France" - }, - { - "author_name": "Marie-Edith Lafon", - "author_inst": "CHU de Bordeaux, Laboratoire de Virologie, UMR 5234, Universite de Bordeaux, Bordeaux, France" - }, - { - "author_name": "Jacques Bonnet", - "author_inst": "Universit\u00e9 BRIC, U 312 INSERM Bordeaux, France" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2023.09.01.555996", "rel_title": "Trapping non-cognate nucleotide upon initial binding for replication fidelity control in SARS-CoV-2 RNA dependent RNA polymerase", @@ -19933,6 +21519,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.08.29.23294793", + "rel_title": "Can long-term COVID-19 vaccination be improved by serological surveillance?: a modeling study for Mozambique", + "rel_date": "2023-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.29.23294793", + "rel_abs": "Seroprevalence provides an estimate of the population-level susceptibility to infection. In this study, we used a transmission model to examine the potential of using serological surveillance to inform the timing of COVID-19 boosters in Mozambique. We simulated using population-level seroprevalence thresholds as an estimate of the risk of outbreaks to trigger the timing of re-vaccination campaigns among older adults. We compare this approach to a strategy of re-vaccination at fixed time intervals. Vaccinating older adults each time the seroprevalence among older adults falls below 50% and 80% resulted in medians of 20% and 71% reduction in deaths, respectively, and number-needed-to-vaccinate to avert one death (NNT) of 1,499 (2.5th-97.5th centile:1,252-1,905) and 3,151 (2,943-3,429), respectively. In comparison, biennial and annual re-vaccination of older adults resulted in medians of 35% and 52% deaths averted, respectively, and NNTs of 1,443 (1,223-1,733) and 1,941 (1,805-2,112), respectively. We conducted sensitivity analysis over a range of antibody waning rates and epidemic scenarios and found that re-vaccination trigger thresholds of 50-60% seroprevalence are most likely to be efficient compared to fixed-time strategies. However, given marginal gains in efficiency even in the best-case scenarios, our results favor the use of simpler fixed-time strategies for long-term control of SARS-CoV-2.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Carol Y Liu", + "author_inst": "Emory University" + }, + { + "author_name": "Kayoko Shioda", + "author_inst": "Boston University" + }, + { + "author_name": "Alicia Kraay", + "author_inst": "University of Illinois Urbana-Champaign" + }, + { + "author_name": "Sergio Massora", + "author_inst": "Centro de Investigacao em Saude de Manhica (CISM)" + }, + { + "author_name": "Auria de Jesus", + "author_inst": "Centro de Investigacao em Saude de Manhica (CISM)" + }, + { + "author_name": "Arsenia Massinga", + "author_inst": "Centro de Investigacao em Saude de Manhica (CISM)" + }, + { + "author_name": "Celso Monjane", + "author_inst": "Mozambique Instituto Nacional de Saude" + }, + { + "author_name": "Saad B Omer", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Samuel M Jenness", + "author_inst": "Emory University" + }, + { + "author_name": "Kristin Nelson", + "author_inst": "Emory University" + }, + { + "author_name": "Stefan Y Flasche", + "author_inst": "LSHTM" + }, + { + "author_name": "Inacio Mandomando", + "author_inst": "Centro de Investigacao em Saude de Manhica (CISM)" + }, + { + "author_name": "Benjamin A Lopman", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.08.29.23294791", "rel_title": "How will COVID-19 persist in the future? Simulating future dynamics of COVID-19 using an agent-based network model", @@ -20098,77 +21751,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.08.30.554497", - "rel_title": "XBB.1.5 Spike Protein COVID-19 Vaccine Induces Broadly Neutralizing and Cellular Immune Responses Against EG.5.1 and Emerging XBB Variants", - "rel_date": "2023-08-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.30.554497", - "rel_abs": "Monovalent SARS-CoV-2 Prototype (Wuhan-Hu-1) and bivalent (Prototype + BA.4/5) COVID-19 vaccines have demonstrated a waning of vaccine-mediated immunity highlighted by lower neutralizing antibody responses against SARS-CoV-2 Omicron XBB sub-variants. The reduction of humoral immunity due to the rapid evolution of SARS-CoV-2 has signaled the need for an update to vaccine composition. A strain change for all authorized/approved vaccines to a monovalent composition with Omicron subvariant XBB.1.5 has been supported by the WHO, EMA, and FDA. Here, we demonstrate that immunization with a monovalent recombinant spike protein COVID-19 vaccine (Novavax, Inc.) based on the subvariant XBB.1.5 induces cross-neutralizing antibodies against XBB.1.5, XBB.1.16, XBB.2.3, EG.5.1, and XBB.1.16.6 subvariants, promotes higher pseudovirus neutralizing antibody titers than bivalent (Prototype + XBB.1.5) vaccine, induces SARS-CoV-2 spike-specific Th1-biased CD4+ T-cell responses against XBB subvariants, and robustly boosts antibody responses in mice and nonhuman primates primed with a variety of monovalent and bivalent vaccines. Together, these data support updating the Novavax vaccine to a monovalent XBB.1.5 formulation for the 2023-2024 COVID-19 vaccination campaign.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Nita Patel", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Jessica F. Trost", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Mimi Guebre-Xabier", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Haixia Zhou", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Jim Norton", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Desheng Jiang", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Zhaohui Cai", - "author_inst": "Novavax Inc." - }, - { - "author_name": "Mingzhu Zhu", - "author_inst": "Novavax Inc." - }, - { - "author_name": "Anthony M Marchese", - "author_inst": "Novavax Inc." - }, - { - "author_name": "Ann M Greene", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Raburn M Mallory", - "author_inst": "Novavax Inc." - }, - { - "author_name": "Raj Kalkeri", - "author_inst": "Novavax Inc." - }, - { - "author_name": "Filip Dubovsky", - "author_inst": "Novavax Inc." - }, - { - "author_name": "Gale Smith", - "author_inst": "Novavax, Inc." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.08.30.555644", "rel_title": "SenePy: Unveiling the Cell-Type Specific Landscape of Cellular Senescence through Single-Cell Analysis in Living Organisms", @@ -21903,6 +23485,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.08.26.554935", + "rel_title": "Self-assembly vascularized human cardiac organoids model cardiac diseases in petri dishes and in mice", + "rel_date": "2023-08-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.26.554935", + "rel_abs": "In this study, we generated self-assembly cardiac organoids (COs) from human pluripotent stem cells by dual-phase modulation of Wnt/{beta}-catenin pathway, utilizing CHIR99021 and IWR-1-endo. The resulting COs exhibited a diverse array of cardiac-specific cell lineages, cardiac cavity-like structures and demonstrated the capacity of spontaneous beating and vascularization in vitro. We further employed these complex and functional COs to replicate conditions akin to human myocardial infarction and SARS-CoV-2 induced fibrosis. These models accurately captured the pathological characteristics of these diseases, in both in vitro and in vivo settings. In addition, we transplanted the COs into NOD SCID mice and observed that they survived and exhibited ongoing expansion in vivo. Impressively, over a span of 75-day transplantation, these COs not only established blood vessel-like structures but also integrated with the host mices vascular system. It is noteworthy that these COs developed to a size of approximately 8 mm in diameter, slightly surpassing the dimensions of the mouse heart. This innovative research highlighted the potential of our COs as a promising avenue for cardiovascular research and therapeutic exploration.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Qixing Zhong", + "author_inst": "West China Hospital, Sichuan University" + }, + { + "author_name": "Yao He", + "author_inst": "Sichuan Junhui Biotechnology Co., Ltd." + }, + { + "author_name": "Li Teng", + "author_inst": "Sichuan Junhui Biotechnology Co., Ltd." + }, + { + "author_name": "Yinqian Zhang", + "author_inst": "West China Hospital, Sichuan University" + }, + { + "author_name": "Ting Zhang", + "author_inst": "West China Hospital, Sichuan University" + }, + { + "author_name": "Yinbing Zhang", + "author_inst": "West China Hospital, Sichuan University" + }, + { + "author_name": "Qinxi Li", + "author_inst": "Sichuan Junhui Biotechnology Co., Ltd." + }, + { + "author_name": "Bangcheng Zhao", + "author_inst": "West China Hospital, Sichuan University" + }, + { + "author_name": "Daojun Chen", + "author_inst": "Sichuan Junhui Biotechnology Co., Ltd." + }, + { + "author_name": "Zhihui Zhong", + "author_inst": "West China Hospital, Sichuan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2023.08.26.23294658", "rel_title": "Limited impact of lifting universal masks on SARS-COV-2 transmission in schools: The crucial role of outcome measurements", @@ -22096,57 +23733,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.08.27.23294685", - "rel_title": "The well-being and work-related stress of senior school leaders in Wales and Northern Ireland during the COVID-19 pandemic: A cross-sectional descriptive study", - "rel_date": "2023-08-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.27.23294685", - "rel_abs": "The COVID-19 pandemic caused far-reaching societal changes, including significant educational impacts, affecting over 1.6 billion pupils and 100 million education practitioners globally. Senior school leaders were at the forefront; an occupation already reporting high work-related stress and large numbers leaving the profession preceding COVID-19, leaders were exposed to high demands relating to the numerous challenges they had to manage during a \"crisis leadership\" period. This cross-sectional descriptive study through the international COVID-HL network aimed to examine the well-being and work-related stress of senior school leaders (n=323) in Wales (n=172) and Northern Ireland (n=151) during COVID-19 (2021-2022). Findings suggest that senior school leaders reported high workloads (54.22{+/-}11.30 hours/week), low well-being (65.2% n=202, mean WHO-5 40.85{+/-}21.57), depressive symptoms (WHO-5 34.8% n=108) and high work-related stress (PSS-10: 29.91{+/-}4.92). High exhaustion (BAT: high/very high 89.0% n=285) and specific psychosomatic complaints (experiencing muscle pain 48.2% n=151) were also reported, and females had statistically higher outcomes in these areas. School leaders were engaging in self-endangering working behaviours; 74.7% (n=239) gave up leisure activities in favour of work and 63.4% (n=202) sacrificed sufficient sleep, which was statistically higher for females. These findings are concerning given that the UK is currently experiencing a \"crisis\" in educational leadership against a backdrop of pandemic-related pressures. Senior leaders high attrition rates further exacerbate this, proving costly to educational systems and placing additional financial and other pressures on educational settings and policy response. This has implications for senior leaders and pupil-level outcomes including health, well-being and educational attainment, requiring urgent tailored and targeted support from the education and health sectors. This is particularly pertinent for Wales and Northern Ireland as devolved nations in the UK, who are both implementing or contemplating major education system level reforms, including new statutory national curricula, requiring significant leadership, engagement and ownership from the education profession.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Emily Marchant", - "author_inst": "Swansea University" - }, - { - "author_name": "Joanna Dowd", - "author_inst": "Freelance Researcher" - }, - { - "author_name": "Lucy Bray", - "author_inst": "Edge Hill University" - }, - { - "author_name": "Gill Rowlands", - "author_inst": "Newcastle University" - }, - { - "author_name": "Nia Miles", - "author_inst": "National Academy for Educational Leadership Wales" - }, - { - "author_name": "Tom Crick", - "author_inst": "Swansea University" - }, - { - "author_name": "Michaela James", - "author_inst": "Swansea University" - }, - { - "author_name": "Kevin Dadaczynski", - "author_inst": "Fulda University of Applied Sciences: Hochschule Fulda" - }, - { - "author_name": "Orkan Okan", - "author_inst": "Technical University Munich School of Medicine: Technische Universitat Munchen Fakultat fur Medizin" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2023.08.25.551434", "rel_title": "Single-cell-resolved interspecies comparison identifies a shared inflammatory axis and a dominant neutrophil-endothelial program in severe COVID-19", @@ -23437,6 +25023,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.08.23.23293081", + "rel_title": "Pediatric and Adult Patients with ME/CFS following COVID-19: A Structured Approach to Diagnosis Using the Munich Berlin Symptom Questionnaire (MBSQ)", + "rel_date": "2023-08-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.23.23293081", + "rel_abs": "PurposeA subset of patients with post-COVID-19 condition (PCC) fulfill the clinical criteria of myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS). To establish the diagnosis of ME/CFS for clinical and research purposes, comprehensive scores have to be evaluated.\n\nMethodsWe developed the Munich Berlin Symptom Questionnaires (MBSQs) and supplementary scoring sheets (SSSs) to allow for a rapid evaluation of common ME/CFS case definitions. The MBSQs were applied to young patients with chronic fatigue and post-exertional malaise (PEM) who presented to the MRI Chronic Fatigue Center for Young People (MCFC). Trials were retrospectively registered (NCT05778006, NCT05638724).\n\nResultsUsing the MBSQs and SSSs, we report on ten patients aged 11 to 25 years diagnosed with ME/CFS after asymptomatic SARS-CoV-2 infection or mild to moderate COVID-19. Results from their MBSQs and from well-established patient-reported outcome measures indicated severe impairments of daily activities and health-related quality of life.\n\nConclusionsME/CFS can follow SARS-CoV-2 infection in patients younger than 18 years, rendering structured diagnostic approaches most relevant for pediatric PCC clinics. The MBSQs and SSSs represent novel diagnostic tools that can facilitate the diagnosis of ME/CFS in children, adolescents, and adults with PCC and other post-viral syndromes.\n\nWhat is knownME/CFS is a frequent debilitating illness. For diagnosis, an extensive differential diagnostic workup is required and the evaluation of clinical ME/CFS criteria. ME/CFS following COVID-19 has been reported in adults but not in pediatric patients younger than 19 years of age.\n\nWhat is newWe present novel questionnairs (MBSQs), as tools to assess common ME/CFS case definitions in pediatric and adult patients with post-COVID-19 condition and beyond. We report on ten patients aged 11 to 25 years diagnosed with ME/CFS following asymptomatic SARS-CoV-2 infection or mild to moderate COVID-19.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Laura C. Peo", + "author_inst": "MRI Chronic Fatigue Center for Young People (MCFC), Children's Hospital, TUM School of Medicine, Technical University of Munich, Munich, Germany" + }, + { + "author_name": "Katharina Wiehler", + "author_inst": "MRI Chronic Fatigue Center for Young People (MCFC), Children's Hospital, TUM School of Medicine, Technical University of Munich, Munich, Germany" + }, + { + "author_name": "Johannes Paulick", + "author_inst": "MRI Chronic Fatigue Center for Young People (MCFC), Children's Hospital, TUM School of Medicine, Technical University of Munich, Munich, Germany" + }, + { + "author_name": "Katrin Gerrer", + "author_inst": "MRI Chronic Fatigue Center for Young People (MCFC), Children's Hospital, TUM School of Medicine, Technical University of Munich, Munich, Germany" + }, + { + "author_name": "Ariane Leone", + "author_inst": "MRI Chronic Fatigue Center for Young People (MCFC), Children's Hospital, TUM School of Medicine, Technical University of Munich, Munich, Germany" + }, + { + "author_name": "Anja Viereck", + "author_inst": "MRI Chronic Fatigue Center for Young People (MCFC), Children's Hospital, TUM School of Medicine, Technical University of Munich, Munich, Germany" + }, + { + "author_name": "Matthias Haegele", + "author_inst": "MRI Chronic Fatigue Center for Young People (MCFC), Children's Hospital, TUM School of Medicine, Technical University of Munich, Munich, Germany" + }, + { + "author_name": "Silvia Stojanov", + "author_inst": "MRI Chronic Fatigue Center for Young People (MCFC), Children's Hospital, TUM School of Medicine, Technical University of Munich, Munich, Germany" + }, + { + "author_name": "Cordula Warlitz", + "author_inst": "MRI Chronic Fatigue Center for Young People (MCFC), Children's Hospital, TUM School of Medicine, Technical University of Munich, Munich, Germany" + }, + { + "author_name": "Silvia Augustin", + "author_inst": "MRI Chronic Fatigue Center for Young People (MCFC), Children's Hospital, TUM School of Medicine, Technical University of Munich, Munich, Germany" + }, + { + "author_name": "Martin Alberer", + "author_inst": "MRI Chronic Fatigue Center for Young People (MCFC), Children's Hospital, TUM School of Medicine, Technical University of Munich, Munich, Germany" + }, + { + "author_name": "Daniel R. B. Hattesohl", + "author_inst": "German Association for ME/CFS, Hamburg, Germany" + }, + { + "author_name": "Laura Froehlich", + "author_inst": "Research Center CATALPA, FernUniversitaet in Hagen, Hagen, Germany" + }, + { + "author_name": "Carmen Scheibenbogen", + "author_inst": "Charite Fatigue Center (CFC), Berlin, Germany" + }, + { + "author_name": "Lorenz L Mihatsch", + "author_inst": "MRI Chronic Fatigue Center for Young People (MCFC), Children's Hospital, TUM School of Medicine, Technical University of Munich, Munich, Germany" + }, + { + "author_name": "Rafael Pricoco", + "author_inst": "MRI Chronic Fatigue Center for Young People (MCFC), Children's Hospital, TUM School of Medicine, Technical University of Munich, Munich, Germany" + }, + { + "author_name": "Uta Behrends", + "author_inst": "MRI Chronic Fatigue Center for Young People (MCFC), Children's Hospital, TUM School of Medicine, Technical University of Munich, Munich, Germany; German Associa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2023.08.23.23294470", "rel_title": "Risk Factors for Post-Traumatic Stress Disorder (PTSD) in COVID Survivors A Cross-Sectional Study", @@ -23534,33 +25203,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.08.24.554651", - "rel_title": "Unveiling the Robustness of Machine Learning Models in Classifying COVID-19 Spike Sequences", - "rel_date": "2023-08-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.24.554651", - "rel_abs": "In the midst of the global COVID-19 pandemic, a wealth of data has become available to researchers, presenting a unique opportunity to investigate the behavior of the virus. This research aims to facilitate the design of efficient vaccinations and proactive measures to prevent future pandemics through the utilization of machine learning (ML) models for decision-making processes. Consequently, ensuring the reliability of ML predictions in these critical and rapidly evolving scenarios is of utmost importance. Notably, studies focusing on the genomic sequences of individuals infected with the coronavirus have revealed that the majority of variations occur within a specific region known as the spike (or S) protein. Previous research has explored the analysis of spike proteins using various ML techniques, including classification and clustering of variants. However, it is imperative to acknowledge the possibility of errors in spike proteins, which could lead to misleading outcomes and misguide decision-making authorities. Hence, a comprehensive examination of the robustness of ML and deep learning models in classifying spike sequences is essential. In this paper, we propose a framework for evaluating and benchmarking the robustness of diverse ML methods in spike sequence classification. Through extensive evaluation of a wide range of ML algorithms, ranging from classical methods like naive Bayes and logistic regression to advanced approaches such as deep neural networks, our research demonstrates that utilizing k-mers for creating the feature vector representation of spike proteins is more effective than traditional one-hot encoding-based embedding methods. Additionally, our findings indicate that deep neural networks exhibit superior accuracy and robustness compared to non-deep-learning baselines. To the best of our knowledge, this study is the first to benchmark the accuracy and robustness of machine-learning classification models against various types of random corruptions in COVID-19 spike protein sequences. The benchmarking framework established in this research holds the potential to assist future researchers in gaining a deeper understanding of the behavior of the coronavirus, enabling the implementation of proactive measures and the prevention of similar pandemics in the future.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Sarwan Ali", - "author_inst": "Georgia State University" - }, - { - "author_name": "Pin-Yu Chen", - "author_inst": "IBM Research, IBM T. J. Watson Research Center, Yorktown Heights, NY, USA" - }, - { - "author_name": "Murray Patterson", - "author_inst": "Georgia State University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.08.23.554537", "rel_title": "Deep proteome analysis of time-series human plasma samples applied to Covid-19 antibody test", @@ -25151,6 +26793,45 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2023.08.20.554012", + "rel_title": "Multi-cell type deconvolution using a probabilistic model for single-molecule DNA methylation haplotypes", + "rel_date": "2023-08-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.20.554012", + "rel_abs": "BackgroundDeconvolution is used to estimate the proportion of mixed cell types from tissue or blood samples based on genomic profiling. DNA methylation is commonly used because specific CpG positions reflect cell type identity and can be accurately measured at either the population or single-molecule level. Methylation sequencing techniques can profile multiple individual CpGs on a single DNA molecule, but few deconvolution models have been developed to exploit these single-molecule methylation haplotypes for cell type deconvolution.\n\nResults and ConclusionsWe used simulated whole-genome methylation data and in silico mixtures of real data to compare existing deconvolution tools with two new models developed here. We found that adapting an existing model CelFiE to incorporate methylation haplotype information improved deconvolution accuracy by [~]30% over other tools, including the original CelFiE. In addition to overall higher accuracy, our new tool CelFiE Integrated Single-molecule Haplotypes (or CelFiE-ISH) outperformed others in detecting rare cell types present at 0.1% and below. Detection of rare cell types is important for the analysis of circulating DNA, which we demonstrate using a patient-derived plasma sequencing dataset.Finally,we show that marker selection strategy has a strong effect on deconvolution accuracy, concluding that haplotype-aware deconvolution can take advantage of markers tailored for that purpose.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Irene Unterman", + "author_inst": "Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, " + }, + { + "author_name": "Dana Avrahami", + "author_inst": "Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel" + }, + { + "author_name": "Efrat Katsman", + "author_inst": "Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, " + }, + { + "author_name": "Timothy J Triche Jr.", + "author_inst": "Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA" + }, + { + "author_name": "Benjamin Glaser", + "author_inst": "Department of Endocrinology and Metabolism, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel" + }, + { + "author_name": "Benjamin P Berman", + "author_inst": "Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, " + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.08.19.23294311", "rel_title": "Seroepidemiology of COVID-19 in pregnant women and their infants in Uganda and Malawi across multiple waves 2020-2022", @@ -25424,33 +27105,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.08.20.23294350", - "rel_title": "Heterogeneous SARS-CoV-2 kinetics due to variable timing and intensity of immune responses", - "rel_date": "2023-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.20.23294350", - "rel_abs": "The viral kinetics of documented SARS-CoV-2 infections exhibit a high degree of inter-individual variability. We identified six distinct viral shedding patterns, which differed according to peak viral load, duration, expansion rate and clearance rate, by clustering data from 810 infections in the National Basketball Association cohort. Omicron variant infections in previously vaccinated individuals generally led to lower cumulative shedding levels of SARS-CoV-2 than other scenarios. We then developed a mechanistic mathematical model that recapitulated 1510 observed viral trajectories, including viral rebound and cases of reinfection. Lower peak viral loads were explained by a more rapid and sustained transition of susceptible cells to a refractory state during infection, as well as an earlier and more potent late, cytolytic immune response. Our results suggest that viral elimination occurs more rapidly during omicron infection, following vaccination, and following re-infection due to enhanced innate and acquired immune responses. Because viral load has been linked with COVID-19 severity and transmission risk, our model provides a framework for understanding the wide range of observed SARS-CoV-2 infection outcomes.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Katherine Owens", - "author_inst": "Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center" - }, - { - "author_name": "Shadisadat Esmaeili-Wellman", - "author_inst": "Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center" - }, - { - "author_name": "Joshua T. Schiffer", - "author_inst": "Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center; Department of Medicine, University of Washington, Seattle" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.08.20.23293987", "rel_title": "Evaluating public health effects of risk-based travel policy for the COVID-19 epidemic in Scotland", @@ -26837,6 +28491,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.08.10.23293925", + "rel_title": "Effect of vaccination certification with mass vaccination and non-pharmaceutical interventions on mitigating COVID-19", + "rel_date": "2023-08-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.10.23293925", + "rel_abs": "As COVID-19 vaccines became abundantly available around the world since the second half of 2021, many countries carried out a vaccination certificate (green pass) policy to encourage vaccination and help reopen their economies. This policy granted certified people more freedom of gathering and movement than unvaccinated individuals. Accordingly, pre-existing non-pharmaceutical interventions (NPIs) were adjusted under the vaccination certificate policy. The vaccination certificate also induced heterogeneous behaviors between unvaccinated and vaccinated groups, which complicates the modeling of COVID-19 transmission. Still, limited work is available in evaluating the impact of the green pass policy on COVID-19 transmission using quantitative methods. To characterize the major changes caused by the green pass policy, a modified susceptible-exposed-infected-removed (SEIR) epidemiological model SEIQRD2 is proposed in this paper. By integrating different behavior patterns of unvaccinated and vaccinated groups under the green pass policy, SEIQRD2 adopts the inherent variability and complexity of human behaviors in the context of vaccination and NPIs and their effect on COVID-19 transmissions. Three countries: Greece, Austria, and Israel are selected as case studies to demonstrate the validity of SEIQRD2. The simulation results illustrate that the combination of NPIs and vaccination still plays a pivotal role in containing the resurgence of COVID-19 by enforcing vaccination certification.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hu Cao", + "author_inst": "Macquarie University" + }, + { + "author_name": "Longbing Cao", + "author_inst": "Macquarie University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.08.10.23293942", "rel_title": "A Susceptible Vaccinated Exposed Infected Hospitalised and Removed/Recovered (SVEIHR) Model Framework for COVID-19", @@ -26946,49 +28623,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.08.11.23293971", - "rel_title": "Individual level analysis of digital proximity tracing for COVID-19 in Belgium highlights major bottlenecks", - "rel_date": "2023-08-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.11.23293971", - "rel_abs": "To complement labour-intensive conventional contact tracing, digital proximity tracing was implemented widely during the COVID-19 pandemic. However, the privacy-centred design of the dominant Google-Apple exposure notification framework has hindered assessment of its effectiveness. Between October 2021 and January 2022, we systematically collected app use and notification receipt data within a test and trace programme for university students in Leuven, Belgium. Due to low success rates in each studied step of the digital notification cascade, only 4.3% of exposed contacts (CI: 2.8-6.1%) received such notifications, resulting in 10 times more cases detected through conventional contact tracing. Moreover, the infection risk of digitally traced contacts (5.0%; CI: 3.0-7.7%) was lower than that of conventionally traced non-app users (9.8%; CI: 8.8-10.7%; p=0.002). Contrary to common perception as near instantaneous, there was a 1.2-day delay (CI: 0.6-2.2) between case PCR result and digital contact notifications. These results highlight major limitations of the dominant digital proximity tracing framework.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Caspar Geenen", - "author_inst": "KU Leuven" - }, - { - "author_name": "Joren Raymenants", - "author_inst": "KU Leuven" - }, - { - "author_name": "Sarah Gorissen", - "author_inst": "KU Leuven" - }, - { - "author_name": "Jonathan Thibaut", - "author_inst": "KU Leuven" - }, - { - "author_name": "Jodie McVernon", - "author_inst": "The Peter Doherty Institute for Infection and Immunity" - }, - { - "author_name": "Natalie Lorent", - "author_inst": "University Hospitals Leuven" - }, - { - "author_name": "Emmanuel Andre", - "author_inst": "KU Leuven" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.08.11.23293472", "rel_title": "\"Getting pregnant during the COVID 19 was a big risk because getting the help from the clinic was not easy\": COVID-19 experiences of women and healthcare providers in Harare, Zimbabwe.", @@ -28163,6 +29797,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.08.06.23293729", + "rel_title": "Why some countries but not others? Urbanisation, GDP and endemic disease predict global SARS-CoV-2 excess mortality patterns.", + "rel_date": "2023-08-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.06.23293729", + "rel_abs": "The global impact of the SARS-CoV-2 pandemic has been uneven, with some regions experiencing significant excess mortality while others have been relatively unaffected. Yet factors which predict this variation remain enigmatic, particularly at large spatial scales. We used spatially explicit Bayesian models that integrate socio-demographic and endemic disease data at the country level to provide robust global estimates of excess SARS-CoV-2 mortality (P scores) for the years 2020 and 2021. We find that gross domestic product (GDP), spatial patterns and urbanization are strong predictors of excess mortality, with countries characterized by low GDP but high urbanization experiencing the highest levels of excess mortality. Intriguingly, we also observed that the prevalence of malaria and human immunodeficiency virus (HIV) are associated with country-level SARS-CoV-2 excess mortality in Africa and the Western Pacific, whereby countries with low HIV prevalence but high malaria prevalence tend to have lower levels of excess mortality. While these associations are correlative in nature at the macro-scale, they emphasize that patterns of endemic disease and socio-demographic factors are needed to understand the global dynamics of SARS-CoV-2.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Nicholas M Fountain-Jones", + "author_inst": "University of Tasmania" + }, + { + "author_name": "Michael Charleston", + "author_inst": "University of Tasmania" + }, + { + "author_name": "Emily Flies", + "author_inst": "University of Tasmania" + }, + { + "author_name": "Scott Carver", + "author_inst": "University of Tasmania" + }, + { + "author_name": "Luke Yates", + "author_inst": "University of Tasmania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.08.07.23293747", "rel_title": "Young Healthcare Workers' Employment Status and Mental Distress over SARS-CoV-2 in Bolivia", @@ -28260,57 +29929,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.08.06.23293725", - "rel_title": "Predicting Clinical Outcomes of SARS-CoV-2 Infection During the Omicron Wave Using Machine Learning", - "rel_date": "2023-08-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.06.23293725", - "rel_abs": "The Omicron SARS-CoV-2 variant continues to strain healthcare systems. Developing tools that facilitate the identification of patients at highest risk of adverse outcomes is a priority. The study objectives are to develop population-scale predictive models that: 1) identify predictors of adverse outcomes with Omicron surge SARS-CoV-2 infections, and 2) predict the impact of prioritized vaccination of high-risk groups for said outcome. We prepared a retrospective longitudinal observational study of a national cohort of 192,984 patients in the U.S. Veteran Health Administration who tested positive for SARS-CoV-2 from January 15 to August 15, 2022. We utilized sociodemographic characteristics, comorbidities, vaccination status, and prior COVID-19 infections, at time of testing positive for SARS-CoV-2 to predict hospitalization, escalation of care (high-flow oxygen, mechanical ventilation, vasopressor use, dialysis, or extracorporeal membrane oxygenation), and death within 30 days. Machine learning models demonstrated that advanced age, high comorbidity burden, lower body mass index, unvaccinated status, prior SARS-CoV-2 infection, and oral anticoagulant use were the important predictors of hospitalization and escalation of care. Similar factors predicted death. However, prior SARS-CoV-2 infection was associated with lower 30-day mortality, and anticoagulant use did not predict mortality risk. The all-cause death model showed the highest discrimination (Area Under the Curve (AUC) = 0.895, 95% Confidence Interval (CI): 0.885, 0.906) followed by hospitalization (AUC = 0.829, CI: 0.825, 0.834), then escalation of care (AUC=0.805, CI: 0.795, 0.814). Assuming a vaccine efficacy range of 70.8 to 78.7%, our simulations projected that targeted prevention in the highest risk group may have reduced 30-day hospitalization, care escalation, and death in more than 2 of 5 unvaccinated patients.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Steven Bradley Cogill", - "author_inst": "VA Palo Alto Cooperative Studies Program Coordinating Center" - }, - { - "author_name": "Shriram Nallamshetty", - "author_inst": "VA Palo Alto Health Care System Palo Alto Division: VA Palo Alto Health Care System" - }, - { - "author_name": "Natalie Fullenkamp", - "author_inst": "VA Palo Alto Health Care System Palo Alto Division: VA Palo Alto Health Care System" - }, - { - "author_name": "Kent Heberer", - "author_inst": "VA Palo Alto Cooperative Studies Coordinating Center" - }, - { - "author_name": "Julie Lynch", - "author_inst": "VA Salt Lake City Health Care System" - }, - { - "author_name": "Kyung Min Lee", - "author_inst": "VA Salt Lake City Health Care System" - }, - { - "author_name": "Mihaela Aslan", - "author_inst": "West Haven CSPCC: West Haven Cooperative Studies Program Coordinating Center" - }, - { - "author_name": "Mei-Chiung Shih", - "author_inst": "VA Palo Alto Cooperative Studies Program" - }, - { - "author_name": "jennifer lee", - "author_inst": "Stanford University School of Medicine" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2023.08.05.23293582", "rel_title": "Dysosmia and dysgeusia as differential diagnostics for clinical triaging of COVID-19 cases", @@ -29665,6 +31283,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.08.03.23293611", + "rel_title": "Work Attendance during Acute Respiratory Illness Before and During the COVID-19 Pandemic, United States, 2018-2022", + "rel_date": "2023-08-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.03.23293611", + "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and influenza viruses can be transmitted by infected persons who are pre-symptomatic or symptomatic. To assess impact of the COVID-19 pandemic on work attendance during illness, we analyzed prospectively collected data from persons with acute respiratory illness (ARI) enrolled in a multi-state study during 2018-2022. Persons with prior experience working from home were significantly less likely than those without this experience to work onsite on the day before illness and during the first 3 days of illness; the effect was more pronounced for the COVID-19 pandemic period than the pre-pandemic influenza seasons. Persons with influenza or COVID-19 were significantly less likely to work onsite than persons with other ARIs. Among persons for whom positive COVID-19 test results were available by the second or third day of illness, few worked onsite. Work-from-home policies may reduce the likelihood of workplace exposures to respiratory viruses.\n\nArticles summary lineWork-from-home policies may reduce the likelihood of workplace exposures to SARS-CoV-2 and influenza viruses.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Faruque Ahmed", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Mary Patricia Nowalk", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Richard Zimmerman", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Todd Bear", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Carlos G Grijalva", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "H. Keipp Talbot", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Ana Florea", + "author_inst": "Kaiser Permanente Southern California" + }, + { + "author_name": "Sara Tartof", + "author_inst": "Kaiser Permanente Southern California" + }, + { + "author_name": "Manjusha Gaglani", + "author_inst": "Baylor Scott and White Health" + }, + { + "author_name": "Michael E Smith", + "author_inst": "Baylor Scott and White Health" + }, + { + "author_name": "Huong Q McLean", + "author_inst": "Marshfield Clinic Research Institute" + }, + { + "author_name": "Jennifer King", + "author_inst": "Marshfield Clinic Research Institute" + }, + { + "author_name": "Emily Toth Martin", + "author_inst": "University of Michigan-Ann Arbor" + }, + { + "author_name": "Arnold Monto", + "author_inst": "University of Michigan-Ann Arbor" + }, + { + "author_name": "Hallie Phillips", + "author_inst": "Kaiser Permanente Washington Health Research Institute" + }, + { + "author_name": "Karen J Wernli", + "author_inst": "Kaiser Permanente Washington Health Research Institute" + }, + { + "author_name": "Brendan Flannery", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jessie Chung", + "author_inst": "US Centers for Disease Control and Prevention" + }, + { + "author_name": "Amra Uzicanin", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.08.03.23293586", "rel_title": "COVID-19 among migrants, refugees, and internally displaced persons: systematic review, meta-analysis and qualitative synthesis of the global empirical literature", @@ -29822,37 +31531,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.03.23293612", - "rel_title": "Influence of Prior SARS-CoV-2 Infection on COVID-19 Severity: Evidence from the National COVID Cohort Collaborative", - "rel_date": "2023-08-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.03.23293612", - "rel_abs": "BackgroundAs SARS-CoV-2 has transitioned from a pandemic to endemic disease, the majority of new infections have been among previously infected individuals. To manage the risks and benefits of ongoing COVID-19 policies, it is important to understand whether prior infection modifies the severity of subsequent infections.\n\nMethodsWe used data from first and second COVID-19 episodes in the National COVID Cohort Collaborative (N3C), a collection of health systems who provide de-identified electronic health records for research purposes. Our analysis was a sequential series of nested trial emulations. In the first of two analytic stages, we created a month-specific model of the probability of prior infection for each individual. In the second stage, we used an ordinal logistic regression with inverse probability weights calculated in the first stage to simulate a series of monthly trials comparing severity between the cohorts of first and second infections. In addition to cohort-wide effect estimates, we also conducted analyses among race/ethnicity, sex, and age subgroups.\n\nResultsFrom an initial cohort of 7,446,481 combined first and second infections, we identified a cohort of 2,227,484 infections, among which 7.6% were second infections. Ninety-four percent of patients with two recorded infections experienced mild disease for both. The overall odds ratio (OR) for more severe disease with prior infection was 1.06 (95% confidence interval [CI]: 1.03 - 1.10). Monthly point estimates of the OR ranged from 0.56 (95% CI: 0.37 - 0.84) in October 2020 to 1.64 (95% CI: 1.33 - 2.00) in February 2023. In most subgroups, the effect of prior infection was significant. In 8 out of 10 subgroups, the maximum monthly OR occurred after the minimum monthly OR, suggesting that protection has waned throughout the pandemic.\n\nConclusionOverall, prior infection was associated with a significant slightly elevated risk of severe disease. This effect varied month to month. As the pandemic proceeded, the effect of prior infection tended to evolve from generally protective during the pre-Omicron era to unprotective during the Omicron era. This points to the need for continued strategies to avert and minimize the harms of COVID-19, rather than relying upon immunity acquired through previous infection.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSDoes prior infection with SARS-CoV-2 affect the severity of subsequent COVID-19 episodes?\n\nFindingsWe observed a mild protective effect of prior infection during the early and mid-stages of the pandemic that waned after the rise of the Omicron variants, ultimately resulting in loss of protection or a tendency toward more severe second infections.\n\nMeaningPrior infection alone is likely not enough to avert the worst public health harms of endemic SARS-CoV-2. Interventions to avoid infection and reduce the severity of COVID-19 will still be important in the post-pandemic era.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Nathaniel Hendrix", - "author_inst": "American Board of Family Medicine" - }, - { - "author_name": "Hythem Sidky", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "David Sahner", - "author_inst": "National Institutes of Health, National Center for Advancing Translational Sciences" - }, - { - "author_name": "- N3C Consortium", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.07.31.23293452", "rel_title": "Racial/Ethnic Differences in COVID-19-Traumatic Symptoms, Sleep, Coping Outcomes in a Group of New-Yorkers", @@ -31283,6 +32961,37 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2023.08.01.23293497", + "rel_title": "Recommended distances for physical distancing during COVID-19 pandemics reveal cultural connections between countries", + "rel_date": "2023-08-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.01.23293497", + "rel_abs": "During COVID-19 pandemic several public health measures were implemented by diverse countries to reduce the risk of COVID-19, including social distancing. Here we collected the minimal distance recommended by each country for physical distancing at the onset of the pandemic and aimed to examine whether it had an impact on the outbreak dynamics and how this specific value was chosen. Despite an absence of data on SARS-CoV-2 viral transmission at the beginning of the pandemic, we found that most countries recommended physical distancing with a precise minimal distance, between one meter/three feet and two meters/six feet. 45% of the countries advised one meter/three feet and 49% advised a higher minimal distance. The recommended minimal distance did not show a clear correlation with reproduction rate nor with the number of new cases per million, suggesting that the overall COVID-19 dynamics in each country depended on multiple interacting factors. Interestingly, the recommended minimal distance correlated with several cultural parameters: it was higher in countries with larger interpersonal distance between two interacting individuals in non-epidemic conditions, and it correlated with civil law systems, and with currency. This suggests that countries which share common conceptions such as civil law systems and currency unions tend to adopt the same public health measures.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Dongwoo Chai", + "author_inst": "Universite Paris Cite" + }, + { + "author_name": "Layla El Mossadeq", + "author_inst": "Universite Paris Cite" + }, + { + "author_name": "Michel Raymond", + "author_inst": "ISEM: Institut des sciences de l'evolution de Montpellier" + }, + { + "author_name": "Virginie Orgogozo", + "author_inst": "Universit\u00e9 Paris Cit\u00e9: Universite Paris Cite" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2023.08.01.23293491", "rel_title": "Health inequalities in SARS-CoV-2 infection during the second wave in England: REACT-1 study", @@ -31472,77 +33181,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.08.01.23293500", - "rel_title": "Lower Urinary Tract Symptoms in a prospective cohort of COVID-19 survivors", - "rel_date": "2023-08-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.01.23293500", - "rel_abs": "PurposeTo analyze the prevalence of lower urinary tract symptoms (LUTS) in patients who survived moderate and severe forms of COVID-19 and the risk factors for LUTS six months after hospital discharge.\n\nMaterials and MethodsIn this prospective cohort study, patients were evaluated six months after being hospitalized due to COVID-19. LUTS were assessed using the International Prostate Symptom Score. General health was assessed through the Hospital Anxiety and Depression Scale and the EQ5D-L5 scale, which evaluates mobility, ability to perform daily activities, pain and discomfort and completed a self-perception health evaluation.\n\nResultsOf 255 participants, 54.1% were men and the median age was 57.3 [44.3 - 66.6] years. Pre-existing comorbidities included diabetes (35.7%), hypertension (54.5%), obesity (30.2%) and physical inactivity (65.5%). 124 (48.6%) had a hospital stay >15 days, 181 (71.0%) were admitted to an ICU and 124 (48.6%) needed mechanical ventilation. Median IPSS score was 6 [3-11] and did not differ between men and women. Moderate to severe LUTS affected 108 (42.4%) patients (40.6% men and 44.4% women; p=0.610). Nocturia (58.4%) and frequency (45.9%) were the most prevalent symptoms and urgency was the only symptom that affected men (29.0%) and women (44.4%) differently (p=0.013). LUTS significantly impacted the quality of life of 60 (23.5%) patients with women more severely affected (p=0.004). Preexisting diabetes, hypertension and self-perception of worse general health were associated with LUTS.\n\nConclusionsLUTS are highly prevalent and bothersome six months after hospitalization due to COVID-19. Assessment of LUTS may help ensure appropriate diagnosis and treatment in these patients.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Cristiano M Gomes", - "author_inst": "University of Sao Paulo School of Medicine" - }, - { - "author_name": "Marcelo Hisano", - "author_inst": "University of Sao Paulo School of Medicine" - }, - { - "author_name": "Julia D Souza", - "author_inst": "University of Sao Paulo School of Medicine" - }, - { - "author_name": "Joao Victor Teixeira Henriques", - "author_inst": "University of Sao Paulo School of Medicine" - }, - { - "author_name": "Jose De Bessa Jr.", - "author_inst": "State University of Feira de Santana" - }, - { - "author_name": "Julyana Moromizato", - "author_inst": "University of Sao Paulo School of Medicine" - }, - { - "author_name": "Thulio Bosi", - "author_inst": "University of Sao Paulo School of Medicine" - }, - { - "author_name": "Rachel Mazoni", - "author_inst": "University of Sao Paulo School of Medicine" - }, - { - "author_name": "Joao Gismondi", - "author_inst": "University of Sao Paulo School of Medicine" - }, - { - "author_name": "Bruno Camargo", - "author_inst": "University of Sao Paulo School of Medicine" - }, - { - "author_name": "Zein M Sammour", - "author_inst": "University of Sao Paulo School of Medicine" - }, - { - "author_name": "Homero Bruschini", - "author_inst": "University of Sao Paulo School of Medicine" - }, - { - "author_name": "Linamara R Battistella", - "author_inst": "Instituto de Medicina Fisica e de Reabilitacao, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo" - }, - { - "author_name": "William C Nahas", - "author_inst": "University of Sao Paulo School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "urology" - }, { "rel_doi": "10.1101/2023.07.28.23293261", "rel_title": "Frequency of Atypical Pulmonary Manifestations of COVID-19 Patients on Chest CTscan: A cross-sectional study", @@ -33289,6 +34927,89 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.07.26.550688", + "rel_title": "Competitive fitness and homologous recombination of SARS-CoV-2 variants of concern", + "rel_date": "2023-07-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.26.550688", + "rel_abs": "SARS-CoV-2 variants continue to emerge and cocirculate in humans and wild animals. The factors driving the emergence and replacement of novel variants and recombinants remain incompletely understood. Herein, we comprehensively characterized the competitive fitness of SARS-CoV-2 wild type (WT) and three variants of concern (VOCs), Alpha, Beta and Delta, by coinfection and serial passaging assays in different susceptible cells. Deep sequencing analyses revealed cell-specific competitive fitness: the Beta variant showed enhanced replication fitness during serial passage in Caco-2 cells, whereas the WT and Alpha variant showed elevated fitness in Vero E6 cells. Interestingly, a high level of neutralizing antibody sped up competition and completely reshaped the fitness advantages of different variants. More importantly, single clone purification identified a significant proportion of homologous recombinants that emerged during the passage history, and immune pressure reduced the frequency of recombination. Interestingly, a recombination hot region located between nucleotide sites 22995 and 28866 of the viral genomes could be identified in most of the detected recombinants. Our study not only profiled the variable competitive fitness of SARS-CoV-2 under different conditions, but also provided direct experimental evidence of homologous recombination between SARS-CoV-2 viruses, as well as a model for investigating SARS-CoV-2 recombination.\n\nImportanceSARS-CoV-2 variants or subvariants keep emerging and the epidemic strains keeps changing in humans and animals. The continued replacement of the epidemic strains was attributed to higher competitive fitness evolved by the newly appeared ones than the older ones, but which factors affect the final outcomes are still not entirely clear. In this study, we performed in vitro coinfection and serial passage with three VOCs and WT under different conditions. Our results showed that the competition outcomes of these viral strains varied in different cell lines or under different immune pressure, confirming the probable effects of these two factors for the competitive fitness of different SARS-CoV-2 viral strains. Meanwhile, strikingly, we found that coinfection and serial passage with different SARS-CoV-2 viral strains can mimic the recombination process of SARS-CoV-2 occurred in coinfection individual, indicating it is a novel model to investigate the SARS-CoV-2 recombination mechanism.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Cheng-Feng Qin", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Qi Chen", + "author_inst": "Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Qin Si", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Hangyu Zhou", + "author_inst": "Chinese Academy of Medical Sciences & Peking Union Medical College" + }, + { + "author_name": "Yong-Qiang Deng", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Pan-Deng Shi", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Hui Zhao", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Xiao-Feng Li", + "author_inst": "Academy of Military Medical Sciences Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Xing-Yao Huang", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Yarong Wu", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Yan Guo", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Guangqian Pei", + "author_inst": "Beijing Institute of Microbiology and Epidemiolog" + }, + { + "author_name": "Yunfei Wang", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Si-Qi Sun", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Zong-Min Du", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Yujun Cui", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Hang Fan", + "author_inst": "Beijing Institute of Microbiology and Epidemiology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.07.26.550660", "rel_title": "Interaction of SCoV-2 NSP7 or NSP8 alone may cause constriction of the RNA entry channel in NSP12: Implications for novel RdRp inhibitor drug discovery", @@ -33474,33 +35195,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2023.07.25.23293143", - "rel_title": "The Cost of Keeping Patients Waiting: Retrospective Treatment-Control Study of Additional Healthcare Utilisation for UK Patients Awaiting Elective Treatment Following COVID-19", - "rel_date": "2023-07-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.25.23293143", - "rel_abs": "ObjectiveThe COVID-19 pandemic has led to increased waiting times for elective treatments in many countries. This study seeks to address a deficit in the literature concerning the effect of long waits on the wider consumption of healthcare resources.\n\nMethodsWe carried out a retrospective treatment-control study in a healthcare system in South West England from 15 June 2021 to 15 December 2021. We compared weekly contacts with health services of patients waiting over 18 weeks for treatment ( Treatments) and people not on a waiting list ( Controls). Controls were matched to Treatments based on age, sex, deprivation and multimorbidity. Treatments were stratified by the clinical specialty of the awaited treatment, with healthcare usage assessed over various healthcare settings. T-tests assessed whether there was an increase in healthcare utilisation and bootstrap resampling was used to estimate the magnitude of any differences.\n\nResultsA total of 44,616 patients were waiting over 18 weeks (the constitutional target in England) for treatment during the study period. Evidence suggests increases (p < 0.05) in healthcare utilisation for all specialties. Patients in the Cardiothoracic Surgery specialty had the largest increase, requiring 17.9 [4.3, 33.8] additional contacts with secondary care and 17.3 [-1.1, 34.1] additional prescriptions per year.\n\nConclusionPeople waiting for treatment consume higher levels of healthcare than comparable individuals not on a waiting list. These findings are relevant for clinicians and managers in better understanding patient need and reducing harm. Results also highlight the possible false economy in failing to promptly resolve long elective waits.\n\nHighlightsO_LILong waits for elective care can result in additional healthcare needs to manage symptoms up to the point of definitive treatment. While previous studies indicate some association, these mainly consider only a single elective specialty and are limited in the range of healthcare settings covered.\nC_LIO_LIThe large number of long-wait pathways produced as a consequence of COVID-19 disruption allows for a more holistic analysis, covering the full range of elective treatment specialties and wider healthcare impacts across primary, secondary, mental health, and community care, as well as emergency service calls and prescriptions.\nC_LIO_LIAnalysis of 44,616 elective care pathways reveals evidence of increases in wider healthcare consumption additional to that expected for similar patients not awaiting elective treatment. This suggests a false economy in failing to promptly resolve elective pathways, which should be reflected by healthcare providers in long-term resource allocation decisions.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Charlotte James", - "author_inst": "University of Bristol" - }, - { - "author_name": "Rachel Denholm", - "author_inst": "University of Bristol" - }, - { - "author_name": "Richard M Wood", - "author_inst": "UK National Health Service (BNSSG ICB)" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2023.07.26.23293188", "rel_title": "Comparative effectiveness of sotrovimab versus no treatment in non-hospitalised high-risk patients with COVID-19 in North West London: aretrospective cohort study using the Discover dataset", @@ -34935,6 +36629,85 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2023.07.24.550352", + "rel_title": "Endothelial SARS-CoV-2 infection is not the underlying cause of COVID19-associated vascular pathology in mice", + "rel_date": "2023-07-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.24.550352", + "rel_abs": "Endothelial damage and vascular pathology have been recognized as major features of COVID-19 since the beginning of the pandemic. Two main theories regarding how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) damages endothelial cells and causes vascular pathology have been proposed: direct viral infection of endothelial cells or indirect damage mediated by circulating inflammatory molecules and immune mechanisms. However, these proposed mechanisms remain largely untested in vivo. Here, we utilized a set of new mouse genetic tools1 developed in our lab to test both the necessity and sufficiency of endothelial human angiotensin-converting enzyme 2 (hACE2) in COVID19 pathogenesis. Our results demonstrate that endothelial ACE2 and direct infection of vascular endothelial cells does not contribute significantly to the diverse vascular pathology associated with COVID-19.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Siqi Gao", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Alan T Tang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Min Wang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "David W Buchholz", + "author_inst": "Cornell University" + }, + { + "author_name": "Brian Imbiakha", + "author_inst": "Cornell University" + }, + { + "author_name": "Jisheng Yang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Xiaowen Chen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Peter Hewins", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Patricia Mericko-Ishizuka", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "N. Adrian Leu", + "author_inst": "University of Pennsylvania School of Veterinary Medicine" + }, + { + "author_name": "Stephanie Sterling", + "author_inst": "University of Pennsylvania School of Veterinary Medicine" + }, + { + "author_name": "Avery August", + "author_inst": "Cornell University" + }, + { + "author_name": "Kellie Jurado", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Edward Morrisey", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Hector Aguilar-Carreno", + "author_inst": "Cornell University" + }, + { + "author_name": "Mark L Kahn", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2023.07.24.550324", "rel_title": "Revealing and evaluation of antivirals targeting multiple druggable sites of RdRp complex in SARS-CoV-2", @@ -35044,69 +36817,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.07.19.23292491", - "rel_title": "High seroprevalence after the second wave of SARS-COV2 respiratory infection in a small settlement in the northern coastal of Peru.", - "rel_date": "2023-07-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.19.23292491", - "rel_abs": "BackgroundDue to more infections from variations that could escape vaccination and immunity by asymptomatic to uninfected transmission, COVID-19s second wave had higher seroprevalence globally. Public health constraints and herd immunity may not work against these novel variations infectivity. This population-based study in Perus Tumbes Region during the second wave of COVID-19 seeks to determine seroprevalence and demographic changes from the first wave.\n\nMethodology/Principal findingsIn Dec 2021-Jan 2022, a study in Tumbes informal settlement sampled individuals over 2 years old from one in every four households. Finger-prick blood samples and symptom surveys were collected. On the second wave, there was a substantial rise in adjusted seroprevalence (50.15%, 95% CI [45.92 - 54.40]) compared with the first wave (24.82 %, 95%CI [22.49 - 27.25]), with females maintaining a higher seroprevalence (53.89; 95% CI [48.48-59.23]) vs. 45.49; 95% CI [38.98-52.12], p=0.042) compare to males. Those under 18 years of age had the highest IgG seropositivity: the 12-17 age group during the second wave (85.14%) and the 2-11 age group (25.25%) during the first wave. Nasal congestion and cough were symptoms associated with seropositivity, unlike the first wave.\n\nConclusions/SignificanceIn Tumbes, the seroprevalence of COVID-19 increased by twofold compared to the initial wave. Inadequate infrastructure and limitations in human resources and supplies in healthcare facilities made the Peruvian health system collapse. We must include in epidemiological surveillance mHealth tools that enable real-time reporting of new cases. Working alongside the community is the only way to improve any new intervention strategy to prevent or control a new pandemic.\n\nAuthor summaryIn Peru, the healthcare system was overwhelmed by the COVID-19 pandemic due to the lack of hospital capacity, oxygen supply, political unrest, and a fragmented healthcare system. During the first wave, the prevalence ranged from 20.8% to 72%, and it was predicted that the second wave would be disastrous. To assess the seroprevalence of SARS-CoV-2, a cross-sectional study was conducted in the settlement \"AAHH Las Flores\" located in front of Tumbes National Universitys main campus. A door-to-door intervention was conducted, and a total of 580/781 (74.26%) individuals over than 2 years and above agreed to participate. After adjusting for sensitivity and specificity, the calculated adjusted seroprevalence was 50.15%. Women had a slightly higher adjusted seroprevalence compared to men, and the age groups with the highest prevalence of IgG seropositive were from 12 to 17 years, from 30 to 59 years, and older than 60 years. More than 80% of seropositive patients were asymptomatic in all age groups. The studys findings suggest that COVID-19 transmission in the settlement was higher during the second wave, and asymptomatic individuals could have played a critical role in spreading the virus.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Angie K. Toledo", - "author_inst": "Centro de Investigaci\u00f3n para la Preservaci\u00f3n de la Vida" - }, - { - "author_name": "Franco Le\u00f3n-Jimenez", - "author_inst": "Universidad Cesar Vallejo" - }, - { - "author_name": "Sofia Cavalcanti", - "author_inst": "Hospital Amistad Peru - Korea" - }, - { - "author_name": "Percy Vilchez Barreto", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "Narcisa Reto", - "author_inst": "Essalud" - }, - { - "author_name": "Jessica Vega", - "author_inst": "Direcci\u00f3n Regional de Salud Tumbes" - }, - { - "author_name": "Lucia M Bolivar", - "author_inst": "Direccion Regional de Salud Tumbes" - }, - { - "author_name": "Matilde Rhor", - "author_inst": "Universidad Nacional de Tumbes" - }, - { - "author_name": "Jhon Ypanaque", - "author_inst": "Universidad Nacional de Tumbes" - }, - { - "author_name": "Henry Silva", - "author_inst": "Universidad Nacional de Tumbes" - }, - { - "author_name": "Luz M. Moyano", - "author_inst": "Universidad Cesar Vallejo" - }, - { - "author_name": "- Group of Neuroepidemiology and Science of Life of Peru", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.07.21.23292994", "rel_title": "Mucosal and Systemic Immune Correlates of Viral Control following SARS-CoV-2 Infection Challenge in Seronegative Adults", @@ -36545,6 +38255,89 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2023.07.17.549425", + "rel_title": "A laboratory framework for ongoing optimisation of amplification based genomic surveillance programs", + "rel_date": "2023-07-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.17.549425", + "rel_abs": "Constantly evolving viral populations affect the specificity of primers and quality of genomic surveillance. This study presents a framework for continuous optimisation of sequencing efficiency for public health surveillance based on the ongoing evolution of the COVID-19 pandemic. SARS-CoV-2 genomic clustering capacity based on three amplification based whole genome sequencing schemes was assessed using decreasing thresholds of genome coverage and measured against epidemiologically linked cases. Overall genome coverage depth and individual amplicon depth were used to calculate an amplification efficiency metric. Significant loss of genome coverage over time was documented which was recovered by optimisation of primer pooling or implementation of new primer sets. A minimum of 95% genome coverage was required to cluster 94% of epidemiologically defined SARS-CoV-2 transmission events. Clustering resolution fell to 70% when only 85% of genome coverage was achieved. The framework presented in this study can provide public health genomic surveillance programs a systematic process to ensure an agile and effective laboratory response during rapidly evolving viral outbreaks.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Connie Lam", + "author_inst": "Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, AUSTRALIA" + }, + { + "author_name": "Jessica Johnson-Mackinnon", + "author_inst": "Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, New South Wales, AUSTRALIA" + }, + { + "author_name": "Kerri Basile", + "author_inst": "Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, AUSTRA" + }, + { + "author_name": "Winkie Fong", + "author_inst": "Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, AUSTRALIA" + }, + { + "author_name": "Carl J.E Suster", + "author_inst": "Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, AUSTRALIA" + }, + { + "author_name": "Mailie Gall", + "author_inst": "Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, AUSTRA" + }, + { + "author_name": "Jessica Aguis", + "author_inst": "Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, AUSTRALIA" + }, + { + "author_name": "Shona Chandra", + "author_inst": "Centre for Infectious Diseases and Microbiology - Public Health, Institute for Clinical Pathology and Medical Research Westmead Hospital, Westmead, AUSTRALIA" + }, + { + "author_name": "Jenny Draper", + "author_inst": "Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, AUSTRA" + }, + { + "author_name": "Elena Martinez", + "author_inst": "Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, AUSTRA" + }, + { + "author_name": "Alexander Drew", + "author_inst": "Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, AUSTRA" + }, + { + "author_name": "Qinning Wang", + "author_inst": "Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, AUSTRA" + }, + { + "author_name": "Sharon Chen", + "author_inst": "Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, AUSTRA" + }, + { + "author_name": "Jen Kok", + "author_inst": "Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute for Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, AUSTRA" + }, + { + "author_name": "Dominic L Dwyer", + "author_inst": "Westmead Hospital" + }, + { + "author_name": "Vitali Sintchenko", + "author_inst": "Institute of Clinical Pathology and Medical Research" + }, + { + "author_name": "Rebecca J Rockett", + "author_inst": "University of Sydney" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2023.07.16.23292705", "rel_title": "Community-onset urinary tract infection in females in the context of COVID-19: a longitudinal population cohort study exploring case presentation, management, and outcomes", @@ -36682,25 +38475,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.07.17.23292772", - "rel_title": "Identification of COVID-19 Vaccine-Hesitancy Predictors in the United States", - "rel_date": "2023-07-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.17.23292772", - "rel_abs": "Vaccine hesitancy is complex, multi-causative phenomenon that undermines public health efforts to contain the spread of infectious diseases. Improving our understanding of the drivers of vaccine hesitancy might improve our capacity to address it. We used the results of the May 2021 ASPEs survey on COVID-19 vaccine-hesitancy which estimated the proportion of adults that felt hesitant of unsure towards taking the COVID-19 vaccine when it becomes available at the county-level. We developed a prediction model to identify the most important predictors of vaccine-hesitancy. The potential predictors included demographic characteristics, the CDCs social vulnerability index, and the Republican Partys voting share in the 2020 presidential election as a proxy of political affiliation, both at the county-level. The most important drivers of hesitancy included low educational attainment, proportion of Black/African American population, and political affiliation. These results deepen our understanding of the phenomenon and could help design more targeted interventions to reduce hesitancy in specific sub-groups of the population.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Enrique M Saldarriaga", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.07.14.23292667", "rel_title": "The scientific chaos phase of the Great Pandemic: A longitudinal analysis and systematic review of the first surge of clinical research concerning COVID-19", @@ -38103,6 +39877,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.07.12.548630", + "rel_title": "Utility of nasal swabs for assessing mucosal immune responses towards SARS-CoV-2", + "rel_date": "2023-07-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.12.548630", + "rel_abs": "SARS-CoV-2 has caused millions of infections worldwide since its emergence in 2019. Understanding how infection and vaccination induce mucosal immune responses and how they fluctuate over time is important, especially since they are key in preventing infection and reducing disease severity. We established a novel methodology for assessing SARS-CoV-2 cytokine and antibody responses at the nasal epithelium by using nasopharyngeal swabs collected longitudinally before and after either SARS-CoV-2 infection or vaccination. We then compared responses between mucosal and systemic compartments. We demonstrate that cytokine and antibody profiles differ markedly between compartments. Nasal cytokines show a wound healing phenotype while plasma cytokines are consistent with pro-inflammatory pathways. We found that nasal IgA and IgG have different kinetics after infection, with IgA peaking first. Although vaccination results in low nasal IgA, IgG induction persists for up to 180 days post-vaccination. This research highlights the importance of studying mucosal responses in addition to systemic responses to respiratory infections to understand the correlates of disease severity and immune memory. The methods described herein can be used to further mucosal vaccine development by giving us a better understanding of immunity at the nasal epithelium providing a simpler, alternative clinical practice to studying mucosal responses to infection.\n\nTeaserA nasopharyngeal swab can be used to study the intranasal immune response and yields much more information than a simple viral diagnosis.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Ericka Kirkpatrick Roubidoux", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "Pamela H Brigleb", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "Kasi Vegesana", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "Aisha Souquette", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "Kendall Whitt", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "Pamela Freiden", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "- St. Jude Investigative Team", + "author_inst": "-" + }, + { + "author_name": "Amanda Green", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "Paul G Thomas", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "Maureen A McGargill", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "Joshua Wolf", + "author_inst": "St. Jude Children's Research Hospital" + }, + { + "author_name": "Stacey Schultz-Cherry", + "author_inst": "St. Jude Children's Research Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.07.13.23292597", "rel_title": "Booster dose of self-amplifying SARS-CoV-2 RNA vaccine vs. mRNA vaccine: a phase 3 comparison of ARCT-154 with Comirnaty", @@ -38264,73 +40101,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.07.11.23292264", - "rel_title": "Efficacy and Safety of 5-Day Oral Ensitrelvir for Patients With Mild-to-Moderate COVID-19: The SCORPIO-SR Randomized Clinical Trial", - "rel_date": "2023-07-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.11.23292264", - "rel_abs": "IMPORTANCETreatment options for coronavirus disease 2019 (COVID-19) that can be used irrespective of risk factors for severe disease are warranted.\n\nOBJECTIVETo assess the efficacy and safety of ensitrelvir in patients with mild-to-moderate COVID-19.\n\nDESIGNThe phase 3 part of a phase 2/3, double-blind, randomized, placebo-controlled study conducted from February 10 to July 10, 2022.\n\nSETTINGA multicenter study conducted at 92 institutions in Japan, Vietnam, and South Korea.\n\nPARTICIPANTSPatients (aged 12 to <70 years) with mild-to-moderate COVID-19 within 120 hours of positive viral testing.\n\nINTERVENTIONSPatients were randomized (1:1:1) to receive once-daily ensitrelvir 125 mg (375 mg on day 1), 250 mg (750 mg on day 1), or placebo for 5 days. Among 1821 randomized patients, 1030 (347, 340, and 343 in the ensitrelvir 125-mg, ensitrelvir 250-mg, and placebo groups, respectively) were randomized in less than 72 hours of disease onset and assessed as the primary analysis population.\n\nMAIN OUTCOMES AND MEASURESThe primary end point was the time to resolution of five COVID-19 symptoms (stuffy or runny nose, sore throat, cough, feeling hot or feverish, and low energy or tiredness). Other end points included virologic efficacy and safety.\n\nRESULTSThe mean age was 35.7, 35.3, and 34.7 years, and 193 (55.6%), 185 (54.4%), and 174 (50.7%) patients were men in the ensitrelvir 125-mg, ensitrelvir 250-mg, and placebo groups, respectively (intention-to-treat, primary analysis population). A significant difference (P=.04 with a Peto-Prentice generalized Wilcoxon test stratified by vaccination history) was observed in the primary end point between ensitrelvir 125 mg and placebo in the primary analysis population (difference in median, -24.3 hours; 95% confidence interval, -78.7 to 11.7). Viral RNA levels on day 4 and time to negative viral titer demonstrated significant reduction vs placebo. The incidence of adverse events was 44.2%, 53.6%, and 24.8% in the ensitrelvir 125-mg, ensitrelvir 250-mg, and placebo groups, respectively. No treatment-related serious adverse events were reported.\n\nCONCLUSIONS AND RELEVANCETreatment with ensitrelvir 125 mg demonstrated clinical and antiviral efficacy without new safety concerns. Generalizability to non-Asian populations should be confirmed.\n\nTRIAL REGISTRATIONJapan Registry of Clinical Trials identifier: jRCT2031210350.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSCan ensitrelvir, an oral severe acute respiratory syndrome coronavirus 2 3C-like protease inhibitor, shorten the duration of symptoms in patients with mild-to-moderate COVID-19 irrespective of risk factors for severe disease?\n\nFindingsIn this phase 3 part of a phase 2/3, double-blind, randomized study SCORPIO-SR, a statistically significant difference was observed in the time to resolution of five COVID-19 symptoms between ensitrelvir 125 mg and placebo in patients randomized in less than 72 hours of disease onset. Viral RNA and viral titer demonstrated significant reduction vs placebo.\n\nMeaningEnsitrelvir 125 mg treatment shortened time to resolution of key COVID-19 symptoms.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Hiroshi Yotsuyanagi", - "author_inst": "The University of Tokyo" - }, - { - "author_name": "Norio Ohmagari", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Yohei Doi", - "author_inst": "University of Pittsburgh School of Medicine, Fujita Health University School of Medicine" - }, - { - "author_name": "Masaya Yamato", - "author_inst": "Rinku General Medical Center" - }, - { - "author_name": "Hoang Bac Nguyen", - "author_inst": "University of Medicine and Pharmacy" - }, - { - "author_name": "Ki Cha Bong", - "author_inst": "Chung-Ang Medical Health Care System Hyundae Hospital" - }, - { - "author_name": "Takumi Imamura", - "author_inst": "Shionogi & Co., Ltd." - }, - { - "author_name": "Takuhiro Sonoyama", - "author_inst": "Shionogi & Co., Ltd." - }, - { - "author_name": "Genki Ichihashi", - "author_inst": "Shionogi & Co., Ltd." - }, - { - "author_name": "Takao Sanaki", - "author_inst": "Shionogi & Co., Ltd." - }, - { - "author_name": "Yuko Tsuge", - "author_inst": "Shionogi & Co., Ltd." - }, - { - "author_name": "Takeki Uehara", - "author_inst": "Shionogi & Co., Ltd." - }, - { - "author_name": "Hiroshi Mukae", - "author_inst": "Nagasaki University Graduate School of Biomedical Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.07.13.23292611", "rel_title": "Genetic Risk Factors for Severe and Fatigue Dominant Long COVID and Commonalities with ME/CFS Identified by Combinatorial Analysis", @@ -39527,7 +41297,7 @@ "rel_date": "2023-07-09", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.08.23292389", - "rel_abs": "Antimicrobial peptides (AMPs) are a complex network of 10-100 amino acid sequence molecules, widely distributed in Nature. Even though more than 300 AMPs have been described in mammals, cathelicidins and defensins remain the most investigated to date.\n\nSome publications examined the role of AMPs in COVID-19, but the findings are preliminary and in vivo studies are still lacking. Here, we report the plasma levels of five AMPs (LL-37, -defensin 1, -defensin 3, {beta}-defensin 1 and {beta}-defensin 3) and five cytokines (tumor necrosis factor-, interleukin-1{beta}, interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1), in 15 healthy volunteers, 36 COVID-19 patients without Acute Kidney Injury (AKI) and 17 COVID-19 patients with AKI, since AKI is a well-known marker of worse prognosis in Sars-CoV-2 infections.\n\nWe found increased levels of -defensin 1, -defensin 3 and {beta}-defensin 3, but not LL-37 or {beta}-defensin 3, in our COVID-19 population, when compared with the healthy controls, in conjunction with higher levels of interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1, putting in evidence that these AMPs and cytokines may have an important role in the systemic inflammatory response and tissue damage that characterizes severe COVID-19.\n\nGraphic Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC=\"FIGDIR/small/23292389v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (45K):\norg.highwire.dtl.DTLVardef@1467c3aorg.highwire.dtl.DTLVardef@85cfc6org.highwire.dtl.DTLVardef@10bdab0org.highwire.dtl.DTLVardef@1428889_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "Antimicrobial peptides (AMPs) are a complex network of 10-100 amino acid sequence molecules, widely distributed in Nature. Even though more than 300 AMPs have been described in mammals, cathelicidins and defensins remain the most investigated to date.\n\nSome publications examined the role of AMPs in COVID-19, but the findings are preliminary and in vivo studies are still lacking. Here, we report the plasma levels of five AMPs (LL-37, -defensin 1, -defensin 3, {beta}-defensin 1 and {beta}-defensin 3) and five cytokines (tumor necrosis factor-, interleukin-1{beta}, interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1), in 15 healthy volunteers, 36 COVID-19 patients without Acute Kidney Injury (AKI) and 17 COVID-19 patients with AKI, since AKI is a well-known marker of worse prognosis in Sars-CoV-2 infections.\n\nWe found increased levels of -defensin 1, -defensin 3 and {beta}-defensin 3, but not LL-37 or {beta}-defensin 3, in our COVID-19 population, when compared with the healthy controls, in conjunction with higher levels of interleukin-6, interleukin-10, interferon-{gamma} and monocyte chemoattractant protein-1, putting in evidence that these AMPs and cytokines may have an important role in the systemic inflammatory response and tissue damage that characterizes severe COVID-19.\n\nGraphic Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC=\"FIGDIR/small/23292389v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (45K):\norg.highwire.dtl.DTLVardef@3c64corg.highwire.dtl.DTLVardef@1cfadbdorg.highwire.dtl.DTLVardef@1977a2dorg.highwire.dtl.DTLVardef@1d638c4_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 5, "rel_authors": [ { @@ -39725,6 +41495,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2023.07.07.23292215", + "rel_title": "Comparative Reconstruction of SARS-CoV-2 transmission in three African countries using a mathematical model integrating immunity data.", + "rel_date": "2023-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.07.23292215", + "rel_abs": "ObjectivesAfrica has experienced fewer coronavirus disease 2019 (COVID-19) cases and deaths than other regions, with a contrasting epidemiological situation between countries, raising questions regarding the determinants of disease spread in Africa.\n\nMethodWe built a susceptible-exposed-infected-recovered model including COVID-19 mortality data where recovery class is structured by specific immunization and modeled by a partial differential equation considering the opposed effects of immunity decline and immunization. This model was applied to Tunisia, Senegal, and Madagascar.\n\nFindingSenegal and Tunisia experienced two epidemic phases. Initially, infections emerged in naive individuals and were limited by social distancing. Variants of concern (VOCs) were also introduced. The second phase was characterized by successive epidemic waves driven by new VOCs that escaped host immunity. Meanwhile, Madagascar demonstrated a different profile, characterized by longer intervals between epidemic waves, increasing the pool of susceptible individuals who had lost their protective immunity. The impact of vaccination in Tunisia and Senegal on model parameters was evaluated.\n\nInterpretationLoss of immunity and vaccination-induced immunity have played crucial role in controlling the African pandemic. Severe acute respiratory syndrome coronavirus 2 has become endemic now and will continue to circulate in African populations. However, previous infections provide significant protection against severe diseases, thus providing a basis for future vaccination strategies.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "bechir neffeti", + "author_inst": "university of Tunis el Manar" + }, + { + "author_name": "amira kebir", + "author_inst": "University of Tunis el Manar" + }, + { + "author_name": "walid ben aribi", + "author_inst": "university of Tunis el manar" + }, + { + "author_name": "Maryam Diarra", + "author_inst": "Instutit Pasteur de Dakar" + }, + { + "author_name": "matthieu schoenhals", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "ines vigan-womas", + "author_inst": "institut pasteur de dakar" + }, + { + "author_name": "koussay dellagi", + "author_inst": "Pasteur Network" + }, + { + "author_name": "slimane ben miled", + "author_inst": "University of Tunis el manar" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.07.05.547902", "rel_title": "SARS-CoV-2 Nsp1 regulates translation start site fidelity to promote infection", @@ -39898,157 +41715,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2023.07.07.548077", - "rel_title": "Novel Spike-stabilized trimers with improved production protect K18-hACE2 mice and golden Syrian hamsters from the highly pathogenic SARS-CoV-2 Beta variant.", - "rel_date": "2023-07-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.07.548077", - "rel_abs": "Most COVID-19 vaccines are based on the SARS-CoV-2 Spike glycoprotein (S) or their subunits. However, the S shows some structural instability that limits its immunogenicity and production, hampering the development of recombinant S-based vaccines. The introduction of the K986P and V987P (S-2P) mutations increases the production of the recombinant S trimer and, more importantly, its immunogenicity, suggesting that these two parameters are related. However, S-2P still shows some molecular instability and it is produced with low yield. Thus, S-2P production can be further optimized. Here we described a novel set of mutations identified by molecular modelling and located in the S2 region of the Spike that increase S-2P production up to five-fold. Besides their immunogenicity, the efficacy of two representative S-2P-based mutants, S-29 and S-21, protecting from a heterologous SARS-CoV-2 Beta variant challenge was assayed in K18-hACE2 mice (an animal model of severe SARS-CoV-2 disease) and golden Syrian hamsters (GSH) (a moderate disease model). S-21 induced higher level of WH1 and Delta variants neutralizing antibodies than S-2P in K18-hACE2 mice three days after challenge. Viral load in nasal turbinate and oropharyngeal samples were reduced in S-21 and S-29 vaccinated mice. Despite that, only the S-29 protein protected 100% of K18-hACE2 mice from severe disease. When GSH were analyzed, all immunized animals were protected from disease development irrespectively of the immunogen they received. Therefore, the higher yield of S-29, as well as its improved immunogenicity and efficacy protecting from the highly pathogenic SARS-CoV-2 Beta variant, pinpoint the S-29 spike mutant as an alternative to the S-2P protein for future SARS-CoV-2 vaccine development.\n\nAuthors summaryThe rapid development of SARS-CoV-2 vaccines have been pivotal in the control of the COVID-19 pandemic worldwide. Most of these vaccines include the S glycoprotein as the main immunogen since this protein, and particularly its receptor binding domain (RBD), is the major target of neutralizing antibodies. SARS-CoV-2 have been evolving from the beginning of the pandemic and several variants with increased transmissibility, pathogenicity or resistance to infection- or vaccine-induced immunity have emerged. Different strategies have been adopted to improve vaccine protection including additional booster doses or the adaptation of the S immunogens to the novel SARS-CoV-2 variants. As a complementary strategy we have identified a combination of non-proline mutations that increase S production by 5-fold (S-29 protein). Despite the sequence of this novel S-29 immunogen is based on the ancestral SARS-CoV-2 WH1 variant, it effectively protects animal model from the highly pathogenic and neutralization resistant SARS-CoV-2 Beta variant. Thus, we describe a novel set of mutations that can increase the production and efficacy of S-based COVID-19 vaccines.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Jorge Carrillo", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Carlos \u00c1vila-Nieto", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "J\u00falia Vergara-Alert", - "author_inst": "IRTA: Institut de Recerca i Tecnologia Agroalimentaries" - }, - { - "author_name": "Pep Amengual-Rigo", - "author_inst": "Barcelona Supercomputing Center: Centro Nacional de Supercomputacion" - }, - { - "author_name": "Erola Ainsua-Enrich", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Marco Brustolin", - "author_inst": "IRTA: Institut de Recerca i Tecnologia Agroalimentaries" - }, - { - "author_name": "Mar\u00eda Luisa Rodr\u00edguez de la Concepci\u00f3n", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "N\u00faria Pedre\u00f1o-Lopez", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Jordi Rodon", - "author_inst": "IRTA: Institut de Recerca i Tecnologia Agroalimentaries" - }, - { - "author_name": "Victor Urrea", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Edwards Pradenas", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Silvia Marfil", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Ester Ballana", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Eva Riveira-Mu\u00f1oz", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "M\u00f2nica P\u00e9rez", - "author_inst": "IRTA: Institut de Recerca i Tecnologia Agroalimentaries" - }, - { - "author_name": "N\u00faria Roca", - "author_inst": "IRTA: Institut de Recerca i Tecnologia Agroalimentaries" - }, - { - "author_name": "Ferran Tarr\u00e9s-Freixas", - "author_inst": "IRTA: Institut de Recerca i Tecnologia Agroalimentaries" - }, - { - "author_name": "Julieta Carabelli", - "author_inst": "irsiCaixa Foundation: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Guillermo Cantero", - "author_inst": "IRTA: Institut de Recerca i Tecnologia Agroalimentaries" - }, - { - "author_name": "Anna Pons-Gr\u00edfols", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Carla Rovirosa", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Carmen Aguilar-Gurrieri", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Raquel Ortiz", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Ana Barajas", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Benjamin Trinit\u00e9", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Rosalba Lepore", - "author_inst": "Barcelona Supercomputing Center: Centro Nacional de Supercomputacion" - }, - { - "author_name": "Jordana Mu\u00f1oz-Basagoiti", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Daniel Perez-Zsolt", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Nuria Izquierdo-Useros", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Alfonso Valencia", - "author_inst": "Barcelona Supercomputing Center: Centro Nacional de Supercomputacion" - }, - { - "author_name": "Juli\u00e0 Blanco", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Bonaventura Clotet", - "author_inst": "IrsiCaixa AIDS Research Institute: IrsiCaixa Institut de Recerca de la Sida" - }, - { - "author_name": "Victor Guallar", - "author_inst": "Barcelona Supercomputing Center: Centro Nacional de Supercomputacion" - }, - { - "author_name": "Joaquim Segal\u00e9s", - "author_inst": "IRTA: Institut de Recerca i Tecnologia Agroalimentaries" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.07.06.548022", "rel_title": "Establishing thresholds for cytokine storm and defining their relationship to disease severity in respiratory viral infections", @@ -41811,6 +43477,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2023.06.30.23292087", + "rel_title": "Pre-pandemic activity on a myalgic encephalomyelitis/chronic fatigue syndrome support forum is highly associated with later activity on a long COVID support forum for a variety of reasons: a mixed methods study.", + "rel_date": "2023-07-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.30.23292087", + "rel_abs": "Encephalomyelitis/chronic fatigue syndrome (ME/CFS) and long COVID share some clinical and social characteristics. We predicted that this would lead to an increased interaction between pre-pandemic members of an ME/CFS online support community and a long COVID community. We performed a mixed-methods retrospective observational study of the Reddit activity of 7,544 users active on Reddits long COVID forum. From among 1600 forums, pre-pandemic activity specifically on a ME/CFS forum is the top predictor of later participation on the long COVID forum versus an acute COVID support forum. In the qualitative portion, motives for this co-participation included seeking mutual support and dual identification with both conditions. Some of this effect may be explained by pre-existing ME/CFS possibly being a risk factor for long COVID and/or SARS-CoV-2 infection being a cause of ME/CFS relapse. The high rate of ME/CFS patients seeking mutual support on a long COVID forum speaks to the longsuffering experience of these patients not feeling heard or respected, and the hope of some ME/CFS patients to gain legitimacy through the publics growing recognition of long COVID.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "William U Meyerson", + "author_inst": "Duke University Health System" + }, + { + "author_name": "Rick H Hoyle", + "author_inst": "Duke University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.06.29.23291797", "rel_title": "Community Antibiotic Prescribing in Patients with COVID-19 Across Three Pandemic Waves: A Population-Based Cohort Study", @@ -41940,305 +43629,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.06.29.23292056", - "rel_title": "Genome-wide Association Study of Long COVID", - "rel_date": "2023-07-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.29.23292056", - "rel_abs": "Infections can lead to persistent or long-term symptoms and diseases such as shingles after varicella zoster, cancers after human papillomavirus, or rheumatic fever after streptococcal infections1, 2. Similarly, infection by SARS-CoV-2 can result in Long COVID, a condition characterized by symptoms of fatigue and pulmonary and cognitive dysfunction3-5. The biological mechanisms that contribute to the development of Long COVID remain to be clarified. We leveraged the COVID-19 Host Genetics Initiative6, 7 to perform a genome-wide association study for Long COVID including up to 6,450 Long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We identified the first genome-wide significant association for Long COVID at the FOXP4 locus. FOXP4 has been previously associated with COVID-19 severity6, lung function8, and cancers9, suggesting a broader role for lung function in the pathophysiology of Long COVID. While we identify COVID-19 severity as a causal risk factor for Long COVID, the impact of the genetic risk factor located in the FOXP4 locus could not be solely explained by its association to severe COVID-19. Our findings further support the role of pulmonary dysfunction and COVID-19 severity in the development of Long COVID.", - "rel_num_authors": 71, - "rel_authors": [ - { - "author_name": "Vilma Lammi", - "author_inst": "Institute for Molecular Medicine Finland (FIMM)" - }, - { - "author_name": "Tomoko Nakanishi", - "author_inst": "Department of Human Genetics" - }, - { - "author_name": "Samuel E Jones", - "author_inst": "Institute for Molecular Medicine Finland (FIMM)" - }, - { - "author_name": "Shea J Andrews", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Juha Karjalainen", - "author_inst": "Institute for Molecular Medicine Finland (FIMM)" - }, - { - "author_name": "Beatriz Cortes", - "author_inst": "Genomes for Life-GCAT lab" - }, - { - "author_name": "Heath E O'Brien", - "author_inst": "Sano Genetics Limited" - }, - { - "author_name": "Brian E Fulton-Howard", - "author_inst": "Genetics and Genomic Sciences" - }, - { - "author_name": "Hele H Haapaniemi", - "author_inst": "Institute for Molecular Medicine Finland (FIMM)" - }, - { - "author_name": "Axel Schmidt", - "author_inst": "Institute of Human Genetics" - }, - { - "author_name": "Ruth E Mitchell", - "author_inst": "Centre for Clinical Brain Sciences" - }, - { - "author_name": "Abdou Mousas", - "author_inst": "Department of Hygiene and Epidemiology" - }, - { - "author_name": "Massimo Mangino", - "author_inst": "Department of Twin Research" - }, - { - "author_name": "Alicia Huerta-Chagoya", - "author_inst": "Departamento de Medicina Genomica y Toxicologia Ambiental" - }, - { - "author_name": "Nasa Sinnott-Armstrong", - "author_inst": "Herbold Computational Biology Program" - }, - { - "author_name": "Elizabeth T Cirulli", - "author_inst": "Helix" - }, - { - "author_name": "Marc Vaudel", - "author_inst": "Mohn Center for Diabetes Precision Medicine" - }, - { - "author_name": "Alex SF Kwong", - "author_inst": "University of Bristol" - }, - { - "author_name": "Amit K Maiti", - "author_inst": "Department of Genetics and Genomics" - }, - { - "author_name": "Minttu M Marttila", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Chiara Batini", - "author_inst": "Department of Population Health Sciences" - }, - { - "author_name": "Francesca Minnai", - "author_inst": "Institute for Biomedical Technologies - National Research Council" - }, - { - "author_name": "Anna R Dearman", - "author_inst": "Institute for Social and Economic Research" - }, - { - "author_name": "CA Robert Warmerdam", - "author_inst": "Department of Genetics" - }, - { - "author_name": "Celia B Sequeros", - "author_inst": "Novo Nordisk Foundation Center for Protein Research" - }, - { - "author_name": "Thomas W Winkler", - "author_inst": "Department of Genetic Epidemiology" - }, - { - "author_name": "Daniel M Jordan", - "author_inst": "Charles Bronfman Institute for Personalized Medicine" - }, - { - "author_name": "Lindsay Guare", - "author_inst": "Department of Pathology and Laboratory Medicine" - }, - { - "author_name": "Ekaterina Vergasova", - "author_inst": "Genotek Ltd." - }, - { - "author_name": "Eirini Marouli", - "author_inst": "William Harvey Research Institute" - }, - { - "author_name": "Pasquale Striano", - "author_inst": "IRCCS G" - }, - { - "author_name": "Ummu Afeera Zainulabid", - "author_inst": "Department of Internal Medicine" - }, - { - "author_name": "Ashutosh Kumar", - "author_inst": "Department of Anatomy" - }, - { - "author_name": "Hajar Fauzan Ahmad", - "author_inst": "Faculty of Industrial Sciences and Technology" - }, - { - "author_name": "Ryuya Edahiro", - "author_inst": "Department of Statistical Genetics" - }, - { - "author_name": "Shuhei Azekawa", - "author_inst": "Division of Pulmonary Medicine" - }, - { - "author_name": "- Long COVID Host Genetics Initiative", - "author_inst": "" - }, - { - "author_name": "- FinnGen", - "author_inst": "" - }, - { - "author_name": "- DBDS Genomic Consortium", - "author_inst": "" - }, - { - "author_name": "- GEN-COVID Multicenter Study", - "author_inst": "" - }, - { - "author_name": "Joseph J Grzymski", - "author_inst": "Center for Genomic Medicine" - }, - { - "author_name": "Makoto Ishii", - "author_inst": "Division of Pulmonary Medicine" - }, - { - "author_name": "Yukinori Okada", - "author_inst": "Department of Statistical Genetics" - }, - { - "author_name": "Noam D Beckmann", - "author_inst": "Charles Bronfman Institute for Personalized Medicine" - }, - { - "author_name": "Meena Kumari", - "author_inst": "Institute for Social and Economic Research" - }, - { - "author_name": "Ralf Wagner", - "author_inst": "Institute of Medical Microbiology & Hygiene" - }, - { - "author_name": "Iris M Heid", - "author_inst": "Department of Genetic Epidemiology" - }, - { - "author_name": "Catherine John", - "author_inst": "Department of Population Health Sciences" - }, - { - "author_name": "Patrick J Short", - "author_inst": "Sano Genetics Limited" - }, - { - "author_name": "Per Magnus", - "author_inst": "Centre for Fertility and Health" - }, - { - "author_name": "Karina Banasik", - "author_inst": "Novo Nordisk Foundation Center for Protein Research" - }, - { - "author_name": "Frank Geller", - "author_inst": "Statens Serum Institute" - }, - { - "author_name": "Lude H Franke", - "author_inst": "Department of Genetics" - }, - { - "author_name": "Alexander Rakitko", - "author_inst": "Genotek Ltd." - }, - { - "author_name": "Emma L Duncan", - "author_inst": "Department of Twin Research and Genetic Epidemiology" - }, - { - "author_name": "Alessandra Renieri", - "author_inst": "Medical Genetics" - }, - { - "author_name": "Konstantinos K Tsilidis", - "author_inst": "Department of Hygiene and Epidemiology" - }, - { - "author_name": "Rafael de Cid", - "author_inst": "Genomes for Life-GCAT lab" - }, - { - "author_name": "Ahmadreza Niavarani", - "author_inst": "Digestive Oncology Research Center" - }, - { - "author_name": "Teresa Tusie-Luna", - "author_inst": "Instituto de Investigaciones Biomedicas Unam/ Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" - }, - { - "author_name": "Shefali S Verma", - "author_inst": "Department of Pathology and Laboratory Medicine" - }, - { - "author_name": "George Davey Smith", - "author_inst": "MRC Integrative Epidemiology Unit at the University of Bristol" - }, - { - "author_name": "Nicholas J Timpson", - "author_inst": "MRC Integrative Epidemiology Unit at the University of Bristol" - }, - { - "author_name": "Mark J Daly", - "author_inst": "Institute for Molecular Medicine Finland (FIMM)" - }, - { - "author_name": "Andrea Ganna", - "author_inst": "Institute for Molecular Medicine Finland (FIMM)" - }, - { - "author_name": "Eva C Schulte", - "author_inst": "Institute of Psychiatric Phenomics & Genomics" - }, - { - "author_name": "J Brent Richards", - "author_inst": "Department of Human Genetics" - }, - { - "author_name": "Kerstin U Ludwig", - "author_inst": "Institute of Human Genetics" - }, - { - "author_name": "Michael Hultstrom", - "author_inst": "Anaesthesiology and Intensive Care Medicine" - }, - { - "author_name": "Hugo Zeberg", - "author_inst": "Department of Evolutionary Genetics" - }, - { - "author_name": "Hanna M Ollila", - "author_inst": "Institute for Molecular Medicine Finland (FIMM)" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2023.06.30.547199", "rel_title": "COVID-related anthropause highlights the impact of marine traffic on breeding little penguins", @@ -44153,6 +45543,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.06.27.546790", + "rel_title": "A human primary airway microphysiological system infected with SARS-CoV-2 distinguishes the treatment efficacy between nirmatrelvir and repurposed compounds fluvoxamine and amodiaquine", + "rel_date": "2023-06-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.27.546790", + "rel_abs": "The COVID-19 pandemic necessitated a rapid mobilization of resources toward the development of safe and efficacious vaccines and therapeutics. Finding effective treatments to stem the wave of infected individuals needing hospitalization and reduce the risk of adverse events was paramount. For scientists and healthcare professionals addressing this challenge, the need to rapidly identify medical countermeasures became urgent, and many compounds in clinical use for other indications were repurposed for COVID-19 clinical trials after preliminary preclinical data demonstrated antiviral activity against SARS-CoV-2. Two repurposed compounds, fluvoxamine and amodiaquine, showed efficacy in reducing SARS-CoV-2 viral loads in preclinical experiments, but ultimately failed in clinical trials, highlighting the need for improved predictive preclinical tools that can be rapidly deployed for events such as pandemic emerging infectious diseases. The PREDICT96-ALI platform is a high-throughput, high-fidelity microphysiological system (MPS) that recapitulates primary human tracheobronchial tissue and supports highly robust and reproducible viral titers of SARS-CoV-2 variants Delta and Omicron. When amodiaquine and fluvoxamine were tested in PREDICT96-ALI, neither compound demonstrated an antiviral response, consistent with clinical outcomes and in contrast with prior reports assessing the efficacy of these compounds in other human cell-based in vitro platforms. These results highlight the unique prognostic capability of the PREDICT96-ALI proximal airway MPS to assess the potential antiviral response of lead compounds.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Landys Lopez Quezada", + "author_inst": "Draper" + }, + { + "author_name": "Felix Mba Medie", + "author_inst": "Draper" + }, + { + "author_name": "Elizabeth P. Gabriel", + "author_inst": "Draper" + }, + { + "author_name": "Rebeccah J. Luu", + "author_inst": "Draper" + }, + { + "author_name": "Logan D. Rubio", + "author_inst": "Draper" + }, + { + "author_name": "Thomas J. Mulhern", + "author_inst": "Draper" + }, + { + "author_name": "Jeffrey T. Borenstein", + "author_inst": "Draper" + }, + { + "author_name": "Christine R. Fisher", + "author_inst": "Draper" + }, + { + "author_name": "Ashley L Gard", + "author_inst": "Draper" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2023.06.28.23291948", "rel_title": "Targeting Multiple Conserved T-Cell Epitopes for Protection against COVID-19 Moderate-Severe Disease by a Pan-Sarbecovirus Vaccine", @@ -44294,33 +45735,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.06.26.23291907", - "rel_title": "The effect of residential aged care facility COVID-19 lockdowns on resident mortality", - "rel_date": "2023-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.26.23291907", - "rel_abs": "AimsThis perspective is exploring the effect of residential aged care facility COVID-19 lockdowns on resident mortality.\n\nRelevancePeople living in residential aged care facilities (RACFs) are at increased risk of COVID-19 infection and death.\n\nIn Australia, COVID-19 infections in RACF residents represented seven percent of recorded infections and the case fatality rate (CFR) was 33%. RACFs were categorised as high-risk settings for COVID-19 and a number of measures to reduce the risk of acquiring COVID-19 were implemented at the National and State and Territory levels, such as strict infection control, monitoring, testing, vaccination and increased clinical capacity\n\nMethodsAll COVID-19 infections and deaths in the 12-months from 15 October 2021 to 14 October 2022 for the cohort of residents living in an Australian RACF (except Western Australia) at the beginning of this period were analysed.\n\nKey pointsO_LILockdowns of RACFs were successful in substantially reducing the number of COVID-19 infections and deaths in RACF residents. This was largely because the infection and mortality rates of COVID-19 were high in 2020 and 2021.\nC_LIO_LIThe findings of this study could be used to evaluate and inform national and local states and territories guidelines on the management of COVID-19 in RACFs.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Maria Gabriela Uribe", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Penelope Fotheringham", - "author_inst": "University of Newcastle" - }, - { - "author_name": "Corey Benjamin Moore", - "author_inst": "NSW Health" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2023.06.22.23291692", "rel_title": "Design and Analysis Heterogeneity in Observational Studies of COVID-19 Booster Effectiveness: A Review and Case Study", @@ -45591,6 +47005,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2023.06.20.23291649", + "rel_title": "Association between post-infection COVID-19 vaccination and symptom severity of post COVID-19 condition among patients on Bonaire, Caribbean Netherlands: a retrospective cohort study", + "rel_date": "2023-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.20.23291649", + "rel_abs": "ObjectivesIn this retrospective cohort study, we aimed to investigate symptom severity change following COVID-19 vaccination among post COVID-19 condition (PCC) patients on Bonaire.\n\nMethodsSymptomatic cases who tested positive for SARS-CoV-2 between the start of the pandemic and 1 October 2021, were unrecovered on the interview day and unvaccinated prior to infection were identified from the national case registry. Patients were interviewed by telephone between 15 November and 4 December 2021 about sociodemographic factors, pre-pandemic health, COVID-19 symptoms and vaccination status. We compared symptom severity change between the acute and post-acute disease phase (>4 weeks after disease onset) of 14 symptoms on a five-point Likert scale for 36 PCC patients having received at least one dose of the BNT162 (BioNTech/Pfizer) vaccine and 11 patients who remained unvaccinated, using separate multiple linear regression models.\n\nResultsMost common post-acute symptoms included fatigue (81%), reduced physical endurance (79%), and reduced muscle strength (64%). Post-infection vaccination was significantly associated with reduced severity of heart palpitations, after adjusting for acute phase severity and duration of illness ({beta} 0.60, 95% CI 0.18-1.02). We did not find a statistically significant association with symptom severity change for other, more prevalent symptoms.\n\nConclusionsLarger prospective studies are needed to confirm our observation in a small study population that post-infection COVID-19 vaccination was associated with reduced severity of heart palpitations among those with this symptom self-attributed to SARS-CoV-2 infection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Danytza Berry", + "author_inst": "National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands" + }, + { + "author_name": "Thomas Dalhuisen", + "author_inst": "National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands" + }, + { + "author_name": "Giramin Marchena", + "author_inst": "Public Health Department Bonaire, Public Entity of Bonaire, Caribbean Netherlands" + }, + { + "author_name": "Ivo Tiemessen", + "author_inst": "Mobilito, Bonaire, Caribbean Netherlands" + }, + { + "author_name": "Eveline Geubbels", + "author_inst": "National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands" + }, + { + "author_name": "Loes Jaspers", + "author_inst": "Public Health Department Bonaire, Public Entity of Bonaire, Caribbean Netherlands" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.06.20.23291688", "rel_title": "Evaluating the buffering role of perceived social support and coping resources against the adult mental health impacts of COVID-19 psychosocial stress: a cross-sectional study in South Africa", @@ -45752,33 +47205,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.06.21.545910", - "rel_title": "Spatial and Temporal Analysis of SARS-CoV-2 Genome Evolutionary Patterns", - "rel_date": "2023-06-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.21.545910", - "rel_abs": "The spread of SARS-CoV-2 virus accompanied by availability of abundant sequence data publicly, provides a window for determining the spatio-temporal patterns of viral evolution in response to vaccination. In this study, SARS-CoV-2 genome sequences were collected from seven countries in the period January 2020-December 2022. The sequences were classified into three phases, namely: pre-vaccination, post-vaccination, and recent period. Comparison was performed between these phases based on parameters like mutation rates, selection pressure (dN/dS ratio), and transition to transversion ratios (Ti/Tv). Similar comparisons were performed among SARS-CoV-2 variants. Statistical significance was tested using Graphpad unpaired t-test. The comparative analysis showed an increase in the percent genomic mutation rates post-vaccination and in recent periods across different countries from the pre-vaccination phase. The dN/dS ratios showed positive selection that increased after vaccination, and the Ti/Tv ratios decreased after vaccination. C[->]U and G[->]U were the most frequent transitions and transversions in all the countries. However, U[->]G was the most frequent transversion in recent period. The Omicron variant had the highest genomic mutation rates, while Delta showed the highest dN/dS ratio. Mutation rates were highest in NSP3, S, N and NSP12b before and increased further after vaccination. NSP4 showed the largest change in mutation rates after vaccination. N, ORF8, ORF3a and ORF10 were under highest positive selection before vaccination. They were overtaken by E, S and NSP1 in the after vaccination as well as recent sequences, with the largest change observed in NSP1. Protein-wise dN/dS ratio was also seen to vary across the different variants.\n\nImportanceIrrespective of the different vaccine technologies used, geographical regions and host genetics, variations in the SARS-CoV-2 genome have maintained similar patterns worldwide. To the best of our knowledge, there exists no other large-scale study of the genomic and protein-wise mutation patterns during the time course of evolution in different countries. Analysing the SARS-CoV-2 evolution patterns in response to spatial, temporal, and biological signals is important for diagnostics, therapeutics, and pharmacovigilance of SARS-CoV-2.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Shubhangi Gupta", - "author_inst": "Netaji Subhas University of Technology" - }, - { - "author_name": "Deepanshu Gupta", - "author_inst": "Netaji Subhas University of Technology" - }, - { - "author_name": "Sonika Bhatnagar", - "author_inst": "Netaji Subhas University of Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.06.19.23291620", "rel_title": "Association of Nirmatrelvir/Ritonavir treatment and COVID-19 neutralizing antibody titers in a longitudinal healthcare worker cohort", @@ -47509,6 +48935,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2023.06.16.23291449", + "rel_title": "Timing and Predictors of Loss of Infectivity among Healthcare Workers with Primary and Recurrent COVID-19: a Prospective Observational Cohort Study", + "rel_date": "2023-06-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.16.23291449", + "rel_abs": "BackgroundThere is a need to understand the duration of infectivity of primary and recurrent COVID-19 and identify predictors of loss of infectivity.\n\nMethodsProspective observational cohort study with serial viral culture, rapid antigen detection test (RADT) and RT-PCR on nasopharyngeal specimens of healthcare workers with COVID-19. The primary outcome was viral culture positivity as indicative of infectivity. Predictors of loss of infectivity were determined using multivariate regression model. The performance of the US CDC criteria (fever resolution, symptom improvement and negative RADT) to predict loss of infectivity was also investigated.\n\nResults121 participants (91 female [79.3%]; average age, 40 years) were enrolled. Most (n=107, 88.4%) had received [≥]3 SARS-CoV-2 vaccine doses, and 20 (16.5%) had COVID-19 previously. Viral culture positivity decreased from 71.9% (87/121) on day 5 of infection to 18.2% (22/121) on day 10. Participants with recurrent COVID-19 had a lower likelihood of infectivity than those with primary COVID-19 at each follow-up (day 5 OR, 0.14; p<0.001]; day 7 OR, 0.04; p=0.003]) and were all non-infective by day 10 (p=0.02). Independent predictors of infectivity included prior COVID-19 (adjusted OR [aOR] on day 5, 0.005; p=0.003), a RT-PCR Ct value <23 (aOR on day 5, 22.75; p<0.001), but not symptom improvement or RADT result.\n\nThe CDC criteria would identify 36% (24/67) of all non-infectious individuals on Day 7. However, 17% (5/29) of those meeting all the criteria had a positive viral culture.\n\nConclusionsInfectivity of recurrent COVID-19 is shorter than primary infections. Loss of infectivity algorithms could be optimized.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Stefka Dzieciolowska", + "author_inst": "McGill University Faculty of Medicine, Montreal, Canada" + }, + { + "author_name": "Hugues Charest", + "author_inst": "Laboratoire de Sante Publique du Quebec, Sainte-Anne-de-Bellevue, Canada" + }, + { + "author_name": "Tonya Roy", + "author_inst": "Laboratoire de Sante Publique du Quebec, Sainte-Anne-de-Bellevue, Canada" + }, + { + "author_name": "Judith Fafard", + "author_inst": "Laboratoire de Sante Publique du Quebec, Institut national de sante publique du Quebec" + }, + { + "author_name": "Sara Carazo", + "author_inst": "Institut national de sante publique du Quebec" + }, + { + "author_name": "Ines Levade", + "author_inst": "Laboratoire de Sante Publique du Quebec, Sainte-Anne-de-Bellevue, Canada" + }, + { + "author_name": "Jean Longtin", + "author_inst": "Centre hospitalier universitaire (CHU) de Quebec" + }, + { + "author_name": "Leighanne Parkes", + "author_inst": "Jewish General Hospital Sir Mortimer B. Davis, Montreal, Canada" + }, + { + "author_name": "Sylvie Nancy Beaulac", + "author_inst": "Laboratoire de Sante Publique du Quebec, Sainte-Anne-de-Bellevue, Canada" + }, + { + "author_name": "Jasmin Villeneuve", + "author_inst": "Institut National de Sante Publique du Quebec, Quebec City, Canada" + }, + { + "author_name": "Patrice Savard", + "author_inst": "Centre Hospitalier de Universite de Montreal (CHUM) and CHUM Research Center, Montreal, Canada" + }, + { + "author_name": "Jacques Corbeil", + "author_inst": "Universite Laval, Quebec City, Canada" + }, + { + "author_name": "Gaston De Serres", + "author_inst": "Institut National de Sante Publique du Quebec, Quebec City, Canada" + }, + { + "author_name": "Yves Longtin", + "author_inst": "Jewish General Hospital Sir Mortimer B. Davis, Montreal, Canada" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.06.15.545172", "rel_title": "SARS-CoV-2 Delta Variant Remains Viable in Environmental Biofilms found in Meat Packaging Plants", @@ -47634,29 +49131,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.06.13.23291332", - "rel_title": "Omicron vs. the Rest: Assessing the Competitive Dynamics and Coinfection Scenarios of COVID-19 Strains on a Social Network", - "rel_date": "2023-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.13.23291332", - "rel_abs": "The rapid spread and evolving nature of COVID-19 variants have raised concerns regarding their competitive dynamics and coinfection scenarios. In this study, we assess the competitive interactions between the Omicron variant and other prominent variants (Alpha, Beta, and Delta) on a social network, considering both single infection and coinfection states. Using the SIRS model, we simulate the progression of these variants and analyze their impact on infection rates, mortality, and overall disease burden. Our findings demonstrate that the Alpha and Beta strains exhibit comparable contagion levels, with the Alpha strain displaying higher infection and mortality rates. Moreover, the Delta strain emerges as the most prevalent and virulent strain, surpassing the other variants. When introduced alongside the less virulent Omicron strain, the Delta strain results in higher infection and mortality rates. However, the Omicron strains dominance leads to an overall increase in disease statistics. Remarkably, our study highlights the efficacy of the Omicron variant in supplanting more virulent strains and its potential role in mitigating the spread of infectious diseases. The Omicron strain demonstrates a competitive advantage over the other variants, suggesting its potential to reduce the severity of the disease and alleviate the burden on healthcare systems. These findings underscore the importance of monitoring and understanding the dynamics of COVID-19 variants, as they can inform effective prevention and mitigation strategies, particularly with the emergence of variants that possess a relative advantage in controlling disease transmission.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Hamed Jebraeilian", - "author_inst": "Tarbiat Modares University" - }, - { - "author_name": "Yousef Jamali", - "author_inst": "Tarbiat Modares University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.06.13.23290674", "rel_title": "Determinants of post-acute COVID-19 syndrome among hospitalized severe COVID-19 patients: a 2-year follow-up study", @@ -49279,6 +50753,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.06.09.23291201", + "rel_title": "SARS-CoV-2 seroprevalence in pregnant women during the first three COVID-19 waves in The Gambia", + "rel_date": "2023-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.09.23291201", + "rel_abs": "ObjectivesSARS-CoV-2 transmission in Sub-Saharan Africa has probably been underestimated. Population-based seroprevalence studies are needed to determine the extent of transmission in the continent.\n\nMethodsBlood samples from a cohort of Gambian pregnant women were tested for SARS-CoV-2 total IgM/IgG before (Pre-pandemic1: October-December 2019 and Pre-pandemic2: February-June 2020) and during the pandemic (Post-wave1: October-December 2020, Post-wave2: May-June 2021; and Post-wave3: October-December 2021). Samples positive for total SARS-CoV-2 IgM/IgG were tested for protein-specific antibodies.\n\nResultsSARS-CoV-2 total IgM/IgG seroprevalence was 0.9% 95%CI (0.2, 4.9) in Pre-pandemic1; 4.1% (1.4, 11.4) in Pre-pandemic2; 31.1% (25.2, 37.7) in Post-wave1; 62.5% (55.8, 68.8) in Post-wave2 and 90.0% (85.1, 93.5) in Post-wave3. S-protein IgG and NCP-protein IgG seroprevalence also increased at each Post-wave period. Although S-protein IgG and NCP-protein IgG seroprevalence was similar at Post-wave1, S-protein IgG seroprevalence was higher at Post-wave2 and Post-wave3, [prevalence difference (PD) 13.5 (0.1, 26.8) and prevalence ratio (PR) 1.5 (1.0, 2.3) in Post-wave2; and 22.9 (9.2, 36.6) and 1.4 (1.1, 1.8) in Post-wave3 respectively, p<0.001].\n\nConclusionSARS-CoV-2 transmission in The Gambia during the first three COVID-19 waves was high, differing significantly from official numbers of COVID-19 cases reported. Our findings are important for policy makers in managing the near-endemic COVID-19.\n\nHighlightsO_LIHigh specificity of the IgM/IgG SARS-CoV-2 test using samples collected prepandemic\nC_LIO_LIVery high (>90%) SARS-CoV-2 seroprevalence after third COVID-19 wave in The Gambia\nC_LIO_LIHigh SARS-CoV-2 transmission contrasts with low number of COVID-19 reported cases\nC_LI", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Ramatoulie E. Janha", + "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, The Gambia" + }, + { + "author_name": "Alasana Bah", + "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, The Gambia" + }, + { + "author_name": "Hawanatu Jah", + "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, The Gambia" + }, + { + "author_name": "Fatima Touray", + "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, The Gambia" + }, + { + "author_name": "Yahaya Idris", + "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, The Gambia" + }, + { + "author_name": "Saikou Keita", + "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, The Gambia" + }, + { + "author_name": "Yassin Gaye", + "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical" + }, + { + "author_name": "Samba Jallow", + "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, The Gambia" + }, + { + "author_name": "Tisbeh Faye-Joof", + "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, The Gambia" + }, + { + "author_name": "Baboucarr Njie", + "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, The Gambia" + }, + { + "author_name": "Rachel Craik", + "author_inst": "Department of Women and Childrens Health, School of Life Course Science, Faculty of Life Sciences and Medicine, Kings College London, 5th Floor, Becket House, 1" + }, + { + "author_name": "Nuredin I Mohammed", + "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, The Gambia" + }, + { + "author_name": "Peter von Dadelszen", + "author_inst": "Department of Women and Childrens Health, School of Life Course Science, Faculty of Life Sciences and Medicine, Kings College London, 5th Floor, Becket House, 1" + }, + { + "author_name": "Umberto D'Alessandro", + "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, The Gambia" + }, + { + "author_name": "Anna Roca", + "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Fajara, P.O. Box 273, Banjul, The Gambia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.06.12.23291266", "rel_title": "Global seasonal activities of respiratory syncytial virus before the COVID-19 pandemic: a systematic review", @@ -49460,37 +51009,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2023.06.09.23290893", - "rel_title": "Risk of Coronavirus Disease 2019 (COVID-19) among Those Up-to-Date and Not Up-to-Date on COVID-19 Vaccination", - "rel_date": "2023-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.09.23290893", - "rel_abs": "BackgroundThe CDC recently defined being \"up-to-date\" on COVID-19 vaccination as having received at least one dose of a COVID-19 bivalent vaccine. The purpose of this study was to compare the risk of COVID-19 among those \"up-to-date\" and \"not up-to-date\".\n\nMethodsEmployees of Cleveland Clinic in Ohio, USA, in employment when the COVID-19 bivalent vaccine first became available, and still employed when the XBB lineages became dominant, were included. Cumulative incidence of COVID-19 since the XBB lineages became dominant was compared across the \"up-to-date\" and \"not up-to-date\" states, by treating COVID-19 bivalent vaccination as a time- dependent covariate whose value changed on receipt of the vaccine. Risk of COVID-19 by vaccination status was also evaluated using multivariable Cox proportional hazards regression adjusting for propensity to get tested for COVID-19, age, sex, most recent prior SARS-CoV-2 infection, and number of prior vaccine doses.\n\nResultsCOVID-19 occurred in 1475 (3%) of 48 344 employees during the 100-day study period. The cumulative incidence of COVID-19 was lower in the \"not up-to-date\" than the \"up-to-date\" state. On multivariable analysis, being \"up-to-date\" was not associated with lower risk of COVID-19 (HR, 1.05; 95% C.I., 0.88-1.25; P-value, 0.58). Results were very similar when those 65 years and older were only considered \"up-to-date\" after 2 doses of the bivalent vaccine.\n\nConclusionsSince the XBB lineages became dominant, adults \"up-to-date\" on COVID-19 vaccination by the CDC definition do not have a lower risk of COVID-19 than those \"not up-to-date\", bringing into question the value of this risk classification definition.\n\nSummaryAmong 48 344 working-aged Cleveland Clinic employees, those \"up-to-date\" on COVID-19 vaccination did not have a lower risk of COVID-19 than those not \"up-to-date\". The current CDC definition provides a meaningless classification of risk of COVID-19 in the adult population.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Nabin K. Shrestha", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Patrick C. Burke", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Amy S. Nowacki", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Steven M. Gordon", - "author_inst": "Cleveland Clinic" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.06.09.23291195", "rel_title": "Characteristics and outcomes of patients with COVID-19 at high risk of disease progression receiving sotrovimab, oral antivirals or no treatment in Scotland", @@ -50857,6 +52375,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, + { + "rel_doi": "10.1101/2023.06.06.23290826", + "rel_title": "OpenSAFELY: The impact of COVID-19 on azathioprine, leflunomide, and methotrexate monitoring, and factors associated with change in monitoring rate.", + "rel_date": "2023-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.06.23290826", + "rel_abs": "BackgroundThe COVID-19 pandemic created unprecedented pressure on healthcare services. This study aimed to investigate if disease-modifying anti-rheumatic drug (DMARD) safety monitoring was affected during the COVID-19 pandemic.\n\nMethodsA population-based cohort study was conducted with the approval of NHS England, using the OpenSAFELY platform to access electronic health record data from 24{middle dot}2 million patients registered at general practices using TPPs SystmOne software. Patients were included for further analysis if prescribed azathioprine, leflunomide, or methotrexate between November 2019 and July 2022. Outcomes were assessed as monthly trends and variation between various sociodemographic and clinical groups for adherence with standard safety monitoring recommendations.\n\nFindingsAn acute increase in the rate of missed monitoring occurred across the study population (+12{middle dot}4 percentage points) when lockdown measures were implemented in March 2020. This increase was more pronounced for some patient groups (70-79 year-olds: +13{middle dot}7 percentage points; females: +12{middle dot}8 percentage points), regions (North West: +17{middle dot}0 percentage points), medications (Leflunomide: +20{middle dot}7 percentage points), and monitoring tests (Blood Pressure: +24{middle dot}5 percentage points). Missed monitoring rates decreased substantially for all groups by July 2022. Substantial and consistent differences were observed in overall missed monitoring rates between several groups throughout the study.\n\nInterpretationDMARD monitoring rates temporarily deteriorated during the COVID-19 pandemic. Deterioration coincided with the onset of lockdown measures, with monitoring rates recovering rapidly as lockdown measures were eased. Differences observed in monitoring rates between medications, tests, regions, and patient groups, highlight opportunities to tackle potential inequalities in the provision or uptake of monitoring services. Further research should aim to evaluate the causes of the differences identified between groups.\n\nFundingNone.\n\nResearch in context Evidence before this studyDisease-modifying anti-rheumatic drugs (DMARDs) are immunosuppressive and/or immunomodulatory drugs, which carry risks of serious adverse effects such as; gastrointestinal, renal, hepatic, and pulmonary toxicity; myelosuppression; and increased susceptibility to infection. To mitigate these safety risks, national safety guidance recommends that patients taking these drugs receive regular monitoring. We searched PubMed, Web of Science and Scopus for studies published between database inception and July 28th, 2022, using the terms ([covid-19] AND [monitoring OR shared care OR dmard OR outcome factors] AND [primary care]), with no language restrictions. Studies that investigated the effect of the COVID-19 pandemic on healthcare services were identified. One key study in England showed disruption to various monitoring services in primary care had occurred during the pandemic. Another English study highlighted a disproportionate impact of the COVID-19 pandemic on health outcomes in certain groups.\n\nAdded value of this studyPrior to this study knowledge of how high-risk drugs, such as DMARDs, were affected by the COVID-19 pandemic was limited. This study reports the impact of COVID-19 on the safety monitoring of DMARDs. Moreover, it reports variation in DMARD monitoring rates between demographic, clinical and regional subgroups, which has not yet been described. This is enabled through use of the OpenSAFELY platform, which provides secure access to pseudonymised primary care patient records in England for the purposes of analysing the COVID-19 pandemic impact.\n\nImplications of all the available evidenceDMARD monitoring rates transiently deteriorated during the COVID-19 pandemic, consistent with previous research on other monitoring tests. Deterioration coincided with the onset of lockdown measures, with performance recovering rapidly as lockdown measures were eased. Differences observed in monitoring rates between demographic, clinical and regional subgroups highlight opportunities to identify and tackle potential inequalities in the provision or uptake of monitoring services. Further research should aim to evaluate the causes of the differences identified between groups, and establish the clinical relevance of missed monitoring. Several studies have demonstrated the capability of the OpenSAFELY platform as a secure and efficient approach for analysing NHS primary care data at scale, generating meaningful insights on service delivery.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "- The OpenSAFELY Collaborative", + "author_inst": "" + }, + { + "author_name": "Andrew D Brown", + "author_inst": "University of Oxford" + }, + { + "author_name": "Louis Fisher", + "author_inst": "University of Oxford" + }, + { + "author_name": "Helen J Curtis", + "author_inst": "University of Oxford" + }, + { + "author_name": "Milan Wiedemann", + "author_inst": "University of Oxford" + }, + { + "author_name": "William J Hulme", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lisa EM Hopcroft", + "author_inst": "University of Oxford" + }, + { + "author_name": "Christine Cunningham", + "author_inst": "University of Oxford" + }, + { + "author_name": "Victoria Speed", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ruth E Costello", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "James B Galloway", + "author_inst": "King's College London" + }, + { + "author_name": "Mark D Russell", + "author_inst": "King's College London" + }, + { + "author_name": "Katie Bechman", + "author_inst": "King's College London" + }, + { + "author_name": "Zeyneb Kurt", + "author_inst": "Northumbria University" + }, + { + "author_name": "Richard Croker", + "author_inst": "University of Oxford" + }, + { + "author_name": "Christopher Wood", + "author_inst": "University of Oxford" + }, + { + "author_name": "Alex J Walker", + "author_inst": "University of Oxford" + }, + { + "author_name": "Andrea L Schaffer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Seb CJ Bacon", + "author_inst": "University of Oxford" + }, + { + "author_name": "Amir Mehrkar", + "author_inst": "University of Oxford" + }, + { + "author_name": "George Hickman", + "author_inst": "University of Oxford" + }, + { + "author_name": "Chris Bates", + "author_inst": "TPP" + }, + { + "author_name": "Jonathan Cockburn", + "author_inst": "TPP" + }, + { + "author_name": "John Parry", + "author_inst": "TPP" + }, + { + "author_name": "Frank Hester", + "author_inst": "TPP" + }, + { + "author_name": "Sam Harper", + "author_inst": "TPP" + }, + { + "author_name": "Ben Goldacre", + "author_inst": "University of Oxford" + }, + { + "author_name": "Brian MacKenna", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2023.06.06.23290982", "rel_title": "Estimating the effectiveness of COVID-19 vaccination against COVID-19 hospitalisation and death: a cohort study based on the 2021 Census, England.", @@ -51090,33 +52735,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.06.05.23290956", - "rel_title": "How could a pooled testing policy have performed in managing the early stages of the COVID-19 pandemic? Results from a simulation study", - "rel_date": "2023-06-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.05.23290956", - "rel_abs": "A coordinated testing policy is an essential tool for responding to emerging epidemics, as was seen with COVID-19. However, it is very difficult to agree on the best policy when there are multiple conflicting objectives. A key objective is minimising cost, which is why pooled testing (a method that involves pooling samples taken from multiple individuals and analysing this with a single diagnostic test) has been suggested. In this paper, we present results from an extensive and realistic simulation study comparing testing policies based on individually testing subjects with symptoms (a policy resembling the UK strategy at the start of the COVID-19 pandemic), individually testing subjects at random or pools of subjects randomly combined and tested. To compare these testing methods, a dynamic model compromised of a relationship network and an extended SEIR model is used. In contrast to most existing literature, testing capacity is considered as fixed and limited rather than unbounded. This paper then explores the impact of the proportion of symptomatic infections on the expected performance of testing policies. Only for less than 50% of infections being symptomatic does pooled testing outperform symptomatic testing in terms of metrics such as total infections and length of epidemic. Additionally, we present the novel feature for testing of non-compliance and perform a sensitivity analysis for different compliance assumptions. Our results suggest for the pooled testing scheme to be superior to testing symptomatic people individually, only a small proportion of the population (> 2%) needs to not comply with the testing procedure.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Bethany Heath", - "author_inst": "MRC Biostatistics Unit, University of Cambridge" - }, - { - "author_name": "Sof\u00eda S. Villar", - "author_inst": "MRC Biostatistics Unit, University of Cambridge" - }, - { - "author_name": "David S. Robertson", - "author_inst": "MRC Biostatistics Unit, University of Cambridge" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.06.05.23290969", "rel_title": "A prospective, single-center, randomized phase 2 trial of etoposide in severe COVID-19", @@ -52639,6 +54257,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pain medicine" }, + { + "rel_doi": "10.1101/2023.05.31.23290799", + "rel_title": "A quantitative evaluation of the impact of vaccine roll-out rate and coverage on reducing deaths from COVID-19: a counterfactual study on the impact of the delayed vaccination programme in Iran", + "rel_date": "2023-06-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.31.23290799", + "rel_abs": "Vaccination has been a crucial factor in the fight against COVID-19 because of its effectiveness in suppressing virus circulation, lowering the risk of severe disease, and ultimately saving lives. Many countries with an early and rapid distribution of COVID-19 vaccines performed much better in reducing their total number of deaths than those with lower coverage and slower roll-out pace. However, we still do not know how many more deaths could have been averted if countries with slower vaccine roll-outs followed the same rate as countries with earlier and faster distribution of vaccines. Here, we investigated counterfactual scenarios for the number of avertable COVID-19 deaths in a given country based on other countries vaccine roll-out rates. As a case study, we compared Iran to eight model countries with similar income brackets and dominant COVID-19 vaccine types. Our analysis revealed that faster roll-outs were associated with higher numbers of averted deaths. While Irans percentage of fully vaccinated individuals would have been similar to Bangladesh, Nepal, Sri Lanka, and Turkey under counterfactual roll-out rates, adopting Turkeys rates could have averted up to 50,000 more deaths, whereas following Bangladeshs rates could have led to up to 52,800 additional losses of lives in Iran. Notably, a counterfactual scenario based on Argentinas early but slow roll-out rate resulted in a smaller number of averted deaths in Iran, up to 12,600 more individuals. Following Montenegros or Bolivias model of faster per capita roll-out rates for Iran could have resulted in more averted deaths in older age groups, particularly during the Alpha and Delta waves, despite their lower overall coverage. Also, following Bahrains model as an upper bound benchmark, Iran could have averted 75,300 deaths throughout the pandemic, primarily in the >50 age groups. This study provides insights into future decisions on the management of infectious disease epidemics through vaccination strategies by comparing the relative performance of different countries in terms of their timing, pace, and coverage of vaccination in preventing COVID-19 deaths.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Mahan Ghafari", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sepanta Hosseinpour", + "author_inst": "University of Queensland" + }, + { + "author_name": "Mohammad Saeid Rezaee-Zavareh", + "author_inst": "Middle East Liver Diseases (MELD) Center" + }, + { + "author_name": "Stefan Dascalu", + "author_inst": "University of Oxford" + }, + { + "author_name": "Somayeh Rostamian", + "author_inst": "Imperial College London" + }, + { + "author_name": "Kiarash Aramesh", + "author_inst": "PennWest University" + }, + { + "author_name": "Kaveh Madani", + "author_inst": "United Nations University Institute for Water, Environment and Health" + }, + { + "author_name": "Shahram Kordasti", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.05.30.23290732", "rel_title": "Challenges of COVID-19 Case Forecasting in the US, 2020-2021", @@ -53196,93 +54861,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.05.25.23290456", - "rel_title": "Effectiveness of mRNA-1273 bivalent (Original and Omicron BA.4/BA.5) COVID-19 vaccine in preventing hospitalizations for COVID-19, medically attended SARS-CoV-2 infections, and hospital death in the United States", - "rel_date": "2023-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.25.23290456", - "rel_abs": "The bivalent (original and Omicron BA.4/BA.5) mRNA-1273 COVID-19 vaccine was authorized to offer broader protection against COVID-19. We conducted a matched cohort study to evaluate the effectiveness of the bivalent vaccine in preventing hospitalization for COVID-19 (primary outcome) and medically attended SARS-CoV-2 infection and hospital death (secondary outcomes). Compared to individuals who did not receive bivalent mRNA vaccination but received [≥]2 doses of any monovalent mRNA vaccine, the relative vaccine effectiveness (rVE) against hospitalization for COVID-19 was 70.3% (95% confidence interval, 64.0%-75.4%). rVE was consistent across subgroups and not modified by time since last monovalent dose or number of monovalent doses received. Protection was durable [≥]3 months after the bivalent booster. rVE against SARS-CoV-2 infection requiring emergency department/urgent care and against COVID-19 hospital death was 55.0% (50.8%-58.8%) and 82.7% (63.7%-91.7%), respectively. The mRNA-1273 bivalent booster provides additional protection against hospitalization for COVID-19, medically attended SARS-CoV-2 infection, and COVID-19 hospital death.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Hung Fu Tseng", - "author_inst": "Kaiser Permanente Southern California" - }, - { - "author_name": "Bradley K. Ackerson", - "author_inst": "Kaiser Permanente Southern California" - }, - { - "author_name": "Lina S. Sy", - "author_inst": "Kaiser Permanente Southern California" - }, - { - "author_name": "Julia E. Tubert", - "author_inst": "Kaiser Permanente Southern California" - }, - { - "author_name": "Yi Luo", - "author_inst": "Kaiser Permanente Southern California" - }, - { - "author_name": "Sijia Qiu", - "author_inst": "Kaiser Permanente Southern California" - }, - { - "author_name": "Gina S. Lee", - "author_inst": "Kaiser Permanente Southern California" - }, - { - "author_name": "Katia J. Bruxvoort", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Jennifer H. Ku", - "author_inst": "Kaiser Permanente Southern California" - }, - { - "author_name": "Ana Florea", - "author_inst": "Kaiser Permanente Southern California" - }, - { - "author_name": "Harpreet S. Takhar", - "author_inst": "Kaiser Permanente Southern California" - }, - { - "author_name": "Radha Bathala", - "author_inst": "Kaiser Permanente Southern California" - }, - { - "author_name": "Cindy Ke Zhou", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Daina Esposito", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Morgan A. Marks", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Evan J. Anderson", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Carla A. Talarico", - "author_inst": "AstraZeneca" - }, - { - "author_name": "Lei Qian", - "author_inst": "Kaiser Permanente Southern California" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.05.25.23290513", "rel_title": "Carotid body dysregulation contributes to the enigma of long COVID", @@ -54037,7 +55615,7 @@ "rel_date": "2023-06-01", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.01.23290768", - "rel_abs": "The authors have withdrawn their manuscript owing to a complete change in methods and results. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the first author.", + "rel_abs": "BackgroundThroughout the surge of the COVID-19 pandemic high rate of chronic diseases have been reported, including respiratory diseases and cardiovascular diseases. The prevalence of coronary artery disease has remained high throughout the COVID-19 pandemic, which also draws great concern towards it. This study seeks to provide a pooled estimate of the burden of coronary artery disease in COVID-19.\n\nObjectiveTo estimate the overall prevalence of coronary artery disease among COVID-19 patients\n\nData SourcesIn this systematic review and meta-analysis, an extensive literature search was conducted in PubMed, Scopus, Embase, EBSCO, Web of Science, Cochrane,Proquest and preprint servers (medRxiv, arXiv, bioRxiv, BioRN, ChiRxiv, ChiRN, and SSRN). References fo eligible articles, forward citation tracking, and expert opinion were used to identify other relevant articles. All published articles until 13 April 2023 were assessed as per the PROSPERO registration protocol (CRD42022367501).\n\nStudy Selection, Data Extraction, and SynthesisPrimary studies that reported coronary artery disease among COVID-19 patients were included. The characteristics of the study and information on the number of cases of coronary artery disease were extracted from the included studies. Individual study estimates were pooled using the random intercept logistic regression model. The heterogeneity between the selected studies was assessed using the I2 statistic, tau, tau-squared, Cochrans Q. Prediction interval was used to identify the range into which future studies are expected to fall. Subgroup analysis based on geography (continent) was done to reduce heterogeneity. Publication bias was analyzed using doi plot and LFK index. The risk of bias in the studies was assessed as per the tools proposed by the National Institute of Health.\n\nMain outcomesThe primary outcome was the pooled prevalence of coronary artery disease among COVID-19 patients within the examined population.\n\nResults510 records were initially retrieved from electronic databases in addition to other sources like reference screening. 33 studies with 40,064 COVID-19 patients were included for quantitative synthesis. The prevalence of coronary artery disease among COVID-19 patients was 15.24% (95% CI: 11.41% - 20.06%). The prediction interval ranged from 2.49% to 55.90%. The studies were highly heterogeneous (tau-sqaured of 0.89), and subgroup analysis significantly reduced it (test of moderators: Q = 14.77, df=2, P=.002). Europe reported the highest prevalence [21.70% (14.80% - 30.65%)], and Asia has the least prevalence [10.07% (6.55% - 15.19%)]. Meta-regression for sample size was not significant (P=.11). A symmetric doi plot and an LFK index of 0.57 revealed no evidence of publication bias or small-study effects.\n\nConclusionThe burden of coronary artery disease has been considerable, varying with geography. and further research in this area is needed. Routine cardiac screening and assessment of COVID-19 patients can help uncover undiagnosed cases, and better optimise the management of all COVID-19 patients.", "rel_num_authors": 10, "rel_authors": [ { @@ -54825,6 +56403,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.05.27.23290638", + "rel_title": "A patient-centered view of symptoms, functional impact, and priorities in post-COVID-19 syndrome: Cross-sectional results from the Quebec Action Post-COVID cohort", + "rel_date": "2023-05-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.27.23290638", + "rel_abs": "BackgroundHealth services planning and mechanism-focused research would benefit from a clearer picture of symptoms, impact, and personal priorities in post-COVID-19 syndrome (PCS). This study aimed to provide estimates of the symptom, function, and quality of life (QOL) impact of PCS.\n\nMethodsPeople living in Quebec, aged [≥]18, were eligible for the Quebec Action for/pour le Post-COVID (QAPC) study if they had symptoms lasting more than 4 weeks post-acute SARS-CoV-2 infection, with or without a positive COVID-19 test. Recruitment was through conventional and social media between September 2022-January 2023. Standardized and individualized questionnaires, in French or English, were accessed through an online portal. We report cross-sectional results from the baseline visit of the first 414 participants in this ongoing longitudinal study.\n\nResultsIndividuals spontaneously reported symptoms attributable to an average of 4.5 organ systems. Fatigue was most frequent. Effects on function and quality of life were moderate to severe, and had already persisted for a year or more in the majority. Personal intervention priorities included fatigue and post-exercise malaise, cognitive symptoms, shortness of breath, and impaired taste and smell. Women and men were similar on PCS impact, while older age was associated with lower impact.\n\nInterpretationSymptom clusters defined a range of severity, with fatigue a pervasive symptom at all levels of severity. Participants in this study are likely to be representative of those seeking health care for post-COVID-19 symptoms in Canada and the results can inform next steps for clinical, research, and health services planning.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Nancy Elizabeth Mayo", + "author_inst": "McGill University" + }, + { + "author_name": "Marie-Josee Brouillette", + "author_inst": "McGill University" + }, + { + "author_name": "Emilia Liana Falcone", + "author_inst": "Montreal Clinical Research Institute" + }, + { + "author_name": "Lesley Fellows", + "author_inst": "McGill University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.05.22.23290323", "rel_title": "Analysing the psychosocial and health impacts of Long COVID in Pakistan: A cross sectional study", @@ -55774,29 +57383,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.05.22.23290291", - "rel_title": "Nurses' perceptions of videoconferencing telenursing: comparing frontal learning vs. online learning before and after the COVID-19 pandemic", - "rel_date": "2023-05-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.22.23290291", - "rel_abs": "IntroductionDuring the COVID-19 pandemic, a digital transformation led to an expansion in telenursing practices and a shift in training to online learning. The aim of this study was to explore the impact of behavioral-related factors, based on both TAM and TPB variables, on the intention to use telenursing through videoconferencing and to compare the effect of frontal (before COVID-19) vs. online (during and after COVID-19) training in post-basic nursing courses on nursing attitudes to telenursing.\n\nMethodsA cross-sectional online survey was conducted in December 2022 among nurses working mainly at hospitals in Israel who underwent post-basic education training between January 2017 and December 2022. A multivariate ordinary least squares (OLS) regression analysis was used to investigate determinants of intention to use telenursing through videoconferencing\n\nResultsNurses have a positive attitude towards telenursing technology via videoconferencing for remote patient care, regardless of whether they learned about it through face-to-face or online training. The ease of use and the perception of the technologys importance by colleagues and supervisors were found to have the most significant impact on the attitude of both research groups towards the use of telelearning.\n\nDiscussionSuccessful implementation of new technology in healthcare requires organizational and collegial support. Therefore, managers should encourage the use of telenursing by providing appropriate training for nurses and the necessary resources and support.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Svetlana Kats", - "author_inst": "Bar-Ilan University, Belinson Hospital" - }, - { - "author_name": "Liora Shmueli", - "author_inst": "Bar-Ilan university" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nursing" - }, { "rel_doi": "10.1101/2023.05.23.23290354", "rel_title": "Long COVID and financial outcomes: Evidence from four longitudinal population surveys", @@ -57547,6 +59133,25 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.05.22.23290349", + "rel_title": "Pandemic Lessons of Sustainability: Higher Covid-19 Mortality in Less Sustainable US States", + "rel_date": "2023-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.22.23290349", + "rel_abs": "This paper intends to contribute to the current debate over what lessons the United States should take away from the Covid-19 pandemic. It focuses on the role that sustainability played in shaping different pandemic outcomes among the 50 states. By the end of 2021, Mississippi reported the highest standardized death rate from Covid-19 in the country, more than five times higher than Vermont, which reported the lowest standardized death rate. If Mississippi had the same rate as Vermont, approximately 83% of the lives lost (7,958 individuals) could have been saved. If all 50 states had the same rate as Vermont, approximately 583,296 individuals (76% of the total deceased) would have survived. The inter-state difference in excess death rates was even larger. It was 18.19% in Arizona, 8.5 times as high as in Hawaii. Political ideology is currently a popular possible explanation for discrepancies among states in pandemic outcomes, given that Republican states tended to have higher death rates compared to Democratic ones. Additionally, partisan politics have been criticized for hindering the US pandemic response, especially in the early stages of the pandemic. However, the current debate lacks an attention to sustainability. This study demonstrates that indicators of sustainability may serve as more significant predictors of the death rates among the US states than political affiliation. Using the percentage of votes for Trump per state in 2020 as a proxy variable, this study found that the correlation between political affiliation and the death rates was significant only when it was the lone parameter. Its effects were overshadowed when vaccination rates and eco-friendliness were included in the equation. Above all, when the Sustainable Development Goal (SDG) index was added to the regression, it became the only significant predictor of the death rates. This suggests that it was not \"red\" or \"blue,\" but rather \"green\" that was the most important factor in determining Covid-19 mortality. Pandemic lessons are lessons of sustainability.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "LEE na LIU", + "author_inst": "University of Central Missouri" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.05.22.23290332", "rel_title": "Wastewater-based reproduction numbers and projections of COVID-19 cases in multiple cities in Japan, 2022", @@ -57756,85 +59361,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2023.05.22.541294", - "rel_title": "Breakthrough infections by SARS-CoV-2 variants boost cross-reactive hybrid immune responses in mRNA-vaccinated Golden Syrian Hamsters", - "rel_date": "2023-05-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.22.541294", - "rel_abs": "Hybrid immunity to SARS-CoV-2 provides superior protection to re-infection. We performed immune profiling studies during breakthrough infections in mRNA-vaccinated hamsters to evaluate hybrid immunity induction. mRNA vaccine, BNT162b2, was dosed to induce binding antibody titers against ancestral spike, but inefficient serum virus neutralization of ancestral SARS-CoV-2 or variants of concern (VoCs). Vaccination reduced morbidity and controlled lung virus titers for ancestral virus and Alpha but allowed breakthrough infections in Beta, Delta and Mu-challenged hamsters. Vaccination primed T cell responses that were boosted by infection. Infection back-boosted neutralizing antibody responses against ancestral virus and VoCs. Hybrid immunity resulted in more cross-reactive sera. Transcriptomics post-infection reflects both vaccination status and disease course and suggests a role for interstitial macrophages in vaccine-mediated protection. Therefore, protection by vaccination, even in the absence of high titers of neutralizing antibodies in the serum, correlates with recall of broadly reactive B and T-cell responses.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Juan Garcia-Bernalt Diego", - "author_inst": "Infectious and Tropical Diseases Research Group (e-INTRO), Biomedical Research Institute of Salamanca-Research Centre for Tropical Diseases at the University of" - }, - { - "author_name": "Gagandeep Singh", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA. Global Health and Emerging Pathogens Institute, Icahn School of Medicine" - }, - { - "author_name": "Sonia Jangra", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA. Global Health and Emerging Pathogens Institute, Icahn School of Medicine" - }, - { - "author_name": "Kim Handrejk", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA. Global Health and Emerging Pathogens Institute, Icahn School of Medicine" - }, - { - "author_name": "Manon Laporte", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA. Global Health and Emerging Pathogens Institute, Icahn School of Medicine" - }, - { - "author_name": "Lauren A Chang", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA. Global Health and Emerging Pathogens Institute, Icahn School of Medicine" - }, - { - "author_name": "Sara S El Zahed", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA. Global Health and Emerging Pathogens Institute, Icahn School of Medicine" - }, - { - "author_name": "Lars Pache", - "author_inst": "NCI Designated Cancer Center, Sanford-Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA" - }, - { - "author_name": "Max W Chang", - "author_inst": "Department of Medicine, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Prajakta Warang", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA. Global Health and Emerging Pathogens Institute, Icahn School of Medicine" - }, - { - "author_name": "Sadaf Aslam", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA. Global Health and Emerging Pathogens Institute, Icahn School of Medicine" - }, - { - "author_name": "Ignacio Mena", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA. Global Health and Emerging Pathogens Institute, Icahn School of Medicine" - }, - { - "author_name": "Brett T Webb", - "author_inst": "Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA" - }, - { - "author_name": "Christopher Benner", - "author_inst": "Department of Medicine, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Adolfo Garcia-Sastre", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA. Global Health and Emerging Pathogens Institute, Icahn School of Medicine" - }, - { - "author_name": "Michael Schotsaert", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai New York, NY, USA. Global Health and Emerging Pathogens Institute, Icahn School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.05.19.541367", "rel_title": "An Atlas of Adaptive Evolution in Endemic Human Viruses", @@ -59309,6 +60835,109 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.05.15.540756", + "rel_title": "A synthetic delivery vector for mucosal vaccination", + "rel_date": "2023-05-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.15.540756", + "rel_abs": "The success of mRNA-based vaccines during the Covid-19 pandemic has highlighted the value of this new platform for vaccine development against infectious disease. However, the CD8+ T cell response remains modest with mRNA vaccines, and these do not induce mucosal immunity, which would be needed to prevent viral spread in the healthy population. To address this drawback, we developed a dendritic cell targeting mucosal vaccination vector, the homopentameric STxB. Here, we describe the highly efficient chemical synthesis of the protein, and its in vitro folding. This straightforward preparation led to a synthetic delivery tool whose biophysical and intracellular trafficking characteristics were largely indistinguishable from recombinant STxB. The chemical approach allowed for the generation of new variants with bioorthogonal handles. Selected variants were chemically coupled to several types of antigens derived from the mucosal viruses SARS-CoV-2 and type 16 human papillomavirus. Upon intranasal administration in mice, mucosal immunity, including resident memory CD8+ T cells and IgA antibodies was induced against these antigens. Our study thereby identifies a novel synthetic antigen delivery tool for mucosal vaccination with an unmatched potential to respond to an urgent medical need.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Anne Billet", + "author_inst": "Institut Curie" + }, + { + "author_name": "Justine Hadjerci", + "author_inst": "Institut Curie" + }, + { + "author_name": "Thi Tran", + "author_inst": "PARCC" + }, + { + "author_name": "Pascal Kessler", + "author_inst": "CEA" + }, + { + "author_name": "Jonathan Ulmer", + "author_inst": "Institut Curie" + }, + { + "author_name": "Gilles Mourier", + "author_inst": "CEA" + }, + { + "author_name": "Marine Ghazarian", + "author_inst": "CEA" + }, + { + "author_name": "Anthony Gonzalez", + "author_inst": "CEA" + }, + { + "author_name": "Robert Thai", + "author_inst": "CEA" + }, + { + "author_name": "Pauline Urquia", + "author_inst": "PARCC" + }, + { + "author_name": "Anne-Cecile Vanbaelen", + "author_inst": "CEA" + }, + { + "author_name": "Annalisa Meola", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Ignacio Fernandez", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Stephanie Deville-Foillard", + "author_inst": "Institut de Chimie des Substances Naturelles" + }, + { + "author_name": "Ewan MacDonald", + "author_inst": "Institut Curie" + }, + { + "author_name": "Lea Paolini", + "author_inst": "PARCC" + }, + { + "author_name": "Frederic Schmidt", + "author_inst": "Institut Curie" + }, + { + "author_name": "Felix A Rey", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Michael S Kay", + "author_inst": "University of Utah" + }, + { + "author_name": "Eric Tartour", + "author_inst": "PARCC" + }, + { + "author_name": "Denis Servent", + "author_inst": "CEA" + }, + { + "author_name": "Ludger Johannes", + "author_inst": "Institut Curie" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2023.05.12.23289890", "rel_title": "Heterogeneous changes in mobility in response to the SARS-CoV-2 Omicron BA.2 outbreak in Shanghai", @@ -59506,45 +61135,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.05.12.23289872", - "rel_title": "Regularized COVID-19 Forecast Ensemble Methods", - "rel_date": "2023-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.12.23289872", - "rel_abs": "Forecasts of COVID-19 outcomes play an essential role in alerting public health and government officials to the trajectory of the pandemic. The sudden and critical need for these forecasts spurred both the proliferation of diverse epidemiological transmission models from academia and industry across the United States and efforts to standardize and curate these model outputs. In many scientific domains, ensemble models, where individual forecasts are aggregated into one, have demonstrated smaller forecasting error than the individual models from which they are constructed. Using COVID-19 deaths as an index outcome, we developed and evaluated several ensemble approaches where point forecast models were combined via weighted sums based on historical individual model or ensemble model performance. We found that a simple method that minimized the error of the past performance of individual models and used L2 regularization to encourage broader distribution of weights across models outperformed a baseline mean ensemble and all other tested methods across US states for both absolute error and weighted interval scores. This suggests that performance-based ensembles can produce accurate forecasts despite training on only point forecasts and recent historical data, provided that sufficient regularization and constraints are used to capture uncertainty. Availability of an accurate and explainable ensemble forecast model can increase trust among stakeholders and the general public, thus bettering preparedness and response efforts during the COVID-19 pandemic.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Alexandra Stephens", - "author_inst": "Johns Hopkins University Applied Physics Laboratory" - }, - { - "author_name": "Luke C. Mullany", - "author_inst": "Johns Hopkins University Applied Physics Laboratory" - }, - { - "author_name": "Matt Kinsey", - "author_inst": "Johns Hopkins University Applied Physics Laboratory" - }, - { - "author_name": "Paul Nicholas", - "author_inst": "Johns Hopkins University Applied Physics Laboratory" - }, - { - "author_name": "Jeffrey Freeman", - "author_inst": "Johns Hopkins University Applied Physics Laboratory" - }, - { - "author_name": "Kaitlin Rainwater-Lovett", - "author_inst": "Johns Hopkins University Applied Physics Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.05.12.23289898", "rel_title": "Disrupted seasonality and association of COVID-19 with medically attended respiratory syncytial virus infections among young children in the US: January 2010-January 2023", @@ -60939,6 +62529,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.05.09.540089", + "rel_title": "Single-cell transcriptome landscape of circulating CD4+ T cell populations in human autoimmune diseases", + "rel_date": "2023-05-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.09.540089", + "rel_abs": "CD4+ T cells are a key mediator of various autoimmune diseases; however, how they contribute to disease development remains obscure primarily because of their cellular heterogeneity. Here, we evaluated CD4+ T cell subpopulations by decomposition-based transcriptome characterization together with canonical clustering strategies. This approach identified 12 independent transcriptional gene programs governing whole CD4+ T cell heterogeneity, which can explain the ambiguity of canonical clustering. In addition, we performed a meta-analysis using public single-cell data sets of over 1.8M peripheral CD4+ T cells from 953 individuals by projecting cells onto the reference and cataloged cell frequency and qualitative alterations of the populations in 20 diseases. The analyses revealed that the 12 transcriptional programs were useful in characterizing each autoimmune disease and predicting its clinical status. Moreover, genetic variants associated with autoimmune diseases showed disease-specific enrichment within the 12 gene programs. The results collectively provide a landscape of single-cell transcriptomes of CD4+ T cell subpopulations involved in autoimmune disease.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Yoshiaki Yasumizu", + "author_inst": "Osaka University" + }, + { + "author_name": "Daiki Takeuchi", + "author_inst": "Osaka university" + }, + { + "author_name": "Reo Morimoto", + "author_inst": "Osaka university" + }, + { + "author_name": "Yusuke Takeshima", + "author_inst": "Osaka university" + }, + { + "author_name": "Tatsusada Okuno", + "author_inst": "Osaka university" + }, + { + "author_name": "Makoto Kinoshita", + "author_inst": "Osaka university" + }, + { + "author_name": "Takayoshi Morita", + "author_inst": "Osaka university" + }, + { + "author_name": "Yasuhiro Kato", + "author_inst": "Osaka university" + }, + { + "author_name": "Min Wang", + "author_inst": "Chinese Academy of Medical Sciences and Peking Union Medical College" + }, + { + "author_name": "Daisuke Motooka", + "author_inst": "Osaka University Research Institute for Microbial Diseases" + }, + { + "author_name": "Daisuke Okuzaki", + "author_inst": "Osaka University Research Institute for Microbial Diseases" + }, + { + "author_name": "Yamami Nakamura", + "author_inst": "Osaka university" + }, + { + "author_name": "Norihisa Mikami", + "author_inst": "Osaka university" + }, + { + "author_name": "Masaya Arai", + "author_inst": "Osaka university" + }, + { + "author_name": "Xuan Zhang", + "author_inst": "PUMC HOSPITAL" + }, + { + "author_name": "A. Kumanogoh", + "author_inst": "Osaka University" + }, + { + "author_name": "Hideki Mochizuki", + "author_inst": "Osaka University Graduate School of Medicine" + }, + { + "author_name": "Naganari Ohkura", + "author_inst": "Osaka university" + }, + { + "author_name": "Shimon Sakaguchi", + "author_inst": "Osaka university" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.05.10.540124", "rel_title": "PandoGen: Generating complete instances of future SARS-CoV2 sequences using Deep Learning", @@ -61116,53 +62797,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.05.09.23289744", - "rel_title": "Surveillance strategies for the detection of new SARS-CoV-2 variants across epidemiological contexts", - "rel_date": "2023-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.09.23289744", - "rel_abs": "Rapid identification of new SARS-CoV-2 variants is a critical component of the public health response to the COVID-19 pandemic. However, we lack a quantitative framework to assess the expected performance of sampling strategies in varying epidemic contexts. To address this gap, we used a multi-patch stochastic model of SARS-CoV-2 spread in New York City to evaluate the impact of the volume of testing and sequencing, geographic representativeness of sampling, location and timing of variant emergence, and relative variant transmissibility on the time to first detection of a new variant. The strategy of targeted sampling of likely emergence locations offered the most improvement in detection speed. Increasing sequencing capacity reduced detection time more than increasing testing volumes. The relative transmissibility of the new variant and the epidemic context of variant emergence also influenced detection times, showing that individual surveillance strategies can result in a wide range of detection outcomes, depending on the underlying dynamics of the circulating variants. These findings help contextualize the design, interpretation, and trade-offs of genomic surveillance strategies.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Kirstin I Oliveira Roster", - "author_inst": "Harvard T. H. Chan School of Public Health" - }, - { - "author_name": "Stephen M Kissler", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Enoma Omoregie", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Jade C Wang", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Helly S Amin", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Steve Di Lonardo", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Scott Hughes", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Yonatan Grad", - "author_inst": "Harvard T. H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.05.04.23289510", "rel_title": "Severity of SARS-CoV-2 Omicron XBB subvariants in Singapore", @@ -62493,6 +64127,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.05.05.23289503", + "rel_title": "Primary series and booster COVID-19 vaccine effectiveness in a cohort of healthcare workers in Albania during a BA.1 and BA.2 variant period, January - May 2022", + "rel_date": "2023-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.05.23289503", + "rel_abs": "BackgroundHealthcare workers (HCWs) have experienced high rates of COVID-19 morbidity and mortality. We estimated COVID-19 two-dose primary series and monovalent booster vaccine effectiveness (VE) against symptomatic SARS-CoV-2 Omicron (BA.1 and BA.2) infection among HCWs in three Albanian hospitals during January-May 2022.\n\nMethodsStudy participants completed weekly symptom questionnaires, underwent PCR testing when symptomatic, and provided quarterly blood samples for serology. We estimated VE using Cox regression models (1-hazard ratio), with vaccination status as the time-varying exposure and unvaccinated HCWs as the reference group, adjusting for potential confounders: age, sex, prior SARS-CoV-2 infection (detected by PCR, rapid-antigen test or serology), and household size.\n\nResultsAt the start of the analysis period, 76% of 1,462 HCWs had received a primary series, 10% had received a booster dose, and 9% were unvaccinated; 1,307 (89%) HCWs had evidence of prior infection. Overall, 86% of primary series and 98% of booster doses received were BNT162b2. The median time interval from the second dose and the booster dose to the start of the analysis period was 289 days (IQR:210- 292) and 30 days (IQR:22-46), respectively. VE against symptomatic PCR-confirmed infection was 34% (95%CI: -36;68) for the primary series and 88% (95%CI: 38;98) for the booster.\n\nConclusionsAmong Albanian HCWs, most of whom had been previously infected, COVID-19 booster dose offered improved VE during a period of Omicron BA.1 and BA.2 circulation. Our findings support promoting booster dose uptake among Albanian HCWs, which, as of January 2023, was only 20%.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Iris Finci", + "author_inst": "World Health Organisation, Regional Office for Europe" + }, + { + "author_name": "Madelyn Yiseth Rojas Castro", + "author_inst": "Epiconcept, Paris, France" + }, + { + "author_name": "Iris Hasibra", + "author_inst": "Institute of Public Health, Tirana, Albania" + }, + { + "author_name": "Jonilda Sulo", + "author_inst": "Southeast European Center for Surveillance and Control of Infectious Disease, Tirana, Albania" + }, + { + "author_name": "Albana Fico", + "author_inst": "Institute of Public Health, Tirana, Albania" + }, + { + "author_name": "Rovena Daja", + "author_inst": "Institute of Public Health, Tirana, Albania" + }, + { + "author_name": "Adela Vasili", + "author_inst": "Institute of Public Health, Tirana, Albania" + }, + { + "author_name": "Majlinda Kota", + "author_inst": "Institute of Public Health, Tirana, Albania" + }, + { + "author_name": "Iria Preza", + "author_inst": "World Health Organization, Country Office Albania, Tirana, Albania" + }, + { + "author_name": "Barbara Muehlemann", + "author_inst": "Institute of Virology, Charite-Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt- Universitaet zu Berlin, and Berlin Institut" + }, + { + "author_name": "Christian Drosten", + "author_inst": "Institute of Virology, Charite-Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin, Humboldt- Universitaet zu Berlin, and Berlin Institut" + }, + { + "author_name": "Richard Pebody", + "author_inst": "World Health Organization Regional Office for Europe, Copenhagen, Denmark" + }, + { + "author_name": "Kathryn E Lafond", + "author_inst": "Influenza Division, US Centers for Disease Control, Atlanta, Georgia" + }, + { + "author_name": "Esther Kissling", + "author_inst": "Epiconcept, Paris, France" + }, + { + "author_name": "Mark A Katz", + "author_inst": "World Health Organization Regional Office for Europe, Copenhagen, Denmark" + }, + { + "author_name": "Silvia Bino", + "author_inst": "Institute of Public Health, Tirana, Albania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.05.05.23289561", "rel_title": "COVID-19 vaccination at a hospital in Paris: spatial analyses and inverse equity hypothesis", @@ -62658,29 +64371,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.05.04.23289498", - "rel_title": "Excess Mortality Resulting from COVID-19 in Turkey during 2020-2021: Regional and Time-Based Analysis", - "rel_date": "2023-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.04.23289498", - "rel_abs": "Turkey experienced substantial excess mortality in 2020 and 2021 related to the COVID-19 pandemic. Methods used to estimate excess mortality vary, making comparisons difficult. This study assessed the impact of the COVID-19 pandemic in Turkey, using the TURKSTAT data which became available on February 23, 2023. We applied a quasi-Poisson model to estimate excess mortality during 2020-2021, comparing excess mortality by time periods and socioeconomic factors. During 2020-2021, Turkey experienced 72,886 excess deaths in 2020 (P-score 16.8%) and 125,540 in 2021 (P-score 28.5%). An additional 80 excess deaths per 100,000 people were recorded in 2020 and 143 in 2021. Excess all-cause mortality varied across socioeconomic levels, with notable social disparities in pandemic deaths as the highest rates were observed in the lowest socioeconomic group. This study highlights the importance of a comprehensive approach to address the diverse impacts of the pandemic on health and well-being while considering socioeconomic disparities, and potential areas for improvement in data collection and reporting.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Salih Keskin", - "author_inst": "Dokuz Eylul University, Faculty of Medicine, Department of Public Health" - }, - { - "author_name": "Gul Ergor", - "author_inst": "Dokuz Eylul University, Department of Public Health, Division of Epidemiology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.05.03.23289479", "rel_title": "Receipt of anti-SARS-CoV-2 pharmacotherapies among non-hospitalized U.S. Veterans with COVID-19, January 2022 to January 2023", @@ -64483,6 +66173,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.05.01.23289307", + "rel_title": "Hear my Voice: Understanding how community health workers in the Peruvian Amazon expanded their roles to mitigate the impact of the COVID-19 pandemic through Community-Based Participatory Action Research", + "rel_date": "2023-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.01.23289307", + "rel_abs": "IntroductionThe COVID-19 pandemic led to the collapse of the Peruvian health system, which disrupted healthcare access for indigenous communities in the Amazon. We aimed to understand how the COVID-19 pandemic transformed the responsibilities of community health workers (CHWs) from indigenous communities in the Peruvian Amazon so policymakers can support indigenous health efforts.\n\nMethodsFourteen CHWs from Loreto, Peru participated in a community-based Participatory Action Research (CBPR) project using Photovoice, a technique that encourages vulnerable groups to take photos and develop stories illustrating their lived experiences. Participants were recruited from Mamas del Rio, a local university-based program, through purposive sampling. CHWs were trained in Photovoice and asked to photograph how the pandemic affected their lives and work. Participants met four times over five months to share photos and develop action items. Data were organized into key themes using a general inductive method. Final photos and action items were shared with policymakers during galleries in Iquitos and Lima.\n\nResultsCHWs took a total of 36 photos with 33 accompanying texts highlighting their roles during the pandemic. Four core themes emerged: (1) the collapse of social infrastructure, (2) the use of medicinal plants versus pharmaceuticals, (3) the community adaptations and struggles, and (4) the importance of CHWs. CHWs expanded their responsibilities or leveraged their leadership across these themes to support COVID-19 patients, vaccination, and mandates without training or resources from the government. CHWs asked policymakers for formal integration into the health system, standardization of CHW training, and better management of community pharmacies.\n\nConclusionCHWs, who work on a voluntary basis, took on additional roles during the pandemic with little to no training from the government. CHWs demonstrated how their roles could be better supported by the government to ameliorate future health catastrophes in the Peruvian Amazon.\n\nShort SummaryHealth care delivery in the Peruvian Amazon collapsed during the COVID-19 pandemic. Community health workers provided frontline care, education, and logistical support without formal training, resources, or compensation from the Ministry of Health. The government can better leverage, supervise, recognize, and integrate the role of community health workers to strengthen the health system.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tina Samsamshariat", + "author_inst": "University of Arizona College of Medicine - Phoenix" + }, + { + "author_name": "Purnima Madhivanan", + "author_inst": "The University of Arizona" + }, + { + "author_name": "Alexandra Reyes", + "author_inst": "Pontificia Universidad Cat\u00f3lica de Per\u00fa" + }, + { + "author_name": "Eva Moya", + "author_inst": "The University of Texas at El Paso, Department of Social Work" + }, + { + "author_name": "Graciela Meza", + "author_inst": "Universidad Nacional de la Amazonia Peruana" + }, + { + "author_name": "Stefan Reinders", + "author_inst": "Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine; Universidad Peruana Cayetano Heredia" + }, + { + "author_name": "Magaly Blas", + "author_inst": "Universidad Peruana Cayetano Heredia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.05.02.23289404", "rel_title": "Sex and age-dependent alterations of drug consumption during the COVID-19 lockdown in Spain: Lessons learned for the future", @@ -64648,65 +66381,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.05.01.23289358", - "rel_title": "Association of SARS-CoV-2 Infection and Cardiopulmonary Long COVID with Exercise Capacity and Chronotropic Incompetence among People with HIV", - "rel_date": "2023-05-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.01.23289358", - "rel_abs": "BackgroundLong COVID has been associated with reduced exercise capacity, but whether SARS-CoV-2 infection or Long COVID is associated with reduced exercise capacity among people with HIV (PWH) has not been reported. We hypothesized that PWH with cardiopulmonary post-acute symptoms of COVID-19 (PASC) would have reduced exercise capacity due to chronotropic incompetence.\n\nMethodsWe conducted cross-sectional cardiopulmonary exercise testing within a COVID recovery cohort that included PWH. We evaluated associations of HIV, prior SARS-CoV-2 infection, and cardiopulmonary PASC with exercise capacity (peak oxygen consumption, VO2) and adjusted heart rate reserve (AHRR, chronotropic measure) with adjustment for age, sex, and body mass index.\n\nResultsWe included 83 participants (median age 54, 35% female). All 37 PWH were virally suppressed; 23 (62%) had prior SARS-CoV-2 infection, and 11 (30%) had PASC. Peak VO2 was reduced among PWH (80% predicted vs 99%; p=0.005), a difference of 5.5 ml/kg/min (95%CI 2.7-8.2, p<0.001). Chronotropic incompetence more prevalent among PWH (38% vs 11%; p=0.002), and AHRR was reduced among PWH (60% vs 83%, p<0.0001). Among PWH, exercise capacity did not vary by SARS-CoV-2 coinfection, but chronotropic incompetence was more common among PWH with PASC: 3/14 (21%) without SARS-CoV-2, 4/12 (25%) with SARS-CoV-2 without PASC, and 7/11 (64%) with PASC (p=0.04 PASC vs no PASC).\n\nConclusionsExercise capacity and chronotropy are lower among PWH compared to SARS-CoV-2 infected individuals without HIV. Among PWH, SARS-CoV-2 infection and PASC were not strongly associated with reduced exercise capacity. Chronotropic incompetence may be a mechanism limiting exercise capacity among PWH.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Matthew S Durstenfeld", - "author_inst": "Division of Cardiology at ZSFG and Department of Medicine, UCSF" - }, - { - "author_name": "Michael J Peluso", - "author_inst": "Division of HIV, Infectious Disease, & Global Medicine, UCSF" - }, - { - "author_name": "Matthew A Spinelli", - "author_inst": "Division of HIV, Infectious Disease, & Global Medicine, UCSF" - }, - { - "author_name": "Danny Li", - "author_inst": "Division of Cardiology at ZSFG and Department of Medicine, UCSF" - }, - { - "author_name": "Rebecca Hoh", - "author_inst": "Division of HIV, Infectious Disease, & Global Medicine, UCSF" - }, - { - "author_name": "Monica Gandhi", - "author_inst": "Division of HIV, Infectious Disease, & Global Medicine, UCSF" - }, - { - "author_name": "Timothy J Henrich", - "author_inst": "Department of Experimental Medicine, UCSF, USA" - }, - { - "author_name": "Mandar A Aras", - "author_inst": "Division of Cardiology, UCSF Health, San Francisco, CA, USA" - }, - { - "author_name": "Carlin S Long", - "author_inst": "Division of Cardiology, UCSF Health, San Francisco, CA, USA" - }, - { - "author_name": "Steven G Deeks", - "author_inst": "Division of HIV, Infectious Disease, & Global Medicine, UCSF" - }, - { - "author_name": "Priscilla Y Hsue", - "author_inst": "Division of Cardiology at ZSFG and Department of Medicine, UCSF" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2023.04.27.23289228", "rel_title": "Researching COVID to enhance recovery (RECOVER) pediatric study protocol: Rationale, objectives and design", @@ -66933,6 +68607,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.04.25.538294", + "rel_title": "Intranasal VLP-RBD vaccine adjuvanted with BECC470 confers immunity against Delta SARS-CoV-2 challenge in K18-hACE2-mice", + "rel_date": "2023-04-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.25.538294", + "rel_abs": "As the COVID-19 pandemic transitions to endemic, seasonal boosters are a plausible reality across the globe. We hypothesize that intranasal vaccines can provide better protection against asymptomatic infections and more transmissible variants of SARS-CoV-2. To formulate a protective intranasal vaccine, we utilized a VLP-based platform. Hepatitis B surface antigen- based virus like particles (VLP) linked with receptor binding domain (RBD) antigen were paired with the TLR4-based agonist adjuvant, BECC 470. K18-hACE2 mice were primed and boosted at four-week intervals with either VLP-RBD-BECC or mRNA-1273. Both VLP-RBD-BECC and mRNA-1273 vaccination resulted in production of RBD-specific IgA antibodies in serum. RBD- specific IgA was also detected in the nasal wash and lung supernatants and were highest in VLP-RBD-BECC vaccinated mice. Interestingly, VLP-RBD-BECC vaccinated mice showed slightly lower levels of pre-challenge IgG responses, decreased RBD-ACE2 binding inhibition, and lower neutralizing activity in vitro than mRNA-1273 vaccinated mice. Both VLP-RBD-BECC and mRNA-1273 vaccinated mice were protected against challenge with a lethal dose of Delta variant SARS-CoV-2. Both vaccines limited viral replication and viral RNA burden in the lungs of mice. CXCL10 is a biomarker of severe SARS-CoV-2 infection and we observed both vaccines limited expression of serum and lung CXCL10. Strikingly, VLP-RBD-BECC when administered intranasally, limited lung inflammation at early timepoints that mRNA-1273 vaccination did not. VLP-RBD-BECC immunization elicited antibodies that do recognize SARS-CoV-2 Omicron variant. However, VLP-RBD-BECC immunized mice were protected from Omicron challenge with low viral burden. Conversely, mRNA-1273 immunized mice had low to no detectable virus in the lungs at day 2. Together, these data suggest that VLP-based vaccines paired with BECC adjuvant can be used to induce protective mucosal and systemic responses against SARS- CoV-2.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Fredrick Heath Damron", + "author_inst": "West Virginia University" + }, + { + "author_name": "Katherine S Lee", + "author_inst": "West Virginia University" + }, + { + "author_name": "Nathaniel A Rader", + "author_inst": "West Virginia University" + }, + { + "author_name": "Olivia A Miller-Stump", + "author_inst": "West Virginia University" + }, + { + "author_name": "Melissa Cooper", + "author_inst": "West Virginia University" + }, + { + "author_name": "Ting Y Wong", + "author_inst": "West Virginia University" + }, + { + "author_name": "Md Shahrier Amin", + "author_inst": "West Virginia University" + }, + { + "author_name": "Mariette Barbier", + "author_inst": "West Virginia University" + }, + { + "author_name": "Justin R. Bevere", + "author_inst": "West Virginia University" + }, + { + "author_name": "Robert K Ernst", + "author_inst": "University of Maryland, College Park" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.04.25.538264", "rel_title": "Surveillance of Vermont wildlife in 2021-2022 reveals no detected SARS-CoV-2 viral RNA", @@ -67234,97 +68963,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.04.25.23289110", - "rel_title": "Comparative Cohort Study of Post-Acute Covid-19 Infection with a Nested, Randomized Controlled Trial of Ivabradine for Those With Postural Orthostatic Tachycardia Syndrome (The COVIVA Study)", - "rel_date": "2023-04-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.25.23289110", - "rel_abs": "BackgroundSignificant clinical similarities have been observed between the recently Described Long-Haul COVID-19 (LHC) syndrome, Postural Orthostatic Tachycardia Syndrome (POTS) and Inappropriate Sinus Tachycardia (IST). Shared symptoms include light-headedness, palpitations, tremulousness, generalized weakness, blurred vision, chest pain, dyspnea, \"brain-fog\", and fatigue. Ivabradine is a selective sinoatrial node blocker FDA-approved for management of tachycardia associated with stable angina and heart failure not fully managed by beta blockers. In our study we aim to identify risk factors underlying LHC, as well as the effectiveness of ivabradine in controlling heart rate dysregulations and POTS/IST related symptoms.\n\nMethods/DesignA detailed prospective phenotypic evaluation combined with multi-omic analysis of 200 LHC volunteers will be conducted to identify risk factors for autonomic dysfunction. A comparator group of 50 volunteers with documented COVID-19 but without LHC will be enrolled to better understand the risk factors for LHC and autonomic dysfunction. Those in the cohort who meet diagnostic criteria for POTS or IST will be included in a nested prospective, randomized, placebo-controlled trial to assess the impact of ivabradine on symptoms and heart rate, assessed non-invasively based on physiologic response and ambulatory electrocardiogram. Additionally, studies on catecholamine production, mast cell and basophil degranulation, inflammatory biomarkers, and indicators of metabolic dysfunction will be measured to potentially provide molecular classification and mechanistic insights.\n\nDiscussionOptimal therapies for dysautonomia, particularly associated with LHC, have yet to be defined. In the present study, ivabradine, one of numerous proposed interventions, will be systematically evaluated for therapeutic potential in LHC-associated POTS and IST. Additionally, this study will further refine the characteristics of the LHC-associated POTS/IST phenotype, genotype and transcriptional profile, including immunologic and multi-omic analysis of persistent immune activation and dysregulation. The study will also explore and identify potential endotheliopathy and abnormalities of the clotting cascade.\n\nTrial registrationClinicalTrials.gov, ID:NCT05481177 Registered on 29 July 2022.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "David Saunders", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Thomas B Arnold", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Jason M Lavendar", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Daoqin Bi", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Karl Alcover", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Lydia D Hellwig", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Sahar T Leazer", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Roshila Mohammed", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Bethelhem Markos", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Kanchana Perera", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Priscilla Kobi", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Martin Evans", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Autumn Mains", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Marian Tanofsky-Kraff", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Emilie Goguet", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Edward Mitre", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Kathleen P Pratt", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Clifton L Dalgard", - "author_inst": "Uniformed Services University School of Medicine" - }, - { - "author_name": "Mark C. Haigney", - "author_inst": "Uniformed Services University of Health Sciences" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2023.04.24.23289029", "rel_title": "Estimation of Near-kink Reproduction Numbers During the Emergent Variants of the COVID-19 Pandemic: Log-quadratic and Forward-imputation Approach", @@ -68887,6 +70525,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.04.19.23288804", + "rel_title": "Assessing Willingness to receive COVID-19 Vaccines, associated factors and reasons for hesitancy among persons aged 13-80 years in Central Uganda. A population-based surveillance Cohort.", + "rel_date": "2023-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.19.23288804", + "rel_abs": "BackgroundVaccination is essential for controlling the COVID-19 pandemic. However adequate vaccine coverage is a critical to the effectiveness of the vaccine at a population level. Data on to acceptability of the vaccine in Urban areas are limited. This study examined the prevalence, factors associated with willingness to receive COVID-19 vaccine and reasons for hesitancy in the predominantly urban in central Uganda (Wakiso)\n\nMethodsData were obtained from a cross-sectional study conducted from March 1st, 2021, to September 30th, 2021 in the urban population-based cohort of the Africa Medical and behavioral Sciences Organization (AMBSO). Multivariable modified Poisson regression analysis was used to estimate adjusted prevalence ratios (aPR) and 95% confidence intervals of willingness to accept the COVID-19 vaccine.\n\nResultsA total of 1,903 participants were enrolled in the study; 61% of whom were females. About 63% of participants indicated willingness to accept the COVID-19 vaccine. Younger age groups (13-19 and 20-29) were less likely to accept the vaccine compared to the persons ages 40-49 years (aPR=0.79; 95% CI: 0.74, 0.84 for the 13-19 years and 0.93; 95% CI: 0.88, 0.98 for age group 20-29, compared to those ages 40-49 years. Post-primary education (aPR=1.05; 95% CI: 1.02, 1.09 compared to primary level), being a students and government staff (APR=1.13; 95% CI: 1.04, 1.23 compared to construction and Mechanic workers) were associated with willingness to receive COVID-19 vaccine. Some of the reported reasons for hesitancy included; concerns about side effects 154(57.0%), about 64(23.7%) did not think the vaccines were effective, and those who did not like the vaccines 32(11.9%).\n\nConclusionA substantial proportion of individuals were not willingness to receive the COVID-19 vaccine. More effort is needed to reduce vaccine hesitancy, especially among the young and people with lower formal education.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "ALEX DAAMA", + "author_inst": "Africa Medical and Behavioral Sciences Organization" + }, + { + "author_name": "Rashid Naziru", + "author_inst": "Makerere University CHS: Makerere University College of Health Sciences" + }, + { + "author_name": "Asani Kasango", + "author_inst": "Makerere University CHS: Makerere University College of Health Sciences" + }, + { + "author_name": "Grace Kigozi Nalwoga", + "author_inst": "Africa Medical and Behavioral Sciences Organization" + }, + { + "author_name": "Fred Nalugoda", + "author_inst": "Africa Medical and Behavioral Sciences Organization" + }, + { + "author_name": "Robert Bulamba", + "author_inst": "Africa Medical and Behavioral Sciences Organization" + }, + { + "author_name": "Emmanuel Kyasanku", + "author_inst": "Africa Medical and Behavioral Sciences Organization" + }, + { + "author_name": "Gertrude Nakigozi", + "author_inst": "Africa Medical and Behavioral Sciences Organization" + }, + { + "author_name": "Godfrey Kigozi", + "author_inst": "Africa Medical and Behavioral Sciences Organization" + }, + { + "author_name": "Joseph Kagaayi", + "author_inst": "Makerere University CHS: Makerere University College of Health Sciences" + }, + { + "author_name": "Stephen Mugamba", + "author_inst": "Africa Medical and Behavioral Sciences Organization" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.04.20.537680", "rel_title": "Establishment of a screening platform based on human coronavirus OC43 for the identification of microbial natural products with antiviral activity", @@ -69068,45 +70765,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.04.19.537521", - "rel_title": "SARS-CoV-2 utilization of ACE2 from different bat species allows for virus entry and replication in vitro", - "rel_date": "2023-04-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.19.537521", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) is believed to have a zoonotic origin. Bats are a suspected natural host of SARS-CoV-2 because of sequence homology with other bat coronaviruses. Understanding the origin of the virus and determining species susceptibility is essential for managing the transmission potential during a pandemic. In a previous study, we established an in vitro animal model of SARS-CoV-2 susceptibility and replication in a non-permissive avian fibroblast cell line (DF1) based on expression of angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) from different animal species. In this work, we express the ACE2 of seven bat species in DF1 cells and determine their ability to support attachment and replication of the original SARS-CoV-2 Wuhan lineage virus, as well as two variants, Delta and Lambda. We demonstrate that the ACE2 receptor of all seven species: little brown bat (Myotis lucifugus), great roundleaf bat (Hipposideros armiger), Pearsons horseshoe bat (Rhinolophus pearsonii), greater horseshoe bat (Rhinolophus ferrumequinum), Brazilian free-tailed bat (Tadarida brasiliensis), Egyptian rousette (Rousettus aegyptiacus), and Chinese rufous horseshoe bat (Rhinolophus sinicus), made the DF1 cells permissible to the three isolates of SARS-CoV-2. However, the level of virus replication differed between bat species and variant tested. In addition, the Wuhan lineage SARS-CoV-2 virus replicated to higher titers (104.5-105.5 TCID50) than either variant virus (103.5-104.5 TCID50) on pass 1. Interestingly, all viruses tested grew to higher titers (approximately 106 TCID50) when cells expressed the human ACE2 gene compared to bat ACE2. This study provides a practical in vitro method for further testing of animal species for potential susceptibility to current and emerging SARS-CoV-2 viruses.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kelsey Briggs", - "author_inst": "U.S. National Poultry Research Center" - }, - { - "author_name": "Ryan Sweeney", - "author_inst": "U.S. National Poultry Research Center" - }, - { - "author_name": "David S Blehert", - "author_inst": "U.S. Geological Survey, National Wildlife Health Center" - }, - { - "author_name": "Erica Spackman", - "author_inst": "US National Poultry Research Center" - }, - { - "author_name": "David L. Suarez", - "author_inst": "U.S. National Poultry Research Center" - }, - { - "author_name": "Darrell R. Kapczynski", - "author_inst": "USDA" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2023.04.19.537460", "rel_title": "Machine learning detection of SARS-CoV-2 high-risk variants", @@ -71201,6 +72859,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2023.04.14.23288559", + "rel_title": "Longitudinal sequencing and variant detection of SARS-CoV-2 across Southern California wastewater from April 2020 - August 2021", + "rel_date": "2023-04-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.14.23288559", + "rel_abs": "Wastewater based epidemiology (WBE) is a useful method to detect pathogen prevalence and may serve to effectively monitor diseases at a broad scale. WBE has been used throughout the COVID-19 pandemic to track localized and population-level disease burden through the quantification of SARS-CoV-2 RNA present in wastewater. Aside from case load estimation, WBE is being used to assay viral genomic diversity and the emergence of potential SARS-CoV-2 variants.\n\nHere, we present a study in which we sequenced RNA extracted from sewage influent samples obtained from eight wastewater treatment plants representing 16 million people in Southern California over April 2020 - August 2021. We sequenced SARS-CoV-2 with two methods: Illumina Respiratory Virus Enrichment and metatranscriptomic sequencing (N = 269), and QIAseq SARS-CoV-2 tiled amplicon sequencing (N = 95). We were able to classify SARS-CoV-2 reads into lineages and sublineages that approximated several named variants across a full year, and we identified a diversity of single nucleotide variants (SNVs) of which many are putatively novel SNVs, and SNVs of unknown potential function and prevalence. Through our retrospective study, we also show that several sublineages of SARS-CoV-2 were detected in wastewater up to several months before clinical detection, which may assist in the prediction of future Variants of Concern. Lastly, we show that sublineage diversity was similar between wastewater treatment plants across Southern California, and that diversity changed by sampling month indicating that WBE is effective across megaregions.\n\nAs the COVID-19 pandemic moves to new phases, and additional SARS-CoV-2 variants emerge, the ongoing monitoring of wastewater is important to understand local and population-level dynamics of the virus. Our study shows the potential of WBE to detect SARS-CoV-2 variants throughout Southern Californias wastewater and track the diversity of viral SNVs and strains in urban and suburban locations. These results will aid in our ability to monitor the evolutionary potential of SARS-CoV-2 and help understand circulating SNVs to further combat COVID-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jason A Rothman", + "author_inst": "University of California: Irvine" + }, + { + "author_name": "Andrew Saghir", + "author_inst": "University of California: Irvine" + }, + { + "author_name": "Amity G Zimmer-Faust", + "author_inst": "Southern California Coastal Water Research Project" + }, + { + "author_name": "Kylie Langlois", + "author_inst": "Southern California Coastal Water Research Project" + }, + { + "author_name": "Joshua A Steele", + "author_inst": "Southern California Coastal Water Research Project" + }, + { + "author_name": "John F Griffith", + "author_inst": "Southern California Coastal Water Research Project" + }, + { + "author_name": "Katrine L Whiteson", + "author_inst": "University of California: Irvine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.04.15.537011", "rel_title": "SARS-CoV-2 shifts transcription of host gene to increase Spike acylation and boost infectivity", @@ -71398,25 +73099,6 @@ "type": "new results", "category": "ecology" }, - { - "rel_doi": "10.1101/2023.04.16.23288641", - "rel_title": "Prevention of cyclical resurgences of COVID-19-like pandemics in the long term: What are the trade-offs?", - "rel_date": "2023-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.16.23288641", - "rel_abs": "Vaccines have facilitated the substantial reduction and containment of COVID-19 transmission in many countries by early 2023. However, the long-term interconnection between vaccines, traits of the pathogen, vaccination strategies, and cases averted/trade-offs of health outcomes is not well understood. Utilizing a compartment-calibrated model, I estimated the aversion/trade-offs effect on six major disease burdens (i.e., total/symptomatic/asymptomatic/hospitalized/ICU/death cases averted) over time conditional on a variety level of scenarios. The findings implied that low-risk immunity profiles of booster doses increased the peak cases averted versus medium- and high-risk counterparts. The effect was most salient for the former paired with enhancing the rollout rate of doses, followed by the medium- and then high-risk scenarios. Positive and temporarily durable aversion effects for the low-risk, in contrast, negative trade-offs and decreasing aversion effects for the suboptimal scenarios were observed. While there are heterogeneities in vaccines, public strategies, social efforts, and other considerations, this work can provide an evidence-based rationale for the long-term trade-off analysis of vaccination.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ichiro Nakamoto", - "author_inst": "Fujian University of Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.04.12.23287815", "rel_title": "Core warming of coronavirus disease 2019 (COVID-19) patients undergoing mechanical ventilation - a pilot study", @@ -72850,6 +74532,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.04.11.23288409", + "rel_title": "A methodological framework for assessing the benefit of SARS-CoV-2 vaccination following previous infection: case study of five to eleven year olds in the UK", + "rel_date": "2023-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.11.23288409", + "rel_abs": "Vaccination rates against SARS-CoV-2 in children aged five to 11 years remain low in many countries. The current benefit of vaccination in this age group has been questioned given that the large majority of children have now experienced at least one SARS-CoV-2 infection. However, protection from infection, vaccination or both wanes over time. National decisions on offering vaccines to this age group have tended to be made without considering time since infection.\n\nThere is an urgent need to evaluate the additional benefits of vaccination in previously infected children and under what circumstances those benefits accrue. We present a novel methodological framework for estimating the potential benefits of COVID-19 vaccination in previously infected children aged five to 11, accounting for waning. We apply this framework to the UK context and for two adverse outcomes: hospitalisation related to SARS-CoV-2 infection and Long Covid.\n\nWe show that the most important drivers of benefit are: the degree of protection provided by previous infection; the protection provided by vaccination; the time since previous infection; and future attack rates. Vaccination can be very beneficial for previously infected children if future attack rates are high and several months have elapsed since the previous major wave in this group.\n\nBenefits are generally larger for Long Covid than hospitalisation, because Long Covid is both more common than hospitalisation and previous infection offers less protection against it.\n\nOur framework provides a structure for policy makers to explore the additional benefit of vaccination across a range of adverse outcomes and different parameter assumptions. It can be easily updated as new evidence emerges.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Christina Pagel", + "author_inst": "University College London" + }, + { + "author_name": "Harrison Wilde", + "author_inst": "University College London" + }, + { + "author_name": "Christopher Tomlinson", + "author_inst": "UCL" + }, + { + "author_name": "Bilal A Mateen", + "author_inst": "University College London" + }, + { + "author_name": "Katherine Brown", + "author_inst": "Great Ormond Street Hospital for Children" + } + ], + "version": "1", + "license": "", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2023.04.11.23288403", "rel_title": "Effectiveness of mRNA COVID-19 monovalent and bivalent vaccine booster doses against Omicron severe outcomes among adults aged >=50 years in Ontario, Canada", @@ -73023,101 +74740,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2023.04.08.536123", - "rel_title": "Antibodies that neutralize all current SARS-CoV-2 variants of concern by conformational locking", - "rel_date": "2023-04-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.08.536123", - "rel_abs": "SARS-CoV-2 continues to evolve and evade most existing neutralizing antibodies, including all clinically authorized antibodies. We have isolated and characterized two human monoclonal antibodies, 12-16 and 12-19, which exhibited neutralizing activities against all SARS-CoV-2 variants tested, including BQ.1.1 and XBB.1.5. They also blocked infection in hamsters challenged with Omicron BA.1 intranasally. Structural analyses revealed both antibodies targeted a conserved quaternary epitope located at the interface between the N-terminal domain and subdomain 1, revealing a previously unrecognized site of vulnerability on SARS-CoV-2 spike. These antibodies prevent viral receptor engagement by locking the receptor-binding domain of spike in the down conformation, revealing a novel mechanism of virus neutralization for non-RBD antibodies. Deep mutational scanning showed that SARS-CoV-2 could mutate to escape 12-19, but the responsible mutations are rarely found in circulating viruses. Antibodies 12-16 and 12-19 hold promise as prophylactic agents for immunocompromised persons who do not respond robustly to COVID-19 vaccines.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Lihong Liu", - "author_inst": "Columbia University" - }, - { - "author_name": "Ryan G Casner", - "author_inst": "Columbia University" - }, - { - "author_name": "Yicheng Guo", - "author_inst": "Columbia University" - }, - { - "author_name": "Qian Wang", - "author_inst": "Columbia University" - }, - { - "author_name": "Sho Iketani", - "author_inst": "Columbia University" - }, - { - "author_name": "Jasper Fuk-Woo Chan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Jian Yu", - "author_inst": "Columbia University" - }, - { - "author_name": "Bernadeta Dadonaite", - "author_inst": "Fred Hutchinson Cancer Center" - }, - { - "author_name": "Manoj S Nair", - "author_inst": "Columbia University" - }, - { - "author_name": "Hiroshi Mohri", - "author_inst": "Columbia University" - }, - { - "author_name": "Eswar R Reddem", - "author_inst": "Columbia University" - }, - { - "author_name": "Shuofeng Yuan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Vincent Kwok-Man Poon", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Chris Chung-Sing Chan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Kwok-Yung Yuen", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Zizhang Sheng", - "author_inst": "Columbia University" - }, - { - "author_name": "Yaoxing Huang", - "author_inst": "Columbia University" - }, - { - "author_name": "Jesse D Bloom", - "author_inst": "Fred Hutchinson Cancer Center" - }, - { - "author_name": "Lawrence Shapiro", - "author_inst": "Columbia University" - }, - { - "author_name": "David D Ho", - "author_inst": "Columbia University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.04.09.536130", "rel_title": "NULISA: a novel proteomic liquid biopsy platform with attomolar sensitivity and high multiplexing", @@ -74816,7 +76438,7 @@ "rel_date": "2023-04-04", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.03.535453", - "rel_abs": "One of the hallmarks of RNA viruses is highly structured untranslated regions (UTRs) in their genomes. These conserved RNA structures are often essential for viral replication, transcription, or translation. In this report, we discovered and optimized a new type of coumarin derivatives, such as C30 and C34, which bind to a four-way RNA helix called SL5 in the 5' UTR of the SARS-CoV-2 RNA genome. To locate the binding site, we developed a novel sequencing-based method namely cgSHAPE-seq, in which the acylating chemical probe was directed to crosslink with the 2'-OH groups of ribose at the ligand binding site. This crosslinked RNA could then create read-through mutations during reverse transcription (i.e., primer extension) at single-nucleotide resolution to uncover the acylation locations. cgSHAPE-seq unambiguously determined that a bulged G in SL5 was the primary binding site of C30 in the SARS-CoV-2 5' UTR, which was validated through mutagenesis and in vitro binding experiments. C30 was further used as a warhead in RNA-degrading chimeras to reduce viral RNA expression levels. We demonstrated that replacing the acylating moiety in the cgSHAPE probe with ribonuclease L recruiter (RLR) moieties yielded RNA degraders active in the in vitro RNase L degradation assay and SARS-CoV-2 5' UTR expressing cells. We further explored another RLR conjugation site on the E ring of C30/C34 and discovered improved RNA degradation activities in vitro and in cells. The optimized RNA-degrading chimera C64 inhibited live virus replication in lung epithelial carcinoma cells.", + "rel_abs": "One of the hallmarks of RNA viruses is highly structured untranslated regions (UTRs) in their genomes. These conserved RNA structures are often essential for viral replication, transcription, or translation. In this report, we discovered and optimized a new type of coumarin derivatives, such as C30 and C34, which bind to a four-way RNA helix called SL5 in the 5 UTR of the SARS-CoV-2 RNA genome. To locate the binding site, we developed a novel sequencing-based method namely cgSHAPE-seq, in which the acylating chemical probe was directed to crosslink with the 2-OH groups of ribose at the ligand binding site. This crosslinked RNA could then create read-through mutations during reverse transcription (i.e., primer extension) at single-nucleotide resolution to uncover the acylation locations. cgSHAPE-seq unambiguously determined that a bulged G in SL5 was the primary binding site of C30 in the SARS-CoV-2 5 UTR, which was validated through mutagenesis and in vitro binding experiments. C30 was further used as a warhead in RNA-degrading chimeras to reduce viral RNA expression levels. We demonstrated that replacing the acylating moiety in the cgSHAPE probe with ribonuclease L recruiter (RLR) moieties yielded RNA degraders active in the in vitro RNase L degradation assay and SARS-CoV-2 5 UTR expressing cells. We further explored another RLR conjugation site on the E ring of C30/C34 and discovered improved RNA degradation activities in vitro and in cells. The optimized RNA-degrading chimera C64 inhibited live virus replication in lung epithelial carcinoma cells.", "rel_num_authors": 6, "rel_authors": [ { @@ -74876,6 +76498,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.04.03.23288102", + "rel_title": "SARS-CoV-2 infection and post-acute risk of non-Covid-19 infectious disease hospitalizations: a nationwide cohort study of Danish adults aged >=50 years", + "rel_date": "2023-04-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.03.23288102", + "rel_abs": "Reports suggest that the potential long-lasting health consequences of SARS-CoV-2 infection may involve persistent dysregulation of some immune populations, but the potential clinical implications are unknown. In a nationwide cohort of 2,430,694 50+-year-olds, we compared the rates of non-Covid-19 infectious disease inpatient hospitalizations (of [≥]5 hours) following the acute phase of SARS-CoV-2 infection in 930,071 individuals with rates among SARS-CoV-2 uninfected from 1 January 2021 to 10 December 2022. The post-acute phase of SARS-CoV-2 infection was associated with an incidence rate ratio of 0.90 (95% confidence interval 0.88-0.92) for any infectious disease hospitalization. Findings were similar for upper- (1.08, 0.97-1.20), lower respiratory tract (0.90, 0.87-0.93), influenza (1.04, 0.94-1.15), gastrointestinal (1.28, 0.78-2.09), skin (0.98, 0.93-1.03), urinary tract (1.01, 0.96-1.08), certain invasive bacterial (0.96, 0.91-0.1.01), and other (0.96, 0.92-1.00) infectious disease hospitalizations and in subgroups. Our study does not support an increased susceptibility to non-Covid-19 infectious disease hospitalization following SARS-CoV-2 infection.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Niklas Worm Andersson", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Emilia Myrup Thiesson", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Ria Lassauniere", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Joergen Vinsloev Hansen", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Anders Hviid", + "author_inst": "Statens Serum Institut" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.04.03.23287498", "rel_title": "Longitudinal Analysis of Humoral and Cellular Immune Response Following SARS-CoV-2 Vaccination Supports Utilizing Point-Of-Care Tests to Enhance COVID-19 Booster Uptake.", @@ -75217,61 +76874,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.04.04.23288110", - "rel_title": "Long-term outcomes of COVID-19 infection in children and young people: a systematic review and meta-analysis", - "rel_date": "2023-04-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.04.23288110", - "rel_abs": "BackgroundChildren and young people (CYP) may experience prolonged symptoms following COVID-19, commonly termed Long-COVID. The nature of this in CYP is unclear, as are the sequalae of acute COVID-19. We aimed to systematically synthesise evidence of the long-term outcomes of COVID-19 in CYP.\n\nMethods13 databases were searched until January 2022. Inclusion criteria: Observational studies reporting outcomes occurring four-weeks or more after COVID-19 in children <18 years old. Exclusion criteria: Outcomes of Paediatric Inflammatory Multisystem Syndrome. Title, abstract and full text screening were conducted independently by two reviewers. Data extraction and risk of bias assessment was by one reviewer with independent verification. Critical appraisal tools appropriate for study type were employed. Results were narratively synthesised with meta-analysis to generate summary estimates of risk of prolonged symptoms in CYP.\n\nFindings94 studies were included. 66 recruited from hospital settings, 8 recruited solely from community settings. >100 symptoms were reported, the most common being fatigue, headache and cognitive symptoms. Summary estimates of risk of prolonged symptoms were higher for hospital samples (31.2%, 95% CI 20.3% to 43.2%) than for community samples (4.6%, 95% CI 3.4% to 5.8). Sequalae including stroke, type-1 diabetes, Guillan-Barre syndrome, and persistent radiological or blood test abnormalities have been reported in CYP following COVID-19. Most studies reporting these are case reports / case series and quality of evidence is low.\n\nInterpretationProlonged symptoms following COVID-19 in children are variable and multi-system. Rates in community samples are lower than hospital. There is limited data on other sequalae in CYP. Heterogeneity in diagnosis of COVID-19, symptom classification, assessment method and duration of follow-up made synthesis less secure.\n\nFundingHT, CB and GS have National Institute for Health and Care Research fellowships. RB, CM and VW are supported by the NIHR West Midlands Applied Research Collaboration. CM Is supported by the NIHR School for Primary Care Research\n\nResearch in context panelO_ST_ABSEvidence before this studyC_ST_ABSAt the time of writing and to the best of our knowledge, the protocol for this systematic review was a novel endeavour to summarise the longer-term effects of COVID-19 in children and young people (CYP). At least three systematic reviews have since been published, summarising the symptom profile and prevalence of Long-COVID in CYP, but prevalence estimates vary widely and the evidence base remains uncertain. In addition, there is very limited information on other sequalae of COVID-19 in this population group.\n\nWe searched thirteen electronic databases (MEDLINE, EMBASE, AMED, HMIC, CINAHLPlus, PsycINFO, Web of Science (Science Citation and Social Science Citation indicies), ASSIA, WHO COVID-19: Global literature on coronavirus disease, Cochrane COVID-19 study register, ProQuest Coronavirus research database, NDLTD and OpenGrey) up to January 2022 for any empirical study including search terms pertaining to longer term symptoms of COVID-19 in CYP (<18 years old). The quality of the studies was mixed. Results were analysed narratively for each objective, and random effects meta-analyses conducted to estimate risk of prolonged symptoms in CYP who have had COVID-19.\n\nAdded value of this studyThis review adds to the evidence of the heterogeneity of prolonged symptoms following COVID-19 in CYP but importantly, stratifies risk of this by recruitment setting. We also synthesise evidence on broader sequalae of the acute infection in this CYP and longer-term effects in CYP with pre-existing conditions, which have not been considered in previous reviews. We purposefully included case studies and case series, to capture emerging patterns of outcomes, which may well be important in a novel condition with a rapidly increasing volume of publications. To our knowledge, this systematic review and meta-analysis is the most comprehensive to date.\n\nImplications of all the available evidenceThis review adds to the evidence that a substantial proportion of CYP do experience effects of COVID-19 that last longer than four-weeks, with the most frequently reported prolonged symptoms being fatigue, headache and cognitive symptoms. The proportion of CYP developing prolonged symptoms in children recruited from community setting was low, although this may translate to a large number of affected CYP at population level. There is a paucity of controlled studies and this limits confidence that prolonged symptoms are attributable to COVID-19. Sequalae including stroke, type-1 diabetes, Guillan-Barre syndrome, and persistent radiological or blood test abnormalities have been reported in CYP following COVID-19 but most studies reporting these are case reports / case series and quality of evidence is low.\n\nTo develop treatment plans and interventions for affected CYP, further studies are needed to better characterise this condition and understand its impact on the lives of CYP and their families and communities. These should ideally recruit from community settings, include population-based control groups and consider using standardised definitions and outcome measures where possible.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Helen Twohig", - "author_inst": "Keele University" - }, - { - "author_name": "Ram Bajpai", - "author_inst": "Keele University" - }, - { - "author_name": "Nadia Corp", - "author_inst": "Keele University" - }, - { - "author_name": "Alice Faux-Nightingale", - "author_inst": "Keele University" - }, - { - "author_name": "Christian Mallen", - "author_inst": "Keele University" - }, - { - "author_name": "Toni Robinson", - "author_inst": "Keele University" - }, - { - "author_name": "Glenys Somayajula", - "author_inst": "Keele University" - }, - { - "author_name": "Danielle van der Windt", - "author_inst": "Keele University" - }, - { - "author_name": "Victoria Welsh", - "author_inst": "Keele University" - }, - { - "author_name": "Claire Burton", - "author_inst": "Keele University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2023.04.04.23288117", "rel_title": "Stratification of Pediatric COVID-19 cases by inflammatory biomarker profiling and machine learning", @@ -76762,6 +78364,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.03.28.23287848", + "rel_title": "Lasting first impression: Pre-existing immunity restricts mucosal antibody responses during Omicron breakthrough", + "rel_date": "2023-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.28.23287848", + "rel_abs": "Understanding mucosal antibody responses from SARS-CoV-2 infection and/or vaccination is crucial to develop strategies for longer term immunity, especially against emerging viral variants. We profiled serial paired mucosal and plasma antibodies from: COVID-19 vaccinated only vaccinees (vaccinated, uninfected), COVID-19 recovered vaccinees (convalescent, vaccinated) and individuals with breakthrough Delta or Omicron BA.2 infections (vaccinated, infected). Saliva from COVID-19 recovered vaccinees displayed improved antibody neutralizing activity, Fc{gamma}R engagement and IgA compared to COVID-19 uninfected vaccinees. Furthermore, repeated mRNA vaccination boosted SARS-CoV-2-specific IgG2 and IgG4 responses in both mucosa biofluids (saliva and tears) and plasma. IgG, but not IgA, responses to breakthrough COVID-19 variants were dampened and narrowed by increased pre-existing vaccine-induced immunity to the ancestral strain. Salivary antibodies delayed initiation of boosting following breakthrough COVID-19 infection, especially Omicron BA.2, however, rose rapidly thereafter. Our data highlight how pre-existing immunity shapes mucosal SARS-CoV-2-specific antibody responses and has implications for long-term protection from COVID-19.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Kevin J Selva", + "author_inst": "Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Pradhipa Ramanathan", + "author_inst": "Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Ebene R Haycroft", + "author_inst": "Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Arnold Reynaldi", + "author_inst": "Kirby Institute, University of NSW" + }, + { + "author_name": "Deborah Cromer", + "author_inst": "Kirby Institute, University of NSW" + }, + { + "author_name": "Chee Wah Tan", + "author_inst": "Programme in Emerging Infectious Diseases, Duke-NUS Medical School" + }, + { + "author_name": "Lin-Fa Wang", + "author_inst": "Programme in Emerging Infectious Diseases, Duke-NUS Medical School" + }, + { + "author_name": "Bruce D Wines", + "author_inst": "Immune Therapies Laboratory, Burnet Institute" + }, + { + "author_name": "P. Mark Hogarth", + "author_inst": "Immune Therapies Laboratory, Burnet Institute" + }, + { + "author_name": "Laura E Downie", + "author_inst": "Department of Optometry and Vision Sciences, University of Melbourne" + }, + { + "author_name": "Samantha K Davis", + "author_inst": "Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Ruth A Purcell", + "author_inst": "Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Helen E Kent", + "author_inst": "Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Jennifer A Juno", + "author_inst": "Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Adam K Wheatley", + "author_inst": "Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Miles Philip Davenport", + "author_inst": "Kirby Institute, University of New South Wales" + }, + { + "author_name": "Stephen J Kent", + "author_inst": "Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Amy W Chung", + "author_inst": "Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.03.26.23287673", "rel_title": "Total-Body Multiparametric PET Quantification of 18F-FDG Delivery and Metabolism in the Study of COVID-19 Recovery", @@ -76947,53 +78636,6 @@ "type": "new results", "category": "synthetic biology" }, - { - "rel_doi": "10.1101/2023.03.30.534873", - "rel_title": "NETosis Induced by Serum of Patients with COVID-19 is Reduced with Reparixin or Antibodies Against DEK and IL-8", - "rel_date": "2023-03-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.30.534873", - "rel_abs": "DEK locates in the nucleus of the cells or the cytoplasmic granules of neutrophils and plays different roles in cellular processes including NETosis, a suicide mechanism of neutrophils. Here we showed that the interaction of rDEK with CXCR2 leads to NETosis, which could be reduced by the CXCR1/CXCR2 inhibitor reparixin. We found that IL-8, IL-6, IL1-{beta}, MPO, and CitH3 were increased whereas DEK was decreased in the serum of COVID-19 patients. Interestingly, reparixin or anti-DEK antibody reduced the NETosis induced by the serums of patients, suggesting that initial cytokine stimulation may further induce the release of DEK. Our results support the use of reparixin as a potential therapeutic strategy in COVID-19 and suggest that DEK-CXCR2 interaction plays a role in NETosis.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Irfan Baki Kilic", - "author_inst": "Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey" - }, - { - "author_name": "Acelya Yasar", - "author_inst": "Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey" - }, - { - "author_name": "Irem Yalim Camci", - "author_inst": "Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey" - }, - { - "author_name": "Turkan Guzel", - "author_inst": "Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey" - }, - { - "author_name": "Aysegul Karahasan", - "author_inst": "Department of Medical Microbiology, Marmara University, Istanbul, Turkey" - }, - { - "author_name": "Tamer Yagci", - "author_inst": "Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey" - }, - { - "author_name": "Naci Cine", - "author_inst": "Department of Medical Genetics, Kocaeli University, Kocaeli, Turkey" - }, - { - "author_name": "Ayten Kandilci", - "author_inst": "Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.03.30.534872", "rel_title": "Broad and potent neutralizing mAbs are elicited in vaccinated individuals following Delta/BA.1 breakthrough infection", @@ -78291,6 +79933,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.03.25.534209", + "rel_title": "AI-Designed, Mutation-Resistant Broad Neutralizing Antibodies Against Multiple SARS-CoV-2 Strains", + "rel_date": "2023-03-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.25.534209", + "rel_abs": "In this study, we generated a Digital Twin for SARS-CoV-2 by integrating data and meta-data with multiple data types and processing strategies, including machine learning, natural language processing, protein structural modeling, and protein sequence language modeling. This approach enabled the computational design of broadly neutralizing antibodies against over 1300 different historical strains of SARS-COV-2 containing 64 mutations in the receptor binding domain (RBD) region. The AI-designed antibodies were experimentally validated in real-virus neutralization assays against multiple strains including the newer Omicron strains that were not included in the initial design base. Many of these antibodies demonstrate strong binding capability in ELISA assays against the RBD of multiple strains. These results could help shape future therapeutic design for existing strains, as well as predicting hidden patterns in viral evolution that can be learned by AI for developing future antiviral treatments.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Yue Kang", + "author_inst": "Ainnocence Inc." + }, + { + "author_name": "Yang Jiao", + "author_inst": "Ainnocence Inc." + }, + { + "author_name": "Kevin Jin", + "author_inst": "Ainnocence Inc." + }, + { + "author_name": "Lurong Pan", + "author_inst": "Ainnocence Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.03.27.23287800", "rel_title": "Lower vaccination coverage against COVID-19 in school-aged children is associated with low socioeconomic status in the Metropolitan Area of Santiago, Chile.", @@ -78460,61 +80133,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.03.24.23287722", - "rel_title": "Facility-based and virtual cardiac rehabilitation in young patients with heart disease during the COVID-19 era", - "rel_date": "2023-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.24.23287722", - "rel_abs": "BackgroundCardiac rehabilitation (CR) is an important tool for improving fitness and quality of life in those with heart disease (HD). Few pediatric centers use CR to care for these patients, and virtual CR is rarely used. Additionally, it is unclear how the COVID-19 era has changed CR outcomes.\n\nObjectivesThis study assessed fitness improvements in young HD patients participating in both facility-based and virtual CR during the COVID-19 pandemic.\n\nMethodsThis retrospective single-center cohort study included new patients who completed CR from March 2020 through July 2022. CR outcomes included physical, performance, and psychosocial measures. Comparison between serial testing was performed with a paired t-test with P<0.05 was considered significant. Data are reported as mean{+/-}standard deviation.\n\nResultsThere were 47 patients (19{+/-}7.3 years-old; 49% male) who completed CR. Improvements were seen in peak oxygen consumption (VO2, 62.3{+/-}16.1 v 71{+/-}18.2% of predicted, p=0.0007), 6-minute walk (6MW) distance (401{+/-}163.8 v 480.7{+/-}119.2 meters, p=<0.0001), sit to stand (16.2{+/-}4.9 v 22.1{+/-}6.6 repetitions; p=<0.0001), Patient Health Questionnaire-9 (PHQ-9) (5.9{+/-}4.3 v 4.4{+/-}4.2; p=0.002), and Physical Component Score (39.9{+/-}10.1 v 44.9{+/-}8.8; p=0.002). Facility-based CR enrollees were less likely to complete CR than virtual patients (60%, 33/55 v 80%, 12/15; p=0.005). Increases in peak VO2 (60{+/-}15.3 v 70.2{+/-}17.8 % of predicted; p=0.002) were seen among those that completed facility-based CR; this was not observed in the virtual group. Both groups demonstrated improvement in 6MW distance, sit-to-stand repetitions, and sit-and-reach distance.\n\nConclusionsCompletion of a CR program resulted in fitness improvements during the COVID-19 era regardless of location.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Elizabeth B Aronoff", - "author_inst": "Cincinnati Children's Hospital Medical Center" - }, - { - "author_name": "Clifford Chin", - "author_inst": "Cincinnati Children's Hospital Medical Center" - }, - { - "author_name": "Alexander Reuben Opotowsky", - "author_inst": "Cincinnati Children's Hospital" - }, - { - "author_name": "Wayne Mays", - "author_inst": "Cincinnati Children's Hospital Medical Center" - }, - { - "author_name": "Sandra K Knecht", - "author_inst": "Cincinnati Children's Hospital Medical Center" - }, - { - "author_name": "Jennah E Goessling", - "author_inst": "Cincinnati Children's Hospital Medical Center" - }, - { - "author_name": "Malloree C Rice", - "author_inst": "Cincinnati Children's Hospital Medical Center" - }, - { - "author_name": "Justine Shertzer", - "author_inst": "Cleveland Clinic Children's Hospital" - }, - { - "author_name": "Samuel Wittekind", - "author_inst": "Seattle Children's" - }, - { - "author_name": "Adam W Powell", - "author_inst": "Cincinnati Children's Hospital" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2023.03.27.23287795", "rel_title": "Effect of an enhanced public health contact tracing intervention on the secondary transmission of SARS-CoV-2 in educational settings: the four-way decomposition analysis", @@ -80073,6 +81691,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.03.22.23287577", + "rel_title": "Coverage of state-initiated contact-tracing during COVID-19 and factors influencing it: evidence from real-world data", + "rel_date": "2023-03-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.22.23287577", + "rel_abs": "BackgroundContact tracing has been one of the central non-pharmaceutical interventions implemented worldwide to try to control the spread of Sars-CoV-2, but its effectiveness strongly depends on its ability to detect contacts.\n\nMethodsWe analysed 166892 concomitant infections occurring at the same address from June 2020 until February 2022 using an extensive operational database of SARS-CoV-2 tests in Geneva and used permutations statistics to compare the total number of secondary infections occurring at the address with those reported through contact tracing.\n\nResultsManual contact tracing captured on average 41% of the secondary infections, with variation in time from 23% during epidemic peaks to 60% during low epidemic activity. People living in wealthy neighbourhoods were less likely to report contacts (adjusted odds ratio (aOR): 1.6). People living in buildings, compared to people living in single house, were also less likely to report contacts than those living in houses, with an aOR of 1.1 to 3.1 depending on the variant, the size of the building and the presence of shops. This under-reporting of contacts in buildings decreased during periods of mandatory face masking and restriction of private gathering.\n\nConclusionsContact tracing alone does not detect enough secondary infections to efficiently reduce the propagation of Sars-CoV-2. Public messages and outreach campaigns targeting specific populations, such as those in affluent areas, could enhance coverage. Additionally, measures like wearing face masks, improving ventilation, and implementing gathering restrictions should also be considered to reduce the number of infections occurring during interactions that may not be perceived as high risk.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Denis Mongin", + "author_inst": "University of Geneva" + }, + { + "author_name": "Nils Burgisser", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "- Covid-SMC Study Group", + "author_inst": "-" + }, + { + "author_name": "Delphine Sophie Courvoisier", + "author_inst": "University of Geneva" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.03.21.23287546", "rel_title": "How influenza vaccination changed over the COVID-19 pandemic?", @@ -80178,97 +81827,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.03.21.533720", - "rel_title": "BCG administration promotes the long-term protection afforded by a single-dose intranasal adenovirus-based SARS-CoV-2 vaccine", - "rel_date": "2023-03-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.21.533720", - "rel_abs": "Despite medical interventions and several approved vaccines, the COVID-19 pandemic is continuing into its third year. Recent publications have explored single-dose intranasal (i.n.) adenovirus-based vaccines as an effective strategy for curbing SARS-CoV-2 in naive animal models. However, the effects of prior immunizations and infections have yet to be considered within these models. Here, we investigate the immunomodulatory effects of Mycobacterium bovis BCG pre-immunization on a subsequent S-protein expressing i.n. Ad vaccination, termed Ad(Spike). We found that Ad(Spike) alone conferred long-term protection from severe SARS-CoV-2 pathology within a mouse model, yet it was unable to limit initial infection 6 months post-vaccination. While i.n. Ad(Spike) retains some protective effect after 6 months, a single administration of BCG-Danish prior to Ad(Spike) vaccination potentiates its ability to control viral replication of the B.1.351 SARS-CoV-2 variant within the respiratory tract. Though BCG-Danish had no effect on the ability of Ad(Spike) to generate and maintain humoral immunity, it promoted the generation of cytotoxic and Th1 responses over suppressive FoxP3+ TREG cells in the lungs of infected mice. These data demonstrate a novel vaccination strategy that may prove useful in limiting future viral pandemics by potentiating the long-term efficacy of next generation mucosal vaccines within the context of the safe and widely distributed BCG vaccine.\n\nOne sentence summaryBCG enhances anti-SARS-CoV-2 immunity and protection afforded by a novel adenovirus-vectored vaccine.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Dilhan J. Perera", - "author_inst": "McGill University" - }, - { - "author_name": "Pilar Domenech", - "author_inst": "McGill University" - }, - { - "author_name": "George Giorgi Babuadze", - "author_inst": "University of Toronto" - }, - { - "author_name": "Maedeh Naghibosadat", - "author_inst": "University of Toronto" - }, - { - "author_name": "Fernando Alvarez", - "author_inst": "McGill University" - }, - { - "author_name": "Cal Koger-Pease", - "author_inst": "McGill University" - }, - { - "author_name": "Lydia Labrie", - "author_inst": "McGill University" - }, - { - "author_name": "Matthew Stuible", - "author_inst": "National Research Council of Canada" - }, - { - "author_name": "Yves Durocher", - "author_inst": "National Research Council of Canada" - }, - { - "author_name": "Ciriaco A. Piccirillo", - "author_inst": "McGill University" - }, - { - "author_name": "Andre Lametti", - "author_inst": "McGill University" - }, - { - "author_name": "Pierre Olivier Fiset", - "author_inst": "McGill University" - }, - { - "author_name": "Seyyed Mehdy Elahi", - "author_inst": "National Research Council of Canada" - }, - { - "author_name": "Gary P. Kobinger", - "author_inst": "Universite Laval" - }, - { - "author_name": "Renald Gilbert", - "author_inst": "National Research Council of Canada" - }, - { - "author_name": "Martin Olivier", - "author_inst": "McGill University" - }, - { - "author_name": "Robert Kozak", - "author_inst": "University of Toronto" - }, - { - "author_name": "Michael B. Reed", - "author_inst": "Research Institute of the McGill University Health Centre" - }, - { - "author_name": "Momar Ndao", - "author_inst": "Research Institute of the McGill University Health Centre" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.03.20.533560", "rel_title": "Nanograms of SARS-CoV-2 Spike Protein Delivered by Exosomes Induce Potent Neutralization of Both Delta and Omicron Variants.", @@ -82018,6 +83576,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.03.17.23287396", + "rel_title": "Demographic and co-morbidity characteristics of patients tested for SARS-CoV-2 from March 2020 to January 2022 in a national clinical research network: results from PCORnet(R)", + "rel_date": "2023-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.17.23287396", + "rel_abs": "BackgroundPrior studies have documented differences in the age, racial, and ethnic characteristics among patients with SARS-CoV-2 infection. However, little is known about how these characteristics changed over time during the pandemic and whether racial, ethnic, and age disparities evident early in the pandemic were persistent over time. This study reports on trends in SARS-CoV-2 infections among U.S. adults from March 1, 2020 to January, 31 2022, using data from electronic health records.\n\nMethods and FindingsWe captured repeated cross-sectional information from 43 large healthcare systems in 52 U.S. States and territories, participating in PCORnet(R), the National Patient-Centered Clinical Research Network. Using distributed queries executed at each participating institution, we acquired information for all patients [≥] 20 years of age who were tested for SARS-CoV-2 (both positive and negative results), including care setting, age, sex, race, and ethnicity by month as well as comorbidities (assessed with diagnostic codes).\n\nDuring this time period, 1,325,563 patients had positive (13% inpatient) and 6,705,868 patients had negative (25% inpatient) viral tests for SARS-CoV-2. Disparities in testing positive were present across racial and ethnic groups, especially in the inpatient setting. Compared to White patients, Black or African American and other race patients had relative risks for testing positive of 1.5 or greater in the inpatient setting for 12 of the 23-month study period. Compared to non-Hispanic patients, Hispanic patients had relative risks for testing positive in the inpatient setting of 1.5 or greater for 16 of 23. Ethnic and racial differences were present in emergency department and ambulatory settings but were less common across time than in inpatient settings. Trends in infections by age group demonstrated higher test positivity for older patients in the inpatient setting only for most months, except for June and July of 2020, April to August 2021, and January 2022. Comorbidities were common, with much higher rates among those hospitalized; hypertension (38% of patients SARS-CoV-2 positive vs. 29% for those negative) and type 2 diabetes mellitus (22% vs. 13%) were the most common.\n\nConclusion and RelevanceRacial and ethnic disparities changed over time among persons infected with SARS-CoV-2. These trends highlight potential underlying mechanisms, such as poor access to care and differential vaccination rates, that may have contributed to greater disparities, especially early in the pandemic. Monitoring data on characteristics of patients testing positive in real time could allow public health officials and policymakers to tailor interventions to ensure that patients and communities most in need are receiving adequate testing, mitigation strategies, and treatment.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Jason P Block", + "author_inst": "Harvard Medical School/Harvard Pilgrim Health Care Institute" + }, + { + "author_name": "Keith A. Marsolo", + "author_inst": "Duke University" + }, + { + "author_name": "Kshema Nagavedu", + "author_inst": "Harvard Pilgrim Health Care Institute: Harvard Pilgrim Health Care" + }, + { + "author_name": "L. Charles Bailey", + "author_inst": "The Children's Hospital of Philadelphia" + }, + { + "author_name": "Tegan K. Boehmer", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Julia Fearrington", + "author_inst": "Harvard Pilgrim Health Care Institute: Harvard Pilgrim Health Care" + }, + { + "author_name": "Aaron M. Harris", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Nedra Garrett", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Alyson B Goodman", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Adi V. Gundlapalli", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Rainu Kaushal", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Abel Kho", + "author_inst": "Northwestern University" + }, + { + "author_name": "Kathleen M. McTigue", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Vinit P. Nair", + "author_inst": "PRACnet" + }, + { + "author_name": "Jon Puro", + "author_inst": "OCHIN: Oregon Community Health Information Network" + }, + { + "author_name": "Elizabeth Shenkman", + "author_inst": "University of Florida College of Medicine" + }, + { + "author_name": "Mark G. Weiner", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Neely Williams", + "author_inst": "Community Partners Network, Inc" + }, + { + "author_name": "Thomas W. Carton", + "author_inst": "Louisiana Public Health Institute" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.03.17.23287411", "rel_title": "Protection against symptomatic SARS-CoV-2 BA.5 infection conferred by the Pfizer-BioNTech Original/BA.4-5 bivalent vaccine compared to the mRNA Original (ancestral) monovalent vaccines - a matched cohort study in France", @@ -82147,57 +83796,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.03.15.23286981", - "rel_title": "Impact of COVID-19 and effects of booster vaccination with BNT162b2 on six-month long COVID symptoms, quality of life, work productivity and activity impairment during Omicron", - "rel_date": "2023-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.15.23286981", - "rel_abs": "BackgroundLongitudinal estimates of long COVID burden during Omicron remain limited. This study characterized long-term impacts of COVID-19 and booster vaccination on symptoms, Health-Related Quality of Life (HRQoL), and Work Productivity Activity Impairment (WPAI).\n\nMethodsOutpatients with [≥]1 self-reported symptom and positive SARS-CoV-2 test at CVS Health United States test sites were recruited between 01/31-04/30/2022. Symptoms, EQ-5D and WPAI were collected via online surveys until 6 months following infection. Both observed and model-based estimates were analyzed. Effect sizes based on Cohens d quantified the magnitude of outcome changes over time, within and between vaccination groups. Mixed models for repeated measures were conducted for multivariable analyses, adjusting for covariates. Logistic regression assessed odds ratio (OR) of long COVID between vaccination groups.\n\nResultsAt long COVID start (Week 4), 328 participants included 87 (27%) Boosted with BNT162b2, 86 (26%) with a BNT162b2 primary series (Primed), and 155 (47%) Unvaccinated. Mean age was 42.0 years, 73.8% were female, 26.5% had [≥]1 comorbidity, 36.9% prior infection, and 39.6% reported [≥]3 symptoms (mean: 3.1 symptoms). At Month 6, among 260 participants, Boosted reported a mean of 1.1 symptoms versus 3.4 and 2.8 in Unvaccinated and Primed, respectively (p<0.001). Boosted had reduced risks of [≥]3 symptoms versus Unvaccinated (observed: OR 0.22, 95% CI, 0.10-0.47, p<0.001; model-based: OR: 0.36, 95% CI, 0.15-0.87, p=0.019) and Primed (observed: OR 0.29, 95% CI, 0.13-0.67, p=0.003; model-based: OR 0.59, 95% CI, 0.21-1.65, p=0.459). Results were consistent using [≥]2 symptoms. Regarding HRQoL, among those with long COVID, Boosted had higher EQ-5D Utility Index (UI) than Unvaccinated (observed: 0.922 versus 0.731, p=0.014; model-based: 0.910 versus 0.758, p-value=0.038) and Primed (0.922 versus 0.648, p=0.014; model-based: 0.910 versus 0.708, p-value=0.008). Observed and model-based estimates for EQ-VAS and UI among Boosted were comparable with pre-COVID since Month 3. Subjects vaccinated generally reported better WPAI scores.\n\nConclusionsLong COVID negatively impacted HRQoL and WPAI. The BNT162b2 booster could have a beneficial effect in reducing the risk and burden of long COVID. Boosted participants reported fewer and less durable symptoms, which contributed to improve HRQoL and maintain WPAI levels. Limitations included self-reported data and small sample size for WPAI.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Manuela Di Fusco", - "author_inst": "Pfizer Inc." - }, - { - "author_name": "Xiaowu Sun", - "author_inst": "CVS Health" - }, - { - "author_name": "Mary M. Moran", - "author_inst": "Pfizer Inc, MDSCA Vaccines, Collegeville, PA, USA" - }, - { - "author_name": "Henriette Coetzer", - "author_inst": "CVS Health, Woonsocket, RI, USA" - }, - { - "author_name": "Joann M. Zamparo", - "author_inst": "Pfizer Inc, Groton, CT, USA" - }, - { - "author_name": "Mary B. Alvarez", - "author_inst": "Pfizer Inc, Field Medical Outcomes and Analytics, New York, NY, USA" - }, - { - "author_name": "Laura Puzniak", - "author_inst": "Pfizer Inc, MDSCA Vaccines, Collegeville, PA, USA" - }, - { - "author_name": "Ying P Tabak", - "author_inst": "CVS Health, Woonsocket, RI, USA" - }, - { - "author_name": "Joseph C. Cappelleri", - "author_inst": "Pfizer Inc, Statistical Research and Data Science Center, Groton, CT, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.17.23287401", "rel_title": "Quantitative LC-MS study of compounds found predictive of COVID-19 severity and outcome", @@ -83832,6 +85430,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.03.14.23287258", + "rel_title": "Left ventricular global longitudinal strain as a parameter of mild myocardial dysfunction in athletes after COVID-19", + "rel_date": "2023-03-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.14.23287258", + "rel_abs": "BackgroundWhether impaired left ventricular (LV) function contributes to persistent cardiopulmonary symptoms or decreased exercise capacity after COVID-19 remains unclear. The aim of this prospective study was to determine differences in LV global longitudinal strain (GLS) between athletes who did not have a history of LV dysfunction but had a positive COVID-19 test (PCAt) and healthy control (CON) athletes and relate them to symptoms during COVID-19.\n\nMethodsWe performed 151 transthoracic echocardiographies in our high-performance laboratory. GLS was determined in four-, two-, and three-chamber views and assessed offline by a blinded investigator in 88 PCAt (35% women) at a median of two months after COVID-19 who trained at least three times per week with more than 20 MET per week and 52 CONs from the German national squad (38% women).\n\nResultsGLS was significantly lower (GLS -18.53{+/-}1.94% vs. -19.94{+/-}1.42%, p<0.001) and diastolic function significantly reduced (E/A 1.54{+/-}0.52 vs. 1.66{+/-}0.43, p=0.020; El 0.15{+/-}0.04 vs. 0.17{+/-}0.04, p=0.009; E/El 5.74{+/-}1.74 vs. 5.22{+/-}1.36, p=0.024) in PCAt. There was no association between GLS and acute symptoms like resting dyspnea, exertional dyspnea during or after COVID-19, palpitations, chest pain or increased resting heart rate. However, there was a trend toward lower GLS in PCAt with subjectively perceived performance limitation (p=0.054).\n\nConclusionsIn a cohort of athletes at a median two months after COVID-19, significantly lower GLS and diastolic function were observed, suggesting mild myocardial dysfunction. GLS could be used as a screening element during return-to-sport examinations.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jana Schellenberg", + "author_inst": "University Hospital Ulm" + }, + { + "author_name": "Magdalena Ahathaller", + "author_inst": "University Hospital of Ulm" + }, + { + "author_name": "Lynn Matits", + "author_inst": "University Hospital of Ulm" + }, + { + "author_name": "Johannes Kirsten", + "author_inst": "University Hospital of Ulm" + }, + { + "author_name": "Johannes Kersten", + "author_inst": "University Hospital of Ulm" + }, + { + "author_name": "Juergen Steinacker", + "author_inst": "University Hospital of Ulm" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2023.03.15.23287292", "rel_title": "Living alone and mental health: parallel analyses in longitudinal population surveys and electronic health records prior to and during the COVID-19 pandemic", @@ -84053,33 +85690,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.03.14.23287265", - "rel_title": "Association of radiological severity with inflammatory biomarkers for prognostic prediction in patients with COVID-19", - "rel_date": "2023-03-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.14.23287265", - "rel_abs": "BackgroundCovid - 19 caused by SARS-CoV2 has become a pandemic. It has a rapid disease progression and causes severe and fatal complications. Associating radiological severity with effective biomarkers like CRP, leucocytes, lymphocytes, D - Dimer, would be helpful in screening, categorizing patient, preventing serious complications.\n\nAims and ObjectivesThe aim of the study was to investigate association between levels of inflammatory biomarkers and correlate it with HRCT chest finding to identify patients at risk of fatal complications.\n\nMaterials and MethodsIt was a retrospective monocentric observational study undertaken at Ibn Tofail hospital COVID-19 dedicated center. 177 Patients>18 year of age who were admitted from september 1, 2020 up to november 30,2020 with laboratory confirmed diagnosis of Covid - 19 were included in the study. Data was collected on demography, disease severity, laboratory measurements, radiology imaging retrospectively from records of patients. The disease severity was classified into light, mild to severe and critic based on CT Severity scoring. HRCT Chest and inflammatory biomarkers were sent in every patient at the time of admission and the outcome was recorded.\n\nResultsThere were 116 male patients, 61 female patients in our study. Average age of patients having severe lung involvement is 61.9years, whereas Average age of patients having non-severe lung involvement is 56.8 years and showed significant association with severity of lung involvement (p value : 0.017). Severity of lung involvement according to HRCT chest findings was greater in patients with both raised values of CRP <0.001), D - Dimer (P value 0.032) and low values of lymphocytes (P value : 0.001). Capillary oxygen SATURATION was also found to be significantly associated with radiological severity among covid-19 patients. Compared with CRP, leukocytes, lymphocytes, and D-Dimeres levels, the CT severity score had higher sensitivity, specificity, and overall accuracy in predicting severe, critical cases, and short-term mortality.\n\nConclusionthe severity of Covid - 19 disease is correlated with radiological severity andinflammatory markers thereby it will help in immediate categorization of patients into different risk groups following diagnosis, to ensure optimal resource allocation.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "yousra zouine", - "author_inst": "cadi ayyad" - }, - { - "author_name": "mariem benzalim", - "author_inst": "cadi ayyad" - }, - { - "author_name": "soumaya alj", - "author_inst": "cadi ayyad" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2023.03.15.23287304", "rel_title": "Latin-American Registry of Cardiovascular Disease and COVID-19: Final Results", @@ -85438,6 +87048,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.03.09.23287033", + "rel_title": "Spatio-temporal distributions of COVID-19 vaccine doses uptake in the Netherlands: A Bayesian ecological modelling analysis", + "rel_date": "2023-03-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.09.23287033", + "rel_abs": "BackgroundIn the transitioning era towards the COVID-19 endemic, there is still a sizable population that has never been vaccinated against COVID-19 in the Netherlands. To identify regions and populations that have a lower chance of vaccination uptake, this study provides a spatio-temporal estimation of the relative chance of COVID-19 vaccination uptake for the first, second, and the booster doses in the Netherlands on both municipality level and the public health services (regional) level.\n\nMethodsData on COVID-19 vaccination uptake were retrieved from the publicly available national COVID-19 surveillance dataset. We used a Bayesian spatio-temporal modelling technique with the integrated nested Laplace approximation to account for the spatial structure and the space-time interaction. Additionally, we used an ecological regression modelling technique which takes into account areal level socio-demographic characteristics to adjust for their potential impact on the chance of the regional vaccination uptake.\n\nResultsOur findings revealed a heterogenous spatio-temporal distribution of the relative chance of COVID-19 vaccination uptake with highly overlapping trends of all three vaccination doses. Internal heterogeneity of COVID-19 vaccination uptake within one public health services region on the municipality level was also identified. The Dutch main urban area and the most religiously conservative regions were identified to have a lower-than-average chance of COVID-19 vaccination uptake compared to the rest of the country. Ecological regression modelling analysis revealed that regions with a higher proportion of non-Western immigrants had a lower chance of COVID-19 vaccination uptake for all vaccination scenarios.\n\nConclusionThe obtained estimates should inform national and local COVID-19 vaccination policies and service strategies in the Netherlands for the ongoing COVID-19 campaign on the second booster. Namely, more regional efforts and services may be needed to close vaccination gaps and optimise COVID-19 health-related outcomes, especially with regard to regions with a relatively higher proportion of marginalised populations.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Haoyi Wang", + "author_inst": "Maastricht University" + }, + { + "author_name": "Tugce Varol", + "author_inst": "Maastricht University" + }, + { + "author_name": "Thomas Gultzow", + "author_inst": "Maastricht University" + }, + { + "author_name": "Hanne M.L. Zimmermann", + "author_inst": "Maastricht University" + }, + { + "author_name": "Robert A.C. Ruiter", + "author_inst": "Maastricht Univrsity" + }, + { + "author_name": "Kai J. Jonas", + "author_inst": "Maastricht University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.03.09.23286855", "rel_title": "Index Cases First Identified by Nasal-Swab Rapid COVID-19 Tests Had More Transmission to Household Contacts Than Cases Identified by Other Test Types", @@ -85587,41 +87236,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.03.09.531961", - "rel_title": "SARS-CoV-2 protein structure and sequence mutations: evolutionary analysis and effects on virus variants SARS-CoV-2 protein structure and sequence mutations:", - "rel_date": "2023-03-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.09.531961", - "rel_abs": "Proteins sequence, structure, and function are related, so that any changes in the protein sequence may cause modifications in its structure and function. Thanks to the exponential growth of data availability, many studies have addressed different questions such as: (i) how structure evolves based on the sequence changes, (ii) how structure and function change over time. Computational experiments have contributed to the study of viral protein structures. For instance the Spike (S) protein has been investigated for its role in binding receptors and infection activity in COVID-19, hence the interest of scientific researchers in studying the effects of virus mutations due to sequence, structure and vaccination effects. Protein Contact Networks (PCNs) can be used for investigating protein structures to detect biological properties thorough network topology. We apply topological studies based on graph theory of the PCNs to compare the structural changes with sequence changes, and find that both node centrality and community extraction analysis play a relevant role in changes in protein stability and functionality caused by mutations. We compare the structural evolution to sequence changes and study mutations from a temporal perspective focusing on virus variants. We finally highlight a timeline correlation between Omicron variant identification and the vaccination campaign.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Lomoio Ugo", - "author_inst": "University of Catanzaro: Universita degli Studi Magna Graecia di Catanzaro" - }, - { - "author_name": "Puccio Barbara", - "author_inst": "University of Catanzaro: Universita degli Studi Magna Graecia di Catanzaro" - }, - { - "author_name": "Tradigo Giuseppe", - "author_inst": "eCampus University: Universita degli Studi eCampus" - }, - { - "author_name": "Pietro Hiram Guzzi", - "author_inst": "Unicz" - }, - { - "author_name": "Veltri Pierangelo", - "author_inst": "University of Calabria Faculty of Engineering: Universita della Calabria" - } - ], - "version": "1", - "license": "cc_by", - "type": "confirmatory results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.03.10.531533", "rel_title": "Ultrapotent SARS coronavirus-neutralizing single-domain antibodies that bind a conserved membrane proximal epitope of the spike", @@ -87292,6 +88906,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2023.03.06.23286877", + "rel_title": "Predictors of mortality among post-COVID-19 discharged patients in Northern India", + "rel_date": "2023-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.06.23286877", + "rel_abs": "BackgroundThe one-year post-discharge all-cause mortality rate of COVID-19 disease is 7.87 % with the majority of patients readmission and mortality occurring within the first 30 days post-discharge.\n\nObjectiveUnderstanding predictors of mortality will help in prioritising patient care and preventive approaches.\n\nMethodsOurs a single-centre unmatched case control study at a tertiary care centre in northern India, conducted from April 2020 to September 2022. The data was extracted retrospectively from the electronic hospital medical records of patients and by trained physicians using standardised data extraction sheet.\n\nResultsA total of 184 patients were enrolled with 92 cases and 92 controls. The mean age of patients was 49.3 {+/-} 17.53 years. The mortality group had a higher mean age (53.24 {+/-} 18.53 yrs) as compared to the control group (45.37 {+/-} 15.58 yrs) [p - 0.002]. Bivariate analysis revealed a significant difference in the two groups with respect to O2 saturation at admission [Case - 91.12 {+/-} 12.49 %, control - 95.46 {+/-} 5.01 %, p - 0.003); Maximum O2 flow rate [L/min] (Case - 11.01 {+/-} 22.2, Control - 6.41 {+/-} 13.31, P - 0.04); ICU need (p - 0.005), Cancer (p - 0.001), O2 need at discharge (p - 0.001) and AKI (p - 0.007). On multiple regression analysis, Cancer (aOR-2.469; 95% CI-1.183-5.150, p-0.016), ICU admission (aOR- 2.446; 95% CI-1.212-4.938, p- 0.013), Oxygen at discharge (aOR- 2.340; 95% CI-0.971-5.640, p-0.0586) and Acute kidney injury (aOR- 5.6; 95% CI-2.351-13.370, p-0.00) only found to be significant.\n\nConclusionOxygen requirement at discharge (2.3 times), Malignancy (2.4 times), ICU admission (2.4 times), and Acute Kidney Injury (5.6 times) were risks of death among COVID-19-recovered patients, post discharge. The presence of these variables would warrant a close follow up for these patients in order to decrease post COVID mortality.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Arjun", + "author_inst": "AIIMS rishikesh" + }, + { + "author_name": "Basavaraj Jatteppanavar", + "author_inst": "AIIMS rishikesh" + }, + { + "author_name": "Prasan Kumar Panda", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Pathik Dhanger", + "author_inst": "AIIMS rishikesh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.03.06.23286853", "rel_title": "Oral SARS-CoV-2 host responses predict the early COVID-19 disease course", @@ -87445,25 +89090,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2023.03.07.23286949", - "rel_title": "The external validity of machine learning-based prediction scores from hematological parameters of COVID-19: A study using hospital records from Brazil, Italy, and Western Europe", - "rel_date": "2023-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.07.23286949", - "rel_abs": "BackgroundThe COVID-19 pandemic is the deadliest threat to humankind caused by the SARS-COV-2 virus in recent times. The gold standard for its detection, quantitative Real-Time Polymerase Chain Reaction (qRT-PCR), has several limitations regarding experimental handling, expense, and time. While the hematochemical values of routine blood tests have been reported as a faster and cheaper alternative, the external validity of the model on a diverse population has yet to be thoroughly investigated. Here we studied the external validity of machine learning-based prediction scores from hematological parameters recorded in Brazil, Italy, and Western Europe.\n\nMethods and FindingsThe publicly available hematological records (raw sample size (n) = 195554) from hospitals of three different territories, Brazil, Italy, and Western Europe, were preprocessed to develop the training, testing, and prediction cohorts for ML models. A total of eight (sub)datasets were trained on seven different ML classifiers. The XGBoost classifier performed consistently better on all the datasets producing eight different models. The working models include a set of either four or fourteen hematological parameters. The internal performances of the XGBoost models (AUC scores range from 84% to 97%) were superior to the ML models reported in the literature for a few datasets (AUC scores range from 84% to 87%). The external performance (AUC score) was 86% when the model was trained and tested on fourteen hematological parameters obtained from the same country (Brazil) but on independent datasets. However, the external performances were reduced when tested across the populations; 69% when trained on datasets from Italy (n=1736) and tested on datasets from Brazil (n=602)) and 65%, when trained on datasets from Italy and tested on datasets from Western Europe (n=1587)) respectively.\n\nConclusionFor the first time, this report showed that the models trained and tested on the same population but on separate records produced reasonably accurate results. The study promises the confidence of these models trained and tested within the same populations and has the potential application to extend those to other demographic locations. Both four- and fourteen-parameter models are publicly available; https://covipred.bits-hyderabad.ac.in/home\n\nAuthor SummaryCOVID-19 has posed the deadliest threat to the human population in the 21st century. Timely detection of the disease could save more lives. The RT-PCR test is considered the gold standard for COVID-19 detection. However, there are several limitations of the technique that suggests developing an alternate detection protocol that would be efficient, fast, and cheap. Among several other alternate detection techniques, hematology based Machine-Learning (ML) prediction is one. All the hematology-based predictions reported so far in the literature were only internally validated. Considering the need to develop an alternate protocol for rapid, near-accurate, and cheaper COVID-19 detection techniques, we aim to externally validate the hematology-based ML prediction. Here external validation indicates use of two independent datasets for model training and testing, in contrast to internal validation where the same dataset splits into train and test sets. We have integrated published clinical records from Brazil, Italy, and West Europe hospitals. Internal ML model performances are superior compared to those reported in literature. The external model performances were equivalent to the internal performances when trained and tested on the same population. However, the external performances were inferior when train and test sets were from different populations. The results promise the utility of these models on the same populations. However, it also warns to train the model on one population and test it on another. The outcome of this work has the potential for an initial screen of COVID-19 based on hematological parameters before qRT-PCR tests.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Debashree Bandyopadhyay", - "author_inst": "Birla Institute of Technology & Science Pilani - Hyderabad Campus" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2023.03.07.23286933", "rel_title": "State-Level Excess Mortality in US Adults During the Delta and Omicron Waves of COVID-19", @@ -89058,6 +90684,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.03.06.23286832", + "rel_title": "Modeling Biases in SARS-CoV-2 infections Prediction using Genome Copies Concentration in Wastewater", + "rel_date": "2023-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.06.23286832", + "rel_abs": "BackgroundSARS-CoV-2, the virus responsible for the COVID-19 pandemic, can be detected in stool samples and subsequently shed in the sewage system. The field of Wastewater-based epidemiology (WBE) aims to use this valuable source of data for epidemiological surveillance, as it has the potential to identify unreported infections and to anticipate the need for diagnostic tests.\n\nObjectivesThe objectives of this study were to analyze the absolute concentration of genome copies of SARS-CoV-2 shed in Catalonias wastewater during the Omicron peak in January 2022, and to develop a mathematical model capable of using wastewater data to estimate the actual number of infections and the temporal relationship between reported and unreported infections.\n\nMethodsWe collected twenty-four-hour composite 1-liter samples of wastewater from 16 wastewater treatment plants (WWTPs) in Catalonia on a weekly basis. We incorporated this data into a compartmental epidemiological model that distinguishes between reported and unreported infections and uses a convolution process to estimate the genome copies shed in sewage.\n\nResultsThe 16 WWTPs showed an average correlation of 0.88 {+/-} 0.08 (ranging from 0.96 to 0.71) and an average delay of 8.7 {+/-} 5.4 days (ranging from 0 to 20 days). Our model estimates that about 53% of the population in our study had been infected during the period under investigation, compared to the 19% of cases that were detected. This under-reporting was especially high between November and December 2021, with values up to 10. Our model also allowed us to estimate the maximum quantity of genome copies shed in a gram of feces by an infected individual, which ranged from 4.15 x 107 gc/g to 1.33 x 108 gc/g.\n\nDiscussionAlthough wastewater data can be affected by uncertainties and may be subject to fluctuations, it can provide useful insights into the current trend of an epidemic. As a complementary tool, WBE can help account for unreported infections and anticipate the need for diagnostic tests, particularly when testing rates are affected by human behavior-related biases.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Mattia Mattei", + "author_inst": "Departament d'Enginyeria Informatica i Matematiques, Universitat Rovira i Virgili" + }, + { + "author_name": "Rosa M. Pinto", + "author_inst": "Enteric Virus Laboratory, School of Biology, University of Barcelona" + }, + { + "author_name": "Susana Guix", + "author_inst": "Enteric Virus Laboratory, School of Biology, University of Barcelona" + }, + { + "author_name": "Albert Bosch", + "author_inst": "Enteric Virus Laboratory, School of Biology, University of Barcelona" + }, + { + "author_name": "Alex Arenas", + "author_inst": "Departament d'Enginyeria Informatica i Matematiques, Universitat Rovira i Virgili and Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.03.05.531213", "rel_title": "The significant yet short-term influence of research covidization on journal citation metrics", @@ -89179,77 +90840,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.03.03.23286750", - "rel_title": "Detection of SARS-CoV-2 in Schools Using Built Environment Testing in Ottawa, Canada: A Multi-Facility Prospective Surveillance Study", - "rel_date": "2023-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.03.23286750", - "rel_abs": "Classroom and staffroom floor swabs across six elementary schools in Ottawa, Canada were tested for SARS-CoV-2. Schools in neighbourhoods with historically elevated COVID-19 burden had lower environmental swab positivity. Environmental test positivity did not correlate with student grade groups, school-level absenteeism, pediatric COVID-19-related hospitalizations, or community SARS-CoV-2 wastewater levels.\n\nSummaryEnvironmental SARS-CoV-2 sampling was performed in six schools in Ottawa, Canada. The percentage of floor swabs detecting SARS-CoV2 was not correlated with absenteeism, pediatric hospitalizations, or wastewater data. Schools in neighbourhoods with previously elevated COVID-19 rates had lower test positivity.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Nisha Thampi", - "author_inst": "Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada; CHEO Research Institute, Ottawa, Ontario, Canada" - }, - { - "author_name": "Tasha Burhunduli", - "author_inst": "CHEO Research Institute, Ottawa, Ontario, Canada" - }, - { - "author_name": "Jamie Strain", - "author_inst": "CHEO Research Institute, Ottawa, Ontario, Canada" - }, - { - "author_name": "Ashley Raudanskis", - "author_inst": "Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada" - }, - { - "author_name": "Jason A. Moggridge", - "author_inst": "Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada" - }, - { - "author_name": "Aaron Hinz", - "author_inst": "Department of Biology, University of Ottawa, Ottawa, Ontario, Canada; Department of Biology, Carleton University, Ottawa, Ontario, Canada" - }, - { - "author_name": "Evgueni Doukhanine", - "author_inst": "DNA Genotek Incorporated, Ottawa, ON K2V 1C2, Canada" - }, - { - "author_name": "Lucas Castellani", - "author_inst": "Sault Area Hospital, Sault Ste. Marie, Ontario, Canada; Clinical Sciences Division, Northern Ontario School of Medicine, Sudbury, Ontario, Canada" - }, - { - "author_name": "Michael Fralick", - "author_inst": "Division of General Internal Medicine, Sinai Health System, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Onta" - }, - { - "author_name": "Rees Kassen", - "author_inst": "Department of Biology, Carleton University, Ottawa, Ontario, Canada" - }, - { - "author_name": "Janine McCready", - "author_inst": "Michael Garron Hospital, Toronto East Health Network, Toronto, Ontario, Canada" - }, - { - "author_name": "Caroline Nott", - "author_inst": "The Ottawa Hospital Research Institute, Ottawa, Ontario, Canada; Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada" - }, - { - "author_name": "Alex Wong", - "author_inst": "Institute for Advancing Health Through Agriculture, Texas AM AgriLife, Fort Worth, Texas, USA" - }, - { - "author_name": "Derek R. MacFadden", - "author_inst": "The Ottawa Hospital Research Institute, Ottawa, Ontario, Canada; Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.03.02.23286683", "rel_title": "Campus Sewage Water Surveillance based dynamics and infection trends of SARS-CoV-2 variants during third wave of COVID-19 in Pune, India", @@ -90712,6 +92302,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2023.02.26.23286471", + "rel_title": "The gray swan: model-based assessment of the risk of sudden failure of hybrid immunity to SARS-CoV-2", + "rel_date": "2023-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.26.23286471", + "rel_abs": "In the fourth year of the COVID-19 pandemic, public health authorities worldwide have adopted a strategy of learning to live with SARS-CoV-2. This has involved the removal of measures for limiting viral spread, resulting in a large burden of recurrent SARS-CoV-2 infections. Crucial for managing this burden is the concept of the so-called wall of hybrid immunity, through repeated reinfections and vaccine boosters, to reduce the risk of severe disease and death. Protection against both infection and severe disease is provided by the induction of neutralizing antibodies (nAbs) against SARS-CoV-2. However, pharmacokinetic (PK) waning and rapid viral evolution both degrade nAb binding titers. The recent emergence of variants with strongly immune evasive potential against both the vaccinal and natural immune responses raises the question of whether the wall of population-level immunity can be maintained in the face of large jumps in nAb binding potency. Here we use an agent-based simulation to address this question. Our findings suggest large jumps in viral evolution may cause failure of population immunity resulting in sudden increases in mortality. As a rise in mortality will only become apparent in the weeks following a wave of disease, reactive public health strategies will not be able to provide meaningful risk mitigation. Learning to live with the virus could thus lead to large death tolls with very little warning. Our work points to the importance of proactive management strategies for the ongoing pandemic, and to the need for multifactorial approaches to COVID-19 disease control.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Madison Stoddard", + "author_inst": "Fractal Therapeutics" + }, + { + "author_name": "Lin Yuan", + "author_inst": "Fractal Therapeutics" + }, + { + "author_name": "Sharanya Sarkar", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Debra Van Egeren", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Laura White", + "author_inst": "Boston University" + }, + { + "author_name": "Arijit Chakravarty", + "author_inst": "Fractal Therapeutics" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.02.27.23286501", "rel_title": "Combining models to generate a consensus effective reproduction number R for the COVID-19 epidemic status in England", @@ -90969,69 +92598,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.02.27.530232", - "rel_title": "SARS-CoV-2 ORF3c suppresses immune activation by inhibiting innate sensing", - "rel_date": "2023-03-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.27.530232", - "rel_abs": "SARS-CoV-2 proteins are translated from subgenomic RNAs (sgRNAs). While most of these sgRNAs are monocistronic, some viral mRNAs encode more than one protein. For example, the ORF3a sgRNA also encodes ORF3c, an enigmatic 4l-amino acid peptide. Here, we show that ORF3c is expressed in SARS-CoV-2 infected cells and suppresses RIG-I- and MDA5-mediated immune activation and IFN-{beta} induction. Mechanistic analyses revealed that ORF3c interacts with the signaling adaptor MAVS, induces its C-terminal cleavage and inhibits the interaction of RIG-I with MAVS. The immunosuppressive activity of ORF3c is conserved among members of the subgenus sarbecovirus, including SARS-CoV and coronaviruses isolated from bats. Notably, however, the SARS-CoV-2 delta and kappa variants harbor premature stop codons in ORF3c demonstrating that this reading frame is not essential for efficient viral replication in vivo and likely compensated by other viral proteins. In agreement with this, disruption of ORF3c did not significantly affect SARS-CoV-2 replication in CaCo-2 or CaLu-3 cells. In summary, we here identify ORF3c as an immune evasion factor of SARS-CoV-2 that suppresses innate sensing in infected cells.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Martin Mueller", - "author_inst": "University Hospital T\u00fcbingen" - }, - { - "author_name": "Alexandra Herrmann", - "author_inst": "Universit\u00e4tsklinikum, Friedrich Alexander Universit\u00e4t" - }, - { - "author_name": "Shigeru Fujita", - "author_inst": "The University of Tokyo" - }, - { - "author_name": "Jan Eric Kolberg", - "author_inst": "University Hospital T\u00fcbingen" - }, - { - "author_name": "Carolin Kruth", - "author_inst": "University Hospital T\u00fcbingen" - }, - { - "author_name": "Adam Strange", - "author_inst": "The University of Tokyo" - }, - { - "author_name": "Markus Schneider", - "author_inst": "University Hospital T\u00fcbingen" - }, - { - "author_name": "Jumpei Ito", - "author_inst": "The University of Tokyo" - }, - { - "author_name": "Armin Ensser", - "author_inst": "Universit\u00e4tsklinikum, Friedrich Alexander Universit\u00e4t" - }, - { - "author_name": "- The Genotype to Phenotype Japan (G2P-Japan) Consortium", - "author_inst": "-" - }, - { - "author_name": "Kei Sato", - "author_inst": "The University of Tokyo" - }, - { - "author_name": "Daniel Sauter", - "author_inst": "University Hospital T\u00fcbingen" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.03.01.530454", "rel_title": "IgG4 serum levels are not elevated in cases of Post-COVID syndrome", @@ -92486,6 +94052,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.02.19.23286159", + "rel_title": "Durable reprogramming of neutralising antibody responses following breakthrough Omicron infection", + "rel_date": "2023-02-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.19.23286159", + "rel_abs": "SARS-CoV-2 breakthrough infection of vaccinated individuals is increasingly common with the circulation of highly immune evasive and transmissible Omicron variants. Here, we report the dynamics and durability of recalled spike-specific humoral immunity following BA.1 or BA.2 breakthrough infection, with longitudinal sampling up to 8 months post-infection. Both BA.1 and BA.2 infection robustly boosted neutralisation activity against the infecting strain while expanding breadth against other Omicron strains. Cross-reactive memory B cells against both ancestral and Omicron spike were predominantly expanded by infection, with limited recruitment of de novo Omicron-specific B cells or antibodies. Modelling of neutralisation titres predicts that protection from symptomatic reinfection against antigenically similar strains will be remarkably durable, but is undermined by novel emerging strains with further neutralisation escape.\n\nOne sentence summaryOmicron breakthrough infection elicits durable neutralising activity by recalling cross-reactive vaccine-elicited memory B cells.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Wen Shi Lee", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Hyon-Xhi Tan", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Arnold Reynaldi", + "author_inst": "Kirby Institute, The University of New South Wales" + }, + { + "author_name": "Robyn Esterbauer", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Marios Koutsakos", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Julie Nguyen", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Thakshila Amarasena", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Helen E Kent", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Anupriya Aggarwal", + "author_inst": "Kirby Institute, The University of New South Wales" + }, + { + "author_name": "Stuart G Turville", + "author_inst": "Kirby Institute, The University of New South Wales" + }, + { + "author_name": "George Taiaroa", + "author_inst": "Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Paul Kinsella", + "author_inst": "Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Kwee Chin Liew", + "author_inst": "Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Thomas Tran", + "author_inst": "Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Deborah A Williamson", + "author_inst": "Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Deborah Cromer", + "author_inst": "Kirby Institute, The University of New South Wales" + }, + { + "author_name": "Miles P Davenport", + "author_inst": "Kirby Institute, The University of New South Wales" + }, + { + "author_name": "Stephen J Kent", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "Jennifer A Juno", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + }, + { + "author_name": "David S Khoury", + "author_inst": "Kirby Institute, The University of New South Wales" + }, + { + "author_name": "Adam K Wheatley", + "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.02.23.23286390", "rel_title": "Was access and quality of healthcare affected during COVID-19 pandemic? A qualitative enquiry into healthcare access for non-communicable diseases in Central India", @@ -92775,45 +94440,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.02.21.23286228", - "rel_title": "Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model", - "rel_date": "2023-02-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.21.23286228", - "rel_abs": "BackgroundProjects such as the European Covid-19 Forecast Hub publish forecasts on the national level for new deaths, new cases, and hospital admissions, but not direct measurements of hospital strain like critical care bed occupancy at the sub-national level, which is of particular interest to health professionals for planning purposes.\n\nMethodsWe present a sub-national French framework for forecasting hospital strain based on a non-Markovian compartmental model, its associated online visualisation tool and a retrospective evaluation of the real-time forecasts it provided from January to December 2021 by comparing to three standard statistical forecasting methods (auto-regression, exponential smoothing, and ARIMA).\n\nResultsFor anticipating risk of critical care unit overload, our model performed worse than pure statistical methods at the one- and two-week horizons, but had better point forecasts at the four-week horizon for 8 of the 13 regions considered. Our model also suffered from over-confidence with respect to its prediction intervals.\n\nConclusionsOnline visualisation tools and consideration of how metrics can be affected by distortion from non-pharmaceutical government interventions are essential in the assessment of forecasting models for hospital strain.\n\nWhat is already known on this topicO_LIThe US and European Covid-19 Forecast Hubs do not provide more direct measurements of hospital strain like critical care bed occupancy at the sub-national level, which was essential for the provisioning of healthcare resources during the COVID-19 pandemic.\nC_LIO_LIIn France, statistical modelling approaches have been proposed to anticipate hospital stain at the sub-national level but are limited by a two-week forecast horizon.\nC_LI\n\nWhat this study addsO_LIWe present a sub-national French modelling framework and online application for anticipating hospital strain at the four-week horizon that can account for abrupt changes in key epidemiological parameters.\nC_LIO_LIIt was the only publicly available real-time non-Markovian mechanistic model for the French epidemic when implemented in January 2021 and, to our knowledge, it still was at the time it stopped in early 2022.\nC_LI\n\nHow this study might affect research, practice or policyO_LIFurther adaptations of this surveillance system can serve as an anticipation tool for hospital strain across sub-national localities to aid in the prevention of short-noticed ward closures and patient transfers.\nC_LI", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Alexander Massey", - "author_inst": "MIVEGEC (University of Montpellier, CNRS, IRD)" - }, - { - "author_name": "Corentin Boennec", - "author_inst": "LAPLACE" - }, - { - "author_name": "Claudia Ximena Restrepo-Ortiz", - "author_inst": "MARBEC" - }, - { - "author_name": "Christophe Blanchet", - "author_inst": "CNRS; Institut Francais de Bioinformatique" - }, - { - "author_name": "Samuel Alizon", - "author_inst": "CNRS" - }, - { - "author_name": "Mircea T. Sofonea", - "author_inst": "MIVEGEC, University of Montpellier" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.02.21.23286227", "rel_title": "COVID-19 preventive measures in Rohingya refugee camps: An assessment of knowledge, attitude and practice toward COVID-19", @@ -94264,6 +95890,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.02.23.23286342", + "rel_title": "Multilevel determinants of Covid-19 vaccine hesitancy and undervaccination among marginalized populations in the United States: A scoping review", + "rel_date": "2023-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.23.23286342", + "rel_abs": "BackgroundAmid persistent disparities in Covid-19 vaccination, we conducted a scoping review to identify multilevel determinants of Covid-19 vaccine hesitancy (VH) and undervaccination among marginalized populations in the U.S.\n\nMethodsWe utilized the scoping review methodology developed by the Joanna Briggs Institute and report all findings according to PRISMA-ScR guidelines. We developed a search string and explored 7 databases to identify peer-reviewed articles published from January 1, 2020-October 31, 2021, the initial period of U.S. Covid-19 vaccine avails.comability. We combine frequency analysis and narrative synthesis to describe factors influencing Covid-19 vaccination among marginalized populations.\n\nResultsThe search captured 2,496 non-duplicated records, which were scoped to 50 peer-reviewed articles: 11 (22%) focused on African American/Black people, 9 (18%) people with disabilities, 4 (8%) justice-involved people, and 2 (4%) each on Latinx, people living with HIV/AIDS, people who use drugs, and LGBTQ+ people. Forty-four articles identified structural factors, 36 social/community, 27 individual, and 40 vaccine-specific factors. Structural factors comprised medical mistrust (of healthcare systems, government public health) and access barriers due to unemployment, unstable housing, lack of transportation, no/low paid sick days, low internet/digital technology access, and lack of culturally and linguistically appropriate information. Social/community factors including trust in a personal healthcare provider (HCP), altruism, family influence, and social proofing mitigated VH. At the individual level, low perceived Covid-19 threat and negative vaccine attitudes were associated with VH.\n\nDiscussionThis review indicates the importance of identifying and disaggregating structural factors underlying Covid-19 undervaccination among marginalized populations, both cross-cutting and population-specific--including multiple logistical and economic barriers in access, and systemic mistrust of healthcare systems and government public health--from individual and social/community factors, including trust in personal HCPs/clinics as reliable sources of vaccine information, altruistic motivations, and family influence, to effectively address individual decisional conflict underlying VH as well as broader determinants of undervaccination.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Peter A. Newman", + "author_inst": "University of Toronto" + }, + { + "author_name": "Thabani Nyoni", + "author_inst": "University of Toronto" + }, + { + "author_name": "Kate Allan", + "author_inst": "University of Toronto" + }, + { + "author_name": "Sophia Fantus", + "author_inst": "The University of Texas at Arlington" + }, + { + "author_name": "Duy Dinh", + "author_inst": "Queen's University" + }, + { + "author_name": "Suchon Tepjan", + "author_inst": "VOICES-Thailand Foundation" + }, + { + "author_name": "Luke Reid", + "author_inst": "University of Toronto" + }, + { + "author_name": "Adrian Guta", + "author_inst": "University of Windsor" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.02.17.23286049", "rel_title": "Evidence of Leaky Protection Following COVID-19 Vaccination and SARS-CoV-2 Infection in a US Correctional Facility Population", @@ -94709,41 +96382,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.02.23.23286343", - "rel_title": "PREVALENCE OF DEPRESSION AND ANXIETY IN COLOMBIA: WHAT HAPPENED DURING COVID-19 PANDEMIC?", - "rel_date": "2023-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.23.23286343", - "rel_abs": "The COVID-19 pandemic has impacted the well-being of millions of people around the globe. During the COVID-19 pandemic, the mental health of the population was affected, which means that governments would need to implement different actions to mitigate and treat mental health disorders result of the pandemic.\n\nThis study aims to estimate the prevalence of anxiety and depression for female and male adolescents and adults in Colombia before the COVID-19 pandemic. It also aimed to estimate the potential increase of the prevalence in each group as a result of the COVID-19 pandemic in 2020. We used the Individual Registry of Health Services Delivery data from 2015 - 2021 to estimate the observed prevalence of anxiety and depression. Using the National Mental Health Survey 2015, we simulated the expected prevalence of anxiety and depression for adolescents (12 to 17 years) and adults (18 or older) from 2016 to 2020. We used an arithmetic static Monte Carlo simulation process to estimate the expected prevalence. The results of the analysis using revealed an important increase in the observed prevalence of these disorders for adults and adolescents and men and women between 2015 and February 2020. When we simulated different scenarios using the National Mental Health Survey and estimated the prevalence of both depression and anxiety for adults and adolescents, we found that the prevalence of depression and anxiety has had an important increase in the last five years for all groups and had an important increase during the 2020. This increase has been greater for women than for men, and for adolescents than adults. Our results show the number of people who need potential attention from the health system in Colombia and highlight the importance to think about how to avoid and detect potential cases of anxiety and depression especially in female adolescents.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sandra Mart\u00ednez-Cabezas", - "author_inst": "Universidad de Los Andes Facultad de Medicina" - }, - { - "author_name": "M\u00f3nica Pinilla-Roncancio", - "author_inst": "Universidad de Los Andes Facultad de Medicina" - }, - { - "author_name": "Gabriel Carrasquilla", - "author_inst": "Asiessalud" - }, - { - "author_name": "Germ\u00e1n Casas", - "author_inst": "Universidad de Los Andes Facultad de Medicina" - }, - { - "author_name": "Catalina Gonz\u00e1lez-Uribe", - "author_inst": "Universidad de los Andes Facultad de Medicina" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.02.23.23286348", "rel_title": "Understanding the impact of a social support program in Immokalee, FL, during the COVID-19 pandemic", @@ -96046,6 +97684,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2023.02.18.23286136", + "rel_title": "Comparative Effectiveness of BNT162b2 and NVX-CoV2373 Vaccines in Korean Adults", + "rel_date": "2023-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.18.23286136", + "rel_abs": "BackgroundVarious types of vaccines against SARS-CoV-2 have reduced the burden of coronavirus diseases 2019 (COVID-19) across the world. We conducted an observational study to evaluate the effectiveness of NVX-CoV2373 and BNT162b2 in providing protection in Korean adults.\n\nMethodsThis study was a retrospective matched cohort study to emulate a target trial of three doses of NVX-CoV2373 (N-N-N) versus three doses of BNT162b2 (B-B-B) vaccines in presumed immune-naive adults. We used data from the Korea COVID-19 Vaccine Effectiveness (K-COVE) cohort, combining all COVID-19 laboratory-confirmed cases and all COVID-19 immunization registry, between February and November 2022. We calculated 40-week risk differences and risk ratios between the two vaccines.\n\nResultsA total of 3,019 recipients of NVX-CoV2373 vaccine and 3,027 recipients of BNT162b2 vaccine were eligible for the study. The 40-week risk ratios for recipients of the NVX-CoV2373 vaccine as compared with recipients of the BNT162b2 vaccine were 1.169 (95% CI, 1.015 to 1.347) for laboratory-confirmed SARS-CoV-2 infection, and 0.504 (95% CI, 0.126 to 2.014) for severe SARS-CoV-2 infection. Estimated risk of severe infection was 0.001 events per 1000 persons (95% CI, 0 to 0.003) for the NVX-CoV2373 vaccine and 0.002 events per 1000 persons (95% CI, 0.001 to 0.006) for BNT162b2 vaccine.\n\nConclusionThis study identifies reduced risk of SARS-CoV-2 infection and severe infection after receipt of three doses of either NVX-CoV2373 or BNT162b2 vaccines in Korean adults. Direct, vaccine-conferred protection may be of importance among high risk persons to mitigate from serious clinical outcome from COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Seon Kyeong Park", + "author_inst": "Korea Disease Control and Prevention Agency" + }, + { + "author_name": "Young June Choe", + "author_inst": "Korea University Anam Hospital" + }, + { + "author_name": "Seung Ah Choe", + "author_inst": "Korea University" + }, + { + "author_name": "Benjamin J Cowling", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Ji Hae Hwang", + "author_inst": "Korea Disease Control and Prevention Agency" + }, + { + "author_name": "Ju Hee Lee", + "author_inst": "Korea Disease Control and Prevention Agency" + }, + { + "author_name": "Kil Hun Lee", + "author_inst": "Korea Disease Control and Prevention Agency" + }, + { + "author_name": "Seonju Yi", + "author_inst": "Korea Disease Control and Prevention Agency" + }, + { + "author_name": "Sang Won Lee", + "author_inst": "Korea Disease Control and Prevention Agency" + }, + { + "author_name": "Geun Yong Kwon", + "author_inst": "Korea Disease Control and Prevention Agency" + }, + { + "author_name": "Eun Jung Jang", + "author_inst": "Korea Disease Control and Prevention Agency" + }, + { + "author_name": "Ryu Kyung Kim", + "author_inst": "Korea Disease Control and Prevention Agency" + }, + { + "author_name": "Young Joon Park", + "author_inst": "Korea Disease Control and Prevention Agency" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.02.17.528968", "rel_title": "Speedy-PASEF: Analytical flow rate chromatography and trapped ion mobility for deep high-throughput proteomics", @@ -96159,81 +97864,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.02.14.527605", - "rel_title": "Protective effect of plasma neutralization from prior SARS-CoV-2 Omicron infection against BA.5 subvariant symptomatic reinfection", - "rel_date": "2023-02-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.14.527605", - "rel_abs": "From December 2022 to January 2023, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections caused by BA.5 and BF.7 subvariants of B.1.1.529 (Omicron) swept across mainland China. It is crucial to estimate the protective effect of the neutralizing antibodies generated by such mass infections against the next potential SARS-CoV-2 reinfection wave, especially if driven by CH.1.1 or XBB.1.5. Previously, we recruited and continuously followed a cohort of individuals that experienced Omicron BA.1, BA.2, and BA.5 breakthrough infections, as well as a control cohort with no history of SARS-CoV-2 infection. In the previously uninfected cohort, the total symptomatic infection rate surveyed during the outbreak was 91.6%, while the symptomatic reinfection rate was 32.9%, 10.5%, and 2.8% among individuals with prior Omicron BA.1, BA.2 and BA.5 infection, respectively, with median intervals between infections of 335, 225 and 94 days. Pseudovirus neutralization assays were performed in plasma samples collected from previously Omicron BA.1-infected individuals approximately 3 months before the outbreak. Results indicate a robust correlation between the plasma neutralizing antibody titers and the protective effect against symptomatic reinfection. The geometric mean of the 50% neutralizing titers (NT50) against D614G, BA.5, and BF.7 were 2.0, 2.5, and 2.3-fold higher in individuals without symptomatic reinfection than in those with symptomatic reinfection (p < 0.01). Low plasma neutralizing antibody titer (below the geometric mean of NT50) was associated with an enhanced cumulative risk of symptomatic reinfection, with a hazard ratio (HR) of 23.55 (95% CI: 9.23-60.06) against BF.7 subvariant. Importantly, neutralizing antibodies titers post one month after BF.7/BA.5 breakthrough infections against CH.1.1 and XBB.1.5 are similar to that against BF.7 from individuals with prior BA.1 infection while not experiencing a symptomatic BF.7/BA.5 reinfection (plasma collected 3 months before the outbreak), suggesting that the humoral immunity generated by the current BF.7/BA.5 breakthrough infection may provide protection against CH.1.1 and XBB.1.5 symptomatic reinfection wave for 4 months. Of note, the higher hACE2 binding of XBB.1.5 may reduce the protection period since the potential increase of infectivity.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Xiaosu Chen", - "author_inst": "Nankai University" - }, - { - "author_name": "Yanli Xu", - "author_inst": "Beijing Ditan Hospital" - }, - { - "author_name": "Yan Xie", - "author_inst": "Tianjin First Central Hospital" - }, - { - "author_name": "Weiliang Song", - "author_inst": "Peking University" - }, - { - "author_name": "Ye Hu", - "author_inst": "Nankai University" - }, - { - "author_name": "Ayijiang Yisimayi", - "author_inst": "Peking University" - }, - { - "author_name": "Fei Shao", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Li Geng", - "author_inst": "Tianjin First Central Hospital" - }, - { - "author_name": "Ying Wang", - "author_inst": "Tianjin First Central Hospital" - }, - { - "author_name": "Hongmei Gao", - "author_inst": "Tianjin First Central Hospital" - }, - { - "author_name": "Yansong Shi", - "author_inst": "Nankai University" - }, - { - "author_name": "Shuo Zhang", - "author_inst": "The Fourth Hospital of Inner Mongolia" - }, - { - "author_name": "Ronghua Jin", - "author_inst": "Beijing Ditan Hospital" - }, - { - "author_name": "Zhongyang Shen", - "author_inst": "Tianjin First Central Hospital" - }, - { - "author_name": "Yunlong Richard Cao", - "author_inst": "Peking University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.02.17.529036", "rel_title": "Tracking and curating putative SARS-CoV-2 recombinants with RIVET", @@ -97728,6 +99358,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.02.16.23286008", + "rel_title": "COVID-19 Vaccine Acceptance in Nigeria: A Rapid Systematic Review and Meta-Analysis", + "rel_date": "2023-02-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.16.23286008", + "rel_abs": "Widespread COVID-19 vaccination is essential to maintaining pandemic control. However, low- and lower-middle-income countries (LMICs) continue to face challenges to care due to unequal access and vaccine fear despite the introduction of safe and effective immunizations. This study aimed to collect information on Nigerias COVID-19 vaccine uptake rates and determinants. Science Direct, PubMed, Google Scholar, African Journal Online, Springer, and Hinari were all systematically searched through and completed in May 2022. Quality assessments of the listed studies were performed using the eight-item Joanna Briggs Institute Critical Appraisal tools for cross-sectional studies. In addition, we undertook a meta-analysis to calculate pooled acceptance rates with 95% confidence intervals (CI). Forty-two studies in total satisfied the inclusion criteria and were reviewed. A total of 24,533 respondents were studied. The total sample size of states in the Northern, Western and Southern parts of Nigeria are 3,206, 4,527 and 5,059, respectively, while 11,741 is the cumulative sample size of all the Nigeria-wide studies. The total COVID-19 vaccination acceptance rate among all the study groups was 52.4% (95% CI: 46.9-57.9%, I2 = 100%), while the total estimated COVID-19 vaccination hesitancy rates was 47.81% (95% CI: 42.2 - 53.4% I2 = 100%). In Nigeria-regions sub-group analyses, the Western region (58.90%, 95% CI: 47.12-70.27%) and Northern region (54.9%, 95% CI: 40.11%-69.4%) showed the highest rates of vaccine acceptance and vaccine hesitancy respectively. The COVID-19 vaccine acceptance rate was highest in 2020, with a pooled rate of 59.56% (46.34, 57.32%, I2 = 98.7%). The acceptance rate in 2021 was only 48.48 (40.78%, 56.22%), while for the studies in 2022, it increased to 52.04% (95% CI: 35.7%, 68.15 %). The sensitization of local authorities and the dissemination of more detailed information about the COVID-19 vaccine and its safety, could significantly increase the countrys vaccination rate.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Victory Chizaram Nnaemeka", + "author_inst": "University of Nigeria, Nsukka." + }, + { + "author_name": "Nnenna Audrey Okafor", + "author_inst": "University of Nigeria, Nsukka" + }, + { + "author_name": "Oluwatosin Qawiyy Orababa", + "author_inst": "University of Warwick" + }, + { + "author_name": "Ruth Anikwe", + "author_inst": "University of Nigeria, Nsukka" + }, + { + "author_name": "Reuben Ogba Onwe", + "author_inst": "University of Nigeria, Nsukka" + }, + { + "author_name": "Nneka Patricia Uzochukwu", + "author_inst": "University of Nigeria, Nsukka." + }, + { + "author_name": "Thomas Sambo Tsiterimam", + "author_inst": "Department of Obstetrics and Gynecology, University of Abuja Teaching Hospital" + }, + { + "author_name": "Nkiru Nenye Nwokoye", + "author_inst": "KNCV TB Foundation, Abuja FCT" + }, + { + "author_name": "Anthony Chibuogwu Ike", + "author_inst": "University of Nigeria, Nsukka." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.02.16.23285816", "rel_title": "Estimates of protection against SARS-CoV-2 infection and severe COVID-19 in Germany before the 2022/2023 winter season - the IMMUNEBRIDGE project", @@ -98061,77 +99742,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2023.02.15.528538", - "rel_title": "Sotrovimab retains activity against SARS-CoV-2 Omicron variant BQ.1.1 in a non-human primate model", - "rel_date": "2023-02-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.15.528538", - "rel_abs": "The SARS-CoV2 Omicron variants have acquired new Spike mutations leading to escape from the most of the currently available monoclonal antibody treatments reducing the options for patients suffering from severe Covid-19. Recently, both in vitro and in vivo data have suggested that Sotrovimab could retain partial activity against recent omicron sub-lineage such as BA.5 variants, including BQ.1.1. Here we report full efficacy of Sotrovimab against BQ.1.1 viral replication as measure by RT-qPCR in a non-human primate challenge model.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Cecile Herate", - "author_inst": "University Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, Fra" - }, - { - "author_name": "Romain Marlin", - "author_inst": "University Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, Fra" - }, - { - "author_name": "Franck Touret", - "author_inst": "Aix Marseille Univ, IRD French Institute of Research for Development, EHESP French School of Public Health & IHU Mediterranee Infection, APHM Public Hospitals o" - }, - { - "author_name": "Nathalie Dereuddre Bosquet", - "author_inst": "University Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, Fra" - }, - { - "author_name": "Flora Donati", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Molecular Genetics of RNA Viruses Unit, Paris, France" - }, - { - "author_name": "Francis Relouzat", - "author_inst": "University Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, Fra" - }, - { - "author_name": "Laura Junges", - "author_inst": "University Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, Fra" - }, - { - "author_name": "Mathilde Galhaut", - "author_inst": "University Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, Fra" - }, - { - "author_name": "Oceane Dehan", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Molecular Genetics of RNA Viruses Unit, Paris, France" - }, - { - "author_name": "Quentin Sconosciutti", - "author_inst": "University Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, Fra" - }, - { - "author_name": "Antoine Nougairede", - "author_inst": "Aix Marseille Univ, IRD French Institute of Research for Development, EHESP French School of Public Health & IHU Mediterranee Infection, APHM Public Hospitals o" - }, - { - "author_name": "Xavier de Lamballerie", - "author_inst": "Aix Marseille Univ, IRD French Institute of Research for Development, EHESP French School of Public Health & IHU Mediterranee Infection, APHM Public Hospitals o" - }, - { - "author_name": "Sylvie van der Werf", - "author_inst": "Institut Pasteur, Universite Paris Cite, CNRS UMR 3569, Molecular Genetics of RNA Viruses Unit, Paris, France" - }, - { - "author_name": "Roger Le Grand", - "author_inst": "University Paris-Saclay, Inserm, CEA, Center for Immunology of Viral, Auto-immune, Hematological and Bacterial Diseases (IMVA-HB/IDMIT), Fontenay-aux-Roses, Fra" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "pathology" - }, { "rel_doi": "10.1101/2023.02.15.528632", "rel_title": "Development and characterization of a multimeric recombinant protein based on the spike protein receptor binding domain of SARS-CoV-2 that can neutralize virus infection", @@ -99694,6 +101304,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2023.02.10.23285603", + "rel_title": "Relative effectiveness of BNT162b2, mRNA-1273, and Ad26.COV2.S vaccines and homologous boosting in preventing COVID-19 in adults in the US", + "rel_date": "2023-02-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.10.23285603", + "rel_abs": "BackgroundFew head-to-head comparisons have been performed on the real-world effectiveness of COVID-19 booster vaccines. We evaluated the relative effectiveness (rVE) of a primary series of mRNA-1273 versus BNT162b2 and Ad26.COV2.S and a homologous mRNA booster against medically-attended, outpatient, and hospitalized COVID-19.\n\nMethodsA dataset linking primary care electronic medical records with medical claims data was used for this retrospective cohort study of US patients [≥]18 years vaccinated with a primary series between February and October 2021 (Part 1) and a homologous mRNA booster between October 2021 and January 2022 (Part 2). Adjusted hazard ratios (HR) were derived from 1:1 matching adjusted across potential covariates. rVE was (1-HRadjusted) x 100. Additional analysis was performed across regions and age groups.\n\nResultsFollowing adjustment, Part 1 rVE for mRNA-1273 versus BNT162b2 was 23% (95% CI: 22%-25%), 23% (22%-25%), and 19% (14%-24%) whilst the rVE for mRNA-1273 versus Ad26.COV2.S was 50% (48%-51%), 50% (48%-52%), and 57% (53%-61%) against any medically-attended, outpatient, and hospitalized COVID-19, respectively. The adjusted rVE in Part 2 for mRNA-1273 versus BNT162b2 was 14% (10%-18%), 13% (8%- 17%), and 19% (1%-34%) against any medically-attended, outpatient, and hospitalized COVID-19, respectively. rVE against medically-attended COVID-19 was higher in adults [≥]65 years (35%; 24%-47%) than those 18-64 years (13%; 9%-17%) after the booster.\n\nConclusionsIn this study, mRNA-1273 was more effective than BNT162b2 or Ad26.COV2.S following primary series during a Delta-dominant period, and than BNT162b2 as a booster during an Omicron-dominant period.\n\nKey pointsmRNA-1273 was associated with a lower risk than BNT162b2 or Ad26.COV2.S of any medically-attended, outpatient, or hospitalized COVID-19 after primary series and of any medically-attended, outpatient, or hospitalized COVID-19 vs BNT162b2 after a homologous mRNA booster", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Van Hung Nguyen", + "author_inst": "VHN vonsulting" + }, + { + "author_name": "Catherine Boileau", + "author_inst": "VHN Consulting Inc." + }, + { + "author_name": "Alina Bogdanov", + "author_inst": "Veradigm" + }, + { + "author_name": "Meg Sredl", + "author_inst": "Veradigm" + }, + { + "author_name": "Mac Bonafede", + "author_inst": "Veradigm" + }, + { + "author_name": "Thierry Ducruet", + "author_inst": "VHN Consulting Inc." + }, + { + "author_name": "Scott Chavers", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Andrew Rosen", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "David Martin", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Philip Buck", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Diana Esposito", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Nicolas Van de Velde", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "James A. Mansi", + "author_inst": "Moderna, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.02.10.23285516", "rel_title": "Epidemiological drivers of transmissibility and severity of SARS-CoV-2 in England", @@ -99839,41 +101516,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.02.09.23285742", - "rel_title": "Long COVID in Elderly Patients: An Epidemiologic Exploration Using a Medicare Cohort", - "rel_date": "2023-02-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.09.23285742", - "rel_abs": "BackgroundIncidence of long COVID in the elderly is difficult to estimate and can be under-reported. While long COVID is sometimes considered a novel disease, many viral or bacterial infections have been known to cause prolonged illnesses. We postulate that some influenza patients might develop residual symptoms that would satisfy the diagnostic criteria for long COVID, a condition we call \"long Flu\". In this study, we estimate the incidence of long COVID and long Flu among Medicare patients using the World Health Organization (WHO) consensus definition. We compare the incidence, symptomatology, and healthcare utilization between long COVID and long Flu patients.\n\nMethods and FindingsThis is a cohort study of Medicare (the U.S. federal health insurance program) beneficiaries over 65. ICD-10-CM codes were used to capture COVID-19, influenza and residual symptoms. Long COVID was identified by a) the designated long COVID-19 code B94.8 (code-based definition), or b) any of 11 symptoms identified in the WHO definition (symptom-based definition), from one to 3 months post infection. A symptom would be excluded if it occurred in the year prior to infection. Long Flu was identified in influenza patients from the combined 2018 and 2019 Flu seasons by the same symptom-based definition for long COVID. Long COVID and long Flu were compared in four outcome measures: a) hospitalization (any cause), b) hospitalization (for long COVID symptom), c) emergency department (ED) visit (for long COVID symptom), and d) number of outpatient encounters (for long COVID symptom), adjusted for age, sex, race, region, Medicare-Medicaid dual eligibility status, prior-year hospitalization, and chronic comorbidities. Among 2,071,532 COVID-19 patients diagnosed between April 2020 and June 2021, symptom-based definition identified long COVID in 16.6% (246,154/1,479,183) and 29.2% (61,631/210,765) of outpatients and inpatients respectively. The designated code gave much lower estimates (outpatients 0.49% (7,213/1,479,183), inpatients 2.6% (5,521/210,765)). Among 933,877 influenza patients, 17.0% (138,951/817,336) of outpatients and 24.6% (18,824/76,390) of inpatients fit the long Flu definition. Long COVID patients had higher incidence of dyspnea, fatigue, palpitations, loss of taste/smell and neurocognitive symptoms compared to long Flu. Long COVID outpatients were more likely to have any-cause hospitalization (31.9% (74,854/234,688) vs. 26.8% (33,140/123,736), odds ratio 1.06 (95% CI 1.05-1.08, p<0.001)), and more outpatient visits than long Flu outpatients (mean 2.9(SD 3.4) vs. 2.5(SD 2.7) visits, incidence rate ratio 1.09 (95% CI 1.08-1.10, p<0.001)). There were less ED visits in long COVID patients, probably because of reduction in ED usage during the pandemic. The main limitation of our study is that the diagnosis of long COVID in is not independently verified.\n\nConclusionsRelying on specific long COVID diagnostic codes results in significant under-reporting. We observed that about 30% of hospitalized COVID-19 patients developed long COVID. In a similar proportion of patients, long COVID-like symptoms (long Flu) can be observed after influenza, but there are notable differences in symptomatology between long COVID and long Flu. The impact of long COVID on healthcare utilization is higher than long Flu.\n\nAuthor summaryO_ST_ABSWhy was this study done?C_ST_ABSO_LIThe quoted incidence of long COVID varies widely because of differences in definition and measurement method. Long COVID in the elderly is likely to be under-reported because they are less likely to respond to surveys, and symptoms may be confused with other chronic diseases. We describe a method of identifying long COVID in the elderly using a standard definition.\nC_LIO_LILingering ill health after infections is not limited to COVID-19. We postulate that some patients may fit the diagnostic criteria of long COVID after a bout of influenza. We call this condition \"long Flu\". Comparing and contrasting long COVID and long Flu may shed light on the understanding of long COVID, a disease still shrouded in mystery.\nC_LI\n\nWhat did the researchers do and find?O_LIWe applied the World Health Organization consensus clinical definition to identify long COVID among 2 million Medicare patients who were diagnosed with COVID-19 between April 2020 and June 2021.\nC_LIO_LIWe applied the symptom-based long COVID definition to almost 900,000 influenza patients during the 2018 and 2019 Flu seasons to identify long Flu.\nC_LIO_LILong COVID occurred in 16.6% of outpatients and 29.2% of inpatients. The corresponding rates for long Flu were 17% and 24.6%. If one had relied solely on the designated diagnostic code to identify long COVID, the estimated rates of long COVID would be 0.5% and 2.6% among outpatients and inpatients, way below the reported rates in most studies.\nC_LIO_LIDespite the similar overall incidence rates, long COVID patients suffered more often from difficulty in breathing, fatigue, palpitations, loss of taste/smell, memory problems, cognitive impairment and sleep disturbance than long Flu patients.\nC_LIO_LILong COVID patients were also more likely to be admitted to hospital and had more outpatient visits on average than long Flu patients.\nC_LI\n\nWhat do these findings mean?O_LIThe use of designated long COVID diagnostic codes alone is likely to result in gross under-reporting.\nC_LIO_LIA similar proportion of influenza patients suffer from a prolonged illness resembling long COVID, but there are notable differences in the incidence of individual symptoms between long COVID and long Flu.\nC_LIO_LILong COVID is associated with higher level of healthcare utilization than long Flu. This means that long COVID is likely to have a bigger impact on the individuals health as well as on society as a whole.\nC_LI", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Kin Wah Fung", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Fitsum Baye", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Seo Hyon Baik", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Zhaonian Zheng", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Clement Joseph McDonald", - "author_inst": "National Institutes of Health" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.02.07.23285612", "rel_title": "Association between calcium and vitamin D in geriatric patients hospitalized for Covid-19: Results from the GERIA-COVID study", @@ -101380,6 +103022,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.02.06.23285542", + "rel_title": "Use of wastewater metrics to track COVID-19 in the U.S.: a national time-series analysis over the first three quarters of 2022", + "rel_date": "2023-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.06.23285542", + "rel_abs": "BackgroundWidespread use of at-home COVID-19 tests hampers determination of community COVID-19 incidence. Using nationwide data available through the US National Wastewater Surveillance System, we examined the performance of two wastewater metrics in predicting high case and hospitalizations rates both before and after widespread use of at-home tests.\n\nMethodsWe performed area under the receiver operating characteristic (ROC) curve analysis (AUC) for two wastewater metrics--viral concentration relative to the peak of January 2022 (\"wastewater percentile\") and 15-day percent change in SARS-CoV-2 (\"percent change\"). Dichotomized reported cases ([≥] 200 or <200 cases per 100,000) and new hospitalizations ([≥] 10 or <10 per 100,000) were our dependent variables, stratified by calendar quarter. Using logistic regression, we assessed the performance of combining wastewater metrics.\n\nResultsAmong 268 counties across 22 states, wastewater percentile detected high reported case and hospitalizations rates in the first quarter of 2022 (AUC 0.95 and 0.86 respectively) whereas the percent change did not (AUC 0.54 and 0.49 respectively). A wastewater percentile of 51% maximized sensitivity (0.93) and specificity (0.82) for detecting high case rates. A model inclusive of both metrics performed no better than using wastewater percentile alone. The predictive capability of wastewater percentile declined over time (AUC 0.84 and 0.72 for cases for second and third quarters of 2022).\n\nConclusionNationwide, county wastewater levels above 51% relative to the historic peak predicted high COVID rates and hospitalization in the first quarter of 2022, but performed less well in subsequent quarters. Decline over time in predictive performance of this metric likely reflects underreporting of cases, reduced testing, and possibly lower virulence of infection due to vaccines and treatments.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Meri Varkila", + "author_inst": "Stanford University" + }, + { + "author_name": "Maria Montez-Rath", + "author_inst": "Stanford University" + }, + { + "author_name": "Joshua Salomon", + "author_inst": "Stanford University" + }, + { + "author_name": "Xue Yu", + "author_inst": "Stanford University" + }, + { + "author_name": "Geoffrey Block", + "author_inst": "U.S. Renal Care" + }, + { + "author_name": "Douglas Owens", + "author_inst": "Stanford University" + }, + { + "author_name": "Glenn Chertow", + "author_inst": "Stanford University" + }, + { + "author_name": "Julie Parsonnet", + "author_inst": "Stanford University" + }, + { + "author_name": "Shuchi Anand", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.02.06.23285411", "rel_title": "Time series analysis of routine immunisation coverage during the COVID-19 pandemic in 2021 shows continued global decline and increases in Zero Dose children", @@ -101493,41 +103186,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.02.08.23285565", - "rel_title": "A Phase 2, Randomized, Double-blind, Placebo-controlled Study of oral RP7214, a DHODH inhibitor, in Patients with Symptomatic Mild SARS-CoV-2 Infection", - "rel_date": "2023-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.08.23285565", - "rel_abs": "IntroductionCOVID-19 pandemic due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is of immense global public health concern. RP7214, a novel, potent, oral, inhibitor of DHODH, has shown preclinical evidence in inhibiting viral replication and lung inflammation.\n\nMethodsThis was a randomized, double-blind, placebo-controlled phase 2 study in patients with symptomatic mild SARS-CoV-2 infection, having at least one high-risk feature (e.g., hypertension, diabetes mellitus) for developing severe Covid-19 infection. The patients received RP7214 (400 mg BID) or a placebo for 14 days in a blinded fashion and were followed up to 30 days. Patients also received supportive therapy (e.g., antipyretics and antitussives for symptomatic relief) at the discretion of the investigator. The endpoints were Covid 19 related hospitalization rate by Day 15, SARS-CoV-2 viral load and clearance on Days 3,7 and 15, clinical symptoms improvement by Day 15, safety, and the immuno-modulatory effect of RP7214.\n\nResultsA total of 163 patients were treated in the study; 82 received RP7214 and 81 received placebo. Of the total patients, 44.2% had received Covid-19 vaccine prior to the study. The symptom onset was [≤] 3 days in 22.1%. None of the patients in the study required hospitalization. There was no difference in the mean change of viral load between RP7214 and placebo. In the subgroup analysis, in patients having symptom onset of [≤] 3 days, RP7214 significantly reduced viral load on Days 3 and 7, respectively. Similarly, in non-vaccinated patients with symptom onset of [≤] 3 days, RP7214 significantly reduced viral load on Day 3. Overall, there was a trend towards better viral load reduction in RP7214-treated patients with a baseline viral load of 5 log units or higher. For all other endpoints, there was no difference between RP7214 and placebo. Majority of the reported AEs were mild and not related either to study treatment.\n\nConclusionsRP7214 at 400 mg BID dose level showed a statistically significant reduction in viral load at an early stage of the disease and in non-vaccinated patients. There was a trend towards better viral load reduction in RP7214-treated patients with a baseline viral load of 5 log units or higher. RP7214 showed a favorable safety profile. Further development of RP7214 in Covid 19 in a mild symptomatic population with co-morbidities and treated at an early stage of disease may show benefit.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Ajit Nair", - "author_inst": "Rhizen Pharmaceticals AG" - }, - { - "author_name": "Prajak Barde", - "author_inst": "Rhizen Pharmaceuticals AG" - }, - { - "author_name": "Kasi V Routhu", - "author_inst": "Rhizen pharmaceuticals AG" - }, - { - "author_name": "Swaroop Vakkalanka", - "author_inst": "Incozen Therapeutics Pvt Ltd" - }, - { - "author_name": "- RP7214-2101 Study Group Investigator Authors (India)", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.02.06.23285532", "rel_title": "Autoantigen profiling reveals a shared post-COVID signature in fully recovered and Long COVID patients", @@ -103034,6 +104692,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.02.05.527173", + "rel_title": "Taxonomical and ontological analysis of verified natural and laboratory human coronavirus hosts", + "rel_date": "2023-02-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.05.527173", + "rel_abs": "To fully understand COVID-19, it is critical to identify and analyze all the possible hosts of SARS-CoV-2 (the pathogen of COVID-19) and compare them with the hosts of other human coronaviruses. In this study, we collected, annotated, and performed taxonomical and ontological analysis of all the reported and verified hosts for all human coronaviruses including SARS-CoV, MERS-CoV, SARS-CoV-2, and four others that cause the common cold. A total of 37 natural hosts and 19 laboratory animal hosts of host human coronaviruses were identified based on experimental or clinical evidence. Our taxonomical ontology-based analysis found that all the verified susceptible natural and laboratory animals belong to therian mammals. Specifically, these 37 natural therian hosts include one wildlife marsupial mammal (i.e., Didelphis virginiana) and 36 Eutheria mammals (a.k.a. placental mammals). The 19 laboratory animal hosts are also classified as placental mammals. While several non-therian animals (including snake, housefly, zebrafish) were reported to be likely SARS-CoV-2 hosts, our analysis excluded them due to the lack of convincing evidence. Genetically modified mouse models with human Angiotensin-converting enzyme 2 (ACE2) or dipeptidyl peptidase-4 (DPP4) protein were more susceptible to virulent human coronaviruses with clear symptoms. Coronaviruses often became more virulent and adaptive in the mouse hosts after a series of viral passages in the mice. To support knowledge standardization and analysis, we have also represented the annotated host knowledge in the Coronavirus Infectious Disease Ontology (CIDO) and provided ways to automatically query the knowledge.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Yang Wang", + "author_inst": "Guizhou University School of Medicine, Guiyang, Guizhou 550025, China." + }, + { + "author_name": "Muhui Ye", + "author_inst": "Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong, China." + }, + { + "author_name": "Fengwei Zhang", + "author_inst": "Guizhou University School of Medicine, Guiyang, Guizhou 550025, China." + }, + { + "author_name": "Zachary Thomas Freeman", + "author_inst": "Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA." + }, + { + "author_name": "Hong Yu", + "author_inst": "Guizhou University School of Medicine, Guiyang, Guizhou 550025, China." + }, + { + "author_name": "Xianwei Ye", + "author_inst": "Guizhou University School of Medicine, Guiyang, Guizhou 550025, China." + }, + { + "author_name": "Yongqun He", + "author_inst": "Center for Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.02.06.23285513", "rel_title": "A Rapid review on the COVID-19 Pandemic's Global Impact on Breast Cancer Screening Participation Rates and Volumes from January-December 2020", @@ -103283,37 +104984,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.02.05.527216", - "rel_title": "Bioinformatic analysis of the spike protein cleavage sites of coronaviruses in the mammalian order Eulipotyphla", - "rel_date": "2023-02-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.05.527216", - "rel_abs": "The mammalian order Eulipotyphla, including hedgehogs and shrews, represent a poorly understood reservoir of coronaviruses with zoonotic potential. Here, we carried out a bioinformatic analyses of these viruses based on the viral spike protein--to illustrate the complexity of coronavirus evolutionary history and the diversity of viruses from these host species, with a focus on the presence of possible furin cleavage sites within the spike protein. We found no evidence for cleavage by furin itself; however, certain strains of Wencheng Sm Shrew coronavirus were shown to have a predicted cleavage site for other member of the proprotein convertases, which are furin family members-- suggesting their spillover potential. As the expanding urbanization and the trade of small mammals in the wet markets enhance the wildlife-human interactions, this may increase pathogen spillover risks. Therefore, we should implement broad wild animal surveillance and be vigilant of contact with these small wild mammals in light of one-health perspectives.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Qinghua Guo", - "author_inst": "Cornell Univ" - }, - { - "author_name": "Annette Choi", - "author_inst": "Cornell Univ" - }, - { - "author_name": "Jean Millet", - "author_inst": "INRAE" - }, - { - "author_name": "Gary Whittaker", - "author_inst": "Cornell Univ" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.02.03.527052", "rel_title": "Automated Agnostic Designation of Pathogen Lineages", @@ -104860,6 +106530,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.31.23285248", + "rel_title": "Using publicly available data to identify priority communities for a SARS-CoV-2 testing intervention in a southern U.S. state", + "rel_date": "2023-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.31.23285248", + "rel_abs": "BackgroundThe U.S. Southeast has a high burden of SARS-CoV-2 infections and COVID-19 disease. We used public data sources and community engagement to prioritize county selections for a precision population health intervention to promote a SARS-CoV-2 testing intervention in rural Alabama during October 2020 and March 2021.\n\nMethodsWe modeled factors associated with county-level SARS-CoV-2 percent positivity using covariates thought to associate with SARS-CoV-2 acquisition risk, disease severity, and risk mitigation practices. Descriptive epidemiologic data were presented to scientific and community advisory boards to prioritize counties for a testing intervention.\n\nResultsIn October 2020, SARS-CoV-2 percent positivity was not associated with any modeled factors. In March 2021, premature death rate (aRR 1.16, 95% CI 1.07, 1.25), percent Black residents (aRR 1.00, 95% CI 1.00, 1.01), preventable hospitalizations (aRR 1.03, 95% CI 1.00, 1.06), and proportion of smokers (aRR 0.231, 95% CI 0.10, 0.55) were associated with average SARS-CoV-2 percent positivity. We then ranked counties based on percent positivity, case fatality, case rates, and number of testing sites using individual variables and factor scores. Top ranking counties identified through factor analysis and univariate associations were provided to community partners who considered ongoing efforts and strength of community partnerships to promote testing to inform intervention.\n\nConclusionsThe dynamic nature of SARS-CoV-2 proved challenging for a modelling approach to inform a precision population health intervention at the county level. Epidemiological data allowed for engagement of community stakeholders implementing testing. As data sources and analytic capacities expand, engaging communities in data interpretation is vital to address diseases locally.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Lynn T. Matthews", + "author_inst": "Division of Infectious Disease, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham" + }, + { + "author_name": "Dustin M. Long", + "author_inst": "Department of Biostatistics, School of Public Health, University of Alabama at Birmingham" + }, + { + "author_name": "Madeline C. Pratt", + "author_inst": "Division of Infectious Disease, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham" + }, + { + "author_name": "Ya Yuan", + "author_inst": "Department of Biostatistics, School of Public Health, University of Alabama at Birmingham" + }, + { + "author_name": "Sonya L. Heath", + "author_inst": "Division of Infectious Disease, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham" + }, + { + "author_name": "Emily B. Levitan", + "author_inst": "Department of Epidemiology, School of Public Health, University of Alabama at Birmingham" + }, + { + "author_name": "Sydney Grooms", + "author_inst": "Center for AIDS Research, Heersink School of Medicine, University of Alabama at Birmingham" + }, + { + "author_name": "Thomas Creger", + "author_inst": "Center for AIDS Research, Heersink School of Medicine, University of Alabama at Birmingham" + }, + { + "author_name": "Aadia Rana", + "author_inst": "Division of Infectious Disease, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham" + }, + { + "author_name": "Michael J Mugavero", + "author_inst": "Division of Infectious Disease, Department of Medicine, Heersink School of Medicine, University of Alabama at Birmingham; Center for AIDS Research, Heersink Sch" + }, + { + "author_name": "Suzanne E. Judd", + "author_inst": "Center for the Study of Community Health, School of Public Health, University of Alabama at Birmingham" + }, + { + "author_name": "- COVID COMET RADXUP Team", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.01.31.23285232", "rel_title": "Cohort profile: Virus Watch: Understanding community incidence, symptom profiles, and transmission of COVID-19 in relation to population movement and behaviour", @@ -105113,45 +106846,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.30.23285171", - "rel_title": "Evaluation of a Commercially Available Rapid RT-PCR Assay's Detection of SARS-CoV-2 Novel Variants", - "rel_date": "2023-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.30.23285171", - "rel_abs": "Rapid molecular diagnostic tests have been critical in the response to the COVID-19 pandemic. It is important to evaluate the ability of these assays to identify variants of concern, particularly across varying collection and storage conditions. Nasal swabs positive for Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.167.2), Gamma (P.1), or Omicron (B.1.1.529) variants of concern (VOCs) were stored in TE buffer and viral transport media (VTM). We evaluated the sensitivity of the Cepheid Xpert(R) Xpress SARS-CoV-2 assay in detecting VOC samples and validated TE buffer for use with the assay. Testing of known VOC positives revealed no substantial reduction of PCR sensitivity. Comparison of TE and VTM samples also revealed no reduction in performance when using TE buffer, validating the use of TE buffer to store SARS-CoV-2 samples. SARS-CoV-2 VOCs collected and stored across various conditions can be detected by the Cepheid Xpert(R) Xpress SARS-CoV-2 assay.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Lewis Back", - "author_inst": "University of Washington" - }, - { - "author_name": "Jennifer K Logue", - "author_inst": "University of Washington" - }, - { - "author_name": "Caitlin Wolf", - "author_inst": "University of Washington" - }, - { - "author_name": "Peter D. Han", - "author_inst": "Brotman Baty Institute" - }, - { - "author_name": "Lea M Starita", - "author_inst": "University of Washington" - }, - { - "author_name": "Helen Chu", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.01.31.23285228", "rel_title": "Road networks to explore COVID-19 infection", @@ -106858,6 +108552,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.01.26.23285076", + "rel_title": "The impact of vaccination frequency on COVID-19 public health outcomes: A model-based analysis", + "rel_date": "2023-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.26.23285076", + "rel_abs": "While the rapid deployment of SARS-CoV-2 vaccines had a significant impact on the ongoing COVID-19 pandemic, rapid viral immune evasion and waning neutralizing antibody titers have degraded vaccine efficacy. Nevertheless, vaccine manufacturers and public health authorities have a number of levers at their disposal to maximize the benefits of vaccination. Here, we use an agent-based modeling framework coupled with the outputs of a population pharmacokinetic model to examine the impact of boosting frequency and durability of vaccinal response on vaccine efficacy. Our work suggests that repeated dosing at frequent intervals (multiple times a year) may offset the degradation of vaccine efficacy, preserving their utility in managing the ongoing pandemic. Our work relies on assumptions about antibody accumulation and the tolerability of repeated vaccine doses. Given the practical significance of potential improvements in vaccinal utility, clinical research to better understand the effects of repeated vaccination would be highly impactful. These findings are particularly relevant as public health authorities worldwide seek to reduce the frequency of boosters to once a year or less. Our work suggests practical recommendations for vaccine manufacturers and public health authorities and draws attention to the possibility that better outcomes for SARS-CoV-2 public health remain within reach.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Madison Stoddard", + "author_inst": "Fractal Therapeutics" + }, + { + "author_name": "Lin Yuan", + "author_inst": "Fractal Therapeutics" + }, + { + "author_name": "Sharanya Sarkar", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Debra Van Egeren", + "author_inst": "Stanford University" + }, + { + "author_name": "Shruthi Mangalaganesh", + "author_inst": "Monash University" + }, + { + "author_name": "Ryan P. Nolan", + "author_inst": "Halozyme Therapeutics" + }, + { + "author_name": "Michael S. Rogers", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Greg Hather", + "author_inst": "Sage Therapeutics" + }, + { + "author_name": "Laura F. White", + "author_inst": "Boston University" + }, + { + "author_name": "Arijit Chakravarty", + "author_inst": "Fractal Therapeutics" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.01.24.23284947", "rel_title": "What interventions or best practice are there to support people with Long COVID, or similar post-viral conditions or conditions characterised by fatigue, to return to normal activities: a rapid review", @@ -107071,69 +108820,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.24.23284952", - "rel_title": "Exploring the Transmission Dynamics of the COVID-19 Outbreaks after Dec. 2022 in Shaanxi Province, China: Analysis of Baseline Data from A Large Scale Cohort", - "rel_date": "2023-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.24.23284952", - "rel_abs": "BackgroundsThe goal of this study is to explore the transmission dynamics for recent large-scale COVID-19 outbreaks in Shaanxi Province on the Chinese mainland. Furthermore, the potential effects of the Spring Festival travel rush on the ongoing COVID-19 pandemic were depicted.\n\nMethodsThis study uses baseline data from a large cohort to investigate the characteristics of the recent COVID-19 epidemic in Shaanxi province. A cluster sampling method was used to recruit the study participants during the COVID-19 pandemic in Shaanxi province since Dec. 1st, 2022. A total of 44 sampling cluster (11 village in rural areas and 33 residences in urban areas) were chosen for enrollment of study participants. A self-developed questionnaire was applied to data collection of socio-demographic and COVID-19 pandemic related information.\n\nResultsA total of 14,744 study participants were enrolled in the baseline survey and 12,111 completed survey data were extracted for analysis. The cumulative infection attack rate (IAR) of COVID-19 among the study participants was 84.7%. The cumulative IAR in urban and rural areas were 85.6% and 83.7%, respectively. A peak of COVID-19 self-reported diagnosis could be observed from Dec. 15th, 2022 to Jan. 1st, 2023 in the provincial level. Beside this major peak of the recent epidemic (around Dec.20th, 2022), a small but steep rise could also be identified between Jan 13th to 14th, 2023. Individuals who escaped the first wave of COVID-19 outbreaks may face danger of infection from returnees during the 2023 Spring Festival.\n\nConclusionAccording to the COVID-19 cumulative IAR data, the herd community was primarily achieved in Shaanxi provinces urban and rural areas. The epidemic in Shaanxi province has been exacerbated by mass population movement during the Spring Festival travel rush in both urban and rural areas. Further surveillance should be performed to monitor the spread of SARS-CoV-2 infections.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Tianxiao Zhang", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Baibing Mi", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Mingwang Shen", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Yunpeng Nian", - "author_inst": "Shaanxi Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Suixia Cao", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Jingchun Liu", - "author_inst": "Xi'an Jiaotong Universtiy" - }, - { - "author_name": "Hao Huang", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Zhongxi Wei", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Lixi Liu", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Qian Wu", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Yi Zhang", - "author_inst": "Shaanxi Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Shaobai Zhang", - "author_inst": "Xi'an Jiaotong University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.01.27.23285082", "rel_title": "COVID-19-related burnout reduces COVID-19 vaccination intention in cardiac patients: a cross-sectional study in Greece", @@ -108668,6 +110354,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.21.23284592", + "rel_title": "TONSILS ARE MAJOR SITES OF PROLONGED SARS-COV-2 INFECTION IN CHILDREN", + "rel_date": "2023-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.21.23284592", + "rel_abs": "In the present study, we show that SARS-CoV-2 can infect palatine tonsils and adenoids in children without symptoms of COVID-19, with no history of recent upper airway infection. We studied 48 children undergoing tonsillectomy due to snoring/OSA or recurrent tonsillitis between October 2020 and September 2021. Briefly, nasal cytobrush (NC), nasal wash (NW) and tonsillar tissue fragments obtained at surgery were tested by RT-PCR, immunohistochemistry (IHC), flow cytometry and neutralization assay. We detected the presence of SARS-CoV-2 in at least one specimen tested in 25% of patients (20% in palatine tonsils and 16.27% in adenoids, 10.41% of NC and 6.25% of NW). Importantly, in 2 of the children there was evidence of laboratory-confirmed acute infection 2 and 5 months before surgery. IHC revealed the presence of SARS-CoV-2 nucleoprotein in epithelial surface and in lymphoid cells in both extrafollicular and follicular regions, in adenoids and palatine tonsils. Flow cytometry showed that CD20+ B lymphocytes were the most infected phenotypes by SARS-CoV-2 NP, followed by CD4+ and CD8+ T lymphocytes, and CD14+ macrophages and dendritic cells. Additionally, IF indicated that SARS-CoV-2-infected tonsillar tissues had increased expression of ACE2 and TMPRSS2. NGS sequencing demonstrated the presence of different SARS CoV-2 variants in tonsils from different tissues. SARS-CoV-2 antigen detection was not restricted to tonsils, but was also detected in nasal cells from the olfactory region. In conclusion, palatine tonsils and adenoids are sites of prolonged infection by SARS-CoV-2 in children, even without COVID-19 symptoms.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Thais Melquiades", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Ronaldo Martins", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Carol Miura", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Maria Vitoria Oliveira", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Murilo Cassiano", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Tamara Rodrigues", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Flavio Veras", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Josane Freitas Souza", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Rogerio Gomes", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Glaucia Almeida", + "author_inst": "Ribeirao Preto Medical Scholl - University of Sao Paulo" + }, + { + "author_name": "Stella Rezende Melo", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Gabriela Conde", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Matheus Dias", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Fabiano Capato", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Maria Lucia Silva", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Veridiana Barros", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Lucas Carenzi", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Dario S Zamboni", + "author_inst": "Universidade de Sao Paulo, School of Medicine Ribeirao Preto" + }, + { + "author_name": "Daniel Macedo", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Edwin Tamashiro", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Wilma Anselmo-Lima", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Fabiana Cardoso Valera", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + }, + { + "author_name": "Eurico Arruda", + "author_inst": "University of Sao Paulo School of Medicine, Ribeirao Preto, Brazil" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.01.22.23284881", "rel_title": "Second monovalent SARS-CoV-2 mRNA booster restores Omicron-specific neutralizing activity in both nursing home residents and health care workers", @@ -108849,93 +110642,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.01.25.525485", - "rel_title": "Long-term respiratory mucosal immune memory to SARS-CoV-2 after infection and vaccination", - "rel_date": "2023-01-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.25.525485", - "rel_abs": "Respiratory mucosal immunity induced by vaccination is vital for protection from coronavirus infection in animal models. In humans, SARS-CoV-2 immunity has been studied extensively in blood. However, the capacity of peripheral vaccination to generate sustained humoral and cellular immunity in the lung mucosa, and how this is influenced by prior SARS-CoV-2 infection, is unknown. Bronchoalveolar lavage samples obtained from vaccinated donors with or without prior infection revealed enrichment of spike-specific antibodies, class-switched memory B cells and T cells in the lung mucosa compared to the periphery in the setting of hybrid immunity, whereas in the context of vaccination alone, local anti-viral immunity was limited to antibody responses. Spike-specific T cells persisted in the lung mucosa for up to 5 months post-vaccination and multi-specific T cell responses were detected at least up to 11 months post-infection. Thus, durable lung mucosal immunity against SARS-CoV-2 seen after hybrid exposure cannot be achieved by peripheral vaccination alone, supporting the need for vaccines targeting the airways.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Elena Mitsi", - "author_inst": "Liverpool School of Tropical Medicine/ Oxford University" - }, - { - "author_name": "Mariana O. Diniz", - "author_inst": "UCL" - }, - { - "author_name": "Jesus Reine", - "author_inst": "Oxford University" - }, - { - "author_name": "Andrea M Collins", - "author_inst": "LSTM" - }, - { - "author_name": "Ryan Robinson", - "author_inst": "LSTM" - }, - { - "author_name": "Angela Hyder-Wright", - "author_inst": "LSTM" - }, - { - "author_name": "Madlen Farrar", - "author_inst": "LSTM" - }, - { - "author_name": "Konstantinos Liatsikos", - "author_inst": "LSTM" - }, - { - "author_name": "Josh Hamilton", - "author_inst": "LSTM" - }, - { - "author_name": "Onyia Onyema", - "author_inst": "LSTM" - }, - { - "author_name": "Britta C Urban", - "author_inst": "LSTM" - }, - { - "author_name": "Carla Solorzano", - "author_inst": "Oxford University" - }, - { - "author_name": "Teresa Lambe", - "author_inst": "Oxford University" - }, - { - "author_name": "Simon J Draper", - "author_inst": "Oxford University" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute For Allergy & Immunology" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Allergy & Immunology" - }, - { - "author_name": "Mala K Maini", - "author_inst": "UCL" - }, - { - "author_name": "Daniela M Ferreira", - "author_inst": "Oxford University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.01.25.524586", "rel_title": "A role for Toll-like receptor 3 in lung vascular remodeling associated with SARS-CoV-2 infection", @@ -109886,7 +111592,7 @@ "rel_date": "2023-01-23", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.22.23284880", - "rel_abs": "With the growing amount of COVID-19 cases, especially in developing countries with limited medical resources, it is essential to accurately and efficiently diagnose COVID-19. Due to characteristic ground-glass opacities (GGOs) and other types of lesions being present in both COVID-19 and other acute lung diseases, misdiagnosis occurs often: 26.6% of the time in manual interpretations of CT scans. Current deep-learning models can identify COVID-19 but cannot distinguish it from other common lung diseases like bacterial pneumonia. Concretely, COVision is a deep-learning model that can differentiate COVID-19 from other common lung diseases, with high specificity using CT scans and other clinical factors. COVision was designed to minimize overfitting and complexity by decreasing the number of hidden layers and trainable parameters while still achieving superior performance. Our model consists of two parts: the CNN which analyzes CT scans and the CFNN (clinical factors neural network) which analyzes clinical factors such as age, gender, etc. Using federated averaging, we ensembled our CNN with the CFNN to create a comprehensive diagnostic tool. After training, our CNN achieved an accuracy of 95.8% and our CFNN achieved an accuracy of 88.75% on a validation set. We found a statistical significance that COVision performs better than three independent radiologists with at least 10 years of experience, especially in differentiating COVID-19 from pneumonia. We analyzed our CNN activation maps through Grad-CAMs and found that lesions in COVID-19 presented peripherally, closer to the pleura, whereas pneumonia lesions presented centrally.", + "rel_abs": "With the growing amount of COVID-19 cases, especially in developing countries with limited medical resources, it is essential to accurately and efficiently diagnose COVID-19. Due to characteristic ground-glass opacities (GGOs) and other types of lesions being present in both COVID-19 and other acute lung diseases, misdiagnosis occurs often -- 26.6% of the time in manual interpretations of CT scans. Current deep-learning models can identify COVID-19 but cannot distinguish it from other common lung diseases like bacterial pneumonia. Concretely, COVision is a deep-learning model that can differentiate COVID-19 from other common lung diseases, with high specificity using CT scans and other clinical factors. COVision was designed to minimize overfitting and complexity by decreasing the number of hidden layers and trainable parameters while still achieving superior performance. Our model consists of two parts: the CNN which analyzes CT scans and the CFNN (clinical factors neural network) which analyzes clinical factors such as age, gender, etc. Using federated averaging, we ensembled our CNN with the CFNN to create a comprehensive diagnostic tool. After training, our CNN achieved an accuracy of 95.8% and our CFNN achieved an accuracy of 88.75% on a validation set. We found a statistical significance that COVision performs better than three independent radiologists with at least 10 years of experience, especially in differentiating COVID-19 from pneumonia. We analyzed our CNNs activation maps through Grad-CAMs and found that lesions in COVID-19 presented peripherally, closer to the pleura, whereas pneumonia lesions presented centrally.", "rel_num_authors": 2, "rel_authors": [ { @@ -110494,6 +112200,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.01.20.23284607", + "rel_title": "Electronic data review, client reminders, and expanded clinic hours for improving cervical cancer screening rates after COVID19 pandemic shutdowns: a multi-component quality improvement program", + "rel_date": "2023-01-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.20.23284607", + "rel_abs": "ObjectiveTo improve cervical cancer screening (CCS) rates, the East Boston Neighborhood Health Center (EBNHC) implemented a Quality Improvement (QI) initiative from March to August 2021.\n\nMethodsStaff training was provided. A 21-provider team validated overdue CCS indicated by electronic medical record data. To improve screening, CCS-only sessions were created during regular clinic hours (n=5) and weekends/evenings (n=8). Patients were surveyed on their experience.\n\nResults6126 charts were reviewed. Of the list of overdue patients, outreach was performed to 1375 patients to schedule the 13 sessions. A total of 459 (33%) of patients completed screening, 622 (45%) could not be reached, and 203 (15%) canceled or missed appointments. The proportion of total active patients who were up to date with CCS increased from 68% in March to 73% in August 2021. Survey results indicated high patient satisfaction, and only 42% of patients would have scheduled CCS without outreach.\n\nConclusionsThe creation of a validated patient chart list and extra clinical sessions devoted entirely to CCS improved up-to-date CCS rates. However, high rates of unsuccessful outreach and cancelations limited sustainability. This information can be used by other community health centers to optimize clinical workflows for CCS.\n\nFundingAll funding was internal from EBNHC Adult Medicine, Family Medicine, and Womens Health Departments.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Sue Ghosh", + "author_inst": "East Boston Neighborhood Health Center" + }, + { + "author_name": "Jackie Fantes", + "author_inst": "East Boston Neighborhood Health Center" + }, + { + "author_name": "Karin Leschly", + "author_inst": "East Boston Neighborhood Health Center" + }, + { + "author_name": "Julio Mazul", + "author_inst": "East Boston Neighborhood Health Center" + }, + { + "author_name": "Rebecca B Perkins", + "author_inst": "Boston University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2023.01.21.23284855", "rel_title": "Safety of bivalent omicron-containing mRNA-booster vaccines: a nationwide cohort study", @@ -110679,73 +112420,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2023.01.19.524762", - "rel_title": "Induction of SARS-CoV-2 N-specific CD8+ T cell immunity in lungs by engineered extracellular vesicles associates with strongly impaired viral replication", - "rel_date": "2023-01-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.19.524762", - "rel_abs": "Induction of effective immunity in lungs should be a pre-requisite for any vaccine designed to control the severe pathogenic effects generated by respiratory infectious agents. In the case of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV)-2 infection, vaccination is expected to associate with significant inhibition of viral replication in lungs. We recently provided evidence that the generation of endogenous extracellular vesicles (EVs) engineered for the incorporation of SARS-CoV-2 Nucleocapsid (N) protein can protect K18-hACE2 transgenic mice from the lethal intranasal infection with the ancestral Wuhan isolate. Actually, it was widely demonstrated that these transgenic mice succumb to SARS-CoV-2 intranasal infection mainly as a consequence of the viral invasiveness of central nervous system, a pathogenetic mechanism almost absent in humans. On the other hand, K18-hACE2 transgenic mice support viral replication in lungs, an event strictly mirroring the major pathogenic signature linked to the severe disease in humans. However, nothing is known about the ability of N-specific CD8+ T cell immunity induced by engineered EVs in controlling viral replication in lungs. To fill the gap, we investigated the immunity generated in lungs by N-engineered EVs in terms of induction of N-specific effectors and resident memory CD8+ T lymphocytes before and after virus challenge carried out three weeks and three months after boosting. At the same time points, viral replication extents in lungs were evaluated. We found that three weeks after second immunization, virus replication was reduced in mice best responding to vaccination by more than 3-logs compared to control group. The impaired viral replication matched with a reduced induction of Spike-specific CD8+ T lymphocytes. The antiviral effect appeared similarly strong when the viral challenge was carried out 3 months after boosting. This inhibitory effect associated with the persistence of a N-specific CD8+ T-resident memory lymphocytes in lungs of N-immunized mice. In view of the quite conserved sequence of the N protein among SARS-CoV-2 variants, these results support the idea that a vaccine strategy focused on the induction of anti-N CD8+ T cell immunity in lungs has the potential to control the replication of emerging variants.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Francesco Manfredi", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Chiara Chiozzini", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Flavia Ferrantelli", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Patrizia Leone", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "katherina Pugliese", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Massimo Spada", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Antonio Di Virgilio", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Andrea Giovannelli", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Mauro Valeri", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Andrea Cara", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Zuleika Michelini", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Mauro Andreotti", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Maurizio Federico", - "author_inst": "Istituto Superiore di Sanita" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.01.19.524784", "rel_title": "Extremely potent pan-sarbecovirus neutralizing antibodies generated by immunization of macaques with an AS03-adjuvanted monovalent subunit vaccine against SARS-CoV-2", @@ -112356,6 +114030,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.16.23284634", + "rel_title": "Prediction of Long COVID Based on Severity of Initial COVID-19 Infection: Differences in predictive feature sets between hospitalized versus non-hospitalized index infections", + "rel_date": "2023-01-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.16.23284634", + "rel_abs": "Long COVID is recognized as a significant consequence of SARS-COV2 infection. While the pathogenesis of Long COVID is still a subject of extensive investigation, there is considerable potential benefit in being able to predict which patients will develop Long COVID. We hypothesize that there would be distinct differences in the prediction of Long COVID based on the severity of the index infection, and use whether the index infection required hospitalization or not as a proxy for developing predictive models. We divide a large population of COVID patients drawn from the United States National Institutes of Health (NIH) National COVID Cohort Collaborative (N3C) Data Enclave Repository into two cohorts based on the severity of their initial COVID-19 illness and correspondingly trained two machine learning models: the Long COVID after Severe Disease Model (LCaSDM) and the Long COVID after Mild Disease Model (LCaMDM). The resulting models performed well on internal validation/testing, with a F1 score of 0.94 for the LCaSDM and 0.82 for the LCaMDM. There were distinct differences in the top 10 features used by each model, possibly reflecting the differences in type and amount of pathophysiological data between the hospitalized and non-hospitalized patients and/or reflecting different pathophysiological trajectories in the development of Long COVID. Of particular interest was the importance of Plant Hardiness Zone in the feature set for the LCaMDM, which may point to a role of climate and/or sunlight in the progression to Long COVID. Future work will involve a more detailed investigation of the potential role of climate and sunlight, as well as refinement of the predictive models as Long COVID becomes increasingly parsed into distinct clinical phenotypes.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Damien Socia", + "author_inst": "University of Vermont Larner College of Medicine" + }, + { + "author_name": "Dale Larie", + "author_inst": "University of Vermont Larner College of Medicine" + }, + { + "author_name": "Solomon Feuerwerker", + "author_inst": "University of Vermont Larner College of Medicine" + }, + { + "author_name": "Gary An", + "author_inst": "University of Vermont" + }, + { + "author_name": "Chase Cockrell", + "author_inst": "University of Vermont Larner College of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.01.14.23284558", "rel_title": "Determinants of protection against SARS-CoV-2 Omicron BA.1 and Delta infections in fully vaccinated outpatients", @@ -112553,29 +114262,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.01.16.23284640", - "rel_title": "Post-pandemic modeling of COVID-19: Waning immunity determines recurrence frequency", - "rel_date": "2023-01-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.16.23284640", - "rel_abs": "There are many factors in the current phase of the COVID-19 pandemic that signal the need for new modeling ideas. In fact, most traditional infectious disease models do not address adequately the waning immunity, in particular as new emerging variants have been able to brake the immune shield acquired either by previous infection by a different strain of the virus, or by inoculation of vaccines not effective for the current variant. Furthermore, in a post-pandemic landscape in which reporting is no longer a default, it is impossible to have reliable quantitative data at the population level. Our contribution to COVID-19 post-pandemic modeling is a simple mathematical predictive model along the age-distributed population framework, that can take into account the waning immunity in a transparent and easily controllable manner. Numerical simulations show that under static conditions, the model produces periodic solutions that are qualitatively similar to the reported data, with the period determined by the immunity waning profile. Evidence from the mathematical model indicates that the immunity dynamics is the main factor in the recurrence of infection spikes, however, irregular perturbation of the transmission rate, due to either mutations of the pathogen or human behavior, may result in suppression of recurrent spikes, and irregular time intervals between consecutive peaks. The spike amplitudes are sensitive to the transmission rate and vaccination strategies, but also to the skewness of the profile describing the waning immunity, suggesting that these factors should be taken into consideration when making predictions about future outbreaks.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Daniela Calvetti", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Erkki Somersalo", - "author_inst": "Case Western Reserve University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.01.16.23284598", "rel_title": "Determinants of Covid-19 vaccine uptake among the elderly aged 58 years and above in Kericho County, Kenya: Institution based cross sectional survey.", @@ -114290,6 +115976,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.01.13.23284341", + "rel_title": "Long-term systemic and mucosal SARS-CoV-2 IgA response and its association with persistent smell and taste disorders.", + "rel_date": "2023-01-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.13.23284341", + "rel_abs": "Current approved COVID-19 vaccines, notably mRNA and adenoviral vectored technologies, still fail to fully protect against infection and transmission of various SARS-CoV-2 variants. The mucosal immunity at the upper respiratory tract represents the first line of defense against respiratory viruses such as SARS-CoV-2 and is thus critical to develop vaccine blocking human-to-human transmission. We measured systemic and mucosal Immunoglobulin A (IgA) response in serum and saliva from 133 healthcare workers from Percy teaching military hospital following a mild infection (SARS-CoV-2 Wuhan strain, n=58) or not infected (n=75), and after SARS-CoV-2 vaccination (Vaxzevria(R)/Astrazeneca and/or Comirnaty(R)/Pfizer). While serum anti-SARS-CoV-2 Spike IgA response lasted up to 16 months post-infection, IgA response in saliva had mostly fallen to baseline level at 6 months post-infection. Vaccination could reactivate the mucosal response generated by prior infection, but failed to induce a significant mucosal IgA response by itself. As breakthrough infections have been correlated with IgA levels, other vaccine platforms inducing a better mucosal immunity are needed to control COVID-19 infection in the future. Early post-COVID-19 serum anti-Spike-NTD IgA titer correlated with seroneutralization titers. Interestingly, its saliva counterpart positively correlated with persistent smell and taste disorders more than one year after mild COVID-19, and could potentially be used as an early prognosis biomarker.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jessica Denis", + "author_inst": "Institut de Recherche Biomedicale des Armees" + }, + { + "author_name": "Annabelle Garnier", + "author_inst": "Institut de Recherche Biomedicale des Armees" + }, + { + "author_name": "Laurence Cheutin", + "author_inst": "Institut de Recherche Biomedicale des Armees" + }, + { + "author_name": "Audrey Ferrier", + "author_inst": "Institut de Recherche Biomedicale des Armees" + }, + { + "author_name": "Hawa Timera", + "author_inst": "Institut de Recherche Biomedicale des Armees" + }, + { + "author_name": "Fanny Jarjaval", + "author_inst": "Institut de Recherche Biomedicale des Armees" + }, + { + "author_name": "Carine Hejl", + "author_inst": "Hopital d'instruction des armees Percy, Ecole du Val-de-Grace" + }, + { + "author_name": "Emmanuelle Billon-Denis", + "author_inst": "Institut de Recherche Biomedicale des Armees, Institut Pasteur de Paris" + }, + { + "author_name": "- Percy ImmunoCovid group", + "author_inst": "" + }, + { + "author_name": "Damien Ricard", + "author_inst": "Institut de Recherche Biomedicale des Armees, Ecole du Val-de-Grace, Centre Borelli ENS Paris-Saclay" + }, + { + "author_name": "Jean-Nicolas Tournier", + "author_inst": "Institut de Recherche Biomedicale des Armees, Ecole du Val-de-Grace, Institut Pasteur de Paris" + }, + { + "author_name": "Aurelie Trignol", + "author_inst": "Institut de Recherche Biomedicale des Armees, Universite Paris Cite" + }, + { + "author_name": "Marie Mura", + "author_inst": "Institut de Recherche Biomedicale des Armees, Institut Pasteur de Paris" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.01.12.23284489", "rel_title": "Cross-sectional Ct distributions from qPCR tests can provide an early warning signal for the spread of COVID-19 in communities", @@ -114451,37 +116204,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.01.13.23284467", - "rel_title": "Coverage of primary and booster vaccination against COVID-19 by socioeconomic level: A nationwide cross-sectional registry study", - "rel_date": "2023-01-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.13.23284467", - "rel_abs": "High and equitable COVID-19 vaccination coverage is important for pandemic control and prevention of health inequity. However, little is known about socioeconomic correlates of booster vaccination coverage. In this cross-sectional study of all Norwegian adults in the national vaccination program (N = 4,190,655), we use individual-level registry data to examine coverage by levels of household income and education of primary ([≥]2 doses) and booster ([≥]3 doses) vaccination against COVID-19. We stratify the analyses by age groups with different booster recommendations and report relative risk ratios (RR) for vaccination by 25 August 2022. In the 18-44 years group, individuals with highest vs. lowest education had 94% vs. 79% primary coverage (adjusted RR (adjRR) 1.15, 95%CI 1.14-1.15) and 67% vs. 38% booster coverage (adjRR 1.55, 95% CI 1.55-1.56), while individuals with highest vs. lowest income had 94% vs. 81% primary coverage (adjRR 1.10, 95%CI 1.10-1.10) and 60% vs. 43% booster coverage (adjRR 1.23, 95%CI 1.22-1.24). In the[≥] 45 years group, individuals with highest vs. lowest education had 96% vs. 92% primary coverage (adjRR 1.02, 95%CI 1.02-1.02) and 88% vs. 80% booster coverage (adjRR 1.09, 95%CI 1.09-1.09), while individuals with highest vs. lowest income had 98% vs. 82% primary coverage (adjRR 1.16, 95%CI 1.16-1.16) and 92% vs. 64% booster coverage (adjRR 1.33, 95%CI 1.33-1.34). In conclusion, we document large socioeconomic inequalities in COVID-19 vaccination coverage, especially for booster vaccination, even though all vaccination was free-of-charge. The results highlight the need to tailor information and to target underserved groups for booster vaccination.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Bo Terning Hansen", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Angela S Labberton", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Prabhjot Kour", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Kristian B Kraft", - "author_inst": "Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.01.12.23284499", "rel_title": "A Scoping Review of Factors used to Explain Disparities in COVID-19 Vaccination Intentions and Uptake among People of Color: United States, December 1, 2020-April 30, 2021", @@ -115976,6 +117698,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.01.09.23284284", + "rel_title": "Using early detection data to estimate the date of emergence of an epidemic outbreak", + "rel_date": "2023-01-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.09.23284284", + "rel_abs": "While the first infection by an emerging disease is often unknown, information on early cases can be used to date it, which is of great interest to trace the diseases origin and understand early infection dynamics. In the context of the COVID-19 pandemic, previous studies have estimated the date of emergence (e.g., first human SARS-CoV-2 infection in Wuhan, emergence of the Alpha variant in the UK) using mainly genomic data. Another dating attempt only relied on case data, estimating a date of emergence using a non-Markovian stochastic model and considering the first case detection. Here, we extend this stochastic approach to use available data of the whole early case dynamics. Our model provides estimates of the delay from the first infection to the N th reported case. We first validate our model using data concerning the spread of the Alpha SARS-CoV-2 variant in the UK. Our results suggest that the first Alpha infection occurred on (median) August 20 (95% interquantile range across retained simulations, IqR: July 20-September 4), 2020. Next, we apply our model to data on the early reported cases of COVID-19. We used data on the date of symptom onset up to mid-January, 2020. We date the first SARS-CoV-2 infection in Wuhan at (median) November 26 (95%IqR: October 31-December 7), 2019. Our results fall within ranges previously estimated by studies relying on genomic data. Our population dynamics-based modelling framework is generic and flexible, and thus can be applied to estimate the starting time of outbreaks, in contexts other than COVID-19, as long as some key parameters (such as transmission and detection rates) are known.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sof\u00eda Jij\u00f3n", + "author_inst": "Sorbonne Universit\u00e9" + }, + { + "author_name": "Peter Czuppon", + "author_inst": "University of M\u00fcnster" + }, + { + "author_name": "Fran\u00e7ois Blanquart", + "author_inst": "Coll\u00e8ge de France" + }, + { + "author_name": "Florence D\u00e9barre", + "author_inst": "CNRS" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.01.10.23284410", "rel_title": "Addressing spatial misalignment in population health research: a case study of US congressional district political metrics and county health data", @@ -116145,61 +117898,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.01.11.23284437", - "rel_title": "A cross sectional survey examining the association of clinician characteristics with perceived changes in cervical cancer screening and colposcopy practice during the COVID-19 pandemic", - "rel_date": "2023-01-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.11.23284437", - "rel_abs": "BackgroundThe COVID-19 pandemic led to reductions in cervical cancer screening and colposcopy. Therefore, in this mixed method study we explored perceived pandemic-related practice changes to cervical cancer screenings and colposcopies.\n\nMethodsIn 2021, a national sample of 1,251 clinicians completed surveys, including 675 clinicians who performed colposcopy; a subset (n=55) of clinicians completed qualitative interviews.\n\nResultsNearly half of all clinicians reported they were currently performing fewer cervical cancer screenings (47%) and colposcopies (44% of those who perform the procedure) than before the pandemic. About one-fifth (18.6%) of colposcopists reported performing fewer LEEPs than prior to the pandemic. Binomial regression analyses indicated that older, non-White, internal medicine and family medicine clinicians (compared to OB-GYNs), and those practicing in community health centers (compared to private practice) had higher odds of reporting reduced screening. Among colposcopists, males, internal medicine physicians, those practicing in community health centers, and in the South had higher odds of reporting reduced colposcopies. Qualitative interviews highlighted pandemic-related care disruptions and lack of tracking systems to identify overdue screenings.\n\nConclusionsReductions in cervical cancer screening and colposcopy among nearly half of clinicians more than one year into the pandemic raise concerns that inadequate screening and follow-up will lead to future increases in preventable cancers.\n\nFundingThis study was funded by the American Cancer Society, who had no role in the studys design, conduct, or reporting.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Lindsay Fuzzell", - "author_inst": "Moffitt Cancer Center" - }, - { - "author_name": "Naomi C Brownstein", - "author_inst": "Medical University of South Carolina" - }, - { - "author_name": "Holly B Fontenot", - "author_inst": "University of Hawaii at Manoa" - }, - { - "author_name": "Paige Lake", - "author_inst": "Moffitt Cancer Center" - }, - { - "author_name": "Alexandra Michel", - "author_inst": "University of Hawaii at Manoa" - }, - { - "author_name": "Ashley Whitmer", - "author_inst": "Moffitt Cancer Center" - }, - { - "author_name": "Sarah L Rossi", - "author_inst": "Boston University" - }, - { - "author_name": "McKenzie McIntyre", - "author_inst": "Moffitt Cancer Center" - }, - { - "author_name": "Susan T Vadaparampil", - "author_inst": "Moffitt Cancer Center" - }, - { - "author_name": "Rebecca B Perkins", - "author_inst": "Boston University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2023.01.09.23284348", "rel_title": "Interleukin-1 receptor antagonist gene (IL1RN) variants modulate the cytokine release syndrome and mortality of SARS-CoV-2", @@ -117566,6 +119264,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.01.06.522349", + "rel_title": "Effects of Variants of Concern Mutations on the Force-Stability of the SARS-CoV-2:ACE2 Interface and Virus Transmissibility", + "rel_date": "2023-01-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.06.522349", + "rel_abs": "Viruses mutate under a variety of selection pressures, allowing them to continuously adapt to their hosts. Mutations in SARS-CoV-2 have shown effective evasion of population immunity and increased affinity to host factors, in particular to the cellular receptor ACE2. However, in the dynamic environment of the respiratory tract forces act on the binding partners, which raises the question whether not only affinity, but also force-stability of the SARS-CoV-2:ACE2 bond, might be a selection factor for mutations. Here, we use magnetic tweezers (MT) to study the effect of amino acid substitutions in variants of concern (VOCs) on RBD:ACE2 bond kinetics with and without external load. We find higher affinity for all VOCs compared to wt, in good agreement with previous affinity measurements in bulk. In contrast, Alpha is the only VOC that shows significantly higher force stability compared to wt. Investigating the RBD:ACE2 interactions with molecular dynamics simulations, we are able to rationalize the mechanistic molecular origins of this increase in force-stability. Our study emphasizes the diversity of contributions to the assertiveness of variants and establishes force-stability as one of several factors for fitness. Understanding fitness-advantages opens the possibility for prediction of likely mutations allowing rapid adjustment of therapeutics, vaccination, and intervention measures.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Magnus S. Bauer", + "author_inst": "Department of Physics and Center for NanoScience (CeNS), LMU Munich, 80799 Munich, Germany; Department of Chemical Engineering, Stanford University; Stanford, C" + }, + { + "author_name": "Sophia Gruber", + "author_inst": "Department of Physics and Center for NanoScience (CeNS), LMU Munich, 80799 Munich, Germany;" + }, + { + "author_name": "Adina Hausch", + "author_inst": "Center for Protein Assemblies, TUM School of Natural Sciences, Technical University of Munich, Germany;" + }, + { + "author_name": "Marcelo C.R. Melo", + "author_inst": "Department of Physics, Auburn University, Auburn, AL 36849, USA;" + }, + { + "author_name": "Priscila S.F.C. Gomes", + "author_inst": "Department of Physics, Auburn University, Auburn, AL 36849, USA;" + }, + { + "author_name": "Thomas Nicolaus", + "author_inst": "Department of Physics and Center for NanoScience (CeNS), LMU Munich, 80799 Munich, Germany;" + }, + { + "author_name": "Lukas F. Milles", + "author_inst": "Institute for Protein Design, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA;" + }, + { + "author_name": "Rafael C. Bernardi", + "author_inst": "Department of Physics, Auburn University, Auburn, AL 36849, USA;" + }, + { + "author_name": "Hermann E. Gaub", + "author_inst": "Department of Physics and Center for NanoScience (CeNS), LMU Munich, 80799 Munich, Germany;" + }, + { + "author_name": "Jan Lipfert", + "author_inst": "Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC Utrecht, The Netherlands;" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2023.01.08.523127", "rel_title": "Bivalent mRNA vaccine improves antibody-mediated neutralization of many SARS-CoV-2 Omicron lineage variants", @@ -117803,49 +119556,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2023.01.06.23284223", - "rel_title": "Nursing Intervention Analysis in COVID-19 Negative Pressure Isolation Wards and General Wards: Observational study", - "rel_date": "2023-01-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.06.23284223", - "rel_abs": "IntroductionWith the global spread of Coronavirus disease (COVID-19) and public health crisis, appropriate allocation of healthcare human resources has been necessitated. Although nursing practice takes up a larger part of medical practice in hospitals, the quantitative assessment of nursing care has not been investigated for human resource allocation in the medical field. The objective of this study to explore the time spent for each nursing intervention, and compared provided amount of nursing intervention between negative pressure isolation wards (NPIWs) and general wards (GWs) provided by COVID-19 hub hospitals.\n\nMethodsThis research is a time-motion (TM) observational study. Three trained external observers recorded their observations for every minute in 19 different work schedules in 2 NPIWs and 2 general respiratory wards. Observation items were chosen based on the standard operating guidelines of Integrated Nursing and Caring Services developed by the Ministry of Health and Welfare and National Health Insurance Service. The average nursing workload per shift was compared by calculating the sum of the spent time of three nurses staffed in each shift in each ward between two groups. In addition, to compare the amount of directed nursing care for patients between two types of wards, nursing work category was divided into directed and undirected nursing interventions.\n\nResultsIn the comparison of demographic characteristics of nursing workforce between two groups, there was no statistically significant difference (p>0.05 respectively). In both groups, the most time-consuming nursing work category was recording in three work shifts. The average duration of those work tasks was 312.5 minutes in NPIWs and 307 minutes (per 3 nurses) in GWs, having no significant difference (p>0.05). Of all nurse duties, the second most time-consuming work category was others (including changing to protective clothing) in NPIWs, and medication administration and transfusion in GWs. The mean duration of performing the category for others that include wearing PPE was 308 minutes in NPIWs and 160 minutes (per 3 nurses) in GWs, showing a significant difference (p<0.05). The greater amount of time was taken for hygiene management in isolation wards. Medication administration and transfusion and nursing assessment were more frequently performed in GWs, demonstrating a statistical significance. In the aggregated spent time for all duties including directed and undirected nursing care, the time spent for directed nursing care was 654 minutes longer in GWs than in NPIWs (per 3 nurses) in each work shift, displaying a significant difference.\n\nConclusionThis study provides the quantitative difference in time-consuming nursing works between NPIWs and GWs by direct observation. Recording was the most time-consuming nursing work category in both NPIWs and GWs. Considering nurses in each duty in GWs provided more directed nursing care than nurse in NIPWs, careful considerations are required in allocation of nursing workforce.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ho Heon Kim", - "author_inst": "Yonsei university" - }, - { - "author_name": "Hyunsoon Park", - "author_inst": "Department of nursing, Gumi University, Gyeongsangbuk-do, Republic of Korea" - }, - { - "author_name": "Mi sug Lee", - "author_inst": "Department of nursing, Bestian Hospital, Chungcheongbuk-do, Republic of Korea" - }, - { - "author_name": "Gyu Min Lee", - "author_inst": "Department of nursing, Chung Goo Sung Sim Hospital, Seoul, Republic of Korea" - }, - { - "author_name": "Hee Oh", - "author_inst": "Department of nursing, Ansan University, Gyeongsangbuk-do, Republic of Korea" - }, - { - "author_name": "Sung Hwangbo", - "author_inst": "Department of nursing student, Gumi University, Gyeongsangbuk-do, Republic of Korea" - }, - { - "author_name": "Sanghyuk Roh", - "author_inst": "Department of nursing student, Gumi University, Gyeongsangbuk-do, Republic of Korea" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nursing" - }, { "rel_doi": "10.1101/2023.01.05.23284239", "rel_title": "Counting Cases and Deaths by Age Tells Us About COVID-19 Infectious and Lethal Components", @@ -119844,6 +121554,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.01.04.522762", + "rel_title": "Urban birds become less fearful following COVID-19 reopenings", + "rel_date": "2023-01-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.04.522762", + "rel_abs": "Following the COVID-19 pandemic, many people around the world stayed home, drastically altering human activity in cities. This exceptional moment provided researchers the opportunity to test how urban animals respond to human disturbance, in some cases testing fundamental questions on the mechanistic impact of urban behaviors on animal behavior. However, at the end of this \"anthropause,\" human activity returned to cities. How might each of these strong shifts affect wildlife in the short and long term? We focused on fear response, a trait essential to tolerating urban life. We measured flight initiation distance--at both individual and population-levels--for an urban bird before, during, and after the anthropause to examine if birds experienced longer-term changes after a year of lowered human presence. Dark-eyed juncos did not change fear levels during the anthropause, but they became drastically less fearful afterwards. These surprising and counter-intuitive findings, made possible by following the behavior of individuals over time, has led to a novel understanding that fear response can be driven by plasticity, yet not habituation-like processes. The pandemic-caused changes in human activity have shown that there is great complexity in how humans modify a behavioral trait fundamental to urban tolerance in animals.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Eleanor Diamant", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Ian MacGregor-Fors", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Daniel T Blumstein", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Pamela J Yeh", + "author_inst": "University of California Los Angeles" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "animal behavior and cognition" + }, { "rel_doi": "10.1101/2023.01.04.522794", "rel_title": "Targets and cross-reactivity of human T cell recognition of Common Cold Coronaviruses", @@ -120005,85 +121746,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.01.03.22284042", - "rel_title": "SARS-CoV-2 Reinfection is Preceded by Unique Biomarkers and Related to Initial Infection Timing and Severity: an N3C RECOVER EHR-Based Cohort Study", - "rel_date": "2023-01-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.03.22284042", - "rel_abs": "Although the COVID-19 pandemic has persisted for over 2 years, reinfections with SARS-CoV-2 are not well understood. We use the electronic health record (EHR)-based study cohort from the National COVID Cohort Collaborative (N3C) as part of the NIH Researching COVID to Enhance Recovery (RECOVER) Initiative to characterize reinfection, understand development of Long COVID after reinfection, and compare severity of reinfection with initial infection. We validate previous findings of reinfection incidence (5.9%), the occurrence of most reinfections during the Omicron epoch, and evidence of multiple reinfections. We present novel findings that Long COVID diagnoses occur closer to the index date for infection or reinfection in the Omicron BA epoch. We report lower albumin levels leading up to reinfection and a statistically significant association of severity between first infection and reinfection (chi-squared value: 9446.2, p-value: 0) with a medium effect size (Cramers V: 0.18, DoF = 4).", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Emily C Hadley", - "author_inst": "RTI International" - }, - { - "author_name": "Yun Jae Yoo", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Saaya V Patel", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Andrea G Zhou", - "author_inst": "University of Virginia" - }, - { - "author_name": "Bryan Laraway", - "author_inst": "TISLab" - }, - { - "author_name": "Rachel Wong", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Alexander J Preiss", - "author_inst": "RTI International" - }, - { - "author_name": "Rob Chew", - "author_inst": "RTI International" - }, - { - "author_name": "Hannah Davis", - "author_inst": "RECOVER Patient Led Research Collaborative (PLRC)" - }, - { - "author_name": "Christopher G Chute", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Emily Pfaff", - "author_inst": "UNC Chapel Hill" - }, - { - "author_name": "Johanna J Loomba", - "author_inst": "University of Virginia" - }, - { - "author_name": "Melissa Haendel", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Elaine L Hill", - "author_inst": "University of Rochester" - }, - { - "author_name": "Richard A Moffitt", - "author_inst": "Emory University" - }, - { - "author_name": "- the N3C and RECOVER Consortia", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.01.04.23284174", "rel_title": "Ethnic differences in the indirect impacts of the COVID-19 pandemic on clinical monitoring and hospitalisations for non-COVID conditions in England: An observational cohort study using OpenSAFELY", @@ -121902,6 +123564,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.01.01.522328", + "rel_title": "SARS-CoV-2 protein NSP2 enhances microRNA-mediated translational repression", + "rel_date": "2023-01-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.01.522328", + "rel_abs": "microRNAs (miRNAs) inhibit mRNA translation initiation by recruiting the GIGYF2/4EHP translation repressor complex to the mRNA 5 cap structure. Viruses utilise miRNAs to impair the host antiviral immune system and facilitate viral infection by expressing their own miRNAs or co-opting cellular miRNAs. We recently reported that the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encoded non-structural protein 2 (NSP2) interacts with GIGYF2. This interaction is critical for blocking translation of the Ifn1-b mRNA that encodes the cytokine Interferon-{beta}, and thereby impairs the host antiviral immune response. However, it is not known whether NSP2 also affects miRNA-mediated silencing. Here, we demonstrate the pervasive augmentation of the miRNA-mediated translational repression of cellular mRNAs by NSP2. We show that NSP2 interacts with Argonaute 2, the core component of the miRNA-Induced Silencing Complex (miRISC) and enhances the translational repression mediated by natural miRNA binding sites in the 3 UTR of cellular mRNAs. Our data reveal an additional layer of the complex mechanism by which SARS-CoV-2 and likely other coronaviruses manipulate the host gene expression program through co-opting the host miRNA-mediated silencing machinery.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Xu Zhang", + "author_inst": "McGill University" + }, + { + "author_name": "Reese Jalal Ladak", + "author_inst": "McGill University" + }, + { + "author_name": "Thomas Duchaine", + "author_inst": "McGill University" + }, + { + "author_name": "Nahum Sonenberg", + "author_inst": "McGill University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2023.01.02.522505", "rel_title": "Nanoparticle-Conjugated TLR9 Agonists Improve the Potency, Durability, and Breadth of COVID-19 Vaccines", @@ -122043,69 +123736,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2022.12.31.522389", - "rel_title": "Nirmatrelvir Resistance in SARS-CoV-2 Omicron_BA.1 and WA1 Replicons and Escape Strategies", - "rel_date": "2023-01-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.31.522389", - "rel_abs": "The antiviral component of Paxlovid, nirmatrelvir (NIR), forms a covalent bond with Cys145 of SARS-CoV-2 nsp5. To explore NIR resistance we designed mutations to impair binding of NIR over substrate. Using 12 Omicron (BA.1) and WA.1 SARS-CoV-2 replicons, cell-based complementation and enzymatic assays, we showed that in both strains, E166V imparted high NIR resistance ([~]55-fold), with major decrease in WA1 replicon fitness ([~]20-fold), but not BA.1 ([~]2-fold). WA1 replicon fitness was restored by L50F. These differences may contribute to a potentially lower barrier to resistance in Omicron than WA1. E166V is rare in untreated patients, albeit more prevalent in paxlovid-treated EPIC-HR clinical trial patients. Importantly, NIR-resistant replicons with E166V or E166V/L50F remained susceptible to a) the flexible GC376, and b) PF-00835231, which forms additional interactions. Molecular dynamics simulations show steric clashes between the rigid and bulky NIR t-butyl and {beta}-branched V166 distancing the NIR warhead from its Cys145 target. In contrast, GC376, through \"wiggling and jiggling\" accommodates V166 and still covalently binds Cys145. PF-00835231 uses its strategically positioned methoxy-indole to form a {beta}-sheet and overcome E166V. Drug design based on strategic flexibility and main chain-targeting may help develop second-generation nsp5-targeting antivirals efficient against NIR-resistant viruses.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Shuiyun Lan", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Grace Neilsen", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Ryan L Slack", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "William A Cantara", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Andres Emanuelli Castaner", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Zachary C Lorson", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Nicole D Lulkin", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Huanchun Zhang", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Jasper Lee", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Maria E Cilento", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Philip R. Tedbury", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Stefan G Sarafianos", - "author_inst": "Emory University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.12.29.522275", "rel_title": "An engineered ACE2 decoy broadly neutralizes Omicron subvariants and shows therapeutic effect in SARS-CoV-2-infected cynomolgus macaques", @@ -123532,6 +125162,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, + { + "rel_doi": "10.1101/2022.12.23.22283884", + "rel_title": "Changes in depression and anxiety among people with cognitive impairment and dementia during the COVID-19 pandemic: Analysis of the English Longitudinal Study of Ageing", + "rel_date": "2022-12-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.23.22283884", + "rel_abs": "BackgroundSome studies have identified declines in mental health over the course of the COVID-19 pandemic across the world and in different age groups, including older people. As anxiety and depression are common neuropsychiatric symptoms among people with dementia or mild cognitive impairment, the mental health experiences of older people during the pandemic should therefore take cognitive function into consideration. This should also be examined using quantitative measures that were assessed prior to the pandemic. This study addresses such gaps in the evidence base on depression and anxiety among older people with cognitive impairment before and throughout the COVID-19 pandemic.\n\nMethods and FindingsUsing data from the English Longitudinal Study of Ageing (ELSA) collected from 2018/19 to Nov/Dec 2020, we estimated changes in depression and anxiety for people aged 50+ in England across three cognitive function groups: no impairment, mild cognitive impairment, and dementia.\n\nWe found that depression (measured with CES-D score) worsened from 2018/19 to Nov/Dec 2020 for people with mild cognitive impairment (1.39 (95%CI: 1.29-1.49) to 2.16 (2.02-2.30)) or no impairment (1.17 (95%CI: 1.12-1.22) to 2.03 (1.96-2.10)). Anxiety, using a single-item rating of 0-10 also worsened among those with mild cognitive impairment (2.48 (2.30-2.66) to 3.14 (2.95-3.33)) or no impairment (2.20 (2.11-2.28) to 2.85 (2.77-2.95)). No statistically significant increases were found for those with dementia. Using a clinical cutoff for likely depression (CES-D[≥]4), we found statistically significant increases in the probability of likely clinical depression between 2018/19 and Nov/Dec 2020 for those with no impairment (0.110 (0.099-0.120) to 0.206 (0.191-0.222)) and those with mild impairment (0.139 (0.120-0.159) to 0.234 (0.204-0.263)).\n\nWe also found that differences according to cognitive function that existed before the pandemic were no longer present by June/July 2020, and there were no statistically significant differences in depression or anxiety among cognitive groups in Nov/Dec 2020.\n\nConclusionsOur findings on measures collected before and during the pandemic suggest a convergence in mental health across cognitive function groups during the pandemic. This suggests mental health services will need to meet an increased demand that will come from older adults, especially those not living with cognitive impairment or dementia. We also found little significant change in mental health outcomes among those with dementia; as their existing need for support will remain, policymakers and care practitioners will need to ensure this group continues to have equitable access to support for their mental health.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Brian Beach", + "author_inst": "University College London" + }, + { + "author_name": "Andrew Steptoe", + "author_inst": "UCL: University College London" + }, + { + "author_name": "Paola Zaninotto", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.12.21.22283740", "rel_title": "Prior infection- and/or vaccine-induced protection against Omicron BA.1, BA.2 and BA.4/BA.5-related hospitalisations in older adults: a test-negative case-control study in Quebec, Canada", @@ -123821,77 +125478,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.12.27.521979", - "rel_title": "Tissue protective role of Ganetespib in SARS-CoV-2-infected Syrian golden hamsters", - "rel_date": "2022-12-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.27.521979", - "rel_abs": "The emergence of new SARS-CoV-2 variants, capable of escaping the humoral immunity acquired by the available vaccines, together with waning immunity and vaccine hesitancy, challenges the efficacy of the vaccination strategy in fighting COVID-19. Improved therapeutic strategies are therefore urgently needed to better intervene particularly in severe cases of the disease. They should aim at controlling the hyper-inflammatory state generated upon infection, at reducing lung tissue pathology and endothelial damages, along with viral replication. Previous research has pointed a possible role for the chaperone HSP90 in SARS-CoV-2 replication and COVID-19 pathogenesis. Pharmacological intervention through HSP90 inhibitors was shown to be beneficial in the treatment of inflammatory diseases, infections and reducing replication of diverse viruses. In this study, we analyzed the effects of the potent HSP90 inhibitor Ganetespib in vitro on alveolar epithelial cells and alveolar macrophages to characterize its effects on cell activation and viral replication. Additionally, to evaluate its efficacy in controlling systemic inflammation and the viral burden after infection in vivo, a Syrian hamster model was used. In vitro, Ganetespib reduced viral replication on AECs in a dose-dependent manner and lowered significantly the expression of pro-inflammatory genes, in both AECs and alveolar macrophages. In vivo, administration of Ganetespib led to an overall improvement of the clinical condition of infected animals, with decreased systemic inflammation, reduced edema formation and lung tissue pathology. Altogether, we show that Ganetespib could be a potential medicine to treat moderate and severe cases of COVID-19.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Luiz Gustavo Teixeira Alves", - "author_inst": "Max Delbrueck Center for Molecular Medicine" - }, - { - "author_name": "Morris Baumgardt", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Judith Hoppe", - "author_inst": "Free University of Berlin" - }, - { - "author_name": "Theresa C. Firsching", - "author_inst": "Free University of Berlin" - }, - { - "author_name": "Julia M. Adler", - "author_inst": "Free University of Berlin" - }, - { - "author_name": "Guido Mastrobuoni", - "author_inst": "Max Delbrueck Center for Molecular Medicine" - }, - { - "author_name": "Jenny Grobe", - "author_inst": "Max Delbrueck Center for Molecular Medicine" - }, - { - "author_name": "Katja Hoenzke", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Stefan Kempa", - "author_inst": "Max Delbrueck Center for Molecular Medicine" - }, - { - "author_name": "Achim D. Gruber", - "author_inst": "Free University of Berlin" - }, - { - "author_name": "Andreas C. Hocke", - "author_inst": "Charite - Universitaetsmedizin" - }, - { - "author_name": "Jakob Trimpert", - "author_inst": "Free University of Berlin" - }, - { - "author_name": "Emanuel Wyler", - "author_inst": "Max Delbrueck Center for Molecular Medicine" - }, - { - "author_name": "Markus Landthaler", - "author_inst": "Max-Delbrueck Center for Molecular Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.12.27.521986", "rel_title": "Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants", @@ -125630,6 +127216,101 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2022.12.25.521784", + "rel_title": "A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates", + "rel_date": "2022-12-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.25.521784", + "rel_abs": "While the rapid development of COVID-19 vaccines has been a scientific triumph, the need remains for a globally available vaccine that provides longer-lasting immunity against present and future SARS-CoV-2 variants of concern (VOCs). Here, we describe DCFHP, a ferritin-based, protein-nanoparticle vaccine candidate that, when formulated with aluminum hydroxide as the sole adjuvant (DCFHP-alum), elicits potent and durable neutralizing antisera in non-human primates against known VOCs, including Omicron BQ.1, as well as against SARS-CoV-1. Following a booster [~]one year after the initial immunization, DCFHP-alum elicits a robust anamnestic response. To enable global accessibility, we generated a cell line that can enable production of thousands of vaccine doses per liter of cell culture and show that DCFHP-alum maintains potency for at least 14 days at temperatures exceeding standard room temperature. DCFHP-alum has potential as a once-yearly booster vaccine, and as a primary vaccine for pediatric use including in infants.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Payton A.-B. Weidenbacher", + "author_inst": "Stanford University" + }, + { + "author_name": "Mrinmoy Sanyal", + "author_inst": "Stanford University" + }, + { + "author_name": "Natalia Friedland", + "author_inst": "Stanford University" + }, + { + "author_name": "Shaogeng Tang", + "author_inst": "Stanford University" + }, + { + "author_name": "Prabhu S Arunachalam", + "author_inst": "Stanford University" + }, + { + "author_name": "Mengyun Hu", + "author_inst": "Stanford University" + }, + { + "author_name": "Ozan S. Kumru", + "author_inst": "University of Kansas" + }, + { + "author_name": "Mary Kate Morris", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Jane Fontenot", + "author_inst": "University of Louisiana at Lafayette" + }, + { + "author_name": "Lisa Shirreff", + "author_inst": "University of Louisiana at Lafayette" + }, + { + "author_name": "Jonathan Do", + "author_inst": "Stanford University" + }, + { + "author_name": "Ya-Chen Cheng", + "author_inst": "Stanford University" + }, + { + "author_name": "Gayathri Vasudevan", + "author_inst": "International AIDS Vaccine Initiative" + }, + { + "author_name": "Mark B. Feinberg", + "author_inst": "International AIDS Vaccine Initiative" + }, + { + "author_name": "Francois J. Villinger", + "author_inst": "University of Louisiana at Lafayette" + }, + { + "author_name": "Carl Hanson", + "author_inst": "California Department of Public Health" + }, + { + "author_name": "Sangeeta B. Joshi", + "author_inst": "University of Kansas" + }, + { + "author_name": "David B. Volkin", + "author_inst": "University of Kansas" + }, + { + "author_name": "Bali Pulendran", + "author_inst": "Stanford University" + }, + { + "author_name": "Peter S. Kim", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.12.22.521696", "rel_title": "Omicron BA.5 infects human brain organoids and is neuroinvasive and lethal in K18-hACE2 mice", @@ -125899,101 +127580,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.12.20.22283750", - "rel_title": "Monkeypox Post COVID19: Knowledge, Worrying, and Vaccine Adoption of the Arabic General Population", - "rel_date": "2022-12-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.20.22283750", - "rel_abs": "BackgroundThe outbreak of monkeypox was designated a global public health emergency by the World Health Organization on July 23, 2022. There have been more reported 60000 cases worldwide, most of which are in places where monkeypox has never been seen due to the travel of people who have the virus. This research aims to evaluate the Arabic general population on monkeypox disease, fears, and vaccine adoption after the WHO proclaimed a monkeypox epidemic and to compare these attitudes to those of the COVID-19 pandemic.\n\nMethodsThis cross-sectional study was performed in some Arabic countries (Syria, Egypt, Qatar, Yemen, Jordan, Sudan, Algeria, and Iraq) between August 18 and September 7, 2022 to examine the Arabic people perspectives on monkeypox disease, fears, and vaccine adoption and to compare these attitudes to those of the COVID-19 pandemic. The inclusion criteria were the general public residing in Arabic nations and older than 18. This questionnaire has 32 questions separated into three sections: sociodemographic variables, prior COVID-19 exposure, and COVID-19 vaccination history. The second portion assesses knowledge and anxieties about monkeypox, while the third section includes the generalized anxiety disorder (GAD7) scale. Logistic regression analysis were performed to compute the adjusted odds ratios (aOR), and their confidence intervals (95%CI) using STATA (version 17.0)\n\nResultsA total of 3665 respondents from 17 Arabic countries were involved in this study. Almost two third (n= 2427, 66.2%) of participants expressed more worried about COVID -19 than monkeypox diseases. Regarding the major cause for concern about monkeypox, 39.5% of participants attributed their anxiety they or a member of their family may contract the illness, while 38.4% were concerned about another worldwide pandemic of monkeypox. According to the GAD 7 score, 71.7% of respondents showed very low anxiety toward monkeypox. 43.8% of the participants scored poor levels of knowledge about monkeypox disease. Participants with previous COVID-19 infection showed greater acceptance to receive the monkeypox vaccine 1.206 times than those with no previous infection. A higher concern for the monkeypox than COVID-19 was shown by the participants who perceived monkeypox as dangerous and virulent 3.097 times than those who didnt. Participants who have a chronic disease (aOR: 1.32; 95%CI: 1.09-1.60); participants worried about monkeypox (aOR: 1.21; 95%CI: 1.04-1.40); and perceived monkeypox as a dangerous and virulent disease (aOR: 2.25; 95%CI: 1.92-2.65); and excellent knowledge level (aOR: 2.28; 95%CI: 1.79-2.90) have emerged as significant predictors.\n\nConclusionOur study reported that three fourth of the participants were more concerned about COVID-19 than monkeypox disease. As well, most of the participants have inadequate levels of knowledge regarding monkeypox disease. Hence immediate action should be taken to address this problem. Consequently, it is crucial to learn about monkeypox and spread information about its prevention.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Sarya Swed", - "author_inst": "University of Aleppo Faculty of Medicine" - }, - { - "author_name": "Haidara Bohsas", - "author_inst": "University of Aleppo Faculty of Medicine" - }, - { - "author_name": "Hidar Alibrahim", - "author_inst": "University of Aleppo Faculty of Medicine" - }, - { - "author_name": "Amine Rakab", - "author_inst": "Weill Cornell Medicine - Qatar" - }, - { - "author_name": "Wael Hafez", - "author_inst": ": Royal Hospital" - }, - { - "author_name": "Bisher Sawaf", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Mohammed Amir Rais", - "author_inst": "University of Algiers: Universite d'Alger 1" - }, - { - "author_name": "Ahmed Sallam Motawei", - "author_inst": "South Valley University Qena Faculty of Medicine: South Valley University Faculty of Medicine" - }, - { - "author_name": "Ahmed Aljabali", - "author_inst": "Jordan University of Science and Technology Faculty of Medicine" - }, - { - "author_name": "Shiekh shoib", - "author_inst": "University of Kashmir" - }, - { - "author_name": "Ismail Atef Ismail Ahmed Ibrahim", - "author_inst": "Fenerbahce Universitesi" - }, - { - "author_name": "Sondos Hussein Ahmad Almashaqbeh", - "author_inst": "UJ: The University of Jordan" - }, - { - "author_name": "Ebrahim Ahmed Qaid Shaddad", - "author_inst": "Sana'a University Faculty of Medicine" - }, - { - "author_name": "Maryam AlShaqsi", - "author_inst": "Oman Medical College" - }, - { - "author_name": "Ahmed abdelrahman", - "author_inst": "Zagazig University" - }, - { - "author_name": "Sherihan fathey", - "author_inst": "New Giza University: Newgiza University" - }, - { - "author_name": "Ren\u00e9 Hurlemann", - "author_inst": "Universitat Oldenburg: Carl von Ossietzky Universitat Oldenburg" - }, - { - "author_name": "Mohamed Elsayed", - "author_inst": "Ulm University: Universitat Ulm" - }, - { - "author_name": "Bijaya Kumar Padhi", - "author_inst": "PGIMER: Post Graduate Institute of Medical Education and Research" - }, - { - "author_name": "Ranjit Sah", - "author_inst": "Tribhuvan University Teaching Hospital" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.12.22.22283850", "rel_title": "Calculation and meaning of \"excess mortality\": A comparison of Covid- and pre-Covid mortality data in 31 Eurostat countries from 1965 to 2021.", @@ -127348,6 +128934,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.21.521431", + "rel_title": "Mechanism of LLPS of SARS-CoV-2 N protein", + "rel_date": "2022-12-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.21.521431", + "rel_abs": "SARS-CoV-2 nucleocapsid (N) protein with low mutation rate is the only structural protein not only functioning to package viral genomic RNA, but also manipulating the host-cell machineries, thus representing a key target for drug development. Recent discovery of its liquid-liquid phase separation (LLPS) not only sheds light on previously-unknown mechanisms underlying the host-SARS-CoV-2 interaction and viral life cycle, but most importantly opens up a new direction for developing anti-SARS-CoV-2 strategies/drugs. However, so far the high-resolution mechanism of LLPS of N protein still remains unknown because it is not amenable for high-resolution biophysical investigations. Here we systematically dissected N protein into differential combinations of domains followed by DIC and NMR characterization. We successfully identified N (1-249), which not only gives high-quality NMR spectra, but phase separates as the full-length N protein. The results together decode for the first time: 1) nucleic acid modulates LLPS by dynamic but specific interactions multivalently over both folded NTD/CTD and Arg/Lys residues within IDRs. 2) ATP, mysteriously with concentrations >mM in all living cells but absent in viruses, not only specifically binds NTD/CTD, but also Arg residues within IDRs with Kd of 2.8 mM. 3) ATP dissolves LLPS by competitively displacing nucleic acid from binding the protein. Therefore, ATP and nucleic acid interplay in modulating LLPS by specific competitions for binding over the highly overlapped binding sites. Our study deciphers the mechanism of LLPS of N protein, which is targetable by small molecules. ATP is not only emerging as a cellular factor controlling the host-SARS-CoV-2 interaction, but also provides a lead for developing anti-SARS-CoV-2 drugs efficient for different variants of SARS-CoV-2. Fundamentally, our results imply that the mechanisms of LLPS of IDR-containing proteins mediated by ATP and nucleic acids appear to be highly conserved from human to virus.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Jianxing Song", + "author_inst": "National University of Singapore" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.12.20.521221", "rel_title": "Structure adaptation in Omicron SARS-CoV-2/hACE2:Biophysical origins of evolutionary driving forces", @@ -127553,33 +129158,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.12.21.521388", - "rel_title": "SARS-CoV-2 variant-specific differences in inhibiting the effects of the PKR-activated integrated stress response", - "rel_date": "2022-12-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.21.521388", - "rel_abs": "The integrated stress response (ISR) is a eukaryotic cell pathway that triggers translational arrest and the formation of stress granules (SGs) in response to various stress signals, including those caused by viral infections. The SARS-CoV-2 nucleocapsid protein has been shown to disrupt SGs, but SARS-CoV-2 interactions with other components of the pathway remains poorly characterized. Here, we show that SARS-CoV-2 infection triggers the ISR through activation of the eIF2-kinase PKR while inhibiting a variety of downstream effects. In line with previous studies, SG formation was efficiently inhibited and the induced eIF2 phosphorylation only minimally contributed to the translational arrest observed in infected cells. Despite ISR activation and translational arrest, expression of the stress-responsive transcripts ATF4 and CHOP was not induced in SARS-CoV-2 infected cells. Finally, we found variant-specific differences in the activation of the ISR between ancestral SARS-CoV-2 and the Delta and Omicron BA.1 variants in that Delta infection induced weaker PKR activation while Omicron infection induced higher levels of p-eIF2 and greatly increased SG formation compared to the other variants. Our results suggest that different SARS-CoV-2 variants can affect normal cell functions differently, which can have an impact on pathogenesis and treatment strategies.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Wanda Christ", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Jonas Klingstrom", - "author_inst": "Center for Infectious Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden" - }, - { - "author_name": "Janne Tynell", - "author_inst": "Helsinki University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.12.19.22283560", "rel_title": "coronabambini.ch: Development and usage of an online decision support tool for pediatric COVID-testing in Switzerland: a cross-sectional analysis", @@ -129186,6 +130764,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.16.22283554", + "rel_title": "Comparison of the mucosal and systemic antibody responses in Covid-19 recovered patients with one dose of mRNA vaccine and unexposed subjects with three doses of mRNA vaccines", + "rel_date": "2022-12-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.16.22283554", + "rel_abs": "BackgroundImmunity acquired from natural SARS-CoV-2 infection and vaccine wanes overtime. This longitudinal prospective study compared the effect of a booster vaccine (BNT162b2) in inducing the mucosal (nasal) and serological antibody between Covid-19 recovered patients and healthy unexposed subjects with two dose of mRNA vaccine (vaccine-only group).\n\nMethodEleven recovered patients and eleven gender-and-age matched unexposed subjects who had mRNA vaccines were recruited. The SARS-CoV-2 spike 1 (S1) protein specific IgA, IgG and the ACE2 binding inhibition to the ancestral SARS-CoV-2 and omicron (BA.1) variant receptor binding domain were measured in their nasal epithelial lining fluid and plasma.\n\nResultIn the recovered group, the booster expanded the nasal IgA dominancy inherited from natural infection to IgA and IgG. They also had a higher S1-specific nasal and plasma IgA and IgG levels with a better inhibition against the omicron BA.1 variant and ancestral SARS-CoV-2 when compared with vaccine-only subjects. The nasal S1-specific IgA induced by natural infection lasted longer than those induced by vaccines while the plasma antibodies of both groups maintained at a high level for at least 21 weeks after booster.\n\nConclusionThe booster benefited all subjects to obtain neutralizing antibody (NAb) against omicron BA.1 variant in plasma while only the Covid-19 recovered subjects had an extra enrichment in nasal NAb against Omicron BA.1 variant.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Shaojun Liu", + "author_inst": "Department of Paediatrics, Faculty of Medicine, The Chinese University of Hong Kong" + }, + { + "author_name": "Joseph GS Tsun", + "author_inst": "Department of Paediatrics, Faculty of Medicine, The Chinese University of Hong Kong" + }, + { + "author_name": "Genevieve PG Fung", + "author_inst": "Department of Paediatrics, Faculty of Medicine, The Chinese University of Hong Kong" + }, + { + "author_name": "Grace CY Lui", + "author_inst": "Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong" + }, + { + "author_name": "Kathy YY Chan", + "author_inst": "Department of Paediatrics, Faculty of Medicine, The Chinese University of Hong Kong" + }, + { + "author_name": "Paul KS Chan", + "author_inst": "Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong" + }, + { + "author_name": "Renee WY Chan", + "author_inst": "Department of Paediatrics, Faculty of Medicine, The Chinese University of Hong Kong; CUHK-Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.12.15.22283474", "rel_title": "Bacillus Calmette-Guerin vaccine to reduce COVID-19 infections and hospitalisations in healthcare workers: a living systematic review and prospective ALL-IN meta-analysis of individual participant data from randomised controlled trials", @@ -129715,53 +131336,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2022.12.16.520835", - "rel_title": "High-Throughput Discovery and Characterization of Viral Transcriptional Effectors in Human Cells", - "rel_date": "2022-12-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.16.520835", - "rel_abs": "Viruses encode transcriptional regulatory proteins critical for controlling viral and host gene expression. Given their multifunctional nature and high sequence divergence, it is unclear which viral proteins can affect transcription and which specific sequences contribute to this function. Using a high-throughput assay, we measured the transcriptional regulatory potential of over 60,000 protein tiles across [~]1,500 proteins from 11 coronaviruses and all nine human herpesviruses. We discovered hundreds of new transcriptional effector domains, including a conserved repression domain in all coronavirus Spike homologs, dual activation-repression domains in VIRFs, and an activation domain in six herpesvirus homologs of the single-stranded DNA-binding protein that we show is important for viral replication and late gene expression in KSHV. For the effector domains we identified, we investigated their mechanisms via high-throughput sequence and chemical perturbations, pinpointing sequence motifs essential for function. This work massively expands viral protein annotations, serving as a springboard for studying their biological and health implications and providing new candidates for compact gene regulation tools.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Connor H Ludwig", - "author_inst": "Stanford University" - }, - { - "author_name": "Abby R Thurm", - "author_inst": "Stanford University" - }, - { - "author_name": "David W Morgens", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Kevin J Yang", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Josh Tycko", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Michael C Bassik", - "author_inst": "Stanford Univeristy" - }, - { - "author_name": "Britt A Glaunsinger", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Lacramioara Bintu", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2022.12.16.520829", "rel_title": "Prewhitening and Normalization Help Detect a Strong Cross-Correlation Between Daily Wastewater SARS-CoV-2 RNA Abundance and COVID-19 Cases in a Community", @@ -131184,6 +132758,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.12.15.22282988", + "rel_title": "Streptococcus pneumoniae re-emerges as a cause of community-acquired pneumonia, including frequent co-infection with SARS-CoV-2, in Germany, 2021", + "rel_date": "2022-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.15.22282988", + "rel_abs": "BackgroundThe COVID-19 pandemic and the associated containment measures had a substantial impact on pathogens causing pneumonia in adults. The objective of this study was to determine the etiology of hospitalized community-acquired pneumonia (CAP) among adults in Germany in 2021, the second year of the COVID-19 pandemic.\n\nMethodsSince January 2021, this on-going, prospective, population-based surveillances study enrolled adult patients with clinically and radiographically confirmed CAP at three hospitals in Thuringia, Germany, serving a population of approximately 280,000. Urine samples were collected from patients and tested for S. pneumoniae using the pneumococcal urinary antigen test (PUAT, BinaxNOW S. pneumoniae) and the proprietary serotype-specific urinary antigen detection (UAD) assays. Nasopharyngeal swabs were tested for 10 respiratory viruses by PCR.\n\nResultsA total of 797 patients were enrolled, of whom 760 were included in the analysis. The median age of patients with CAP was 67 years; in-hospital case-fatality rate was 8.4%. A respiratory pathogen was detected in 553 (72.8%) patients. The most common pathogen was SARS-CoV-2 (n=498, 68.2%), followed by S. pneumoniae (n=40, 6.4%). Serotypes contained in the 13-valent, 15-valent and 20-valent pneumococcal conjugate vaccine were detected in 42.5%, 45.0%, and 70.0% of the pneumococcal CAP cases. Between the first and second half of 2021, the proportion of CAP cases associated with S. pneumoniae increased from 1.1% to 5.6% in patients aged 18-59 years and from 2.5% to 12.4% in those aged [≥]60 years; coinfection of SARS-CoV-2 and S. pneumoniae among COVID-19 patients increased from 0.7% (2/283 cases) to 6.0% (13/215) in patients aged [≥]18 years, and from 1.0% (2/195) to 8.7% (11/127) in those aged [≥]60 years.\n\nConclusionIn Germany, the proportion of CAP cases associated with S. pneumoniae rebounded to a near-pandemic level in the second half of 2021 and many pneumococcal infections occurred in patients with COVID-19. Vaccination uptake against respiratory pathogens, including S. pneumoniae, should be strengthened.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Juliane Ankert", + "author_inst": "Institute for Infectious Diseases and Infection Control, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany" + }, + { + "author_name": "Stefan Hagel", + "author_inst": "Institute for Infectious Diseases and Infection Control, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany" + }, + { + "author_name": "Claudia Schwarz", + "author_inst": "Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer, Collegeville, PA, USA" + }, + { + "author_name": "Kaijie Pan", + "author_inst": "Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer, Collegeville, PA, USA" + }, + { + "author_name": "Liz Wang", + "author_inst": "Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer, Collegeville, PA, USA" + }, + { + "author_name": "Christof von Eiff", + "author_inst": "Pfizer Pharma GmbH, Berlin, Germany" + }, + { + "author_name": "Bradford D. Gessner", + "author_inst": "Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer, Collegeville, PA, USA" + }, + { + "author_name": "Christian Theilacker", + "author_inst": "Vaccines Medical Development, Scientific and Clinical Affairs, Pfizer, Collegeville, PA, USA" + }, + { + "author_name": "Mathias W. Pletz", + "author_inst": "Institute for Infectious Diseases and Infection Control, Jena University Hospital, Friedrich Schiller University Jena, Jena, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.12.15.22283522", "rel_title": "Estimating the transmission dynamics of Omicron in Beijing, November to December 2022", @@ -131349,85 +132974,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.12.15.520606", - "rel_title": "Identification of broad, potent antibodies to functionally constrained regions of SARS-CoV-2 spike following a breakthrough infection", - "rel_date": "2022-12-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.15.520606", - "rel_abs": "The antiviral benefit of antibodies can be compromised by viral escape especially for rapidly evolving viruses. Therefore, durable, effective antibodies must be both broad and potent to counter newly emerging, diverse strains. Discovery of such antibodies is critically important for SARS-CoV-2 as the global emergence of new variants of concern (VOC) has compromised the efficacy of therapeutic antibodies and vaccines. We describe a collection of broad and potent neutralizing monoclonal antibodies (mAbs) isolated from an individual who experienced a breakthrough infection with the Delta VOC. Four mAbs potently neutralize the Wuhan-Hu-1 vaccine strain, the Delta VOC, and also retain potency against the Omicron VOCs through BA.4/BA.5 in both pseudovirus-based and authentic virus assays. Three mAbs also retain potency to recently circulating VOCs XBB.1.5 and BQ.1.1 and one also potently neutralizes SARS-CoV-1. The potency of these mAbs was greater against Omicron VOCs than all but one of the mAbs that had been approved for therapeutic applications. The mAbs target distinct epitopes on the spike glycoprotein, three in the receptor binding domain (RBD) and one in an invariant region downstream of the RBD in subdomain 1 (SD1). The escape pathways we defined at single amino acid resolution with deep mutational scanning show they target conserved, functionally constrained regions of the glycoprotein, suggesting escape could incur a fitness cost. Overall, these mAbs are novel in their breadth across VOCs, their epitope specificity, and include a highly potent mAb targeting a rare epitope outside of the RBD in SD1.\n\nSignificance StatementSARS-CoV-2 infections can result in diverse clinical outcomes, including severe disease. Monoclonal antibodies (mAbs) have been used therapeutically to treat infection, but the emergence of variants has compromised their efficacy. Thus, identifying mAbs that are more durable in the face of SARS-CoV-2 evolution is a pressing need. Here, we describe four new mAbs isolated from a Delta-breakthrough infection, that can potently neutralize diverse variants, including multiple Omicron variants. In addition, one mAb shows broader activity against coronaviruses. The breadth of these mAbs is due to their focus on highly conserved regions of the viral protein antigen, including regions that are required for the virus to enter the cell. These properties make them promising candidates for therapeutic use.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Jamie Guenthoer", - "author_inst": "Fred Hutchinson Cancer Center" - }, - { - "author_name": "Michelle Lilly", - "author_inst": "Fred Hutchinson Cancer Center" - }, - { - "author_name": "Tyler N Starr", - "author_inst": "University of Utah" - }, - { - "author_name": "Bernadeta Dadonaite", - "author_inst": "Fred Hutchinson Cancer Center" - }, - { - "author_name": "Klaus N Lovendahl", - "author_inst": "University of Washington" - }, - { - "author_name": "Jacob T Croft", - "author_inst": "University of Washington" - }, - { - "author_name": "Caitlin I Stoddard", - "author_inst": "Fred Hutchinson Cancer Center" - }, - { - "author_name": "Vrasha Chohan", - "author_inst": "Fred Hutchinson Cancer Center" - }, - { - "author_name": "Shilei Ding", - "author_inst": "Centre de Recherche du CHUM" - }, - { - "author_name": "Felicitas Ruiz", - "author_inst": "Fred Hutchinson Cancer Center" - }, - { - "author_name": "Mackenzie S Kopp", - "author_inst": "Fred Hutchinson Cancer Center" - }, - { - "author_name": "Andr\u00e9s Finzi", - "author_inst": "Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Jesse D Bloom", - "author_inst": "Fred Hutchinson Cancer Center" - }, - { - "author_name": "Helen Y Chu", - "author_inst": "University of Washington" - }, - { - "author_name": "Kelly K Lee", - "author_inst": "University of Washington" - }, - { - "author_name": "Julie Overbaugh", - "author_inst": "Fred Hutchinson Cancer Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.12.15.520679", "rel_title": "Molecular evolution and structural analyses of spike protein COVID-19 variants in Negeri Sembilan of peninsular Malaysia", @@ -133182,6 +134728,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.12.12.22283367", + "rel_title": "Milk antibody response after 3rd dose of COVID-19 mRNA vaccine and SARS-CoV-2 breakthrough infection and implications for infant protection", + "rel_date": "2022-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.12.22283367", + "rel_abs": "Anti-SARS-CoV-2 antibodies have been found in human-milk after COVID-19 infection and vaccination. However, little is known about their persistence in milk after booster vaccination and breakthrough infection. In this study, human-milk, saliva and blood samples were collected from 33 lactating individuals before and after mRNA-based vaccination and COVID-19 breakthrough infections. Antibody levels were measured using ELISA and symptoms were assessed using questionnaires. Evaluation of maternal and infant symptomatology revealed that infected mothers reported more symptoms than vaccinated mothers. We found that after vaccination, human-milk anti-SARS-CoV-2 antibodies persisted for up to 8 months. In addition, distinct patterns of human milk IgA and IgG production we observed after breakthrough infection compared to 3-dose vaccination series alone, indicating a differential central and mucosal immune profiles in hybrid compared with vaccine-induced immunity. To investigate passively-derived milk antibody protection in infants, we examined the persistence of these antibodies in infant saliva after breastfeeding. We found that IgA was more abundant in infant saliva compared to IgG and persist in infant saliva longer after feeding. Our results delineate the differences in milk antibody response to vaccination as compared to breakthrough infection and emphasize the importance of improving the secretion of IgA antibodies to human milk after vaccination to improve the protection of breastfeeding infants.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Yarden Golan", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Mikias Ilala", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Caryl Gay", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Soumya Hunagund", + "author_inst": "University of California San Francisco, California" + }, + { + "author_name": "Christine Y. Lin", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Arianna G. Cassidy", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Unurzul Jigmeddagva", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Lin Li", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Nida Ozarslan", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Ifeyinwa V. Asiodu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Nadav Ahituv", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Valerie J. Flaherman", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Stephanie L. Gaw", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Mary Prahl", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.12.22283388", "rel_title": "The Impact of COVID-19 Pandemic on Mental Health: A Scoping Review", @@ -133335,73 +134952,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2022.12.12.22283381", - "rel_title": "Identifying and preventing fraudulent responses in online public health surveys: Lessons learned during the COVID-19 pandemic", - "rel_date": "2022-12-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.12.22283381", - "rel_abs": "Web-based survey data collection has become increasingly popular, and limitations on in-person data collection during the COVID-19 pandemic have fueled this growth. However, the anonymity of the online environment increases the risk of fraud, which pose major risks to data integrity. As part of a study of COVID-19 and the return to in-person school, we implemented a web-based survey of parents in Maryland, USA, between December 2021 and July 2022. Recruitment relied, in part, on social media advertisements. Despite implementing many existing best practices, the survey was challenged by sophisticated fraudsters. In this paper, we describe efforts to identify and prevent fraudulent online survey responses and provide specific, actionable recommendations for identifying and preventing online survey fraud. Some strategies can be deployed within the web-based data collection platform such as Internet Protocol address logging to identify duplicate responses and comparison of client-side and server-side time stamps to identify responses that may have been completed by respondents outside of the surveys target geography. Additional approaches include the use of a 2-stage survey design, repeated within-survey and cross-survey validation questions, the addition of \"speed bump\" questions to thwart careless or computerized responders, and the use of optional open-ended survey responses to identify irrelevant responses. We describe best practices for ongoing survey data review and verification, including algorithms to simplify aspects of this review.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Sara B. Johnson", - "author_inst": "Johns Hopkins School of Medicine: Johns Hopkins University School of Medicine" - }, - { - "author_name": "June Wang", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Gabriela Calderon", - "author_inst": "Johns Hopkins Hospital: Johns Hopkins Medicine" - }, - { - "author_name": "Erin R. Hager", - "author_inst": "Johns Hopkins University Bloomberg School of Public Health" - }, - { - "author_name": "Lorece V. Edwards", - "author_inst": "Morgan State University Department of Behavioral Health Sciences: Morgan State University School of Community Health and Policy" - }, - { - "author_name": "Andrea A. Berry", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Yisi Liu", - "author_inst": "Johns Hopkins School of Medicine: Johns Hopkins University School of Medicine" - }, - { - "author_name": "Janny Dinh", - "author_inst": "Johns Hopkins University Bloomberg School of Public Health" - }, - { - "author_name": "Amber C. Summers", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Katherine A. Connor", - "author_inst": "Johns Hopkins School of Medicine: Johns Hopkins University School of Medicine" - }, - { - "author_name": "Megan E. Collins", - "author_inst": "Johns Hopkins School of Medicine: Johns Hopkins University School of Medicine" - }, - { - "author_name": "Laura Pritchett", - "author_inst": "Johns Hopkins: Johns Hopkins University" - }, - { - "author_name": "Beth R. Marshall", - "author_inst": "Johns Hopkins University Bloomberg School of Public Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.12.09.22283256", "rel_title": "Emergence and Spread of SARS-CoV-2 Variants of Concern in Canada: a Retrospective Analysis from Clinical and Wastewater Data", @@ -134939,6 +136489,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.07.22283234", + "rel_title": "Machine learning identifies a COVID-19-specific phenotype in university students using a mental health app", + "rel_date": "2022-12-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.07.22283234", + "rel_abs": "Advances in smartphone technology have allowed people to access mental healthcare via digital apps from wherever and whenever they choose. University students experience a high burden of mental health concerns. Although these apps improve mental health symptoms, user engagement has remained low. Studies have shown that users can be subgrouped based on unique characteristics that just-in-time adaptive interventions (JITAIs) can use to improve engagement. To date, however, no studies have examined the effect of the COVID-19 pandemic on these subgroups. Here, we use machine learning to examine user subgroup characteristics across three COVID-19-specific timepoints: during lockdown, immediately following lockdown, and three months after lockdown ended. We demonstrate that there are three unique subgroups of university students who access mental health apps. Two of these, with either higher or lower mental well-being, were defined by characteristics that were stable across COVID-19 timepoints. The third, situational well-being, had characteristics that were timepoint-dependent, suggesting that they are highly influenced by traumatic stressors and stressful situations. This subgroup also showed feelings and behaviours consistent with burnout. Overall, our findings clearly suggest that user subgroups are unique: they have different characteristics and therefore likely have different mental healthcare goals. Our findings also highlight the importance of including questions and additional interventions targeting traumatic stress(ors), reason(s) for use, and burnout in JITAI-style mental health apps to improve engagement.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Artur Shvetcov", + "author_inst": "Black Dog Institute" + }, + { + "author_name": "Alexis Whitton", + "author_inst": "Black Dog Institute" + }, + { + "author_name": "Suranga Kasturi", + "author_inst": "Black Dog Institute" + }, + { + "author_name": "Wu-Yi Zheng", + "author_inst": "Black Dog Institute" + }, + { + "author_name": "Joanne Beames", + "author_inst": "Black Dog Institute" + }, + { + "author_name": "Omar Ibrahim", + "author_inst": "Black Dog Institute" + }, + { + "author_name": "Jin Han", + "author_inst": "Black Dog Institute" + }, + { + "author_name": "Leonard Hoon", + "author_inst": "Deakin University" + }, + { + "author_name": "Kon Mouzakis", + "author_inst": "Deakin University" + }, + { + "author_name": "Sunil Gupta", + "author_inst": "Deakin University" + }, + { + "author_name": "Svetha Venkatesh", + "author_inst": "Deakin University" + }, + { + "author_name": "Helen Christensen", + "author_inst": "Black Dog Institute" + }, + { + "author_name": "Jill Newby", + "author_inst": "Black Dog Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.12.11.520008", "rel_title": "Using machine learning to detect coronaviruses potentially infectious to humans", @@ -135056,41 +136673,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2022.12.10.519730", - "rel_title": "Dynamical nonequilibrium molecular dynamics simulations identify allosteric sites and positions associated with drug resistance in the SARS-CoV-2 main protease", - "rel_date": "2022-12-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.10.519730", - "rel_abs": "The SARS-CoV-2 main protease (Mpro) plays an essential role in the coronavirus lifecycle by catalysing hydrolysis of the viral polyproteins at specific sites. Mpro is the target of drugs, such as nirmatrelvir, though resistant mutants have emerged that threaten drug efficacy. Despite its importance, questions remain on the mechanism of how Mpro binds its substrates. Here, we apply dynamical nonequilibrium molecular dynamics (D-NEMD) simulations to evaluate structural and dynamical responses of Mpro to the presence and absence of a substrate. The results highlight communication between the Mpro dimer subunits and identify networks, including some far from the active site, that link the active site with a known allosteric inhibition site, or which are associated with nirmatrelvir resistance. They imply that some mutations enable resistance by altering the allosteric behaviour of Mpro. More generally, the results show the utility of the D-NEMD technique for identifying functionally relevant allosteric sites and networks including those relevant to resistance.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "H. T Henry Chan", - "author_inst": "University of Oxford" - }, - { - "author_name": "A. Sofia F. Oliveira", - "author_inst": "University of Bristol" - }, - { - "author_name": "Christopher J. Schofield", - "author_inst": "University of Oxford" - }, - { - "author_name": "Adrian J. Mulholland", - "author_inst": "University of Bristol" - }, - { - "author_name": "Fernanda Duarte", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2022.12.11.22283310", "rel_title": "Regime type and Data Manipulation: Evidence from the COVID-19 Pandemic", @@ -136765,6 +138347,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.06.519322", + "rel_title": "A Binary RNA and DNA Self-Amplifying Platform for Next Generation Vaccines and Therapeutics", + "rel_date": "2022-12-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.06.519322", + "rel_abs": "Conventional mRNA-based vaccines were instrumental in lowering the burden of the pandemic on healthcare systems and in reducing mortality. However, such first-generation vaccines have significant weaknesses. Here, we describe a high-performance binary recombinant vectoral platform offering the flexibility to be used as a self-amplifying mRNA or a self-amplifying DNA. Both formats drive long-lasting expression and actuate robust antibody responses against SAR-CoV-2 spike, and neither format require encapsulation with lipid nanoparticles (LNP) in the generation immune responses. The platform combines the power of conventional mRNA with the low-dosage of self-amplifying vectors together with the simplicity, rapid creation, ease of storage, and convenience of distribution of plasmid DNA vectors. This platform promises to pave the way for more effective, less expensive, and truly democratized vaccines and therapeutics.\n\nOne-Sentence SummaryGemini: a versatile platform that improves on existing vaccine formats in terms of effectiveness, manufacturing, distribution, and cost.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Wilfred Jefferies", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Kyung Bok Choi", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Paolo Ribeca", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Suresh Kari", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Jay Young", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Elizabeth Hui", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Simon Yong Qi", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Emmanuel Garrosvillas", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Pamela Lincez", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Tracy Welch", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Iryna Saranchova", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Cheryl G Pfeifer", + "author_inst": "University of British Columbia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.12.07.519460", "rel_title": "Reduced SARS-CoV-2 mRNA vaccine immunogenicity and protection in mice with diet-induced obesity and insulin resistance.", @@ -136862,29 +138507,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.12.05.22283130", - "rel_title": "Utilization of Cycle Threshold Values of RTPCR SARS-Cov-2 Among Admitted Patients in a Public Hospital", - "rel_date": "2022-12-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.05.22283130", - "rel_abs": "Coronavirus 2019 (COVID-19) was caused by the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and not just affected the Philippines but also globally. Data on real-time PCR cycle threshold (Ct) values were accessible in the healthcare facility and previous studies did not support its direct clinical significance on patients management. The aim of this study was to investigate the RT-PCR Ct values of admitted COVID-19 confirmed patients in the epidemiologic context from April 2021 to November 2021.\n\nA total of 1,245 were tested and out of the 1,038 confirmed COVID-19 admitted patients, 579 (55.78%) were females and 459 were males (44.22%). There were 4 genes detected, namely: N, E, ORF1ab and RdRP genes, and the majority was N gene 925 (88.94%) while the least detected was 203 E gene of SARS-CoV-2. This study described the utilization of five (5) different COVID-19 test kits.\n\nComparing the Ct values between the male and female groups, this study showed no significant differences. To compare between the different age groups and the three classifications of CT values was shown in Table 6. For the N gene, the current study showed a significant difference of CT value <25 among 0-17 years old vs 46-60 years old (p=0.00054), and among 0-17 years old vs >61 (senior citizens) years old group (p=0.00945). Moreover, a significant difference was observed for CT value >30 among 0-17 years vs 18-45 years old (p=0.00411) and among 0-17 years old vs >61 years old group (p=0.00025). CT values for the ORF gene showed significant differences. CT value <25 showed significant differences among 0-17 years versus 45-60 years old (p=0.00907) and 0-17 years versus >60 years old (p=0.04298). Moreover, CT value >30 showed significant differences among 0-17 years versus 46-60 years old (p=0.02344) and 0-17 years versus >60 years old (p=0.3411).\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@18c1e44org.highwire.dtl.DTLVardef@170741org.highwire.dtl.DTLVardef@1dd6474org.highwire.dtl.DTLVardef@1ee218eorg.highwire.dtl.DTLVardef@dd25e9_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 6.C_FLOATNO O_TABLECAPTIONThe distribution of different age group relative to the different genes and CT values among COVID-19 admitted patients.\n\nC_TABLECAPTION C_TBL Comparing the mean CT values of two consecutive months from April to Nov, this study showed a significant difference between April and May (p value= 0.0004), August and September (p value= 0.0212), and September and October (p value= 0.002). There was no significant difference with the following months: May and June, June and July, July and August, and October and November (Table 9).\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@e41feforg.highwire.dtl.DTLVardef@ecb6a1org.highwire.dtl.DTLVardef@ca3ceborg.highwire.dtl.DTLVardef@165a53aorg.highwire.dtl.DTLVardef@42afa9_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 9.C_FLOATNO O_TABLECAPTIONFrequency and mean of test kits used among COVID-19 admitted patients relative to the cycle threshold cycles (CT) values. (n=1040)\n\nC_TABLECAPTION C_TBL", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Arbeen Acosta Laurito", - "author_inst": "JUSTINIANO R. BORJA GENERAL HOSPITAL" - }, - { - "author_name": "Alyanna Mae Cuerquis Arengo", - "author_inst": "JUSTINIANO R. BORJA GENERAL HOSPITAL" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.12.06.22283023", "rel_title": "Have there been sustained impacts of the Covid-19 pandemic on trends in smoking prevalence, uptake, quitting, use of treatment, and relapse? A monthly population study in England, 2017-2022", @@ -138423,6 +140045,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.12.03.518956", + "rel_title": "Bioinformatics techniques for efficient structure prediction of SARS-CoV-2 protein ORF7a via structure prediction approaches", + "rel_date": "2022-12-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.03.518956", + "rel_abs": "Protein is the building block for all organisms. Protein structure prediction is always a complicated task in the field of proteomics. DNA and protein databases can find the primary sequence of the peptide chain and even similar sequences in different proteins. Mainly, there are two methodologies based on the presence or absence of a template for Protein structure prediction. Template-based structure prediction (threading and homology modeling) and Template-free structure prediction (ab initio). Numerous web-based servers that either use templates or do not can help us forecast the structure of proteins. In this current study, ORF7a, a transmembrane protein of the SARS-coronavirus, is predicted using Phyre2, IntFOLD, and Robetta. The protein sequence is straightforwardly entered into the sequence bar on all three web servers. Their findings provided information on the domain, the region with the disorder, the global and local quality score, the predicted structure, and the estimated error plot. Our study presents the structural details of the SARS-CoV protein ORF7a. This immunomodulatory component binds to immune cells and induces severe inflammatory reactions.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Aleeza Kazmi", + "author_inst": "Shaheed Benazir Bhutto Women University" + }, + { + "author_name": "Muhammad Kazim", + "author_inst": "Medical Officer, Tehsil Headquarter Hospital, Kallur Kot, Bhakkar, Punjab, Pakistan" + }, + { + "author_name": "Faisal Aslam", + "author_inst": "Tehsil Headquarter Hospital, Ahmad Pur East, Bahawalpur, Punjab, Pakistan" + }, + { + "author_name": "Syeda Mahreen-ul-Hassan Kazmi", + "author_inst": "Department of Microbiology, Shaheed Benazir Bhutto Women University (SBBWU), Peshawar, Pakistan" + }, + { + "author_name": "Abdul Wahab", + "author_inst": "Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China" + }, + { + "author_name": "Rafid Magid Mikhlef", + "author_inst": "Department of Biotechnology, University of Samarra, Iraq" + }, + { + "author_name": "Chandni Khizar", + "author_inst": "Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore, Pakistan" + }, + { + "author_name": "Abeer Kazmi", + "author_inst": "Department of Genetics, Institute of Hydrobiology, University of Chinese Academy of Sciences (UCAS), Wuhan, China" + }, + { + "author_name": "Nadeem Ullah Wazir", + "author_inst": "Department of Pharmacy, COMSATS University Islamabad, Abbottabad Campus, KPK, Pakistan" + }, + { + "author_name": "Ram Parsad Mainali", + "author_inst": "National Agriculture Genetic Resource Center (National Genebank), NARC, Khumaltar, Nepal" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.12.02.518937", "rel_title": "Deep mutational scanning to predict antibody escape in SARS-CoV-2 Omicron subvariants", @@ -138640,73 +140317,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.12.05.519151", - "rel_title": "Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane", - "rel_date": "2022-12-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.05.519151", - "rel_abs": "Entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into host cells depends on refolding of the virus-encoded spike protein from a prefusion conformation, metastable after cleavage, to a lower energy, stable postfusion conformation. This transition overcomes kinetic barriers for fusion of viral and target cell membranes. We report here a cryo-EM structure of the intact postfusion spike in a lipid bilayer that represents single-membrane product of the fusion reaction. The structure provides structural definition of the functionally critical membraneinteracting segments, including the fusion peptide and transmembrane anchor. The internal fusion peptide forms a hairpin-like wedge that spans almost the entire lipid bilayer and the transmembrane segment wraps around the fusion peptide at the last stage of membrane fusion. These results advance our understanding of the spike protein in a membrane environment and may guide development of intervention strategies.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Wei Shi", - "author_inst": "Boston Childrens Hospital/Harvard Medical School" - }, - { - "author_name": "Yongfei Cai", - "author_inst": "Boston Childrens Hospital/Harvard Medical School" - }, - { - "author_name": "Haisun Zhu", - "author_inst": "Institute for Protein Innovation/Harvard Institutes of Medicine" - }, - { - "author_name": "Hanqin Peng", - "author_inst": "Boston Childrens Hospital" - }, - { - "author_name": "Jewel Voyer", - "author_inst": "Boston Childrens Hospital" - }, - { - "author_name": "Sophia Rits-Volloch", - "author_inst": "Boston Childrens Hospital" - }, - { - "author_name": "Hong Cao", - "author_inst": "Codex BioSolutions, Inc." - }, - { - "author_name": "Megan L. Mayer", - "author_inst": "The Harvard Cryo-EM Center for Structural Biology" - }, - { - "author_name": "Kangkang Song", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Chen Xu", - "author_inst": "University of Massachusetts Medical School" - }, - { - "author_name": "Jianming Lu", - "author_inst": "Codex BioSolutions, Inc." - }, - { - "author_name": "Jun Zhang", - "author_inst": "Boston Childrens Hospital/Harvard Medical School" - }, - { - "author_name": "Bing Chen", - "author_inst": "Boston Childrens Hospital/Harvard Medical School" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2022.12.03.518997", "rel_title": "Covidscope: An atlas-scale COVID-19 resource for single-cell meta analysis at sample and cell levels", @@ -140493,6 +142103,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.12.01.518643", + "rel_title": "Immunopeptidome profiling of human coronavirus OC43-infected cells identifies CD4 T cell epitopes specific to seasonal coronaviruses or cross-reactive with SARS-CoV-2", + "rel_date": "2022-12-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.01.518643", + "rel_abs": "Seasonal \"common-cold\" human coronaviruses are widely spread throughout the world and are mainly associated with mild upper respiratory tract infections. The emergence of highly pathogenic coronaviruses MERS-CoV, SARS-CoV, and most recently SARS-CoV-2 has prompted increased attention to coronavirus biology and immunopathology, but identification and characterization of the T cell response to seasonal human coronaviruses remain largely uncharacterized. Here we report the repertoire of viral peptides that are naturally processed and presented upon infection of a model cell line with seasonal human coronavirus OC43. We identified MHC-I and MHC-II bound peptides derived from the viral spike, nucleocapsid, hemagglutinin-esterase, 3C-like proteinase, and envelope proteins. Only three MHC-I bound OC43-derived peptides were observed, possibly due to the potent MHC-I downregulation induced by OC43 infection. By contrast, 80 MHC-II bound peptides corresponding to 14 distinct OC43-derived epitopes were identified, including many at very high abundance within the overall MHC-II peptidome. These peptides elicited low-abundance recall T cell responses in most donors tested. In vitro assays confirmed that the peptides were recognized by CD4+ T cells and identified the presenting HLA alleles. T cell responses cross-reactive between OC43, SARS-CoV-2, and the other seasonal coronaviruses were confirmed in samples of peripheral blood and peptide-expanded T cell lines. Among the validated epitopes, S903-917 presented by DPA1*01:03/DPB1*04:01 and S1085-1099 presented by DRB1*15:01 shared substantial homology to other human coronaviruses, including SARS-CoV-2, and were targeted by cross-reactive CD4 T cells. N54-68 and HE128-142 presented by DRB1*15:01 and HE259-273 presented by DPA1*01:03/DPB1*04:01 are immunodominant epitopes with low coronavirus homology that are not cross-reactive with SARS-CoV-2. Overall, the set of naturally processed and presented OC43 epitopes comprise both OC43-specific and human coronavirus cross-reactive epitopes, which can be used to follow T cell cross-reactivity after infection or vaccination and could aid in the selection of epitopes for inclusion in pan-coronavirus vaccines.\n\nAuthor SummaryThere is much current interest in cellular immune responses to seasonal common-cold coronaviruses because of their possible role in mediating protection against SARS-CoV-2 infection or pathology. However, identification of relevant T cell epitopes and systematic studies of the T cell responses responding to these viruses are scarce. We conducted a study to identify naturally processed and presented MHC-I and MHC-II epitopes from human cells infected with the seasonal coronavirus HCoV-OC43, and to characterize the T cell responses associated with these epitopes. We found epitopes specific to the seasonal coronaviruses, as well as epitopes cross-reactive between HCoV-OC43 and SARS-CoV-2. These epitopes should be useful in following immune responses to seasonal coronaviruses and identifying their roles in COVID-19 vaccination, infection, and pathogenesis.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Aniuska Becerra-Artiles", + "author_inst": "UMass Chan: University of Massachusetts Medical School" + }, + { + "author_name": "Padma P Nanaware", + "author_inst": "UMass Chan Medical School: University of Massachusetts Medical School" + }, + { + "author_name": "Khaja Muneeruddin", + "author_inst": "UMass Chan: University of Massachusetts Medical School" + }, + { + "author_name": "Grant C Weaver", + "author_inst": "UMass Chan: University of Massachusetts Medical School" + }, + { + "author_name": "Scott A Shaffer", + "author_inst": "UMass Chan Medical School: University of Massachusetts Medical School" + }, + { + "author_name": "Jaime Mauricio Calvo-Calle", + "author_inst": "UMass Chan Medical School: University of Massachusetts Medical School" + }, + { + "author_name": "Lawrence J. Stern", + "author_inst": "University of Massachusetts Medical School" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.12.01.518149", "rel_title": "SARS-CoV-2 mRNA vaccine is re-adenylated in vivo, enhancing antigen production and immune response", @@ -140686,41 +142339,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.12.01.22282978", - "rel_title": "Pilot Study Demonstrates Benefits of Nursing Home Air Purification on COVID-19 Outcomes", - "rel_date": "2022-12-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.01.22282978", - "rel_abs": "Improving indoor air quality is one potential strategy to reduce the transmission of SARS-CoV-2 in any setting, including nursing homes, where staff and residents have been disproportionately and negatively affected by the COVID-19 pandemic. We used an interrupted time series design to compare trends in weekly COVID-19 cases and deaths before and after installation of ultraviolet air purification in 84 nursing homes in Florida, Georgia, North Carolina, and South Carolina from September 31, 2020 to December 27, 2020. Compared to pre-installation, weekly COVID-19 cases per 1,000 residents (-1.69, 95%CI: -4.32, 0.95) and the weekly probability of reporting any COVID-19 case (-0.02, 95%CI: -0.04, 0.00) declined in the post-installation period. We did not find any difference pre- and post-installation in COVID-19-related mortality (0.00 95%CI: -0.01, 0.02). Our findings from this small number of nursing homes in the southern US demonstrate the potential benefits of air purification in nursing homes on COVID-19 outcomes. We recommend a stronger experimental design to estimate the causal effect of installing air purification devices like this one on improving COVID-19 outcomes in nursing homes.\n\nPractical ImplicationsImproving indoor air quality is one potential strategy to reduce the burden of COVID-19 in nursing homes and nursing homes are eligible to receive Civil Monetary Penalty funding for purchases that improve air quality. Intervening on air quality may have a wide impact without placing significant burden on individuals to modify their behavior. In this pilot evaluation, we found that installing ultraviolet air purification may be an effective strategy to reduce COVID-19 cases in nursing homes. We recommend a stronger experimental design to determine the causal effect of indoor air interventions, such as air purification, on COVID-19 in this setting.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Eric Jutkowitz", - "author_inst": "Brown University" - }, - { - "author_name": "Peter Shwemaker", - "author_inst": "Brown University" - }, - { - "author_name": "Ann Reddy", - "author_inst": "Brown University" - }, - { - "author_name": "Joseph Braun", - "author_inst": "Brown University" - }, - { - "author_name": "Rosa Baier", - "author_inst": "Brown University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2022.11.30.22282833", "rel_title": "High SARS-CoV-2 seroprevalence in Lagos, Nigeria with robust antibody and cellular responses", @@ -142151,6 +143769,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.11.25.22282676", + "rel_title": "The influence of COVID-19 risk perception and vaccination status on the number of social contacts across Europe: insights from the CoMix study", + "rel_date": "2022-11-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.25.22282676", + "rel_abs": "BackgroundThe SARS-CoV-2 transmission dynamics have been greatly modulated by human contact behaviour. To curb the spread of the virus, global efforts focused on implementing both Non-Pharmaceutical Interventions (NPIs) and pharmaceutical interventions such as vaccination. This study was conducted to explore the influence of COVID-19 vaccination status and risk perceptions related to SARS-CoV-2 on the number of social contacts of individuals in 16 European countries. This is important since insights derived from the study could be utilized in guiding the formulation of risk communication strategies.\n\nMethodsWe used data from longitudinal surveys conducted in the 16 European countries to measure social contact behaviour in the course of the pandemic. The data consisted of representative panels of participants in terms of gender, age and region of residence in each country. The surveys were conducted in several rounds between December 2020 and September 2021. We employed a multilevel generalized linear mixed effects model to explore the influence of risk perceptions and COVID-19 vaccination status on the number of social contacts of individuals.\n\nResultsThe results indicated that perceived severity played a significant role in social contact behaviour during the pandemic after controlling for other variables. More specifically, participants who perceived COVID-19 to be a serious illness made fewer contacts compared to those who had low or neutral perceptions of the COVID-19 severity. Additionally, vaccinated individuals reported significantly higher number of contacts than the non-vaccinated. Further-more, individual-level factors played a more substantial role in influencing contact behaviour than country-level factors.\n\nConclusionOur multi-country study yields significant insights on the importance of risk perceptions and vaccination in behavioral changes during a pandemic emergency. The apparent increase in social contact behaviour following vaccination would require urgent intervention in the event of emergence of an immune escaping variant. Hence, insights derived from this study could be taken into account when designing, implementing and communicating COVID-19 interventions.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "James Wambua", + "author_inst": "Data Science Institute, I-BioStat, Hasselt University, Hasselt, Belgium." + }, + { + "author_name": "Neilshan Loedy", + "author_inst": "Data Science Institute, I-BioStat, Hasselt University, Hasselt, Belgium." + }, + { + "author_name": "Christopher I Jarvis", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel " + }, + { + "author_name": "Kerry LM Wong", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel " + }, + { + "author_name": "Christel Faes", + "author_inst": "Data Science Institute, I-BioStat, Hasselt University, Hasselt, Belgium." + }, + { + "author_name": "Rok Grah", + "author_inst": "European Centre for Disease Prevention and Control (ECDC), Gustav III:s Boulevard 40, 169 73 Solna, Sweden." + }, + { + "author_name": "Bastian Prasse", + "author_inst": "European Centre for Disease Prevention and Control (ECDC), Gustav III:s Boulevard 40, 169 73 Solna, Sweden." + }, + { + "author_name": "Frank Sandmann", + "author_inst": "European Centre for Disease Prevention and Control (ECDC), Gustav III:s Boulevard 40, 169 73 Solna, Sweden." + }, + { + "author_name": "Rene Niehus", + "author_inst": "European Centre for Disease Prevention and Control (ECDC), Gustav III:s Boulevard 40, 169 73 Solna, Sweden." + }, + { + "author_name": "Helen Johnson", + "author_inst": "European Centre for Disease Prevention and Control (ECDC), Gustav III:s Boulevard 40, 169 73 Solna, Sweden. Current address (Health Emergency Preparedness and R" + }, + { + "author_name": "W.John Edmunds", + "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel " + }, + { + "author_name": "Philippe Beutels", + "author_inst": "Centre for Health Economics Research and Modelling Infectious Diseases, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium. AND The" + }, + { + "author_name": "Niel Hens", + "author_inst": "Data Science Institute, I-BioStat, Hasselt University, Hasselt, Belgium. AND Centre for Health Economics Research and Modelling Infectious Diseases, Vaccine & I" + }, + { + "author_name": "Pietro Coletti", + "author_inst": "Data Science Institute, I-BioStat, Hasselt University, Hasselt, Belgium." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.11.29.22282856", "rel_title": "The Detection of COVID-19 in Chest X-Rays Using Ensemble CNN Techniques", @@ -142264,53 +143953,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.11.24.22282643", - "rel_title": "Wastewater genomic surveillance captures early detection of Omicron in Utah", - "rel_date": "2022-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.24.22282643", - "rel_abs": "Wastewater-based epidemiology has emerged as a powerful public health tool to trace new outbreaks, detect trends in infection and provide an early warning of COVID-19 community spread. Here, we investigated the spread of SARS-CoV-2 infections across Utah by characterizing lineages and mutations detected in wastewater samples. We sequenced over 1,200 samples from 32 sewersheds collected between November 2021 and March 2022. Wastewater sequencing confirmed the presence of Omicron (B.1.1.529) in Utah in samples collected on November 19, 2021, up to ten days before its corresponding detection via clinical sequencing. Analysis of diversity of SARS-CoV-2 lineages revealed Delta as the most frequently detected lineage during November, 2021 (67.71%), but it started declining in December, 2021 with the onset of Omicron (B.1.1529) and its sub-lineage BA.1 (6.79%). Proportion of Omicron increased to [~]58% by January 4th 2022 and completely displaced Delta by February 7th, 2022. Wastewater genomic surveillance revealed the presence of Omicron sub-lineage BA.3, a lineage that is yet to be identified from Utahs clinical surveillance. Interestingly, several Omicron-defining mutations began to appear in early November, 2021 and increased in prevalence across sewersheds from December to January. Our study suggests that tracking epidemiologically relevant mutations is critical in detecting emerging lineages in the early stages of an outbreak. Wastewater genomic epidemiology provides an unbiased representation of community-wide infection dynamics and is an excellent complementary tool to SARS-CoV-2 clinical surveillance, with the potential of guiding public health action and policy decisions.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Pooja Gupta", - "author_inst": "Utah Public Health Laboratory, Utah Department of Health and Human Services" - }, - { - "author_name": "Stefan Liao", - "author_inst": "Utah Public Health Laboratory, Utah Department of Health and Human Services" - }, - { - "author_name": "Maleea Ezekiel", - "author_inst": "Utah Public Health Laboratory, Utah Department of Health and Human Services" - }, - { - "author_name": "Nicolle Novak", - "author_inst": "Utah Public Health Laboratory, Utah Department of Health and Human Services" - }, - { - "author_name": "Alessandro Rossi", - "author_inst": "Utah Public Health Laboratory, Utah Department of Health and Human Services" - }, - { - "author_name": "Nathan LaCross", - "author_inst": "Utah Department of Health and Human Services" - }, - { - "author_name": "Kelly Oakeson", - "author_inst": "Utah Public Health Laboratory, Utah Department of Health and Human Services" - }, - { - "author_name": "Andreas Rohrwasser", - "author_inst": "Utah Public Health Laboratory, Utah Department of Health and Human Services" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.11.29.22282848", "rel_title": "Opinions of Former Jail Residents about Self-collection of SARS-CoV-2 Specimens, Paired with Wastewater Surveillance: A Qualitative Study Rapidly Examining Acceptability of COVID-19 Mitigation Measures", @@ -144061,6 +145703,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.11.23.22282478", + "rel_title": "Population Pharmacokinetics and Exposure-Response Analysis of Sotrovimab in the Early Treatment of COVID-19", + "rel_date": "2022-11-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.23.22282478", + "rel_abs": "Sotrovimab is a recombinant human monoclonal antibody that has been shown to prevent progression to hospitalization or death from severe disease in non-hospitalized high-risk patients with mild-to-moderate COVID-19 following either intravenous (IV) or intramuscular (IM) administration. Population pharmacokinetic (popPK) and exposure-response (ER) analyses were performed to characterize sotrovimab PK and the relationship between exposure and response (probability of progression), as well as covariates that may contribute to between-participant variability in sotrovimab PK and efficacy following IV or IM administration. Sotrovimab PK was described by a two-compartment model with linear elimination; IM absorption was characterized by a sigmoid absorption model. PopPK covariate analysis led to the addition of the effect of body weight on systemic clearance and peripheral volume of distribution, sex on IM bioavailability and first-order absorption rate (KA), and body mass index on KA. However, the magnitude of covariate effect was not pronounced and was therefore not expected to be clinically relevant based on available data to date. For ER analysis, sotrovimab exposure measures were predicted using the final popPK model. An ER model was developed using the exposure measure of sotrovimab concentration at 168 hours that described the relationship between exposure and probability of progression within the ER dataset for COMET-TAIL. The number of risk factors ([≤]1 vs >1) was incorporated as an additive shift on the model-estimated placebo response but had no impact on overall drug response. Limitations in the ER model may prevent generalization of these results to describe the sotrovimab exposure-progression relationship across SARS-COV-2 variants.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Jennifer Sager", + "author_inst": "Vir Biotechnology" + }, + { + "author_name": "Asma El-Zailik", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Julie Passarell", + "author_inst": "Cognigen Division, Simulations Plus, Inc." + }, + { + "author_name": "Stefan Roepcke", + "author_inst": "Cognigen Division, Simulations Plus, Inc." + }, + { + "author_name": "Xiaobin Li", + "author_inst": "GSK, Upper Providence" + }, + { + "author_name": "Melissa Aldinger", + "author_inst": "Vir Biotechnology, Inc." + }, + { + "author_name": "Ahmed Nader", + "author_inst": "GSK, Upper Providence" + }, + { + "author_name": "Andrew Skingsley", + "author_inst": "GSK, Brentford" + }, + { + "author_name": "Elizabeth L. Alexander", + "author_inst": "Vir Biotechnology, Inc." + }, + { + "author_name": "Wendy W. Yeh", + "author_inst": "Vir Biotechnology, Inc." + }, + { + "author_name": "Erik Mogalian", + "author_inst": "Vir Biotechnology, Inc." + }, + { + "author_name": "Chad Garner", + "author_inst": "Vir Biotechnology, Inc." + }, + { + "author_name": "Amanda Peppercorn", + "author_inst": "GSK, Cambridge" + }, + { + "author_name": "Adrienne E Shapiro", + "author_inst": "University of Washington" + }, + { + "author_name": "Maribel Reyes", + "author_inst": "Vir Biotechnology, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pharmacology and therapeutics" + }, { "rel_doi": "10.1101/2022.11.23.22282463", "rel_title": "Heterogeneity of treatment effect of higher dose dexamethasone by geographic region in patients with COVID-19 and severe hypoxemia - A post hoc evaluation of the COVID STEROID 2 trial", @@ -144258,33 +145975,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "addiction medicine" }, - { - "rel_doi": "10.1101/2022.11.22.22282637", - "rel_title": "Prediction of Covid-19 vaccine effectiveness in adult populations and in clinically-vulnerable subgroups", - "rel_date": "2022-11-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.22.22282637", - "rel_abs": "Predictions of Covid vaccine effectiveness could support rapid and effective measures against the pandemic. Our modelling boosts the accuracy and applications of these predictions, especially to subgroups. We model the symptomatic effectiveness of Comirnaty or Vaxzevria with 50% neutralising antibody titres from a large UK immunogenicity study and with up to 68 effectiveness estimates from 23 vaccine studies. We predicted effectiveness in adult populations, age and disease subgroups, with 45% (95% CI: 27-63) predicted against Omicron BA.1 for Comirnaty boosters in haemodialysis patients. Prediction errors for two Comirnaty doses in adults were 1.9%, 2.6% and 0.4%, against the Alpha, Beta and Delta variants, versus 3.6%, 28% and 8.7% with a state-of-the-art alternative; and for Vaxzevria, 1.1% and 0.7% against Alpha and Delta, versus 18% and 20.4%. Identical titres implied between 18% (95% CI: 1-33) and 31% (95% CI: 13-50) lower Comirnaty effectiveness against Omicron BA.1 than Delta.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Oleg Volkov", - "author_inst": "Xitific LTD" - }, - { - "author_name": "Svetlana Borozdenkova", - "author_inst": "Xitific LTD" - }, - { - "author_name": "Alexander Gray", - "author_inst": "IDEAPharma" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.11.23.517619", "rel_title": "Feline Coronavirus Infection of Domestic Cats Causes Development of Cross-Reactive Antibodies to SARS-CoV-2 Receptor Binding Domain", @@ -145919,6 +147609,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2022.11.21.22282569", + "rel_title": "COVID-19-related testing, knowledge and behaviors among severe and chronic non-communicable disease patients in Neno District, Malawi: A prospective cohort study.", + "rel_date": "2022-11-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.21.22282569", + "rel_abs": "ObjectiveTo assess changes over time in COVID-19 knowledge, risks, symptoms, testing, and infection prevention practices among patients with complex non-communicable disease (NCD) receiving care at Neno District and Lisungwi Community Hospitals, Malawi.\n\nDesign and participantsWe conducted a prospective open cohort study using telephone-based data collection among patients enrolled in NCD clinics. We conducted four rounds of data collection between November 2020 and October 2021.\n\nSettingRural southwestern Malawi in Neno District which has a population of 150, 211 persons.\n\nPrimary and secondary outcome measuresWe used descriptive statistics to characterize the population and assess COVID-19-related knowledge and behaviors. Linear and logistic regression models were used to assess significant changes over time.\n\nResultsAcross four rounds of data collection, the most commonly reported COVID-19-related risks among patients included visiting health facilities (range: 35-49%), attending mass gatherings (range: 33-36%), and travelling outside the district (range: 14-19%). Patients reporting having ever experienced COVID-like symptoms increased from 30% in December 2020 to 41% in October 2021, however, as of the end of study period, only 13% of patients had ever received a COVID-19 test. Overall, respondents answered about two thirds (range: 67-70%) of the COVID-19 knowledge questions correctly with no significant changes over time. Hand washing, wearing of face masks and maintaining safe distance were the most frequently reported strategies used to prevent spreading of COVID-19. Wearing of facemask significantly improved from 63% to 96% over time (p<0.001).\n\nConclusionsHouseholds of advanced chronic disease patients reported accurate knowledge about COVID-19 and improved adherence to wearing of face masks over time. However, patients commonly visit locations where they could be exposed to COVID-19 and often experience COVID-like symptoms but are rarely tested for COVID-19. We urge the government and other stakeholders to increase COVID-19 testing accessibility to primary facility and community levels.\n\nStrengths and limitations of this studyO_LIAssessed COVID-19-related outcomes among a highly vulnerable group of patients in a rural African setting\nC_LIO_LILongitudinal follow-up allowed us to assess changes over time from December 2020 to September 2021\nC_LIO_LIData can inform COVID-19 infection preventive measures in a setting with persistently poor access to COVID-19 vaccines\nC_LIO_LIThe telephone survey was conducted among severe and chronic NCD patients in rural Malawi and is not generalizable to urban areas or rural populations without cellular service\nC_LIO_LIData was self-reported data and vulnerable to social desirability bias\nC_LI", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Haules Robbins Zaniku", + "author_inst": "Neno District Health Office" + }, + { + "author_name": "Moses Banda Aron", + "author_inst": "Partners in Health, Malawi" + }, + { + "author_name": "Kaylin Vrkljan", + "author_inst": "Harvard College, Harvard University, USA" + }, + { + "author_name": "Kartik Tyagi", + "author_inst": "Gillings School of Global Public Health, University of North Carolina at Chapel Hill" + }, + { + "author_name": "Myness Kasanda Ndambo", + "author_inst": "Malawi Epidemiology and Intervention Research Unit (MEIRU), Malawi" + }, + { + "author_name": "Gladys Mtalimanja Banda", + "author_inst": "Neno District Health Office, Malawi" + }, + { + "author_name": "Revelation Nyirongo", + "author_inst": "Partners in Health, Malawi" + }, + { + "author_name": "Isaac Mphande", + "author_inst": "Partners in Health, Malawi" + }, + { + "author_name": "Bright Mailosi", + "author_inst": "Partners in Health, Malawi" + }, + { + "author_name": "George Talama", + "author_inst": "Partners in Hope, Malawi" + }, + { + "author_name": "Fabien Munyaneza", + "author_inst": "Partners in Health, Malawi" + }, + { + "author_name": "Emilia Connolly", + "author_inst": "Partners in Health, Malawi" + }, + { + "author_name": "Luckson Dullie", + "author_inst": "Partners in Health, Malawi" + }, + { + "author_name": "Dale A. Barnhart", + "author_inst": "Partners in Health, Rwanda" + }, + { + "author_name": "Todd Ruderman", + "author_inst": "Partners in Health, Malawi" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.11.21.517390", "rel_title": "Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England", @@ -146012,25 +147777,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2022.11.20.517236", - "rel_title": "Polymorphic regions in BA.2.12.1, BA.4 and BA.5 likely implicated in immunological evasion of Omicron subvariant BQ.1.1", - "rel_date": "2022-11-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.20.517236", - "rel_abs": "In this work, 45 Spike glycoprotein Chain B polypeptides were used in the subvariants BA.2.12.1, BA.4 and BA.5 were recovered from GENBANK. All sequences were publicly available on the National Biotechnology Information Center (NCBI) platform. The results indicate the existence of informative polymorphic and parsimony sites that may be implicated in the level of diversity of the studied strains, as well as reflect the immunological evasion potential of the subvariant BQ1.1. of the variant Omicron d and SARS-CoV-2. The results also suggest the formation of ancestral polymorphism with slight retention, and the probable is responsible the diversity of the whole studied set.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Pierre Teodosio Felix Sr.", - "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA, Vitoria de Santo Antao, Pernambuco, Brazil." - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.11.18.517139", "rel_title": "SARS-CoV-2 variant transition dynamics are associated with vaccination rates, number of co-circulating variants, and natural immunity", @@ -147601,6 +149347,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2022.11.17.22282473", + "rel_title": "Perceptions and compliance with COVID-19 preventive measures in Southern and Central regions of Mozambique: a quantitative in-person household survey in the districts of Manhica and Quelimane", + "rel_date": "2022-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.17.22282473", + "rel_abs": "BackgroundThe COVID-19 pandemic has led countries into urgent implementation of stringent preventive measures at the population level. However, implementing these measures in low-income countries like Mozambique was incredibly difficult, coupled with lack of scientific evidence on the community understanding and compliance with these measures. This study assessed the perceptions and implementation of COVID-19 preventive measures recommended by Mozambican authorities in Manhica and Quelimane districts, taking confinement, social distancing, frequent handwashing, mask wearing, and quarantine as the key practices to evaluate.\n\nMethodsA quantitative survey interviewing households heads in-person was conducted in October 2020 and February 2021; collecting data on perceptions of COVID-19, symptoms, means of transmission/prevention; including self-evaluation of compliance with the key measures, existence of handwashing facilities, and the ratio of face-masks per person. The analysis presents descriptive statistics on perceptions and compliance with anti-COVID-19 measures at individual and household levels, comparing by district and other variables. T-test was performed to assess the differences on proportions between the districts or categories of respondents in the same district.\n\nResultsThe study interviewed 770 individuals of which 62.3% were heads of households, 18.6% their spouses, and 11.0% sons/daughters. Most participants (98.7%) had heard of COVID-19 disease. The most difficult measure to comply with was staying at home (35.8% of respondents said they could not comply with it at all); followed by avoiding touching the month/nose/eyes (28.7%), and social distancing at home (27.3%). Mask wearing in public places was the measure that more respondents (48.8%) thought they complied 100% with it, followed by avoiding unnecessary traveling (40.0%), avoiding crowed places (34.0%), and social distancing outside home (29.0%). Only 30.4% of households had handwashing devices or disinfectant (36.7% in Manhica and 24.1% in Quelimane); and of those with devices, only 41.0% had water in the device, 37.6% had soap, and 22.6% had other disinfectant. The ratio of masks per person was only 1, which suggests that people may have used the same mask for longer periods than recommended.\n\nConclusionsCommunity members in Manhica and Quelimane were aware of COVID-19 but they lacked understanding for implementing the preventive measures. This, together with socio-economic constraints, led to lower levels of compliance with the key measures. Understanding and addressing the factors affecting proper implementation of these measures is crucial for informing decision-makers about ways to improve community knowledge and practices to prevent infectious diseases with epidemic potential.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Ariel Nhacolo", + "author_inst": "CISM: Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Amilcar Maga\u00e7o", + "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a: Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Felizarda Amosse", + "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a: Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Aura Hunguana", + "author_inst": "Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Teodomiro Matsena", + "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a: Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Arsenio Nhacolo", + "author_inst": "Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Elisio Xerinda", + "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a: Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Quique Bassat", + "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a: Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Charfudin Sacoor", + "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a: Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Inacio Mandomando", + "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a: Centro de Investigacao em Saude de Manhica" + }, + { + "author_name": "Khatia Munguambe", + "author_inst": "Centro de Investiga\u00e7\u00e3o em Sa\u00fade de Manhi\u00e7a: Centro de Investigacao em Saude de Manhica" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.11.17.22282452", "rel_title": "Association between long COVID symptoms and employment status", @@ -147738,85 +149543,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.11.18.517047", - "rel_title": "Innate immune response to SARS-1 CoV-2 infection contributes to neuronal damage in human iPSC-derived peripheral neurons", - "rel_date": "2022-11-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.18.517047", - "rel_abs": "Severe acute respiratory coronavirus 2 (SARS-CoV-2) infection causes neurological disease in some patients suggesting that infection can affect both the peripheral and central nervous system (PNS and CNS, respectively). It is not clear whether the outcome of SARS-CoV-2 infection of PNS and CNS neurons is similar, and which are the key factors that cause neurological disease: SARS-CoV-2 infection or the subsequent immune response. Here, we addressed these questions by infecting human induced-pluripotent stem cell-derived CNS and PNS neurons with the {beta} strain of SARS-CoV-2. Our results show that SARS-CoV-2 infects PNS neurons more efficiently than CNS neurons, despite lower expression levels of angiotensin converting enzyme 2. Infected PNS neurons produced interferon {lambda}1, several interferon stimulated genes and proinflammatory cytokines. They also displayed neurodegenerative-like alterations, as indicated by increased levels of sterile alpha and Toll/interleukin receptor motif-containing protein 1, amyloid precursor protein and -synuclein and lower levels of nicotinamide mononucleotide adenylyltransferase 2 and {beta}-III-tubulin. Interestingly, blockade of the Janus kinase and signal transducer and activator of transcription pathway by Ruxolitinib did not increase SARS-CoV-2 infection, but reduced neurodegeneration, suggesting that an exacerbated neuronal innate immune response contributes to pathogenesis in the PNS.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Vania Passos", - "author_inst": "Institute of Virology, Hannover Medical School, Hannover, Germany" - }, - { - "author_name": "Lisa M Henkel", - "author_inst": "Department of Neurology, Hannover Medical School, Hannover, Germany" - }, - { - "author_name": "Jiayi Wang", - "author_inst": "Institute of Virology, Hannover Medical School, Hannover, Germany" - }, - { - "author_name": "Francisco J Zapatero-Belinchon", - "author_inst": "University of Veterinary Medicine Hannover, Foundation, Hannover, Germany" - }, - { - "author_name": "Rebecca Moeller", - "author_inst": "University of Veterinary Medicine Hannover, Foundation, Hannover, Germany" - }, - { - "author_name": "Guorong Sun", - "author_inst": "Institute of Virology, Hannover Medical School, Hannover, Germany" - }, - { - "author_name": "Inken Waltl", - "author_inst": "Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre f" - }, - { - "author_name": "Birgit Ritter", - "author_inst": "Institute of Virology, Hannover Medical School" - }, - { - "author_name": "Kai A Kropp", - "author_inst": "Institute of Virology, Hannover Medical School, Hannover, Germany" - }, - { - "author_name": "Shuyong Zhu", - "author_inst": "Institute of Virology, Hannover Medical School, Hannover, Germany" - }, - { - "author_name": "Michela Deleidi", - "author_inst": "German Center for Neurodegenerative Diseases (DZNE), Tuebingen, Germany; Center of Neurology, Hertie Institute for Clinical Brain Research, University of Tuebin" - }, - { - "author_name": "Ulrich Kalinke", - "author_inst": "Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre f" - }, - { - "author_name": "Guenter Hoeglinger", - "author_inst": "Department of Neurology, Hannover Medical School, Hannover, Germany" - }, - { - "author_name": "Gisa Gerold", - "author_inst": "University of Veterinary Medicine Hannover, Foundation, Hannover, Germany" - }, - { - "author_name": "Florian Wegner", - "author_inst": "Department of Neurology, Hannover Medical School, Hannover, Germany" - }, - { - "author_name": "Abel Viejo-Borbolla", - "author_inst": "Hannover Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.11.17.516978", "rel_title": "Human Early Syncytiotrophoblasts Are Highly Susceptible to SARS-CoV-2 Infection", @@ -149323,6 +151049,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.15.516323", + "rel_title": "The SARS-CoV-2 protein ORF3c is a mitochondrial modulator of innate immunity", + "rel_date": "2022-11-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.15.516323", + "rel_abs": "The SARS-CoV-2 genome encodes a multitude of accessory proteins. Using comparative genomic approaches, an additional accessory protein, ORF3c, has been predicted to be encoded within the ORF3a sgmRNA. Expression of ORF3c during infection has been confirmed independently by ribosome profiling. Despite ORF3c also being present in the 2002-2003 SARS-CoV, its function has remained unexplored. Here we show that ORF3c localises to mitochondria during infection, where it inhibits innate immunity by restricting IFN-{beta} production, but not NF-{kappa}B activation or JAK-STAT signalling downstream of type I IFN stimulation. We find that ORF3c acts after stimulation with cytoplasmic RNA helicases RIG-I or MDA5 or adaptor protein MAVS, but not after TRIF, TBK1 or phospho-IRF3 stimulation. ORF3c co-immunoprecipitates with the antiviral proteins MAVS and PGAM5 and induces MAVS cleavage by caspase-3. Together, these data provide insight into an uncharacterised mechanism of innate immune evasion by this important human pathogen.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Hazel Stewart", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Yongxu Lu", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Anusha Valpadashi", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Luis Daniel Cruz-Zaragoza", + "author_inst": "University Medical Center Goettingen" + }, + { + "author_name": "Hendrik A Michel", + "author_inst": "Harvard Graduate Program in Virology" + }, + { + "author_name": "Samantha K Nguyen", + "author_inst": "University of Cambridge" + }, + { + "author_name": "George W Carnell", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Nina Lukhovitskaya", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Rachel Milligan", + "author_inst": "University of Bristol" + }, + { + "author_name": "Irwin Jungreis", + "author_inst": "MIT" + }, + { + "author_name": "Valeria Lulla", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Andrew D Davidson", + "author_inst": "University of Bristol" + }, + { + "author_name": "David A Matthews", + "author_inst": "University of Bristol" + }, + { + "author_name": "Stephen High", + "author_inst": "University of Manchester" + }, + { + "author_name": "Peter Rehling", + "author_inst": "Univ. Goettingen" + }, + { + "author_name": "Edward Emmott", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Jonathan Luke Heeney", + "author_inst": "University of Cambridge" + }, + { + "author_name": "James R Edgar", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Geoffrey L. Smith", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Andrew E Firth", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.11.14.22282297", "rel_title": "Using Genome Sequence Data to Predict SARS-CoV-2 Detection Cycle Threshold Values", @@ -149428,29 +151249,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.11.14.22282128", - "rel_title": "Assessment of level of depression and associated factors among COVID-19 recovered patients: a cross sectional study", - "rel_date": "2022-11-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.14.22282128", - "rel_abs": "ObjectivesThe Corona Virus Disease-2019 (COVID-19) pandemic has psychological consequences such as increased risk of depression, anxiety, and stress problems, exacerbating human health disparities. This study aimed to analyze depression and its causes in COVID-19-recovered patients in Bangladesh.\n\nMethodA cross-sectional study was conducted on COVID-19 recovered patients, who attended for follow-up after 14 days to 3 months at Dhaka Medical College Hospital (DMCH) and Dhaka North City Corporation Hospital (DNCCH), Dhaka, Bangladesh from 1st January to 31st December, 2021. Respondents were face-to-face interviewed with a semi-structured questionnaire after written agreement. The Patient Health Questionnaire (PHQ-9) was used to assess respondents depression, and data were analyzed using SPSS version-23, with p < 0.05 indicating statistical significance.\n\nResultsA total of 325 COVID-19 recovered patients aged from 15 to 65 years (mean 44.34 {+/-}13.87 years) of age were included in this study, highest 23.1% of them belonged to 46-55 years, and majority (61.5%) of them were male. There were 69.5% of respondents had no signs of depression while 31% of them had with 26.7 % being mildly depressed, 2.5 % being extremely depressed, and 1.2 % being severely depressed. Diabetes mellitus, hospitalization duration, social distancing, the social media post on COVID-19, loss of employment, family damage, and fear of re-infection were significantly associated with depression level of respondents.\n\nConclusionThis study gives us a glimpse into the psychological health of COVID-19 recovered patients, and its findings highlight the imperative of alleviating their psychological anguish in Bangladesh.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Mst.Khadeza Khatun", - "author_inst": "Dhaka Medical college Hospital" - }, - { - "author_name": "Nasreen Farhana", - "author_inst": "National Institute of Preventive and Social Medicine (NIPSOM), Mohakhali, Dhaka, Bangladesh" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.11.13.22282222", "rel_title": "Acute and Post-Acute COVID-19 Outcomes Among Immunologically Nai\u0308ve Adults During Delta Versus Omicron Waves", @@ -151241,6 +153039,57 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2022.11.09.22282120", + "rel_title": "Selection of long COVID symptoms influences prevalence estimates in a prospective cohort", + "rel_date": "2022-11-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.09.22282120", + "rel_abs": "BackgroundStudies on long COVID differ in the selection of symptoms used to define the condition. We aimed to assess to what extent symptom selection impacts prevalence estimates of long COVID.\n\nMethodsIn a prospective cohort of patients who experienced mild to critical coronavirus disease 2019 (COVID-19), we used longitudinal data on the presence of 20 different symptoms to evaluate changes in the prevalence of long COVID over time when altering symptom selection.\n\nResultsChanging symptom selection resulted in wide variation in long COVID prevalence, even within the same study population. Long COVID prevalence at 12 months since illness onset ranged from 39.6% (95%CI=33.4-46.2) when using a limited selection of symptoms to 80.6% (95%CI=74.8-85.4) when considering any reported symptom to be relevant.\n\nConclusionsComparing the occurrence of long COVID is already complex due to heterogeneity in study design and population. Disparate symptom selection may further hamper comparison of long COVID estimates between populations. Harmonised data collection tools could be one means to achieve greater reproducibility and comparability of results.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Elke Wynberg", + "author_inst": "Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands" + }, + { + "author_name": "Godelieve J. de Bree", + "author_inst": "Department of Infectious Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands" + }, + { + "author_name": "Tjalling Leenstra", + "author_inst": "National Institute for Public Health and the Environment (Rijksinstituut voor Volksgezondheid en Milieu; RIVM), Bilthoven, Netherlands" + }, + { + "author_name": "Anouk Verveen", + "author_inst": "Department of Medical Psychology, Amsterdam UMC, Amsterdam Public Health Research Institute, University of Amsterdam, Amsterdam, the Netherlands" + }, + { + "author_name": "Hugo D.G. van Willigen", + "author_inst": "Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, th" + }, + { + "author_name": "Menno de Jong", + "author_inst": "Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, th" + }, + { + "author_name": "Maria Prins", + "author_inst": "Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands" + }, + { + "author_name": "Anders Boyd", + "author_inst": "Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands; Stichting hiv monitoring, Amsterdam, the Netherlands" + }, + { + "author_name": "- the RECoVERED Study Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.11.11.516114", "rel_title": "A broad-spectrum macrocyclic peptide inhibitor of the SARS-CoV-2 spike protein", @@ -151502,57 +153351,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.11.11.516107", - "rel_title": "Crystal structure and activity profiling of deubiquitinating inhibitors-bound to SARS-CoV-2 papain like protease revealed new allosteric sites for antiviral therapies", - "rel_date": "2022-11-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.11.516107", - "rel_abs": "Emerging variants of SARS-CoV-2 still threaten the effectiveness of currently deployed vaccines, and antivirals can prove to be an effective therapeutic option for attenuating it. The papain-like protease (PLpro) is an attractive target due to its sequence conservation and critical role in the replication and pathogenesis of SARS-CoV-2. PLpro also plays very important role in modulation of host immune responses by deubiquitinating (DUBs) or deISGylating host proteins. Thus, targeting PLpro serves as a two-pronged approach to abate SARS-CoV-2. Due to its structural and functional similarities with the host DUB enzymes, an in-house library of DUB inhibitors was constituted in this study. Five promising compounds exhibiting high binding affinities with the substrate binding site of PLpro were identified from a library of 81 compounds with in silico screening, docking, and simulation studies. Interestingly, lithocholic acid, linagliptin, teneligliptin, and flupenthixol significantly inhibited the proteolytic activity of PLpro. Each of these compounds abrogated in vitro replication of SARS-CoV-2 with EC50 values in the range of 5-21 M. In addition, crystal structure of SARS-CoV-2 PLpro and its complex with inhibitors have been determined that revealed their inhibitory mechanism. The findings of this study provide the proof-of-principle that the DUB inhibitors hold high potential as a new class of therapeutics against SARS-CoV-2. Additionally, this is the first study that has opened a new avenue towards not only targeting PLpro active site but also simultaneously directing towards restoration of antiviral immune response of the host for deterring SARS-CoV-2.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=173 SRC=\"FIGDIR/small/516107v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (51K):\norg.highwire.dtl.DTLVardef@1f7d0c6org.highwire.dtl.DTLVardef@ab9c13org.highwire.dtl.DTLVardef@93d3f3org.highwire.dtl.DTLVardef@14021e6_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Shweta Choudhary", - "author_inst": "Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India 247667" - }, - { - "author_name": "Sanketkumar Nehul", - "author_inst": "Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India 247667" - }, - { - "author_name": "K Amith Kumar", - "author_inst": "Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India 247667" - }, - { - "author_name": "Swati Sharma", - "author_inst": "Shiv Nadar University, Uttar Pradesh (201314), India" - }, - { - "author_name": "Ruchi Rani", - "author_inst": "Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India 247667" - }, - { - "author_name": "Ankita Saha", - "author_inst": "Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India 247667" - }, - { - "author_name": "Gaurav Kumar Sharma", - "author_inst": "Centre for Animal Disease Research and Diagnosis (CADRAD), Indian veterinary Research Institute, Bareilly (IVRI, Bareilly) Uttar Pradesh, India" - }, - { - "author_name": "Shailly Tomar", - "author_inst": "Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India 247667" - }, - { - "author_name": "Pravindra Kumar", - "author_inst": "Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand, India 247667" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2022.11.10.22282132", "rel_title": "Year-round RSV Transmission in the Netherlands Following the COVID-19 Pandemic - A Prospective Nationwide Observational and Modeling Study", @@ -152887,6 +154685,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.11.07.22282054", + "rel_title": "Durability and determinants of anti-SARS-CoV-2 spike antibodies following the second and third doses of mRNA COVID-19 vaccine", + "rel_date": "2022-11-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.07.22282054", + "rel_abs": "BackgroundEpidemiological data regarding differences in durability and its determinants of humoral immunity following 2- and 3-dose COVID-19 vaccination are scarce.\n\nMethodsWe repeatedly assessed the anti-spike IgG antibody titers of 2- and 3-dose mRNA vaccine recipients among the staff of a medical and research center in Tokyo. Linear mixed models were used to estimate trajectories of antibody titers from 14 to 180 days after the last immune-conferred event (vaccination or infection) and compare antibody waning rates across prior infection and vaccination status, and across background factors in infection-naive participants.\n\nResultsA total of 6901 measurements from 2964 participants (median age, 35 years; 30% male) were analyzed. Antibody waning rate (per 30 days [95% CI]) was slower after 3-dose (25% [23-26]) than 2-dose (36% [35-37]). Participants with hybrid immunity (vaccination and infection) had further slower waning rates: 2-dose plus infection (16% [9-22]); 3-dose plus infection (21% [17-25]). Older age, male sex, obesity, coexisting diseases, immunosuppressant use, smoking, and alcohol drinking were associated with lower antibody titers, whereas these associations disappeared after 3-dose, except for sex (lower in female participants) and immunosuppressant use. Antibody waning was faster in older participants, females, and alcohol drinkers after 2-dose, whereas it did not differ after 3-dose across except sex.\n\nConclusionsThe 3-dose mRNA vaccine conferred higher durable antibody titers, and previous infection further enhanced its durability. The antibody levels at a given time point and waning speed after 2-dose differed across background factors; however, these differences mostly diminished after 3-dose.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Shohei Yamamoto", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Yusuke Oshiro", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Natsumi Inamura", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Takashi Nemoto", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Kumi Horii", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Kaori Okudera", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Maki Konishi", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Mitsuru Ozeki", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Tetsuya Mizoue", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Haruhito Sugiyama", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Nobuyoshi Aoyanagi", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Wataru Sugiura", + "author_inst": "Naional Center for Global Health and Medicine" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "Kokuritsu Kenkyu Kaihatsu Hojin Kokuritsu Kokusai Iryo Kenkyu Center" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.11.08.515436", "rel_title": "Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection.", @@ -153136,41 +155001,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2022.11.08.515673", - "rel_title": "Prediction of Transport, Deposition, and Resultant Immune Response of Nasal Spray Vaccine Droplets using a CFPD-HCD Model in a 6-Year-Old Upper Airway Geometry to Potentially Prevent COVID-19", - "rel_date": "2022-11-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.08.515673", - "rel_abs": "This study focuses on the transport, deposition, and triggered immune response of intranasal vaccine droplets to the Angiotensin-converting enzyme 2-rich region (i.e., the olfactory region (OR)) in the nasal cavity of a 6-year-old female to possibly prevent COVID-19. To investigate how administration strategy can influence nasal vaccine efficiency, a validated multiscale model (i.e., computational fluid-particle dynamics (CFPD) and host-cell dynamics (HCD) model) was employed. Droplet deposition fraction, size change, residence time, and the area percentage of OR covered by the vaccine droplets and triggered immune system response were predicted with different spray cone angles, initial droplet velocities, and compositions. Numerical results indicate that droplet initial velocity and composition have negligible influences on the vaccine delivery efficiency to OR. In contrast, the spray cone angle can significantly impact the vaccine delivery efficiency. The triggered immunity was not significantly influenced by the administration investigated in this study, due to the low percentage of OR area covered by the droplets. To enhance the effectiveness of the intranasal vaccine to prevent COVID-19 infection, it is necessary to optimize the vaccine formulation and administration strategy so that the vaccine droplets can cover more epithelial cells in OR to minimize the available receptors for SARS-CoV-2.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Hamideh Hayati", - "author_inst": "Oklahoma State University" - }, - { - "author_name": "Yu Feng", - "author_inst": "Oklahoma State University" - }, - { - "author_name": "Xiaole Chen", - "author_inst": "Nanjing Normal University" - }, - { - "author_name": "Emily Kolewe", - "author_inst": "University of Delaware" - }, - { - "author_name": "Catherine Fromen", - "author_inst": "University of Delaware" - } - ], - "version": "1", - "license": "cc_no", - "type": "confirmatory results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2022.11.07.515557", "rel_title": "Normalized Semi-Covariance Co-Efficiency Analysis of Spike Proteins from SARS-CoV-2 variant Omicron and Other Coronaviruses for their Infectivity and Virulence", @@ -154529,6 +156359,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.02.22281822", + "rel_title": "Augmenting vaccine efficacy against delta variant with Mycobacterium-w mediated modulation of NK-ADCC and TLR-MYD88 pathways", + "rel_date": "2022-11-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.02.22281822", + "rel_abs": "Mycobacterium-w (Mw), was shown to boost adaptive natural killer (ANK) cells and protect against COVID-19 during the first wave of the pandemic. As a follow-up of the trial, 50 healthcare workers (HCW) who had received Mw in September 2020 and subsequently received at least one dose of ChAdOx1 nCoV-19 vaccine (Mw+ChAdOx1 group) were monitored for symptomatic COVID-19, during a major outbreak with the delta variant of SARS-CoV-2 (April-June, 2021), along with 201 HCW receiving both doses of the vaccine without Mw (ChAdOx1 group). Despite 48% having received just a single dose of the vaccine in Mw+ChAdOx1 group, only 2 had mild COVID-19, compared to 36 infections in the ChAdOx1 group (HR-0.46, p=0.009). Transcriptomic studies revealed an enhanced adaptive NK cell-dependent ADCC in the Mw+ChAdOx1 group, along with downregulation of TLR2-MYD88 pathway and concomitant attenuation of downstream inflammatory pathways. This might have resulted in robust protection during the pandemic with the delta variant.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Sarita Rani Jaiswal", + "author_inst": "Dharamshila Narayana Superspeciality Hospital, New Delhi-96" + }, + { + "author_name": "Ashraf Saifullah", + "author_inst": "Dharamshila Narayana Superspeciality Hospital, New Delhi-96" + }, + { + "author_name": "Jaganath Arunachalam", + "author_inst": "Manashi Chakrabarti Foundation, New Delhi-96" + }, + { + "author_name": "Rohit Lakhchaura", + "author_inst": "Dharamshila Narayana Superspeciality Hospital, New Delhi-96" + }, + { + "author_name": "Dhanir Tailor", + "author_inst": "Oregon Health & Science University, USA" + }, + { + "author_name": "Anupama Mehta", + "author_inst": "Dharamshila Narayana Superspeciality Hospital, New Delhi-96" + }, + { + "author_name": "Gitali bhagawati", + "author_inst": "Dharamshila Narayana Superspeciality Hospital, New Delhi-96" + }, + { + "author_name": "Hemamalini Iyer", + "author_inst": "Dharamshila Narayana Superspeciality Hospital, New Delhi-96" + }, + { + "author_name": "Subhrajit Biswas", + "author_inst": "Amity University, Uttar Pradesh, INDIA" + }, + { + "author_name": "Bakulesh M Khamar", + "author_inst": "Cadila Pharmaceuticals Limited" + }, + { + "author_name": "Sanjay V Malhotra", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Suparno Chakrabarti", + "author_inst": "Manashi Chakrabarti Foundation, New Delhi-96" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.11.04.22281910", "rel_title": "Surveillance of COVID-19 vaccine safety among elderly persons aged 65 years and older", @@ -154702,101 +156595,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.11.01.22281746", - "rel_title": "Population-based sero-epidemiological estimates of real-world vaccine effectiveness against Omicron infection in an infection-naive population, Hong Kong, January to July 2022", - "rel_date": "2022-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.01.22281746", - "rel_abs": "The SARS-CoV-2 Omicron variant has demonstrated enhanced transmissibility and escape of vaccine-derived immunity. While current vaccines remain effective against severe disease and death, robust evidence on vaccine effectiveness (VE) against all Omicron infections (i.e. irrespective of symptoms) remains sparse. We addressed this knowledge-gap using a community-wide serosurvey with 5,310 subjects by estimating how vaccination histories modulated risk of infection in Hong Kong (which was largely infection naive) during a large wave of Omicron epidemic during January-July 2022. We estimated that Omicron infected 45% (41-48%) of the Hong Kong population. Three and four doses of BNT162b2 or CoronaVac were effective against Omicron infection (VE of 47% (95% credible interval 34-68%) and 70% (43-99%) for three and four doses of BNT162b2 respectively; VE of 31% (1-73%) and 59% (10-99%) for three and four doses of CoronaVac respectively) seven days after vaccination, but protection waned with half-lives of 15 (3-47) weeks for BNT162b2 and 5 (1-37) weeks for CoronaVac. Our findings suggest that booster vaccination can temporarily enhance population immunity ahead of anticipated waves of infections.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Jonathan J Lau", - "author_inst": "WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Ko" - }, - { - "author_name": "Samuel MS Cheng", - "author_inst": "School of Public Health, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong SAR, China" - }, - { - "author_name": "Kathy Leung", - "author_inst": "WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Ko" - }, - { - "author_name": "Cheuk Kwong Lee", - "author_inst": "Hong Kong Red Cross Blood Transfusion Service, Hospital Authority, Hong Kong SAR, People's Republic of China" - }, - { - "author_name": "Asmaa Hachim", - "author_inst": "HKU-Pasteur Research Pole, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China" - }, - { - "author_name": "Leo CH Tsang", - "author_inst": "School of Public Health, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong SAR, China" - }, - { - "author_name": "Kenny WH Yam", - "author_inst": "School of Public Health, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong SAR, China" - }, - { - "author_name": "Sara Chaothai", - "author_inst": "School of Public Health, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong SAR, China" - }, - { - "author_name": "Kelvin KH Kwan", - "author_inst": "School of Public Health, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong SAR, China" - }, - { - "author_name": "Zacary YH Chai", - "author_inst": "School of Public Health, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong SAR, China" - }, - { - "author_name": "Tiffany HK Lo", - "author_inst": "WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Ko" - }, - { - "author_name": "Masashi Mori", - "author_inst": "Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Japan" - }, - { - "author_name": "Chao Wu", - "author_inst": "Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA." - }, - { - "author_name": "Sophie A Valkenburg", - "author_inst": "Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Gaya K Amarasinghe", - "author_inst": "Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA" - }, - { - "author_name": "Eric HY Lau", - "author_inst": "WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Ko" - }, - { - "author_name": "David S Hui", - "author_inst": "Chinese University of Hong Kong, Hong Kong SAR, China" - }, - { - "author_name": "Gabriel M Leung", - "author_inst": "WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Ko" - }, - { - "author_name": "Malik Peiris", - "author_inst": "School of Public Health, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong SAR, China" - }, - { - "author_name": "Joseph T. Wu", - "author_inst": "WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Ko" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.11.03.515011", "rel_title": "Evaluation of antibody kinetics and durability in health subjects vaccinated with inactivated COVID-19 vaccine (CoronaVac): A cross-sectional and cohort study in Zhejiang, China", @@ -156143,6 +157941,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.10.31.514483", + "rel_title": "An optimised method for recovery and quantification of laboratory generated SARS-CoV-2 aerosols by plaque assay.", + "rel_date": "2022-11-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.31.514483", + "rel_abs": "We present an optimised method for the recovery of laboratory generated SARS-CoV-2 virus by plaque assay. This method allows easy incorporation into existing standard operating procedures of biological containment level 3 (BCL3) laboratories.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Rachel L Byrne", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Susan Gould", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Thomas Edwards", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Dominic Wooding", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Barry Atkinson", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Ginny Moore", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Kieran Collings", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Cedric Boisdon", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Simon Maher", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Giancarlo Biagini", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Emily R Adams", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Tom Fletcher", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Shaun H Pennington", + "author_inst": "Liverpool School of Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2022.10.27.22281585", "rel_title": "Phase-wise Impact Analysis of the Indian National Lockdown against COVID-19 Outcomes", @@ -156185,20 +158050,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.10.26.22281561", - "rel_title": "FULL-SCALE DEEPLY SUPERVISED ATTENTION NETWORK FOR SEGMENTING COVID-19 LESIONS", - "rel_date": "2022-11-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.26.22281561", - "rel_abs": "Automated delineation of COVID-19 lesions from lung CT scans aids the diagnosis and prognosis for patients. The asymmetric shapes and positioning of the infected regions make the task extremely difficult. Capturing information at multiple scales will assist in deciphering features, at global and local levels, to encompass lesions of variable size and texture. We introduce the Full-scale Deeply Supervised Attention Network (FuDSA-Net), for efficient segmentation of corona-infected lung areas in CT images. The model considers activation responses from all levels of the encoding path, encompassing multi-scalar features acquired at different levels of the network. This helps segment target regions (lesions) of varying shape, size and contrast. Incorporation of the entire gamut of multi-scalar characteristics into the novel attention mechanism helps prioritize the selection of activation responses and locations containing useful information. Determining robust and discriminatory features along the decoder path is facilitated with deep supervision. Connections in the decoder arm are remodeled to handle the issue of vanishing gradient. As observed from the experimental results, FuDSA-Net surpasses other state-of-the-art architectures; especially, when it comes to characterizing complicated geometries of the lesions.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2022.10.31.22281754", "rel_title": "Informed consent and trial prioritization for human subject research during the COVID-19 pandemic. Stakeholder experiences and viewpoints.", @@ -157524,6 +159375,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.10.27.22281632", + "rel_title": "Application of a Multiplicative Cascade Model to Detect the Early Signs of SARS-CoV-2 Infection Using Heart Rate Data", + "rel_date": "2022-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.27.22281632", + "rel_abs": "BackgroundWrist-worn devices can keep track of a persons daily health status, including those likely to become infected with the SARS-CoV-2 virus. Technological solutions using mobile devices are being developed to predict the time course of COVID-19.\n\nObjectiveIn this proof-of-concept study, we use heart rate data to detect the first sign of infection in people who have been diagnosed with COVID-19 and to monitor the time-course of the illness.\n\nMethodsThe heart-rate data were analysed using a multiplicative cascade driven by a Gaussian process. This provides two parameters, mean and standard deviation, which when combined with similar parameters estimated from control series, provide a Health Index.\n\nResultsFor 90% of 31 cases, the Health Index tracked COVID-19 infection with the virus and subsequent recovery. The first-sign of COVID-19 was detected on average nine days before symptoms were reported.\n\nConclusionsEarly detection of COVID-19 may lead to a reduction in the spread of the virus. The Heath Indexs potential use for the early detection of complications arising from Long COVID would be an important innovation.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Rachel Ann Heath", + "author_inst": "School of Psychological Sciences, University of Newcastle, Australia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.10.27.514012", "rel_title": "Vitamin D deficiency and SARS-CoV-2 infection: Big-data analysis from March 2020 to March 2021. D-COVID study", @@ -157677,261 +159547,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.27.514070", - "rel_title": "A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients", - "rel_date": "2022-10-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.27.514070", - "rel_abs": "The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells. Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.", - "rel_num_authors": 60, - "rel_authors": [ - { - "author_name": "Yered Pita-Juarez", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA, Harvard Medical School, Boston, MA, USA, Broad Institute of MIT and Harvard, Cam" - }, - { - "author_name": "Dimitra Karagkouni", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA, Harvard Medical School, Boston, MA, USA, Broad Institute of MIT and Harvard, Cam" - }, - { - "author_name": "Nikolaos Kalavros", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Spatial Technologies Uni" - }, - { - "author_name": "Johannes C. Melms", - "author_inst": "Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA, Columbia Center for Translational Immunol" - }, - { - "author_name": "Sebastian Niezen", - "author_inst": "Harvard Medical School, Boston, MA, USA, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA, Division of Gastroenterology, Hepatology" - }, - { - "author_name": "Toni M. Delorey", - "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Adam L Essene", - "author_inst": "Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA, Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA, Division o" - }, - { - "author_name": "Olga R. Brook", - "author_inst": "Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA, USA" - }, - { - "author_name": "Deepti Pant", - "author_inst": "Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA, Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA, Division o" - }, - { - "author_name": "Disha Skelton-Badlani", - "author_inst": "Harvard Medical School, Boston, MA, USA, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA, Division of Gastroenterology, Hepatology" - }, - { - "author_name": "Pourya Naderi", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Pinzhu Huang", - "author_inst": "Harvard Medical School, Boston, MA, USA, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA, Division of Gastroenterology, Hepatology" - }, - { - "author_name": "Liuliu Pan", - "author_inst": "NanoString Technologies, Inc., Seattle, WA, USA" - }, - { - "author_name": "Tyler Hether", - "author_inst": "NanoString Technologies, Inc., Seattle, WA, USA" - }, - { - "author_name": "Tallulah S. Andrews", - "author_inst": "Ajmera Transplant Centre, Toronto General Research Institute, University Health Network, Toronto, ON, Canada" - }, - { - "author_name": "Carly G.K. Ziegler", - "author_inst": "Harvard Medical School, Boston, MA, USA, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Program in Health Sciences & Technology, Harvard Medical School" - }, - { - "author_name": "Jason Reeves", - "author_inst": "NanoString Technologies, Inc., Seattle, WA, USA" - }, - { - "author_name": "Andriy Myloserdnyy", - "author_inst": "Harvard Medical School, Boston, MA, USA, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA, Division of Gastroenterology, Hepatology" - }, - { - "author_name": "Rachel Chen", - "author_inst": "Harvard Medical School, Boston, MA, USA, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA, Division of Gastroenterology, Hepatology" - }, - { - "author_name": "Andy Nam", - "author_inst": "NanoString Technologies, Inc., Seattle, WA, USA" - }, - { - "author_name": "Stefan Phelan", - "author_inst": "NanoString Technologies, Inc., Seattle, WA, USA" - }, - { - "author_name": "Yan Liang", - "author_inst": "NanoString Technologies, Inc., Seattle, WA, USA" - }, - { - "author_name": "Amit Dipak Amin", - "author_inst": "Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA, Columbia Center for Translational Immunol" - }, - { - "author_name": "Jana Biermann", - "author_inst": "Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA, Columbia Center for Translational Immunol" - }, - { - "author_name": "Hanina Hibshoosh", - "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA" - }, - { - "author_name": "Molly Veregge", - "author_inst": "Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA, Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA, Division o" - }, - { - "author_name": "Zachary Kramer", - "author_inst": "Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA, Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA, Division o" - }, - { - "author_name": "Christopher Jacobs", - "author_inst": "Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA, Department of Medicine, Beth Israel Deaconess Medical Center, MA, USA, Division o" - }, - { - "author_name": "Yusuf Yalcin", - "author_inst": "Harvard Medical School, Boston, MA, USA, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA, Division of Gastroenterology, Hepatology" - }, - { - "author_name": "Devan Phillips", - "author_inst": "Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA" - }, - { - "author_name": "Michal Slyper", - "author_inst": "Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA" - }, - { - "author_name": "Ayshwarya Subramanian", - "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Orr Ashenberg", - "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Zohar Bloom-Ackermann", - "author_inst": "Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Victoria M. Tran", - "author_inst": "Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "James Gomez", - "author_inst": "Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Alexander Sturm", - "author_inst": "Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Shuting Zhang", - "author_inst": "Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Stephen J. Fleming", - "author_inst": "Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, " - }, - { - "author_name": "Sarah Warren", - "author_inst": "NanoString Technologies, Inc., Seattle, WA, USA" - }, - { - "author_name": "Joseph Beechem", - "author_inst": "NanoString Technologies, Inc., Seattle, WA, USA" - }, - { - "author_name": "Deborah Hung", - "author_inst": "Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Department of Genetics, Harvard Medical School, Boston, MA, U" - }, - { - "author_name": "Mehrtash Babadi", - "author_inst": "Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Precision Cardiology Laboratory, Broad Institute of MIT and Harvard, Cambridge, " - }, - { - "author_name": "Gary D. Bader", - "author_inst": "Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada, The Donnelly Centre, Toronto, ON, Canada" - }, - { - "author_name": "Nasser Imad", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA" - }, - { - "author_name": "Eric Miller", - "author_inst": "NanoString Technologies, Inc., Seattle, WA, USA" - }, - { - "author_name": "Stefan Riedel", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Caroline B.M. Porter", - "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Alexandra-Chloe Villani", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA, Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital," - }, - { - "author_name": "Linus T.-Y. Tsai", - "author_inst": "Harvard Medical School, Boston, MA, USA, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Department of Medicine, Beth Israel Deaconess Medical Center, B" - }, - { - "author_name": "Winston Hide", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Gyongyi Szabo", - "author_inst": "Harvard Medical School, Boston, MA, USA, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Department of Medicine, Beth Israel Deaconess Medical Center, B" - }, - { - "author_name": "Jonathan Hecht", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Orit Rozenblatt-Rosen", - "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA" - }, - { - "author_name": "Alex K. Shalek", - "author_inst": "Harvard Medical School, Boston, MA, USA, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Program in Health Sciences & Technology, Harvard Medical School" - }, - { - "author_name": "Benjamin Izar", - "author_inst": "Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA, Columbia Center for Translational Immunol" - }, - { - "author_name": "Aviv Regev", - "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA, Current address: Genentech, 1 DNA Way, South San Francisco, CA, USA" - }, - { - "author_name": "Yury Popov", - "author_inst": "Harvard Medical School, Boston, MA, USA, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA, Division of Gastroenterology, Hepatology" - }, - { - "author_name": "Z. Gordon Jiang", - "author_inst": "Harvard Medical School, Boston, MA, USA, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA, Division of Gastroenterology, Hepatology" - }, - { - "author_name": "Ioannis S. Vlachos", - "author_inst": "Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA, USA, Harvard Medical School, Boston, MA, USA, Broad Institute of MIT and Harvard, Cam" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2022.10.27.514096", "rel_title": "Tocilizumab treatment leads to early resolution of myeloid dysfunction and lymphopenia in patients hospitalized with COVID-19", @@ -159902,6 +161517,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.10.25.22281247", + "rel_title": "Occupational risk of SARS-CoV-2 infection: a nationwide register-based study of the Danish workforce during the Covid-19 pandemic 2020-21", + "rel_date": "2022-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.25.22281247", + "rel_abs": "ObjectivesMost earlier studies on occupational risk of Covid-19 covering the entire workforce are based on relatively rare outcomes such as hospital admission and mortality. This study examines the incidence of SARS-CoV-2 infection by occupational group based upon real-time polymerase chain reaction tests (RT-PCR).\n\nMethodsThe cohort includes 2.4 million Danish employees, 20-69 years of age. All data were retrieved from public registries. The sex-specific incidence rate ratios (IRR) of first-occurring positive RT-PCR test from week 8 of 2020 through week 50 of 2021 were computed by Poisson regression for each 4-digit DISCO-08 job code with more than 100 employees (337 in men; 297 in women). Occupational groups with low risk of workplace infection according to a job exposure matrix constituted the reference group. Risk estimates were adjusted by demographic, social and health characteristics including household size, completed Covid-19 vaccination, pandemic wave and occupation-specific frequency of testing.\n\nResultsIRRs of SARS-CoV-2 infection were elevated in 34 occupations comprising 12 % of male employees and 45 occupations comprising 41 % of female employees. All IRR estimates were below 2.0. Decreased IRRs were observed in 85 occupations in men but none in women.\n\nDiscussionWe observed a modestly increased risk of SARS-CoV-2 infection among employees in numerous occupations indicating a large potential for preventive actions, especially in the female workforce. Cautious interpretation of observed risk in specific occupations is needed because of methodological issues inherent in analyses of RT-PCR-test results and because of multiple statistical tests.\n\nWHAT IS ALREADY KNOW ABOUT THIS TOPIC?O_LIEpidemiological studies suggest that the workplace contribute to the Covid-19 pandemic\nC_LIO_LIResults are mostly based upon studies of less frequent outcomes as Covid-19 morbidity or mortality which limits inference about risk in specific occupations\nC_LI\n\nWHAT THIS STUDY ADDSO_LIThe risk of Covid-19 infection was increased in 34 of 337 occupations in men and in 45 of 297 occupations in women\nC_LIO_LISome 12% of the Danish male workforce and 41% of the female workforce are at increased risk of Covid-19 infection\nC_LI\n\nHOW THIS RESEARCH MIGHT AFFECT RESEARCH, PRACTICE OR POLICY?O_LIPreventive actions targeting the workplace may contribute substantially to alleviate disease occurrence in the ongoing Covid-19 and similar future pandemics.\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jens Peter Ellekilde Bonde", + "author_inst": "Department of Occupational and Environmental Medicine, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark" + }, + { + "author_name": "Luise Moelenberg Begtrup", + "author_inst": "Department of Occupational and Environmental Medicine, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark" + }, + { + "author_name": "Johan Hoej Jensen", + "author_inst": "Department of Occupational and Environmental Medicine, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark" + }, + { + "author_name": "Esben Meulengracht Flachs", + "author_inst": "Department of Occupational and Environmental Medicine, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark" + }, + { + "author_name": "Vivi Schlunssen", + "author_inst": "Department of Public Health, Research Unit for Environment, Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark" + }, + { + "author_name": "Henrik Albert Kolstad", + "author_inst": "Department of Occupational Medicine, Danish Ramazzini Centre, Aarhus University Hospital, Denmark" + }, + { + "author_name": "Kristina Jakobsson", + "author_inst": "School of Public Health and Community Medicine, Sahlgrenska Academy, University of Gothenburg, Sweden" + }, + { + "author_name": "Christel Nielsen", + "author_inst": "Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden" + }, + { + "author_name": "Kerstin Nielsson", + "author_inst": "Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden" + }, + { + "author_name": "Lars Rylander", + "author_inst": "Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden" + }, + { + "author_name": "Andreas Vilhelmsson", + "author_inst": "Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University, Lund, Sweden" + }, + { + "author_name": "Kajsa Kirstine Ugelvig Petersen", + "author_inst": "Department of Occupational and Environmental Medicine, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark" + }, + { + "author_name": "Sandra Soegaard Toettenborg", + "author_inst": "Department of Occupational and Environmental Medicine, Copenhagen University Hospital - Bispebjerg and Frederiksberg, Copenhagen, Denmark" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2022.10.24.22281104", "rel_title": "Which curve are we flattening? The disproportionate impact of COVID-19 among economically marginalized communities in Ontario, Canada, was unchanged from wild-type to omicron", @@ -160051,29 +161733,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.10.21.22281271", - "rel_title": "NC-COVID: A Time-Varying Compartmental Model for Estimating SARS-CoV-2 Infection Dynamics in North Carolina, US", - "rel_date": "2022-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.21.22281271", - "rel_abs": "Efforts to track and model SARS-CoV-2 infection dynamics in the population have been complicated by certain aspects of the transmission characteristics, which include a pre-symptomatic infectious phase as well as asymptomatic infectious individuals. Another problem is that many models focus on case count, as there has been (and is) limited data regarding infection status of members of the population, which is the most important aspect for constructing transmission models. This paper describes and explains the parameterization, calibration, and revision of the NC-COVID model, a compartmental model to estimate SARS-CoV-2 infection dynamics for the state of North Carolina, US. The model was developed early in the pandemic to provide rapid, up-to-date state-level estimates of the number of people who were currently infected, were immune from a prior infection, and remained susceptible to infection. As a post modeling exercise, we assessed the veracity of the model by comparing its output to SARS-CoV-2 viral particle concentrations detected in wastewater data and to estimates of people infected using COVID-19 deaths. The NC-COVID model was highly correlated with these independently derived estimates, suggesting that it produced accurate estimates of SARS-CoV-2 infection dynamics in North Carolina.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Paul L Delamater", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Rachel L Woodul", - "author_inst": "University of North Carolina at Chapel Hill" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.10.23.22281408", "rel_title": "Scoping review and meta-analysis of COVID-19 epidemiological parameters for modeling from early Asian studies", @@ -162180,6 +163839,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.21.22281171", + "rel_title": "Comparison of the risk of hospitalisation among BA.1 and BA.2 COVID-19 cases treated with Sotrovimab in the community in England", + "rel_date": "2022-10-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.21.22281171", + "rel_abs": "ObjectivesSotrovimab is one of several therapeutic agents that have been licensed to treat people at risk of severe outcomes following COVID-19 infection. However, there are concerns that it has reduced efficacy to treat people with the BA.2 sub-lineage of the Omicron (B.1.1.529) SARS-CoV-2 variant. We compared individuals with the BA.1 or BA.2 sub-lineage of the Omicron variant treated Sotrovimab in the community to assess their risk of hospital admission.\n\nMethodsWe performed a retrospective cohort study of individuals treated with Sotrovimab in the community and either had BA.1 or BA.2 variant classification.\n\nResultsUsing a Stratified Cox regression model it was estimated that the hazard ratios (HR) of hospital admission with a length of stay of two or more days was 1.17 for BA.2 compared to BA.1 (95% CI 0.74-1.86) and for such admissions where COVID-19 ICD-10 codes was recorded the HR was 0.98 (95% CI 0.58-1.65).\n\nConclusionThese results suggest that the risk of hospital admission is similar between BA.1 and BA.2 cases treated with Sotrovimab in the community.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Katie Harman", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Sophie G Nash", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Harriet H Webster", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Natalie Groves", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Jo Hardstaff", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Jessica Bridgen", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Paula B Blomquist", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Russell Hope", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Efejiro Ashano", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Richard Myers", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Sakib Rokadiya", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Susan Hopkins", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Colin S Brown", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Meera Chand", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Gavin Dabrera", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Simon Thelwall", + "author_inst": "UK Health Security Agency" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.10.19.22281256", "rel_title": "Changes in Treatment and Severity of Multisystem Inflammatory Syndrome in Children: An EHR-based cohort study from the RECOVER program", @@ -162333,41 +164071,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.18.22281237", - "rel_title": "Did Risk-based or Age-based Vaccine Prioritization for Covid-19 Save More Lives?", - "rel_date": "2022-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.18.22281237", - "rel_abs": "ImportanceAll U.S. states provided Covid-19 vaccine access to frontline healthcare workers first, but after that, states varied in whether they gave earlier access to the elderly, versus the vulnerable with comorbidities, or school employees or essential workers, reflecting the underlying scientific and policy uncertainty.\n\nObjectiveTo evaluate if risk-based or age-based prioritization is more effective at reducing reported Covid-19 cases and deaths.\n\nDesignA serial cross-sectional study\n\nSetting50 U.S. states and Washington D.C.\n\nParticipants60+ years of age, high-risk individuals, K-12 school employees, and essential workers\n\nMain Outcomes and MeasuresHospitalizations and deaths\n\nResultsSeven to nine weeks after 60-year-olds became eligible for a vaccine, there was a statistically significant 40-50% decline in Covid-19 hospitalizations in that state. In contrast, there was no statistically detectable change in hospitalizations in the 7-9 weeks after K-12 employees become eligible for vaccines. Vaccine eligibility of \"high-risk adults\" and \"essential workers\" produces effects somewhere in the middle, with reductions in hospitalization of about 25%. There was a large statistically significant decline in death rates (25-38%) 10 to 11 weeks after people aged over 60 became vaccine-eligible. These effects were generally statistically larger than high risk individuals, K-12 school employees, and essential workers.\n\nConclusions and RelevancePanel data analysis of weekly variation in Covid-19 health outcomes reveals that prioritizing adults 60+ years of age is associated with the largest reduction in hospitalizations and Covid-19 cases, followed by vaccines for adults with high-risk comorbidities. Vaccinations extended to K-12 school employees and essential workers is associated with the smallest reductions in hospitalizations and deaths.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSDid Risk-based or Age-based Vaccine Prioritization for Covid-19 Save More Lives?\n\nFindingsPanel data analysis of weekly variation in Covid-19 health outcomes reveals that prioritizing adults 60+ years of age is associated with the largest reduction in hospitalizations and Covid-19 cases, followed by vaccines for adults with high-risk comorbidities. Vaccinations extended to K-12 school employees and essential workers is associated with the smallest reductions in hospitalizations and deaths.\n\nMeaningPrioritizing adults 60+ years of age can lead to a higher estimated reduction in hospitalizations and deaths, followed by a strategy of prioritizing adults with high-risk comorbidities. Our findings add to the limited evidence for the roadmap for prioritizing use of Covid-19 vaccines, and help address uncertainties about the relative effectiveness of different vaccine strategies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Joeri Smits", - "author_inst": "Harvard Kennedy School" - }, - { - "author_name": "Amyn Abdul Malik", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Jad A Elharake", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Ahmed Mushfiq Mobarak", - "author_inst": "Yale University" - }, - { - "author_name": "Saad B. Omer", - "author_inst": "Yale Institute for Global Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.18.22281049", "rel_title": "Estimating the effectiveness of shielding during pregnancy against SARS-CoV-2 in New York City during the first year of the COVID-19 pandemic", @@ -164222,6 +165925,117 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.10.20.512999", + "rel_title": "Altered infective competence of the human gut microbiome in COVID-19", + "rel_date": "2022-10-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.20.512999", + "rel_abs": "ObjectivesInfections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19.\n\nDesignWe used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group.\n\nResultsWe found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19 positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19 positive individuals compared to healthy controls.\n\nConclusionOur analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Laura de Nies", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Valentina Galata", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Camille Martin-Gallausiaux", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Milena Despotovic", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Susheel Bhanu Busi", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Chantal J. Snoeck", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Lea Delacour", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Deepthi Poornima Budagavi", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Cedric Christian Laczny", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Janine Habier", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Paula-Cristina Lupu", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Rashi Halder", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Joelle V. Fritz", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Taina Marques", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Estelle Sandt", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Soumyabrata Ghosh", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Venkata Satagopam", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "- CON-VINCE Consortium", + "author_inst": "-" + }, + { + "author_name": "Rejko Kruger", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Guy Fagherazzi", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Markus Ollert", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Feng Q. Hefeng", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Patrick May", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Paul Wilmes", + "author_inst": "University of Luxembourg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.10.19.512957", "rel_title": "SARS-CoV-2 infected cells sprout actin-rich filopodia that facilitate viral invasion", @@ -164399,37 +166213,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.18.22281212", - "rel_title": "ALCOHOLIC LIVER BIOMARKERS: DETERMINANTS FOR ADMISSION TO REHABILITATION CENTRES DURING THE COVID 19 PERIOD IN KENYA", - "rel_date": "2022-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.18.22281212", - "rel_abs": "Consumption of alcohol is a practice world over that dates back to 10,000 Before Christ. Evaluation on the damages caused by the alcohol on the human organs such as the liver is paramount. There is no direct evaluation to liver parenchyma before admission rather blood samples are evaluated to show damage or no damage to the liver cells. The outcome of the blood samples denote the health status of the liver cells before admission. Alcohol biomarkers are usually elevated when there is damage to the liver parenchyma. This was a quantitative descriptive cross sectional study. Purpose sampling was used to select two Counties with the highest number of alcohol consumers. Simple Random sampling method was used to select participants for liver biomarkers. Participants were requested to consent for blood donation and confidentiality was maintained. Blood samples collected were separated for serum and cells using centrifuge within one hour after donation. The samples were transported for storage using cool boxes and temperature was maintained between -8 and +8 degrees during transportation. The blood samples were stored at -8 and +8 degrees in the deep freezer. Majority (97%) of the participants had alanine aminotransferase levels of 41 to 80 IU/L. Eighty eight percent of the participants had aspartate aminotransferase elevated to between 35 and 68 IU/L. Gamma Glutamyl aminotransferase was elevated in all of the participants while alanine phosphatase was elevated in 99% of the participants. Most participants had elevated liver biomarkers before admission to rehabilitation centre.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "GEORGE NJOROGE", - "author_inst": "MOUNT KENYA UNIVERSITY" - }, - { - "author_name": "CATHERINE MWENDA", - "author_inst": "SOUTH EASTERN KENYA UNIVERSITY" - }, - { - "author_name": "EZEKIEL MECHA", - "author_inst": "UNIVERSITY OF NAIROBI" - }, - { - "author_name": "STANLEY WAITHAKA", - "author_inst": "MOUNT KENYA UNIVERSITY" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "addiction medicine" - }, { "rel_doi": "10.1101/2022.10.18.22281225", "rel_title": "Cumulative COVID-19 incidence indicators should account for the population-at-risk dynamics", @@ -166268,6 +168051,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.10.17.22281168", + "rel_title": "A systematic review on outbreaks of COVID-19 among children within households in the European region", + "rel_date": "2022-10-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.17.22281168", + "rel_abs": "ObjectivesThis systematic review aims to identify the secondary attack rates (SAR) to adults and other children when children are the index cases within household settings.\n\nMethodsThis literature review assessed European-based studies published in Medline and Embase between January 2020 and January 2022 that assessed the secondary transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within household settings. The inclusion criteria were based on the PEO framework (P-Population, E-Exposure, O-Outcome) for systematic reviews. Thus, the study population was restricted to humans within the household setting in Europe (population), in contact with pediatric index cases 1-17 years old (exposure) that led to the transmission of SARS-CoV-2 reported as either a SAR or the probability of onward infection (outcome).\n\nResultsOf 1,819 studies originally identified, 25 met the inclusion criteria. Overall, the SAR ranged from 13% to 75% in 23 studies, while there was no evidence of secondary transmission from children to other household members in two studies. Evidence indicated that asymptomatic SARS-CoV-2 index cases also have a lower SAR than those with symptoms and that younger children may have a lower SAR than adolescents (>12 years old) within household settings.\n\nConclusionsSARS-CoV-2 secondary transmission from paediatric index cases ranged from 0% to 75%, within household settings between January 2020 and January 2022, with differences noted by age and by symptomatic/asymptomatic status of the index case. Given the anticipated endemic circulation of SARS-CoV-2, continued monitoring and assessment of household transmission is necessary.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Constantine Vardavas", + "author_inst": "School of Medicine, University of Crete, Heraklion, Crete, Greece" + }, + { + "author_name": "Katerina Nikitara", + "author_inst": "University of Crete" + }, + { + "author_name": "Katerina Aslanoglou", + "author_inst": "School of Medicine, University of Crete, Heraklion, Crete, Greece" + }, + { + "author_name": "Apostolos Kamekis", + "author_inst": "School of Medicine, University of Crete, Heraklion, Crete, Greece" + }, + { + "author_name": "Nithya Ramesh", + "author_inst": "Department of Oral Health Policy and Epidemiology, Harvard School of Dental Medicine, Harvard University, Boston, MA, USA" + }, + { + "author_name": "Emmanouil Symvoulakis", + "author_inst": "School of Medicine, University of Crete, Heraklion, Crete, Greece" + }, + { + "author_name": "Israel Agaku", + "author_inst": "Department of Oral Health Policy and Epidemiology, Harvard School of Dental Medicine, Harvard University, Boston, MA, USA" + }, + { + "author_name": "Revati Phalkey", + "author_inst": "Centre for Evidence Based Healthcare, Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, UK" + }, + { + "author_name": "Jo Leonardi-Bee", + "author_inst": "Centre for Evidence Based Healthcare, Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, UK" + }, + { + "author_name": "Esteve Fernandez", + "author_inst": "Catalan Institute of Oncology, Barcelona, Spain" + }, + { + "author_name": "Orla Condell", + "author_inst": "European Centre for Disease Prevention and Control (ECDC), Solna, Sweden" + }, + { + "author_name": "Favelle Lamb", + "author_inst": "European Centre for Disease Prevention and Control (ECDC), Solna, Sweden" + }, + { + "author_name": "Charlotte Deogan", + "author_inst": "European Centre for Disease Prevention and Control (ECDC), Solna, Sweden" + }, + { + "author_name": "Jonathan E Suk", + "author_inst": "European Centre for Disease Prevention and Control (ECDC), Solna, Sweden" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.17.22281175", "rel_title": "Reconstruction of SARS-CoV-2 outbreaks in a primary school using epidemiological and genomic data", @@ -166461,213 +168315,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.10.17.22281058", - "rel_title": "Eleven key measures for monitoring general practice clinical activity during COVID-19 using federated analytics on 48 million adults' primary care records through OpenSAFELY", - "rel_date": "2022-10-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.17.22281058", - "rel_abs": "BackgroundThe COVID-19 pandemic has had a significant impact on delivery of NHS care. We have developed the OpenSAFELY Service Restoration Observatory (SRO) to describe this impact on primary care activity and monitor its recovery.\n\nObjectivesTo develop key measures of primary care activity and describe the trends in these measures throughout the COVID-19 pandemic.\n\nMethodsWith the approval of NHS England we developed an open source software framework for data management and analysis to describe trends and variation in clinical activity across primary care electronic health record (EHR) data on 48 million adults.\n\nWe developed SNOMED-CT codelists for key measures of primary care clinical activity selected by a expert clinical advisory group and conducted a population cohort-based study to describe trends and variation in these measures January 2019-December 2021, and pragmatically classified their level of recovery one year into the pandemic using the percentage change in the median practice level rate.\n\nResultsWe produced 11 measures reflective of clinical activity in general practice. A substantial drop in activity was observed in all measures at the outset of the COVID-19 pandemic. By April 2021, the median rate had recovered to within 15% of the median rate in April 2019 in six measures. The remaining measures showed a sustained drop, ranging from a 18.5% reduction in medication reviews to a 42.0% reduction in blood pressure monitoring. Three measures continued to show a sustained drop by December 2021.\n\nConclusionsThe COVID-19 pandemic was associated with a substantial change in primary care activity across the measures we developed, with recovery in most measures. We delivered an open source software framework to describe trends and variation in clinical activity across an unprecedented scale of primary care data. We will continue to expand the set of key measures to be routinely monitored using our publicly available NHS OpenSAFELY SRO dashboards with near real-time data.", - "rel_num_authors": 48, - "rel_authors": [ - { - "author_name": "Louis Fisher", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Helen J Curtis", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Richard Croker", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Milan Wiedemann", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Victoria Speed", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Christopher Wood", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Andrew Brown", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Lisa EM Hopcroft", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Rose Higgins", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Jon Massey", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Alex J Walker", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Jessica Morley", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Seb Bacon", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "George Hickman", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Orla Macdonald", - "author_inst": "Oxford Health NHS FT" - }, - { - "author_name": "Tom Lewis", - "author_inst": "Royal Devon University Healthcare NHS Foundation Trust," - }, - { - "author_name": "Marion Wood", - "author_inst": "NHS England" - }, - { - "author_name": "Martin Myers", - "author_inst": "Lancashire Teaching Hospitals NHS Foundation Trust" - }, - { - "author_name": "Miriam Samuel", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Robin Conibere", - "author_inst": "Beacon Medical Group" - }, - { - "author_name": "Wasim Baqir", - "author_inst": "NHS England" - }, - { - "author_name": "Harpreet Sood", - "author_inst": "Sternhall Lane Surgery" - }, - { - "author_name": "Charles Drury", - "author_inst": "Herefordshire and Worcestershire Health and Care NHS Trus" - }, - { - "author_name": "Kiren Collison", - "author_inst": "NHS England" - }, - { - "author_name": "Chris Bates", - "author_inst": "TPP" - }, - { - "author_name": "David Evans", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Iain Dillingham", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Tom Ward", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Simon Davy", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Rebecca M Smith", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "William Hulme", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Amelia Green", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "John Parry", - "author_inst": "TPP" - }, - { - "author_name": "Frank Hester", - "author_inst": "TPP" - }, - { - "author_name": "Sam Harper", - "author_inst": "TPP" - }, - { - "author_name": "Jonathan Cockburn", - "author_inst": "TPP" - }, - { - "author_name": "Shaun O'Hanlon", - "author_inst": "EMIS" - }, - { - "author_name": "Alex Eavis", - "author_inst": "EMIS" - }, - { - "author_name": "Richard Jarvis", - "author_inst": "EMIS" - }, - { - "author_name": "Dima Avramov", - "author_inst": "EMIS" - }, - { - "author_name": "Paul Griffiths", - "author_inst": "EMIS" - }, - { - "author_name": "Aaron Fowles", - "author_inst": "EMIS" - }, - { - "author_name": "Nasreen Parkes", - "author_inst": "EMIS" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "Bennett Institute for Applied Data Science, University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2022.10.14.22281103", "rel_title": "No evidence that analgesic use after COVID-19 vaccination negatively impacts antibody responses", @@ -168150,6 +169797,173 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.10.11.22280868", + "rel_title": "High titers of infectious SARS-CoV-2 in COVID-19 corpses", + "rel_date": "2022-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.11.22280868", + "rel_abs": "BackgroundThe prolonged presence of infectious severe acute respiratory syndrome coronavirus (SARS-CoV-2) in deceased coronavirus disease 2019 (COVID-19) patients has been reported. However, infectious virus titers have not been determined. Such information is important for public health, death investigation, and handling corpses.\n\nAimThe aim of this study was to assess the level of SARS-CoV-2 infectivity in COVID-19 corpses.\n\nMethodsWe collected 11 nasopharyngeal swabs and 19 lung tissue specimens from 11 autopsy cases with COVID-19 in 2021. We then investigated the viral genomic copy number by real-time reverse transcription-polymerase chain reaction and infectious titers by cell culture and virus isolation.\n\nResultsInfectious virus was present in 6 of 11 (55%) cases, 4 of 11 (36%) nasopharyngeal swabs, and 9 of 19 (47%) lung specimens. The virus titers ranged from 6.00E + 01 plaque-forming units (PFU)/mL to 2.09E + 06 PFU/g. In all cases in which an infectious virus was found, the time from death to discovery was within 1 day and the longest postmortem interval was 13 days.\n\nConclusionCOVID-19 corpses may have high titers of infectious virus after a long postmortem interval (up to 13 days). Therefore, appropriate infection control measures must be taken when handling corpses.", + "rel_num_authors": 38, + "rel_authors": [ + { + "author_name": "Hisako Saitoh", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Yuko Tagawa Sakai", + "author_inst": "Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo" + }, + { + "author_name": "Sayaka Nagasawa", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Suguru Torimitsu", + "author_inst": "Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Kazumi Kubota", + "author_inst": "Department of Healthcare Information Management, The University of Tokyo Hospital" + }, + { + "author_name": "Yuichiro Hirata", + "author_inst": "Department of Pathology, National Institute of Infectious Diseases" + }, + { + "author_name": "Kiyoko Horimoto Iwatsuki", + "author_inst": "Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo" + }, + { + "author_name": "Ayumi Motomura", + "author_inst": "Department of Legal Medicine, International University of Health and Welfare" + }, + { + "author_name": "Namiko Ishii", + "author_inst": "Department of Legal Medicine, International University of Health and Welfare" + }, + { + "author_name": "Keisuke Okaba", + "author_inst": "Department of Legal Medicine, International University of Health and Welfare" + }, + { + "author_name": "Kie Horioka", + "author_inst": "Department of Legal Medicine, International University of Health and Welfare" + }, + { + "author_name": "Hiroyuki Abe", + "author_inst": "Department of Pathology, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Masako Ikemura", + "author_inst": "Department of Pathology, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Hirofumi Rokutan", + "author_inst": "Department of Pathology, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Munetoshi Hinata", + "author_inst": "Department of Pathology, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Department of Pathology, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Yoichi Yasunaga", + "author_inst": "Department of Pathology, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Makoto Nakajima", + "author_inst": "Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Rutsuko Yamaguchi", + "author_inst": "Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Shigeki Tsuneya", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Kei Kira", + "author_inst": "Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Susumu Kobayashi", + "author_inst": "Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Go Inokuchi", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Fumiko Chiba", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Yumi Hoshioka", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Aika Mori", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Isao Yamamoto", + "author_inst": "Department of Forensic Medicine, Kanagawa Dental University" + }, + { + "author_name": "Kimiko Nakagawa", + "author_inst": "Department of Forensic Medicine, Kanagawa Dental University" + }, + { + "author_name": "Harutaka Katano", + "author_inst": "Department of Pathology, National Institute of Infectious Diseases" + }, + { + "author_name": "Shun Iida", + "author_inst": "Department of Pathology, National Institute of Infectious Diseases" + }, + { + "author_name": "Tadaki Suzuki", + "author_inst": "Department of Pathology, National Institute of Infectious Diseases" + }, + { + "author_name": "Shinji Akitomi", + "author_inst": "Japan Medical Association Research Institute" + }, + { + "author_name": "Iwao Hasegawa", + "author_inst": "Department of Forensic Medicine, Kanagawa Dental University" + }, + { + "author_name": "Tetsuo Ushiku", + "author_inst": "Department of Pathology, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Daisuke Yajima", + "author_inst": "Department of Legal Medicine, International University of Health and Welfare" + }, + { + "author_name": "Hirotaro Iwase", + "author_inst": "Department of Legal Medicine, Graduate School of Medicine, Chiba University" + }, + { + "author_name": "Yohsuke Makino", + "author_inst": "Department of Forensic Medicine, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Yoshihiro Kawaoka", + "author_inst": "University of Wisconsin-Madison" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.10.22280850", "rel_title": "Anti-SARS-CoV-2 antibody containing plasma improves outcome in patients with hematologic or solid cancer and severe COVID-19 via increased neutralizing antibody activity. A randomized clinical trial", @@ -168455,61 +170269,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.10.12.22280997", - "rel_title": "Utility of human judgment ensembles during times of pandemic uncertainty: A case study during the COVID-19 Omicron BA.1 wave in the USA", - "rel_date": "2022-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.12.22280997", - "rel_abs": "Responding to a rapidly evolving pandemic like COVID-19 is challenging, and involves anticipating novel variants, vaccine uptake, and behavioral adaptations. Human judgment systems can complement computational models by providing valuable real-time forecasts. We report findings from a study conducted on Metaculus, a community forecasting platform, in partnership with the Virginia Department of Health, involving six rounds of forecasting during the Omicron BA.1 wave in the United States from November 2021 to March 2022. We received 8355 probabilistic predictions from 129 unique users across 60 questions pertaining to cases, hospitalizations, vaccine uptake, and peak/trough activity. We observed that the case forecasts performed on par with national multi-model ensembles and the vaccine uptake forecasts were more robust and accurate compared to baseline models. We also identified qualitative shifts in Omicron BA.1 wave prognosis during the surge phase, demonstrating rapid adaptation of such systems. Finally, we found that community estimates of variant characteristics such as growth rate and timing of dominance were in line with the scientific consensus. The observed accuracy, timeliness, and scope of such systems demonstrates the value of incorporating them into pandemic policymaking workflows.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Srinivasan Venkatramanan", - "author_inst": "University of Virginia" - }, - { - "author_name": "Juan Cambeiro", - "author_inst": "Metaculus" - }, - { - "author_name": "Tom Liptay", - "author_inst": "Metaculus" - }, - { - "author_name": "Bryan Lewis", - "author_inst": "University of Virginia" - }, - { - "author_name": "Mark Orr", - "author_inst": "University of Virginia" - }, - { - "author_name": "Gaia Dempsey", - "author_inst": "Metaculus" - }, - { - "author_name": "Alex Telionis", - "author_inst": "Virginia Department of Health" - }, - { - "author_name": "Justin Crow", - "author_inst": "Virginia Department of Health" - }, - { - "author_name": "Chris Barrett", - "author_inst": "University of Virginia" - }, - { - "author_name": "Madhav Marathe", - "author_inst": "University of Virginia" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.10.10.511625", "rel_title": "Statistical challenges for inferring multiple SARS-CoV-2 spillovers with early outbreak phylodynamics", @@ -170096,6 +171855,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.10.10.22280915", + "rel_title": "Infection-induced immunity is associated with protection against SARS-CoV-2 infection, but not decreased infectivity during household transmission", + "rel_date": "2022-10-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.10.22280915", + "rel_abs": "BackgroundUnderstanding the impact of infection-induced immunity on SARS-CoV-2 transmission will provide insight into the transition of SARS-CoV-2 to endemicity. Here we estimate the effects of prior infection induced immunity and children on SARS-CoV-2 transmission in households.\n\nMethodsWe conducted a household cohort study between March 2020-June 2022 in Managua, Nicaragua where when one household member tests positive for SARS-CoV-2, household members are closely monitored for SARS-CoV-2 infection. Using a pairwise survival model, we estimate the association of infection period, age, symptoms, and infection-induced immunity with secondary attack risk.\n\nResultsOverall transmission occurred in 72.4% of households, 42% of household contacts were infected and the secondary attack risk was 13.0% (95% CI: 11.7, 14.6). Prior immunity did not impact the probability of transmitting SARS-CoV-2. However, participants with pre-existing infection-induced immunity were half as likely to be infected compared to naive individuals (RR 0.53, 95% CI: 0.39, 0.72), but this reduction was not observed in children. Likewise, symptomatic infected individuals were more likely to transmit (RR 24.4, 95% CI: 7.8, 76.1); however, symptom presentation was not associated with infectivity of young children. Young children were less likely to transmit SARS-CoV-2 than adults. During the omicron era, infection-induced immunity remained protective against infection.\n\nConclusionsInfection-induced immunity is associated with protection against infection for adults and adolescents. While young children are less infectious, prior infection and asymptomatic presentation did not reduce their infectivity as was seen in adults. As SARS-CoV-2 transitions to endemicity, children may become more important in transmission dynamics.\n\nArticle summaryInfection-induced immunity protects against SARS-CoV-2 infection for adolescents and adults; however, there was no protection in children. Prior immunity in an infected individual did not impact the probability they will spread SARS-CoV-2 in a household setting.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Aaron M Frutos", + "author_inst": "University of Michigan" + }, + { + "author_name": "Guillermina Kuan", + "author_inst": "Health Center Socrates Flores Vivas, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua, Nicaragua" + }, + { + "author_name": "Roger Lopez", + "author_inst": "Laboratorio Nacional de Virologia, Centro Nacional de Diagnostico y Referencia, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua," + }, + { + "author_name": "Sergio Ojeda", + "author_inst": "Sustainable Sciences Institute, Managua, Nicaragua" + }, + { + "author_name": "Abigail Shotwell", + "author_inst": "Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA" + }, + { + "author_name": "Nery Sanchez", + "author_inst": "Sustainable Sciences Institute, Managua, Nicaragua" + }, + { + "author_name": "Saira Saborio", + "author_inst": "Laboratorio Nacional de Virologia, Centro Nacional de Diagnostico y Referencia, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua," + }, + { + "author_name": "Miguel Plazaola", + "author_inst": "Sustainable Sciences Institute, Managua, Nicaragua" + }, + { + "author_name": "Carlos Barilla", + "author_inst": "Sustainable Sciences Institute, Managua, Nicaragua" + }, + { + "author_name": "Eben Kenah", + "author_inst": "Biostatistics Division, College of Public Health, The Ohio State University, Columbus, OH, USA" + }, + { + "author_name": "Angel Balmaseda", + "author_inst": "Laboratorio Nacional de Virologia, Centro Nacional de Diagnostico y Referencia, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua," + }, + { + "author_name": "Aubree Gordon", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.10.11.22280942", "rel_title": "Impact of the COVID-19 pandemic on exercise habits and overweight in Japan: a nation-wide panel survey", @@ -170281,73 +172103,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.11.22280953", - "rel_title": "CoViD-19 rRT-PCR Testing Capacity in Ghana; Indications of Preparedness for Marburg virus Outbreak?", - "rel_date": "2022-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.11.22280953", - "rel_abs": "IntroductionGhana, as of July 2022, has had 168,350 Real-Time Reverse Transcription-Polymerase Chain Reaction (rRT-PCR)-confirmed cases of CoViD-19 infections and 1,458 deaths. Besides, 2 cases of Marburg virus diseases (MVD) were confirmed in the country within the same month. Both CoViD-19 and MVD require rRT-PCR for diagnosis, however, rRT-PCR facilities are scarce in Ghana - especially, hitherto, the CoViD-19 pandemic. The objectives of this study were to assess the current testing capacity of CoViD-19 rRT-PCR in Ghana, and to make some recommendations in case of an MVD outbreak, or recurrence of the CoViD-19 pandemic.\n\nMethodsThe study was cross-sectional. Questionnaires were administered to 100 health professionals actively involved in the testing cycle of CoViD-19 across rRT-PCR testing institutions. Responses with regards to CoViD-19 rRT-PCR testing, biosafety, and relationship with Surveillance Outbreak Response Management and Analysis System (SORMAS), PanaBios and Zipline, were obtained for 2020-through-2022. The responses were analyzed with Microsoft Excel office-365 and SPSS v.23.\n\nResultsThirty-five (35) of the 53 testing institutions were in the Greater Accra Region, but none in seven (7) regions of the country. Many (49%) were privately owned. Nine (9) different professionals were involved in rRT-PCR testing. The testing institutions increased from 2 (in March 2020) to 53 by June-ending 2022, and most (90%) had Biosafety Cabinet class II (BSCII). PPEs were inadequate between march and June, 2020 (25%), but enough (100%) by June 2022. Zipline, SORMAS, and PanaBios, respectively, saw transactions from 28%, 81%, and 77% of the institutions.\n\nConclusionGhana is adequately resourced for recurrence of CoViD-19, or any MVD outbreak, in terms of diagnosis with rRT-PCR. However, the country needs redistribution of these testing resources, expand the services of Zipline and SORMAS, satisfy additional biosafety requirements for MVD testing and equip over 180 GeneXpert facilities to help in accessible and affordable testing.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Eric NY Nyarko", - "author_inst": "Department of Chemical Pathology, University of Ghana Medical School" - }, - { - "author_name": "Justice Kumi", - "author_inst": "Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana" - }, - { - "author_name": "Emmanuel K Ofori", - "author_inst": "Department of Chemical Pathology, University of Ghana Medical School" - }, - { - "author_name": "Richmond Owusu Ateko", - "author_inst": "Department of Chemical Pathology, University of Ghana Medical School" - }, - { - "author_name": "Michael Appiah", - "author_inst": "Department of Medical Laboratory Technology, Accra Technical University" - }, - { - "author_name": "Afua B Bontu", - "author_inst": "Department of Chemical Pathology, University of Ghana Medical School" - }, - { - "author_name": "Derrick N.D Dodoo", - "author_inst": "Department of Medical Laboratory Sciences, Baldwin University College" - }, - { - "author_name": "Broderick Yeboah Amoah", - "author_inst": "Department of Medical Laboratory Science, School of Biomedical and Allied Health Sciences, University of Ghana" - }, - { - "author_name": "Sandra ANA Crabbe", - "author_inst": "Department of Chemical Pathology, University of Ghana Medical School" - }, - { - "author_name": "Ebenezer K Amakye", - "author_inst": "Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, University for Development Studies" - }, - { - "author_name": "Seth D Amanquah", - "author_inst": "Department of Chemical Pathology, University of Ghana Medical School" - }, - { - "author_name": "Christian Obirikorang", - "author_inst": "Global Health and Infectious Diseases Group, Kumasi Centre for Collaborative Research, KNUST, Ghana" - }, - { - "author_name": "Henry Asare-Anane", - "author_inst": "Department of Chemical Pathology, University of Ghana Medical School" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.10.11.22280952", "rel_title": "Perceptions and predictors of COVID-19 vaccine hesitancy among health care providers across five countries in sub-Saharan Africa", @@ -171950,6 +173705,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.10.06.22280798", + "rel_title": "Impact of vaccination on post-acute sequelae of SARS CoV-2 infection in patients with rheumatic diseases", + "rel_date": "2022-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.06.22280798", + "rel_abs": "ObjectiveVaccination decreases the risk of severe COVID-19 but its impact on post-acute sequelae of COVID-19 (PASC) is unclear among patients with systemic autoimmune rheumatic diseases (SARDs) who may have blunted vaccine immunogenicity and be vulnerable to PASC.\n\nMethodsWe prospectively enrolled SARD patients from a large healthcare system who survived acute infection to complete surveys. The symptom-free duration and the odds of PASC (any symptom lasting [≥] 28 or 90 days) were evaluated using restricted mean survival time and multivariable logistic regression, respectively, among those with and without breakthrough infection ([≥] 14 days after initial vaccine series).\n\nResultsAmong 280 patients, the mean age was 53 years, 80% were female, and 82% were white. The most common SARDs were inflammatory arthritis (59%) and connective tissue disease (24%). Those with breakthrough infection had more upper respiratory symptoms, and those with non-breakthrough infection had more anosmia, dysgeusia, and joint pain. Compared to those with non-breakthrough COVID-19 infection (n=164), those with breakthrough infection (n=116) had significantly more symptom-free days over the follow-up period (+28.9 days, 95% CI: 8.83, 48.89; p=0.005) and lower odds of PASC at 28 and 90 days (aOR 0.49, 95% CI: 0.29, 0.83 and aOR 0.10, 95% CI: 0.04, 0.22, respectively).\n\nConclusionVaccinated patients with SARDs were less likely to experience PASC compared to those not fully vaccinated. These findings support the benefits of vaccination for patients with SARDs and suggest that the immune response to acute infection is important in the pathogenesis of PASC in SARD patients.\n\nKey MessagesO_ST_ABSWhat is already known on this topic?C_ST_ABSO_LIPost-acute sequelae of COVID-19 (PASC) affects 20-50% of COVID-19 survivors, though the impact of vaccination on the risk and severity of PASC is unclear, especially among those with systemic autoimmune rheumatic diseases (SARDs) who may have impaired responses to vaccines and be particularly vulnerable to PASC.\nC_LI\n\nWhat this study adds?O_LIIn this prospective cohort of SARD patients recovering from COVID-19, we found that those with breakthrough vs non-breakthrough infection had more symptom-free days over the follow-up period (adjusted difference +28.9 days, 95% CI: 8.38, 48.89; p=0.005) and a lower odds of PASC at 28 days (aOR 0.49, 95% CI: 0.29, 0.83) and at 90 days (aOR 0.10, 95% CI: 0.04, 0.22).\nC_LIO_LIPatient-reported pain and fatigue scores were lower, reflecting less severe pain and fatigue, in those with breakthrough infection compared to those with non-breakthrough infection.\nC_LI\n\nHow this study might affect research, practice, or policy?O_LIThis study extends our understanding of the benefits of vaccination against COVID-19 in patients living with SARDs and reinforces the importance of vaccinating this vulnerable population.\nC_LIO_LIOur findings suggest that the initial immune response to acute SARS-CoV-2, as influenced by vaccination, affects PASC risk but this requires further study.\nC_LI", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Naomi J Patel", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Claire Cook", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Kathleen MM Vanni", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Xiaoqing Fu", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Xiaosong Wang", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Yumeko Kawano", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Grace Qian", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Buuthien Hang", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Shruthi Srivatsan", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Emily Banasiak", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Emily Kowalski", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Katarina Bade", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Yuqing Zhang", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Jeffrey A. Sparks", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Zachary S Wallace", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2022.10.06.22280795", "rel_title": "Long COVID Risk and Pre-COVID Vaccination: An EHR-Based Cohort Study from the RECOVER Program", @@ -172183,117 +174013,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.10.07.511319", - "rel_title": "Development of SARS-CoV-2 mRNA vaccines encoding spike N-terminal and receptor binding domains", - "rel_date": "2022-10-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.07.511319", - "rel_abs": "With the success of mRNA vaccines against coronavirus disease 2019 (COVID-19), strategies can now focus on improving vaccine potency, breadth, and stability. We present the design and preclinical evaluation of domain-based mRNA vaccines encoding the wild-type spike-protein receptor-binding (RBD) and/or N-terminal domains (NTD). An NTD-RBD linked candidate vaccine, mRNA-1283, showed improved antigen expression, antibody responses, and stability at refrigerated temperatures (2-8{degrees}C) compared with the clinically available mRNA-1273, which encodes the full-length spike protein. In mice administered mRNA-1283 as a primary series, booster, or variant-specific booster, similar or greater immune responses and protection from viral challenge were observed against wild-type, beta, delta, or omicron (BA. 1) compared with mRNA-1273 immunized mice, especially at lower vaccine dosages. These results support clinical assessment of mRNA-1283 (NCT05137236).\n\nOne Sentence SummaryA domain-based mRNA vaccine, mRNA-1283, is immunogenic and protective against SARS-CoV-2 and emerging variants in mice.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Guillaume Stewart-Jones", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Sayda M. Elbashir", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Kai Wu", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Diana Lee", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Isabella Renzi", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Baoling Ying", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Matthew Koch", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Angela Choi", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Bradley Whitener", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Dario Garcia-Dominguez", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Carole Henry", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Angela Woods", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "LingZhi Ma", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Daniela Montes Berrueta", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Laura E. Avena", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Julian Quinones", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Samantha Falcone", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Chiaowen J. Hsiao", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Suzanne M. Scheaffer", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Larissa B. Thackray", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Phil White", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Michael S. Diamond", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Darin K. Edwards", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Andrea Carfi", - "author_inst": "Moderna, Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.10.07.511252", "rel_title": "Baculoviral COVID-19 Delta DNA vaccine cross-protects against SARS-CoV2 variants in K18-ACE2 transgenic mice", @@ -173792,6 +175511,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.05.22280716", + "rel_title": "Kinetics of naturally induced binding and neutralizing anti-SARS-CoV-2 antibody levels and potencies among Kenyan patients with diverse grades of COVID-19 severity", + "rel_date": "2022-10-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.05.22280716", + "rel_abs": "BackgroundGiven the low levels of COVID-19 vaccine coverage in Sub-Saharan Africa, despite high levels of natural SARS-CoV-2 exposures, strategies for extending the breadth and longevity of naturally acquired immunity are warranted. Designing such strategies will require a good understanding of natural immunity.\n\nMethodsWe used ELISA to measure whole-spike IgG and spike-receptor binding domain (RBD) total immunoglobulins (Igs) on 585 plasma samples collected longitudinally over five successive time points within six months of COVID-19 diagnosis in 309 COVID-19 patients. We measured antibody neutralizing potency against the wild-type (Wuhan) SARS-CoV-2 pseudo-virus in a subset of 51 patients over three successive time points. Binding and neutralizing antibody levels and potencies were then tested for correlations with COVID-19 severities, graded according to the National Institute of Health (NIH), USA criteria.\n\nResultsRates of sero-conversion increased from Day 0 (day of PCR testing) to Day 180 (six months) (63.6% to 100 %) and (69.3 % to 97%) for anti-spike IgG and anti-spike-RBD binding Igs, respectively. Levels of these binding antibodies peaked at Day 28 (P<0.0001) and were subsequently maintained for six months without significant decay (p>0.99). Similarly, antibody neutralizing potencies peaked at Day 28 (p<0.0001) but had decreased by three-folds, six months after COVID-19 diagnosis (p<0.0001). Binding antibodies levels were highly correlated with neutralizing antibody potencies at all the time points analyzed (r>0.6, P<0.0001). Levels and potencies of binding and neutralizing antibodies increased with disease severity.\n\nConclusionMost COVID-19 patients from Sub-Saharan Africa generate SARS-CoV-2 specific binding antibodies that remain stable during the first six months of infection. Although antibody binding levels and neutralizing potencies were directly correlated, the respective neutralizing antibodies decayed three-fold by the sixth month of COVID-19 diagnosis suggesting that they are short-lived, consistent with what has been observed elsewhere. Thus, just like for other populations, regular vaccination boosters will be required to broaden and sustain the high levels of predominantly naturally acquired anti-SARS-CoV-2 neutralizing antibodies.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "John Kimotho", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Yiakon Sein", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Shahin M Sayed", + "author_inst": "Aga Khan University - Kenya" + }, + { + "author_name": "Reena Shah", + "author_inst": "Aga Khan University - Kenya" + }, + { + "author_name": "Kennedy Mwai", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Mansoor Saleh", + "author_inst": "Aga Khan University-Kenya" + }, + { + "author_name": "Perpetual Wanjiku", + "author_inst": "KEMRI Wellcome" + }, + { + "author_name": "Jedida Mwacharo", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "James Nyangwange", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Henry Karanja", + "author_inst": "KEMRI Wellcome" + }, + { + "author_name": "Bernadette Kutima", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "John Gitonga", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Daisy Mugo", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Ann Karanu", + "author_inst": "Aga Khan University-Kenya" + }, + { + "author_name": "Linda Moranga", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Viviane Oluoch", + "author_inst": "Aga Khan University-Kenya" + }, + { + "author_name": "Jasmit Shah", + "author_inst": "Aga Khan University-Kenya" + }, + { + "author_name": "Julius Mutiso", + "author_inst": "Aga Khan University-Kenya" + }, + { + "author_name": "Afred G Mburu", + "author_inst": "Aga Khan University-Kenya" + }, + { + "author_name": "Zaitun Nneka", + "author_inst": "Aga Khan University-Kenya" + }, + { + "author_name": "Peter Betti", + "author_inst": "Agha Khan University-Kenya" + }, + { + "author_name": "Wanzila U Mutinda", + "author_inst": "Pwani University-Kenya" + }, + { + "author_name": "Abdirahman I Abdi", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Philip Bejon", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Isabella L Ochola", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "George M Warimwe", + "author_inst": "KEMRI-Wellcome Trust Research Programme - Kenya" + }, + { + "author_name": "Eunice Nduati", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + }, + { + "author_name": "Francis M Ndungu", + "author_inst": "KEMRI - Wellcome Research Programme - Kenya" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.04.22280459", "rel_title": "Association between COVID-19 mRNA vaccination and COVID-19 illness and severity during Omicron BA.4 and BA.5 sublineage periods", @@ -174149,105 +175995,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.04.510657", - "rel_title": "Relevance of the viral Spike protein/cellular Estrogen Receptor-\u03b1 interaction for endothelial-based coagulopathy induced by SARS-CoV-2", - "rel_date": "2022-10-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.04.510657", - "rel_abs": "Severe coagulopathy has been observed at the level of the microcirculation in several organs including lungs, heart and kidneys in patients with COVID-19, and in a minority of subjects receiving the SARS-CoV-2 vaccine. Various mechanisms have been implicated in these effects, including increases in circulating neutrophil extracellular traps, excessive inflammation, and endothelial dysfunction. Even if a correlation between infection by SARS-CoV-2 and upregulation of coagulation cascade components has been established in the lung, no direct proofs have been yet provided about the transcriptional machinery controlling the expression of these factors. Recent results obtained by us reported a novel transcriptional function of the SARS-CoV-2 Spike (S) viral protein involving a direct protein-protein interaction with the human Estrogen Receptor- (ER). Given the implications of ER in the control of key effectors in the coagulation cascade, we hypothesized that S-protein might increase the pro-coagulation activity of endothelial cells via the transcriptional activity of the ER, thus justifying the enhanced risk of thrombosis. To assess this, we tested the effects of S-protein on the expression of Tissue Factor (TF) and the overall procoagulation activity in a human endothelial cell line and confirmed this finding by overexpressing S-protein by gene transfer in mice. We then designed and tested two-point mutations in the S2 S-protein sequence that abolished the pro-coagulation function of S-protein in vitro and in vivo, without compromising its immunogenicity. In addition to reveal a new potential transcriptional function of S-protein, these results inspire the design of new vaccines with lower risk of thrombogenesis. Indeed, while the benefit/risk ratio remains overwhelming in favor of COVID-19 vaccination, our results shed light on the causal mechanisms of some rare anti-SARS-CoV-2 vaccine adverse events, and are thus essential for current and future vaccination and booster campaigns.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Silvia Stella Barbieri", - "author_inst": "Centro Cardiologico Monzino, IRCCS" - }, - { - "author_name": "Franca Cattani", - "author_inst": "Dompe farmaceutici S.p.A," - }, - { - "author_name": "Leonardo Sandrini", - "author_inst": "Centro Cardiologico Monzino, IRCCS" - }, - { - "author_name": "Magda Maria Grillo", - "author_inst": "Centro Cardiologico Monzino, IRCCS" - }, - { - "author_name": "Carmine Talarico", - "author_inst": "EXSCALATE, Dompe farmaceutici S.p.A" - }, - { - "author_name": "Daniela Iaconis", - "author_inst": "Dompe Farmacenutici, S.p.A." - }, - { - "author_name": "Lucia Lione", - "author_inst": "Takis S.r.l." - }, - { - "author_name": "Erika Salvatori", - "author_inst": "Takis S.r.l." - }, - { - "author_name": "Patrizia Amadio", - "author_inst": "Centro Cardiologico Monzino, IRCCS" - }, - { - "author_name": "Gloria Garoffolo", - "author_inst": "Centro Cardiologico Monzino, IRCCS" - }, - { - "author_name": "Mariano Maffei", - "author_inst": "Dompe Farmaceutici S.P.A." - }, - { - "author_name": "Francesca Galli", - "author_inst": "Dompe Farmaceutici, S.p.A." - }, - { - "author_name": "Andrea Rosario Beccari", - "author_inst": "Dompe Farmaceutici, S.p.A." - }, - { - "author_name": "Emanuele Marra", - "author_inst": "Takis, S.r.l." - }, - { - "author_name": "Marica Zoppi", - "author_inst": "Centro Cardiologico Monzino, IRCCS" - }, - { - "author_name": "Michael Michaelides", - "author_inst": "National Institute on Drug Abuse Intramural Research Program" - }, - { - "author_name": "Giuseppe Roscilli", - "author_inst": "Takis S.r.l." - }, - { - "author_name": "Luigi Aurisicchio", - "author_inst": "Takis S.r.l." - }, - { - "author_name": "Riccardo Bertini", - "author_inst": "Atreius S.a.s." - }, - { - "author_name": "Marcello Allegretti", - "author_inst": "Dompe Farmaceutici S.p.A." - }, - { - "author_name": "Maurizio Pesce", - "author_inst": "Centro Cardiologico Monzino, IRCCS" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2022.10.03.510677", "rel_title": "An agent-based modeling approach for lung fibrosis in response to COVID-19", @@ -176042,6 +177789,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.09.30.22280586", + "rel_title": "COVID treatment and in-hospital length of stay inequalities between race in the US over time", + "rel_date": "2022-10-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.30.22280586", + "rel_abs": "IntroductionDemonstrated health inequalities persist in the United States. SARS-CoV-2 (COVID) has been no exception, with access to treatment and hospitalization differing across race or ethnic group. Here we aim to assess differences in treatment with remdesivir and hospital length of stay across four waves of the pandemic.\n\nMethodsUsing a subset of the Truveta data we examine odds ratios (OR) of in-hospital remdesivir treatment and risk ratios (RR) of in-hospital length of stay between Black or African American (Black) to white patients. We adjusted for confounding factors such as age, sex, and comorbidity status.\n\nResultsThere were statically significant lower rates of remdesivir treatment and longer in-hospital lengths of stay comparing Black patients to white patients early in the pandemic (OR for treatment: 0.88, 95% confidence interval [CI]: 0.80, 0.96; RR for length of stay: 1.17, CI: 1.06, 1.21). Rates became close to parity between groups as the pandemic progressed.\n\nConclusionsWhile inpatient remdesivir treatment rates increased and length of stay decreased over the beginning course of the pandemic, there are still inequalities in patient care.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Benjamin Muir Althouse", + "author_inst": "Truveta" + }, + { + "author_name": "Charlotte Baker", + "author_inst": "Truveta" + }, + { + "author_name": "Peter D Smits", + "author_inst": "Truveta" + }, + { + "author_name": "Samuel Gratzl", + "author_inst": "Truveta" + }, + { + "author_name": "Ryan H Lee", + "author_inst": "Truveta" + }, + { + "author_name": "Brianna M Goodwin Cartwright", + "author_inst": "Truveta" + }, + { + "author_name": "Michael Siminov", + "author_inst": "Truveta" + }, + { + "author_name": "Michael D Wang", + "author_inst": "Truveta" + }, + { + "author_name": "Nicholas Stucky", + "author_inst": "Truveta" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.29.22280522", "rel_title": "A simple non-invasive C reactive protein-based score can predict outcome in patients with COVID-19", @@ -176191,41 +177989,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.28.22280467", - "rel_title": "The impact of a home-based personalized computerized training program on cognitive dysfunction associated with Long COVID: a before-and-after feasibility study", - "rel_date": "2022-09-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.28.22280467", - "rel_abs": "BackgroundLong COVID--also known as post-acute sequelae of COVID-19 or PASC--is a systemic syndrome affecting a large number of persons in the aftermath of the pandemic. Cognitive dysfunction (or brain fog) is one of its most common manifestations of PACS, and there are no effective interventions to mitigate it. Home-based personalized computerized cognitive training (CCT), which has shown effectiveness to improve other conditions, could offer hope to relieve the cognitive dysfunction in people with a previous history of COVID-19.\n\nObjectiveTo evaluate the feasibility and potential benefit of a personalized CCT intervention to improve cognitive function among people living with PACS.\n\nMethodsAdult individuals who self-reported cognitive dysfunction more than 3 months after a diagnosis of COVID-19 were recruited through an online platform designed for the study. Those who were eligible assessed their general cognitive function before completing as many cognitive daily training sessions as they wished during an 8-week period, using a personalized CCT application at home. The sessions included gamified tasks that tapped into five cognitive domains (attention, coordination, memory, perception and reasoning) and were tailored to the specific cognitive strengths and weaknesses detected at each point. At the end of this period, participants repeated the general cognitive function assessment. The differences between the scores at 8 weeks and baseline was the main outcome, complemented with analyses of the changes based on the participants age, training time, self-reported health level at baseline and time since the initial COVID-19 infection. Participants cognitive assessment scores were also computed in terms of percentiles according to the normative database of the test, considering their corresponding age- and gender-based reference sample.\n\nResultsThe participants had significant cognitive dysfunction at baseline, even though 80% of them had had the initial episode of COVID-19 more than a year before enrolling in the study. Eighty nine percent reported negative levels of self-reported health at baseline. On average, 51 training sessions (range: 10 to 251) were completed over a mean time of 435 minutes (range 78 to 2448). Most of the participants obtained higher scores after CCT in each of the domains as compared with baseline (attention: 81% of the sample; memory: 86%; coordination: 82%; perception: 88%; reasoning: 77%). The magnitude of the score increase at post-test was high across domains (attention: 31% of change; memory: 37%; coordination: 52%; perception: 42%; reasoning: 26%). Following CCT, there were also improvements in the percentile data in all the domains (attention: 14 points; memory: 18 points; coordination: 18 points; perception: 17 points; reasoning: 11 points).\n\nConclusionsThis study suggests that a self-administered CCT based on gamified cognitive tasks could be an effective way to ameliorate cognitive dysfunction in persons with PASC.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jon Andoni Dunabeitia", - "author_inst": "Universidad Nebrija" - }, - { - "author_name": "Francisco Mera", - "author_inst": "Blue Health Care" - }, - { - "author_name": "Oscar Baro", - "author_inst": "Centro de Salud de Galapagar" - }, - { - "author_name": "Tamen Jadad-Garcia", - "author_inst": "Vivenxia Group" - }, - { - "author_name": "Alejandro R Jadad", - "author_inst": "Centre for Digital Therapeutics" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.09.28.22280464", "rel_title": "Incidence Rates of Medically Attended COVID-19 in Infants Less than 6 Months of Age", @@ -177856,6 +179619,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.26.22280387", + "rel_title": "Duration of viral infectiousness and correlation with symptoms and diagnostic testing in non-hospitalized adults during acute SARS-CoV-2 infection: A longitudinal cohort study", + "rel_date": "2022-09-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.26.22280387", + "rel_abs": "BackgroundGuidelines for SARS-CoV-2 have relied on limited data on duration of viral infectiousness and correlation with COVID-19 symptoms and diagnostic testing.\n\nMethodsWe enrolled ambulatory adults with acute SARS-CoV-2 infection and performed serial measurements of COVID-19 symptoms, nasal swab viral RNA, nucleocapsid (N) and spike (S) antigens, and replication-competent SARS-CoV-2 by culture. We determined average time from symptom onset to a first negative test result and estimated risk of infectiousness, as defined by a positive viral culture.\n\nResultsAmong 95 adults, median [interquartile range] time from symptom onset to first negative test result was 9 [5] days, 13 [6] days, 11 [4] days, and >19 days for S antigen, N antigen, viral culture growth, and viral RNA by RT-PCR, respectively. Beyond two weeks, viral cultures and N antigen titers were rarely positive, while viral RNA remained detectable among half (26/51) of participants tested 21-30 days after symptom onset. Between 6-10 days from symptom onset, N antigen was strongly associated with viral culture positivity (relative risk=7.61, 95% CI: 3.01-19.2), whereas neither viral RNA nor symptoms were associated with culture positivity. During the 14 days following symptom onset, presence of N antigen (adjusted relative risk=7.66, 95% CI: 3.96-14.82), remained strongly associated with viral culture positivity, regardless of COVID-19 symptoms.\n\nConclusionsMost adults have replication-competent SARS-CoV-2 for 10-14 after symptom onset, and N antigen testing is a strong predictor of viral infectiousness. Within two weeks from symptom onset, N antigen testing, rather than absence of symptoms or viral RNA, should be used to safely discontinue isolation.\n\nFundingBill and Melinda Gates Foundation", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Paul K Drain", + "author_inst": "University of Washington" + }, + { + "author_name": "Ronit R Dalmat", + "author_inst": "University of Washington" + }, + { + "author_name": "LINHUI HAO", + "author_inst": "University of Washington" + }, + { + "author_name": "Meagan J Bemer", + "author_inst": "University of Washington" + }, + { + "author_name": "Elvira Budiawan", + "author_inst": "University of Washington" + }, + { + "author_name": "Jennifer F Morton", + "author_inst": "University of Washington" + }, + { + "author_name": "Renee C Ireton", + "author_inst": "University of Washington" + }, + { + "author_name": "Tien-Ying Hsiang", + "author_inst": "University of Washington" + }, + { + "author_name": "Zarna Marfatia", + "author_inst": "University of Washington" + }, + { + "author_name": "Roshni Prabhu", + "author_inst": "University of Washington" + }, + { + "author_name": "Claire Woosley", + "author_inst": "University of Washington" + }, + { + "author_name": "Adenech Gichamo", + "author_inst": "University of Washington" + }, + { + "author_name": "Elena Rechkina", + "author_inst": "University of Washington" + }, + { + "author_name": "Daphne Hamilton", + "author_inst": "University of Washington" + }, + { + "author_name": "Michalina Montano", + "author_inst": "University of Washington" + }, + { + "author_name": "Jason L Cantera", + "author_inst": "Global Health Labs" + }, + { + "author_name": "Alexey Ball", + "author_inst": "Global Health Labs" + }, + { + "author_name": "Inah Golez", + "author_inst": "University of Washington" + }, + { + "author_name": "Elise Smith", + "author_inst": "University of Washington" + }, + { + "author_name": "Alex Greninger", + "author_inst": "University of Washington" + }, + { + "author_name": "M Juliana McElrath", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Matthew Thompson", + "author_inst": "University of Washington" + }, + { + "author_name": "Benjamin D Grant", + "author_inst": "Global Health Labs" + }, + { + "author_name": "Allison Meisner", + "author_inst": "Fred Hutch Cancer Research Center" + }, + { + "author_name": "Geoffrey S Gottlieb", + "author_inst": "University of Washington" + }, + { + "author_name": "Michael J Gale Jr.", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.26.22280362", "rel_title": "Household transmission of SARS-CoV-2 during the Omicron wave in Shanghai, China: a case-ascertained study", @@ -178081,37 +179963,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.09.27.22280400", - "rel_title": "Direct modelling from GPS data reveals daily-activity-dependency of effective reproduction number in COVID-19 pandemic", - "rel_date": "2022-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.27.22280400", - "rel_abs": "During the COVID-19 pandemic, governments faced difficulties in implementing mobility restriction measures, as no clear quantitative relationship between human mobility and infection spread in large cities is known. We developed a model that enables quantitative estimations of the infection risk for individual places and activities by using smartphone GPS data for the Tokyo metropolitan area. The effective reproduction number is directly calculated from the number of infectious social contacts defined by the square of the population density at each location. The difference in the infection rate of daily activities is considered, where the stay-out activity, staying at someplace neither home nor workplace, is more than 28 times larger than other activities. Also, the contribution to the infection strongly depends on location. We imply that the effective reproduction number is sufficiently suppressed if the highest-risk locations or activities are restricted. We also discuss the effects of the Delta variant and vaccination.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jun'ichi Ozaki", - "author_inst": "Tokyo Institute of Technology" - }, - { - "author_name": "Yohei Shida", - "author_inst": "Tokyo Institute of Technology" - }, - { - "author_name": "Hideki Takayasu", - "author_inst": "Sony Computer Science Laboratories, Inc." - }, - { - "author_name": "Misako Takayasu", - "author_inst": "Tokyo Institute of Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.09.27.22280238", "rel_title": "Emergence and Persistent Dominance of Omicron BA.2.3.7 Variant in Community Outbreaks in Taiwan", @@ -179742,6 +181593,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.09.26.509459", + "rel_title": "Nanobodies for the treatment of SARS-CoV-2 in animals: a meta-analysis", + "rel_date": "2022-09-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.26.509459", + "rel_abs": "This meta-analysis aimed to find the effect of variable domain of heavy-chain antibodies (VHHs) for the treatment of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in animals. The databases of the PubMed, China National Knowledge Infrastructure (CNKI), Wan fang data, Cochrane Library, and Embase were searched for articles published before August 2022 on the protective effects of VHHs in animals. The articles retrieved were screened using inclusion and exclusion criteria. The data were analyzed using Review Manager 5.4. Six articles were selected from 667 articles based on the inclusion and exclusion criteria in VHHs. A forest plot showed that VHHs could offer protection against SARS-CoV-2 infection in animals [Mantel-Haenszel (MH) = 172.94, 95% confidence interval (CI) = (43.96, 678.42), P < 0.00001]. There was almost no heterogeneity in this study (I2 = 0). A funnel plot showed that the bias of the data analysis was small. This is a special meta-analysis proved that VHHs could treat and prevent SARS-CoV-2 in animals.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "jiao jiao", + "author_inst": "shihezi university" + }, + { + "author_name": "shu lan lin", + "author_inst": "shihezi university" + }, + { + "author_name": "zhen qi liang", + "author_inst": "shihezi university" + }, + { + "author_name": "Peng Wu", + "author_inst": "Shehezi University" + } + ], + "version": "1", + "license": "cc_no", + "type": "confirmatory results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.09.25.509344", "rel_title": "Comprehensive structural analysis reveals broad-spectrum neutralizing antibodies against Omicron", @@ -180103,117 +181985,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.26.509485", - "rel_title": "Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease", - "rel_date": "2022-09-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.26.509485", - "rel_abs": "SARS-CoV-2 is the causative agent of COVID-19. The highly conserved viral NSP15 endoribonuclease, NendoU, is a key enzyme involved in viral immune evasion, and a promising target for the development of new classes of antivirals. Yet, the broad variety of recognition sequences, complex assembly and kinetics, and lack of structural complexes hampers the development of new competitive or allosteric inhibitors for this target. Here, we performed enzymatic characterization of NendoU in its monomeric and hexameric form, showing that hexamers are allosteric enzymes with a positive cooperative index of 2. By using cryo-EM at distinct pHs combined with X-ray crystallography and structural analysis, we demonstrate the potential for NendoU to shift between open and closed states, and assembly in larger supramolecular entities, which might serve as a mechanism of self-regulation. Further, we report results from a large fragment screening campaign against NendoU, revealing multiple new allosteric sites for the development of inhibitors.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Andre Schutzer Godoy", - "author_inst": "Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil" - }, - { - "author_name": "Aline Minalli Nakamura", - "author_inst": "Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil" - }, - { - "author_name": "Alice Douangamath", - "author_inst": "Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, UK" - }, - { - "author_name": "Yun Song", - "author_inst": "Electron Bio-imaging Centre, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, OX11 0QX, UK" - }, - { - "author_name": "Gabriela Dias Noske", - "author_inst": "Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil" - }, - { - "author_name": "Victor Oliveira Gawriljuk", - "author_inst": "Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil" - }, - { - "author_name": "Rafaela Sachetto Fernandes", - "author_inst": "Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil" - }, - { - "author_name": "Humberto D. Muniz Pereira", - "author_inst": "Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil" - }, - { - "author_name": "Ketllyn Irene Zagato Oliveira", - "author_inst": "Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil" - }, - { - "author_name": "Daren Fearon", - "author_inst": "Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, UK" - }, - { - "author_name": "Alexandre Dias", - "author_inst": "Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, UK" - }, - { - "author_name": "Tobias Krojer", - "author_inst": "BioMAX, MAX IV Laboratory, Fotongatan 2, Lund 224 84, Sweden" - }, - { - "author_name": "Michael Fairhead", - "author_inst": "Centre for Medicines Discovery, Oxford University, OX1 3QU, UK" - }, - { - "author_name": "Alisa Powell", - "author_inst": "Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, UK" - }, - { - "author_name": "Louise Dunnet", - "author_inst": "Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, UK" - }, - { - "author_name": "Jose Brandao-Neto", - "author_inst": "Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, UK" - }, - { - "author_name": "Rachael Skyner", - "author_inst": "Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, UK" - }, - { - "author_name": "Rod Chalk", - "author_inst": "Centre for Medicines Discovery, Oxford University, OX1 3QU, UK" - }, - { - "author_name": "Frank von Delft", - "author_inst": "Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, UK" - }, - { - "author_name": "David Bajusz", - "author_inst": "Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudosok krt. 2, 1117 Budapest, Hungary" - }, - { - "author_name": "Miklos Bege", - "author_inst": "Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary" - }, - { - "author_name": "Aniko Borbas", - "author_inst": "Department of Pharmaceutical Chemistry, University of Debrecen, Egyetem ter 1, 4032 Debrecen, Hungary" - }, - { - "author_name": "Gyorgy Miklos Keseru", - "author_inst": "Medicinal Chemistry Research Group, Research Centre for Natural Sciences. 2, 1117 Budapest, Hungary" - }, - { - "author_name": "Glaucius Oliva", - "author_inst": "Sao Carlos Institute of Physics, University of Sao Paulo, Av. Joao Dagnone, 1100 - Jardim Santa Angelina, Sao Carlos, 13563-120, Brazil" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2022.09.23.22280297", "rel_title": "Development of Q-LAAD, an allonamer-based antigen test for the rapid detection of SARS-CoV-2", @@ -182472,6 +184243,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2022.09.22.22280222", + "rel_title": "Effects of SARS-CoV-2 Infection on Attention, Memory, and Sensorimotor Performance", + "rel_date": "2022-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.22.22280222", + "rel_abs": "BackgroundRecovery after SARS-CoV-2 infection is extremely variable, with some individuals recovering quickly, and others experiencing persistent long-term symptoms or developing new symptoms after the acute phase of infection, including fatigue, poor concentration, impaired attention, or memory deficits. Many existing studies reporting cognitive deficits associated with SARS-CoV-2 infection are limited by the exclusive use of self-reported measures or a lack of adequate comparison groups.\n\nMethodsForty-five participants, ages 18-70, (11 Long-COVID, 14 COVID, and 20 No-COVID) underwent behavioral testing with the NIH Toolbox Neuro-Quality of Life survey and selected psychometric tests, including a flanker interference task and the d2 Test of Attention.\n\nResultsWe found greater self-reported anxiety, apathy, fatigue, emotional dyscontrol, sleep disturbance and cognitive dysfunction in COVID compared No-COVID groups. After categorizing COVID patients according to self-reported concentration problems, we observed declining performance patterns in multiple attention measures across No-COVID controls, COVID and Long-COVID groups. COVID participants, compared to No-COVID controls, exhibited worse performance on NIH Toolbox assessments, including the Eriksen Flanker, Nine-Hole Pegboard and Auditory Verbal Learning tests.\n\nConclusionThis study provides convergent evidence that previous SARS-CoV-2 infection is associated with impairments in sustained attention, processing speed, self-reported fatigue and concentration. The finding that some patients have cognitive and visuomotor dysfunction in the absence of self-reported problems suggests that SARS-CoV-2 infection can have unexpected and persistent subclinical consequences.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Erin O'Connor", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Nikita Rednam", + "author_inst": "univrsity of Marylnd School of Medicine" + }, + { + "author_name": "Rory OBrien", + "author_inst": "Lantern Laboratory" + }, + { + "author_name": "Shea OBrien", + "author_inst": "Lantern Laboratory" + }, + { + "author_name": "Peter Rock", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Andrea Levine", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Thomas A Zeffiro", + "author_inst": "University of Maryland School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.21.22280219", "rel_title": "Excess death estimates from multiverse analysis in 2009-2021", @@ -182597,73 +184411,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.21.508922", - "rel_title": "Evolution of antibody immunity following Omicron BA.1 breakthrough infection", - "rel_date": "2022-09-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.21.508922", - "rel_abs": "Understanding the evolution of antibody immunity following heterologous SAR-CoV-2 breakthrough infection will inform the development of next-generation vaccines. Here, we tracked SARS-CoV-2 receptor binding domain (RBD)-specific antibody responses up to six months following Omicron BA.1 breakthrough infection in mRNA-vaccinated individuals. Cross-reactive serum neutralizing antibody and memory B cell (MBC) responses declined by two- to four-fold through the study period. Breakthrough infection elicited minimal de novo Omicron-specific B cell responses but drove affinity maturation of pre-existing cross-reactive MBCs toward BA.1. Public clones dominated the neutralizing antibody response at both early and late time points, and their escape mutation profiles predicted newly emergent Omicron sublineages. The results demonstrate that heterologous SARS-CoV-2 variant exposure drives the evolution of B cell memory and suggest that convergent neutralizing antibody responses continue to shape viral evolution.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Chengzi I. Kaku", - "author_inst": "Adimab LLC, The Scripps Research Institute" - }, - { - "author_name": "Tyler N. Starr", - "author_inst": "Fred Hutchinson Cancer Research Center, \t Fred Hutchinson Cancer Research Center The University of Utah School of Medicine" - }, - { - "author_name": "Panpan Zhou", - "author_inst": "The Scripps Research Institute; International Aids Vaccine Initiative Neutralizing Antibody Center; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scr" - }, - { - "author_name": "Haley L. Dugan", - "author_inst": "Adimab LLC" - }, - { - "author_name": "Paul Khalife", - "author_inst": "Adimab LLC" - }, - { - "author_name": "Ge Song", - "author_inst": "Scripps Research Institute Immunology and Microbiology; Scripps Research Institute Immunology and Microbiology International Aids Vaccine Initiative Neutralizin" - }, - { - "author_name": "Elizabeth R. Champney", - "author_inst": "Adimab LLC" - }, - { - "author_name": "Daniel W. Mielcarz", - "author_inst": "Dartmouth-Hitchcock Norris Cotton Cancer Center" - }, - { - "author_name": "James C. Geoghegan", - "author_inst": "Adimab LLC" - }, - { - "author_name": "Dennis R. Burton", - "author_inst": "Scripps Research Institute Immunology and Microbiology; International Aids Vaccine Initiative Neutralizing Antibody Center; Consortium for HIV/AIDS Vaccine Deve" - }, - { - "author_name": "Raiees Andrabi", - "author_inst": "The Scripps Research Institute; International Aids Vaccine Initiative Neutralizing Antibody Center; Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scr" - }, - { - "author_name": "Jesse D. Bloom", - "author_inst": "Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute University of Washington, University of Washington Department of Genome Sciences" - }, - { - "author_name": "Laura M. Walker", - "author_inst": "Invivyd Inc" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.09.21.508816", "rel_title": "Preclinical Study on SARS-CoV-2 Sublingual Vaccine with RBD Antigen and Poly(I:C) Adjuvant in Cynomolgus Macaques", @@ -184406,6 +186153,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2022.09.20.22280135", + "rel_title": "Host immunological responses facilitate development of SARS-CoV-2 mutations in patients receiving monoclonal antibody treatments", + "rel_date": "2022-09-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.20.22280135", + "rel_abs": "The role of host immunity in emergence of evasive SARS-CoV-2 Spike mutations under therapeutic monoclonal antibody (mAb) pressure remains to be explored. Here, we show that patients treated with various anti-SARS-CoV-2 mAb regimens develop evasive Spike mutations with remarkable speed and high specificity to the targeted mAb-binding sites. Mutations develop more frequently in immunocompromised patients and strongly correlate not only with the neutralizing capacity of the therapeutic mAbs, but also with an anti-inflammatory and healing-promoting host milieu. Machine-learning models based on soluble host-derived biomarkers identified patients at high risk of developing escape mutations against therapeutic mAbs with high accuracy. While our data demonstrate that host-driven immune and non-immune responses are essential for development of mutant SARS-CoV-2, these data could also support point-of-care decision making in reducing the risk of mAb treatment failure and improving mitigation strategies for possible dissemination of escape SARS-CoV-2 mutants.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Akshita Gupta", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Angelina Konnova", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Mathias Smet", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Matilda Berkell", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Alessia Savoldi", + "author_inst": "University of Verona" + }, + { + "author_name": "Matteo Morra", + "author_inst": "University of Verona" + }, + { + "author_name": "Vincent Van averbeke", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Fien De Winter", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Denise Peserico", + "author_inst": "University of Verona" + }, + { + "author_name": "Elisa Danese", + "author_inst": "University of Verona" + }, + { + "author_name": "An Hotterbeekx", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Elda Righi", + "author_inst": "University of Verona" + }, + { + "author_name": "- mAb ORCHESTRA working group", + "author_inst": "-" + }, + { + "author_name": "Pasquale De Nardo", + "author_inst": "University of Verona" + }, + { + "author_name": "Evelina Tacconelli", + "author_inst": "University of Verona" + }, + { + "author_name": "Surbhi Malhotra-Kumar", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Samir Kumar-Singh", + "author_inst": "University of Antwerp" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.20.22280138", "rel_title": "Prevalence of SARS-CoV-2 and co-occurrence/co-infection with malaria during the first wave of the pandemic (the Burkina Faso case)", @@ -184547,29 +186377,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2022.09.18.22279896", - "rel_title": "Application of the SEIR Model to a Logistic Formula and the Basic Reproduction Number of COVID-19 in Japan", - "rel_date": "2022-09-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.18.22279896", - "rel_abs": "The SEIR model is one of modified models of SIR, especially taken into account of exposed people. SEIR equations can be solved numerically, but it is hard to obtain analytically. Here, we propose some approximate solutions of SEIR equations, one of which is related with the logistic formula in Biology. As the second aim, the SEIR model is applied to the 7th-wave of COVID-19 in Japan. The basic reproduction number () in the SEIR model is estimated for the Omicron wave. We make use of data of the removed number R(t) rather than that of the infective number, because the latter seems to be ambiguous. This analysis gives = 10 with{gamma} = 1 and {sigma} = 0.5.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Takesi Saito", - "author_inst": "Kwansei Gakuin University" - }, - { - "author_name": "Kazuyasu Shigemoto", - "author_inst": "Tezukayama University" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.09.19.22280078", "rel_title": "Antibody avidity maturation favors SARS-CoV-2 convalescents over vaccinated individuals granting breadth in neutralizability and tolerance against variants", @@ -186156,6 +187963,125 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2022.09.15.507787", + "rel_title": "Imprinted SARS-CoV-2 humoral immunity induces converging Omicron RBD evolution", + "rel_date": "2022-09-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.15.507787", + "rel_abs": "Continuous evolution of Omicron has led to a rapid and simultaneous emergence of numerous variants that display growth advantages over BA. 5. Despite their divergent evolutionary courses, mutations on their receptor-binding domain (RBD) converge on several hotspots. The driving force and destination of such convergent evolution and its impact on humoral immunity remain unclear. Here, we demonstrate that these convergent mutations can cause striking evasion of neutralizing antibody (NAb) drugs and convalescent plasma, including those from BA.5 breakthrough infection, while maintaining sufficient ACE2 binding capability. BQ.1.1.10, BA.4.6.3, XBB, and CH. 1.1 are the most antibody-evasive strain tested, even exceeding SARS-CoV-1 level. To delineate the origin of the convergent evolution, we determined the escape mutation profiles and neutralization activity of monoclonal antibodies (mAbs) isolated from BA.2 and BA.5 breakthrough-infection convalescents. Importantly, due to humoral immune imprinting, BA.2 and especially BA.5 breakthrough infection caused significant reductions in the epitope diversity of NAbs and increased proportion of non-neutralizing mAbs, which in turn concentrated humoral immune pressure and promoted convergent evolution. Moreover, we showed that the convergent RBD mutations could be accurately inferred by integrated deep mutational scanning (DMS) profiles, and the evolution trends of BA.2.75/BA.5 subvariants could be well-simulated through constructed convergent pseudovirus mutants. Together, our results suggest current herd immunity and BA.5 vaccine boosters may not provide good protection against infection. Broad-spectrum SARS-CoV-2 vaccines and NAb drugs development should be highly prioritized, and the constructed mutants could help to examine their effectiveness in advance.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Yunlong Cao", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University; Changping Laboratory" + }, + { + "author_name": "Fanchong Jian", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" + }, + { + "author_name": "Jing Wang", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" + }, + { + "author_name": "Yuanling Yu", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Weiliang Song", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" + }, + { + "author_name": "Ayijiang Yisimayi", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" + }, + { + "author_name": "Jing Wang", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Ran An", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Xiaosu Chen", + "author_inst": "Institute for Immunology, College of Life Sciences, Nankai University" + }, + { + "author_name": "Na Zhang", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Yao Wang", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Peng Wang", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Lijuan Zhao", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Haiyan Sun", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Lingling Yu", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Sijie Yang", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" + }, + { + "author_name": "Xiao Niu", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" + }, + { + "author_name": "Tianhe Xiao", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" + }, + { + "author_name": "Qingqing Gu", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Fei Shao", + "author_inst": "Changping Laboratory, Beijing, P.R. China." + }, + { + "author_name": "Xiaohua Hao", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China." + }, + { + "author_name": "Yanli Xu", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China." + }, + { + "author_name": "Ronghua Jin", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China." + }, + { + "author_name": "Zhongyang Shen", + "author_inst": "Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University" + }, + { + "author_name": "Youchun Wang", + "author_inst": "Changping Laboratory; Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug C" + }, + { + "author_name": "Xiaoliang Sunney Xie", + "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University; Changping Laboratory" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.09.15.508120", "rel_title": "SARS-CoV-2 and HSV-1 Induce Amyloid Aggregation in Human CSF", @@ -186405,57 +188331,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.09.16.508278", - "rel_title": "Semantic and population analysis of the genetic targets related to COVID-19 and its association with genes and diseases", - "rel_date": "2022-09-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.16.508278", - "rel_abs": "SARS-CoV-2 is a coronavirus responsible for one of the most serious, modern worldwide pandemics, with lasting and multi-faceted effects. By late 2021, SARS-CoV-2 has infected more than 180 million people and has killed more than 3 million. The virus gains entrance to human cells through binding to ACE2 via its surface spike protein and causes a complex disease of the respiratory system, termed COVID-19. Vaccination efforts are being made to hinder the viral spread and therapeutics are currently under development. Towards this goal, scientific attention is shifting towards variants and SNPs that affect factors of the disease such as susceptibility and severity. This genomic grammar, tightly related to the dark part of our genome, can be explored through the use of modern methods such as natural language processing. We present a semantic analysis of SARS-CoV-2 related publications, which yielded a repertoire of SNPs, genes and disease ontologies. Population data from the 100Genomes Project were subsequently integrated into the pipeline. Data mining approaches of this scale have the potential to elucidate the complex interaction between COVID-19 pathogenesis and host genetic variation; the resulting knowledge can facilitate the management of high-risk groups and aid the efforts towards precision medicine.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Louis Papageorgiou", - "author_inst": "Agricultural University of Athens" - }, - { - "author_name": "Eleni Papakonstantinou", - "author_inst": "Agricultural University of Athens" - }, - { - "author_name": "Io Diakou", - "author_inst": "Agricultural University of Athens" - }, - { - "author_name": "Katerina Pierouli", - "author_inst": "Agricultural University of Athens" - }, - { - "author_name": "Konstantina Dragoumani", - "author_inst": "Agricultural University of Athens" - }, - { - "author_name": "Flora Bacopoulou", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "George P Chrousos", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Elias Eliopoulos", - "author_inst": "Agricultural University of Athens" - }, - { - "author_name": "Dimitrios Vlachakis", - "author_inst": "Agricultural University of Athens" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.09.14.22279916", "rel_title": "Humoral and Cellular Immunogenicity and Safety of 3 Doses of CoronaVac and BNT162b2 in Young Children and Adolescents with Kidney Diseases", @@ -188162,6 +190037,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.09.14.507948", + "rel_title": "HLA variants and TCR diversity against SARS-CoV-2 in the pre-COVID-19 era", + "rel_date": "2022-09-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.14.507948", + "rel_abs": "HLA antigen presentation and T-cell immunity are critical to control viral infection such as SARS-CoV-2. This study performed on samples collected in the pre-COVID-19 era demonstrates that individuals are fully equiped at the genetic level in terms of TCR repertoire and HLA variants to recognize and kill SARS-CoV-2 infected cells. HLA diversity, heterologous immunity and random somatic TCR recombination could explain these observations.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Stephane Buhler", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Zuleika Calderin Sollet", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Florence Bettens", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Antonia Schaefer", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Marc Ansari", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Sylvie Ferrari-Lacraz", + "author_inst": "Geneva University Hospitals" + }, + { + "author_name": "Jean Villard", + "author_inst": "Geneva University Hospitals" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.09.14.507904", "rel_title": "The SARS-CoV-2 spike N-terminal domain engages 9-O-acetylated \u03b12-8-linked sialic acids", @@ -188339,77 +190257,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.09.12.22279850", - "rel_title": "SARS-CoV-2 containment was achievable during the early stage of the pandemic: a retrospective modelling study of the Xinfadi outbreak in Beijing", - "rel_date": "2022-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.12.22279850", - "rel_abs": "Prior to the emergence of the Omicron variant, many cities in China had been able to maintain a \"Zero-COVID\" policy. They were able to achieve this without blanket city-wide lockdown and through widespread testing and an extensive set of nonpharmaceutical interventions (NPIs), such as mask wearing, contact tracing, and social distancing. We wanted to examine the effectiveness of such a policy in containing SARS-CoV-2 in the early stage of the pandemic. Therefore, we developed a fully stochastic, spatially structured, agent-based model of SARS-CoV-2 ancestral strain and reconstructed the Beijing Xinfadi outbreak through computational simulations. We found that screening for symptoms and among high-risk populations served as methods to discover cryptic community transmission in the early stage of the outbreak. Effective contact tracing could greatly reduce transmission. Targeted community lockdown and temporal mobility restriction could slow down the spatial spread of the virus, with much less of the population being affected. Population-wide mass testing could further improve the speed at which the outbreak is contained. Our analysis suggests that the containment of SARS-CoV-2 ancestral strains was certainly possible. Outbreak suppression and containment at the beginning of the pandemic, before the virus had the opportunity to undergo extensive adaptive evolution with increasing fitness in the human population, could be much more cost-effective in averting the overall pandemic disease burden and socioeconomic cost.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Yan Wang", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China" - }, - { - "author_name": "Kaiyuan Sun", - "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, NIH" - }, - { - "author_name": "Yang Pan", - "author_inst": "Beijing Center for Disease Prevention and Control (CDC), Beijing 100013, China" - }, - { - "author_name": "Lan Yi", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China" - }, - { - "author_name": "Da Huo", - "author_inst": "Beijing Center for Disease Prevention and Control (CDC), Beijing 100013, China" - }, - { - "author_name": "Yanpeng Wu", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China" - }, - { - "author_name": "Shuaibing Dong", - "author_inst": "Beijing Center for Disease Prevention and Control (CDC), Beijing 100013, China" - }, - { - "author_name": "Jinxin Guo", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China" - }, - { - "author_name": "Xiangfeng Dou", - "author_inst": "Beijing Center for Disease Prevention and Control (CDC), Beijing 100013, China" - }, - { - "author_name": "Wei Wang", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China" - }, - { - "author_name": "Shuangsheng Wu", - "author_inst": "Beijing Center for Disease Prevention and Control (CDC), Beijing 100013, China" - }, - { - "author_name": "Xufang Bai", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China" - }, - { - "author_name": "Hongjie Yu", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China" - }, - { - "author_name": "Quanyi Wang", - "author_inst": "Beijing Center for Disease Prevention and Control (CDC), Beijing 100013, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.09.13.22279912", "rel_title": "Increasing Cases of SARS-CoV-2 Omicron Reinfection Reveals Ineffective Post-COVID-19 Immunity in Denmark and Conveys the Need for Continued Next-Generation Sequencing", @@ -189928,6 +191775,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.09.09.507303", + "rel_title": "Expression profiling of immune-response-genes common in SARS-CoV-1 and influenza A virus disease, viz-a-viz neutropenia disorder, using integrated bioinformatics tools", + "rel_date": "2022-09-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.09.507303", + "rel_abs": "Viral diseases have proven to be an existential threat to man due to its fatality and its consistent emergence and re-emergence, so the need for novel ideas in combating this menace. Advances in genetic studies has proven to be indispensable in this fight as knowledge of organismal genetic variability has been useful in therapy development, as well as in mounting defense against the treacherous infectious agents. However, there are still fallow grounds needing to be explored in this war which informed this study, with focus on expression profiling of similar immune-responsegenes in SARS-COV-1 and influenza A virus (AIV) in respect to neutropenia (NP), using integrated bioinformatics techniques such as extraction of microarray dataset in the gene expression omnibus (GEO) database, generation of DEGs using GEO2R tool, construction of protein-protein interaction (PPI) network using string and Cytoscape software, Venn diagram analysis and then gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) for enrichment and pathway analysis respectively. Ten genes which includes ELANE, ITGA2B, CXCR1, CSF3R, SPI1, MS4A3, MMP8, CEACAM8, RNASE3, and DEFA4 were identified, with ELANE gene moreover identified as a key gene, which might be responsible in the regulation of immune response during viral infection, based on its characteristic feature in the PPI network.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ayinde Charles Olaniyi", + "author_inst": "Ladoke Akintola University of Technology" + }, + { + "author_name": "Obasanmi Dorcas Oluwadamilola", + "author_inst": "university of Lagos" + }, + { + "author_name": "Alabi Temitope Oluwabunmi", + "author_inst": "Ladoke Akintola University of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2022.09.09.22279725", "rel_title": "Effectiveness of incentivized peer referral to increase enrollment in a community-based chlamydia screening and treatment study among young Black men", @@ -190173,133 +192047,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.09.08.22279459", - "rel_title": "Population Normalization in SARS-CoV-2 Wastewater-Based Epidemiology: Implications from Statewide Wastewater Monitoring in Missouri", - "rel_date": "2022-09-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.08.22279459", - "rel_abs": "O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC=\"FIGDIR/small/22279459v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (24K):\norg.highwire.dtl.DTLVardef@debf50org.highwire.dtl.DTLVardef@1e21da2org.highwire.dtl.DTLVardef@78708org.highwire.dtl.DTLVardef@3239ee_HPS_FORMAT_FIGEXP M_FIG C_FIG The primary objective of this study was to identify a universal wastewater biomarker for population normalization for SARS-CoV-2 wastewater-based epidemiology (WBE). A total of 2,624 wastewater samples (41 weeks) were collected weekly during May 2021-April 2022 from 64 wastewater facilities across Missouri, U.S. Three wastewater biomarkers, caffeine and its metabolite, paraxanthine, and pepper mild mottle virus (PMMoV), were compared for the population normalization effectiveness for wastewater SARS-CoV-2 surveillance. Paraxanthine had the lowest temporal variation and strongest relationship between population compared to caffeine and PMMoV. This result was confirmed by data from ten different Wisconsins WWTPs with gradients in population sizes, indicating paraxanthine is a promising biomarker of the real-time population across a large geographical region. The estimated real-time population was directly compared against the population patterns with human movement mobility data. Of the three biomarkers, population normalization by paraxanthine significantly strengthened the relationship between wastewater SARS-CoV-2 viral load and COVID-19 incidence rate the most (40 out of 61 sewersheds). Caffeine could be a promising population biomarker for regions where no significant exogenous caffeine sources (e.g., discharges from food industries) exist. In contrast, PMMoV showed the highest variability over time, and therefore reduced the strength of the relationship between sewage SARS-CoV-2 viral load and the COVID-19 incidence rate, as compared to wastewater data without population normalization and the population normalized by either recent Census population or the population estimated based on the number of residential connections and average household size for that municipality from the Census. Overall, the findings of this long-term surveillance study concluded that the paraxanthine has the best performance as a biomarker for population normalization for SARS-CoV-2 wastewater-based epidemiology.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Chenhui Li", - "author_inst": "School of Natural Resources, University of Missouri, Columbia" - }, - { - "author_name": "Mohamed Bayati", - "author_inst": "School of Natural Resources, University of Missouri, Columbia" - }, - { - "author_name": "Shu-Yu Hsu", - "author_inst": "School of Natural Resources, University of Missouri, Columbia" - }, - { - "author_name": "Hsin-Yeh Hsieh", - "author_inst": "School of Natural Resources, University of Missouri, Columbia" - }, - { - "author_name": "Wilfing Lindsi", - "author_inst": "School of Natural Resources, University of Missouri, Columbia" - }, - { - "author_name": "Anthony Belenchia", - "author_inst": "Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services" - }, - { - "author_name": "Sally A. Zemmer", - "author_inst": "Water Protection Program, Missouri Department of Natural Resources" - }, - { - "author_name": "Jessica Klutts", - "author_inst": "Water Protection Program, Missouri Department of Natural Resources" - }, - { - "author_name": "Mary Samuelson", - "author_inst": "Water Protection Program, Missouri Department of Natural Resources" - }, - { - "author_name": "Melissa Reynolds", - "author_inst": "Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services" - }, - { - "author_name": "Elizabeth Semkiw", - "author_inst": "Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services" - }, - { - "author_name": "Hwei-Yiing Johnson", - "author_inst": "Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services" - }, - { - "author_name": "Trevor Foley", - "author_inst": "Missouri Department of Corrections" - }, - { - "author_name": "Chris G. Wieberg", - "author_inst": "Water Protection Program, Missouri Department of Natural Resources" - }, - { - "author_name": "Jeff Wenzel", - "author_inst": "Bureau of Environmental Epidemiology, Division of Community and Public Health, Missouri Department of Health and Senior Services" - }, - { - "author_name": "Terri D. Lyddon", - "author_inst": "Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center" - }, - { - "author_name": "Mary LePique", - "author_inst": "Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center" - }, - { - "author_name": "Clayton Rushford", - "author_inst": "Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center" - }, - { - "author_name": "Braxton B Salcedo", - "author_inst": "Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center" - }, - { - "author_name": "Kara Young", - "author_inst": "Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center" - }, - { - "author_name": "Madalyn Graham", - "author_inst": "Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center" - }, - { - "author_name": "Reinier Suarez", - "author_inst": "Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center" - }, - { - "author_name": "Anarose Ford", - "author_inst": "Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center" - }, - { - "author_name": "Dagmara S. Antkiewicz", - "author_inst": "Wisconsin State Laboratory of Hygiene, University of Wisconsin Madison" - }, - { - "author_name": "Kayley H. Janssen", - "author_inst": "Wisconsin State Laboratory of Hygiene, University of Wisconsin Madison" - }, - { - "author_name": "Martin M. Shafer", - "author_inst": "Wisconsin State Laboratory of Hygiene, University of Wisconsin Madison" - }, - { - "author_name": "Marc C. Johnson", - "author_inst": "Department of Molecular Microbiology and Immunology, University of Missouri, School of Medicine and the Christopher S. Bond Life Sciences Center" - }, - { - "author_name": "Chung-Ho Lin", - "author_inst": "School of Natural Resources, University of Missouri, Columbia" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.09.08.22279690", "rel_title": "A phase 3, randomised, double-blind, placebo-controlled clinical trial for adult evaluation of the efficacy and safety of a SARS-CoV-2 recombinant spike RBD protein vaccine (ABDALA-3 Study).", @@ -192222,6 +193969,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.09.05.22279623", + "rel_title": "Modeling vaccine allocation and equity implications of COVID-19 containment strategies", + "rel_date": "2022-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.05.22279623", + "rel_abs": "Given the shortage of global COVID-19 vaccines, a critical public concern is whether the strategy of allocation exerts a heterogeneous effect on settings that have imbalanced accessibility. Exacerbated by the mutational characteristics of the pathogen, traits of immunity protection of vaccines, and diversification of human behaviors, the pathway to the full eradication of the COVID-19 pandemic is becoming increasingly complicated and indeterminate. Population-wide evaluation of public interventions remains crucial to evaluate the performance of epidemiology policies. This study employs a mathematical compartmental model combined with the observational data of the United States to examine the potential effect of vaccine allocation on the trajectory of COVID-19 transmission and the elicited equity implications. The outcomes imply that allocation strategies substantially impact the cumulative equilibrium size of a pandemic controlling for confounding factors. Under a framework of a two-dose primary vaccination strategy aiming to curb the total infections for high-accessibility settings (HAS) and low-accessibility settings(LAS), the traits of vaccination, pathogen, and human effort integrally affect the equilibrium of the COVID-19 pandemic in the medium perspective (i.e., up to 5 years). Vaccine allocation increases the healthcare and cost burden for HAS temporarily, in contrast, it reduces the risk of COVID-19 transmission for the LAS. The effects are consistent across a variety of profiles. By enhancing the administration rates of primary doses (i.e., mainly through dose 1 and dose 2), the magnitude of the COVID-19 pandemic decreases contingent on confounding factors. To minimize the magnitude of infection, it is of importance to dynamically monitor the immunity protection of vaccines, the dynamics of virus transmission, and the gap in the human effort.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ichiro Nakamoto", + "author_inst": "Fujian University of Technology, School of Internet Economics and Business" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.09.09.22279760", "rel_title": "Parental experiences of the impacts of COVID-19 on the care of young children; qualitative interview findings from the Nairobi Early Childcare in Slums (NECS) Project", @@ -192391,25 +194157,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2022.09.04.22279016", - "rel_title": "The Most Cost-Efficient And Effective Set Of COVID-19 Policies To Reduce Monthly COVID-19 Case Increase Rates", - "rel_date": "2022-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.04.22279016", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe coronavirus is one of the most unprecedented pandemics in recent decades. Countries have been struggling to identify the appropriate policies to prevent COVID-19 spread efficiently. As coronavirus case and death numbers fluctuated among countries in the past two years, questions of which policies are most cost-efficient and effective in preventing coronavirus spread have yet to be answered. There are no worldwide agreed guidelines to follow, to the authors best knowledge. Countries are prone to making policy and implementation errors that could cost lives and cause tremendous economic loss. Although much research on COVID-19 has been done and many focused on policy effectiveness, few focused on the cost-efficiency and effectiveness of COVID-19 policies. This research identifies the most Cost-Efficient and Effective Set of COVID-19 Policies to Reduce Monthly COVID-19 Case Increase Rates through a quantitative, big-data-driven, and machine-learning enabled approach. The research collected and analyzed 13 COVID-19 policies and associated daily COVID-19 case numbers across 180 countries from January 2020 to June 2021, developed Policy Cost Model, defined Policy Efficiency and Effectiveness Index, and developed a Fully-Automated Best Policy Group Finder Python Program to find the most cost efficient and effective policy group. This research found that 1) Before Vaccinations are available, the most cost-efficient and effective policy group includes Facial Covering, Testing Policy, and Contact Tracing. Its cost-efficiency is a 1% monthly case decrease rate per billion of dollars spent. Its effectiveness is a 37% monthly case decrease rate. It is 1474 times more cost-efficient, 11 times more effective, and costs around $5336.83 Billion less than implementing all 12 common COVID-19 policies as the U.S. and many other countries did before vaccinations were available; 2) After Vaccinations are available, the most cost-efficient and effective policy group includes Facial Coverings, Contact Tracing, and Vaccinations. Its cost-efficiency is a 2.7% monthly case decrease rate per billion of dollars spent. Its effectiveness is a 52% monthly case decrease rate. It is 3835 times more cost-efficient, 21.5 times more effective, and costs around $5350 Billion less than implementing all 13 common COVID-19 policies as the U.S. and many other countries did. The research results will help countries, especially underdeveloped ones with very limited budgets, to identify and implement the most cost-efficient and effective policies so they can spend much less but reduce monthly cases much more.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Charline Chen", - "author_inst": "Irvine High School" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.09.04.22279587", "rel_title": "Effectiveness of inactivated and Ad5-nCoV COVID-19 vaccines against SARS-CoV-2 Omicron BA. 2 variant infection, severe illness, and death", @@ -194060,6 +195807,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.09.05.506626", + "rel_title": "Immune dynamics at single cell protein level after delta/omicron infection in COVID-19 vaccinated convalescent individuals", + "rel_date": "2022-09-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.05.506626", + "rel_abs": "Both COVID-19 mRNA or recombinant Adenovirus vector (rAdVV) based vaccines have shown a great efficacy in generating humoral and cellular immune responses. Two doses of the COVID-19 vaccines generate enough antibodies and generate spike-specific T cell responses. However, after 6-8 months there is a decline in antibody production and T cell responses. Due to the rise of new SARS-CoV-2 variants of concern, a third or even fourth dose of vaccine was recommended for the elderly, immune comprised and frontline medical health care workers. However, despite additional booster doses given, those who were infected with either delta or omicron (during December 2021 - March 2022) had symptoms of illness. By what means these COVID-19 vaccines provide immunity against the SARS-CoV-2 virus at the molecular level is not explored extensively yet and, it is an emerging research field as to how the SARS-CoV-2 virus is able to evade the host immunity. Most of the infected people had mild symptoms whilst some were asymptomatic. Many of the people had developed nucleocapsid antibodies against the SARS-CoV-2 delta/omicron variants confirming a humoral immune response against viral infection. Furthermore, cellular analysis shows that post-vaccinated recovered COVID-19 individuals have significantly reduced NK cells and increased T naive CD4+, TEM CD8+ and B cells. This decrease in cellular immunity corresponds to individuals who recovered from alpha variants infection and had mild symptoms. Our results highlight that booster doses clearly reduce the severity of infection against delta/omicron infection. Furthermore, our cellular and humoral immune system is trained by vaccines and ready to deal with breakthrough infections in the future.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Rimpi Bajaj", + "author_inst": "Tuebingen University" + }, + { + "author_name": "Zhiqi Yang", + "author_inst": "FK, Tuebingen University, Tuebingen" + }, + { + "author_name": "Vincent Hammer", + "author_inst": "IMGAG Tuebingen University" + }, + { + "author_name": "Simone Poeschel", + "author_inst": "Tuebingen University Hospital" + }, + { + "author_name": "Kristin Beiber", + "author_inst": "Tuebingen University Hospital" + }, + { + "author_name": "Madhuri S Salker", + "author_inst": "FK Tuebingen University" + }, + { + "author_name": "Nicolas Casadei", + "author_inst": "Tuebingen University" + }, + { + "author_name": "Stephan Ossowski", + "author_inst": "University of Tuebingen" + }, + { + "author_name": "Olaf Riess", + "author_inst": "Tuebingen University" + }, + { + "author_name": "Yogesh Singh", + "author_inst": "Tuebingen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.09.06.506714", "rel_title": "Heterologous boost with mRNA vaccines against SARS-CoV-2 Delta/Omicron variants following an inactivated whole-virus vaccine", @@ -194277,181 +196079,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.05.22279572", - "rel_title": "Distinct immune signatures discriminate SARS-CoV-2 vaccine combinations", - "rel_date": "2022-09-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.05.22279572", - "rel_abs": "Several vaccines have been found effective against COVID-19, usually administered in homologous regimens, with the same vaccine used for the prime and boost doses. However, recent studies have demonstrated improved protection via heterologous mix-and-match COVID-19 vaccine combinations, and a direct comparison among these regimens is needed to identify the best employment strategies. Here, we show a single-cohort comparison of changes to the humoral and cellular immune compartments following five different COVID-19 vaccines spanning three technologies (adenoviral, mRNA and inactivated vaccines). These vaccines were administered in a combinatorial fashion, resulting in sixteen different homologous and heterologous regimens. SARS-CoV-2-targeting antibody titres were highest when the boost dose consisted of mRNA-1273, independent of the vaccine used for priming. Priming with BBIBP-CorV induced less class-switching among spike-binding memory B cells and the highest antigen-specific T cell responses in heterologous combinations. These were generally more immunogenic in terms of specific antibodies and cellular responses compared to homologous regimens. Finally, single-cell analysis of 754 samples revealed specific B and T cell signatures of the vaccination regimens, indicating distinctive differences in the immune responses. These data provide new insights on the immunological effects of COVID-19 vaccine combinations and a framework for the design of improved vaccination strategies for other pathogens and cancer.", - "rel_num_authors": 40, - "rel_authors": [ - { - "author_name": "Nicolas Nunez", - "author_inst": "University of Zurich" - }, - { - "author_name": "Jonas Schmid", - "author_inst": "University of Zurich" - }, - { - "author_name": "Laura Power", - "author_inst": "University of Zurich" - }, - { - "author_name": "Chiara Alberti", - "author_inst": "University of Zurich" - }, - { - "author_name": "Sinduya Krishnarajah", - "author_inst": "University of Zurich" - }, - { - "author_name": "Stefanie Kreutmair", - "author_inst": "University of Zurich" - }, - { - "author_name": "Susanne Unger", - "author_inst": "University of Zurich" - }, - { - "author_name": "Sebastian Blanco", - "author_inst": "Universidad Nacional de Cordoba" - }, - { - "author_name": "Brenda Konigheim", - "author_inst": "InViV-CONICET, Universidad Nacional de Cordoba" - }, - { - "author_name": "Constanza Marin", - "author_inst": "Universidad de Cordoba" - }, - { - "author_name": "Luisina Onofrio", - "author_inst": "Universidad de Cordoba" - }, - { - "author_name": "Jenny Christine Kienzler", - "author_inst": "University of Zurich" - }, - { - "author_name": "Sara Pereira", - "author_inst": "University of Zurich" - }, - { - "author_name": "Florian Ingelfinger", - "author_inst": "University of Zurich" - }, - { - "author_name": "Marina E. Pasinovich", - "author_inst": "Msal" - }, - { - "author_name": "Juan M Castelli", - "author_inst": "Msal" - }, - { - "author_name": "Carla Vizzotti", - "author_inst": "Msal" - }, - { - "author_name": "Maximilian Schaefer", - "author_inst": "University of Zurich" - }, - { - "author_name": "Juan Villar-Vesga", - "author_inst": "University of Zurich" - }, - { - "author_name": "Carla Helena Merten", - "author_inst": "University of Zurich" - }, - { - "author_name": "Aakriti Sethi", - "author_inst": "University of Zurich" - }, - { - "author_name": "Tobias Wertheimer", - "author_inst": "University of Zurich" - }, - { - "author_name": "Mirjam Lutz", - "author_inst": "University of Zurich" - }, - { - "author_name": "Danusia Vanoaica", - "author_inst": "University of Zurich" - }, - { - "author_name": "Claudia Sotomayor", - "author_inst": "Universidad Nacional de Cordoba" - }, - { - "author_name": "Adriana Gruppi", - "author_inst": "Universidad de Cordoba" - }, - { - "author_name": "Christian Munz", - "author_inst": "University of Zurich" - }, - { - "author_name": "Diego Cardozo", - "author_inst": "Msal Cordoba" - }, - { - "author_name": "Gabriela Barbas", - "author_inst": "Msal CBA" - }, - { - "author_name": "Laura Lopez", - "author_inst": "Msal CBA" - }, - { - "author_name": "Paula Carreno", - "author_inst": "Msal CBA" - }, - { - "author_name": "Gonzalo Castro", - "author_inst": "Msal CBA" - }, - { - "author_name": "Elias Raboy", - "author_inst": "Msal CBA" - }, - { - "author_name": "Sandra Gallego", - "author_inst": "Universidad de Cordoba" - }, - { - "author_name": "Gabriel Moron", - "author_inst": "Universidad de Cordoba" - }, - { - "author_name": "Laura Cervi", - "author_inst": "Universidad de Cordoba" - }, - { - "author_name": "Eva V Acosta Rodriguez", - "author_inst": "Universidad de Cordoba" - }, - { - "author_name": "Belkys Maletto", - "author_inst": "Universidad de Cordoba" - }, - { - "author_name": "Mariana Maccioni", - "author_inst": "Universidad de Cordoba" - }, - { - "author_name": "Burkhard Becher", - "author_inst": "University of Zurich" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.09.05.22279589", "rel_title": "Safety and immunogenicity of a broad-spectrum mosaic vaccine as a booster dose against SARS-CoV-2 Omicron and other circulating variants", @@ -196110,6 +197737,101 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.09.02.506305", + "rel_title": "Novel monoclonal antibodies showing broad neutralizing activity for SARS-CoV-2 variants including Omicrons BA.5 and BA.2.75", + "rel_date": "2022-09-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.02.506305", + "rel_abs": "We identified novel neutralizing monoclonal antibodies against SARS-CoV-2 variants (including Omicron) from individuals received two doses of mRNA vaccination after they had been infected with wildtype. We named them MO1, MO2 and MO3. MO1 shows high neutralizing activity against authentic variants: D614G, Delta, BA.1, BA.1.1, BA.2, and BA.2.75 and BA.5. Our findings confirm that the wildtype-derived vaccination can induce neutralizing antibodies that recognize the epitopes conserved among the SARS-CoV-2 variants (including BA.5 and BA.2.75). The monoclonal antibodies obtained herein could serve as novel prophylaxis and therapeutics against not only current SARS-CoV-2 viruses but also future variants that may arise.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Hanako Ishimaru", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Mitsuhiro Nishimura", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Lidya Handayani Tjan", + "author_inst": "Kobe university Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Silvia Sutandhio", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Maria Istiqomah Marini", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Gema Barlian Effendi", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Hideki Shigematsu", + "author_inst": "Japan Synchrotron Radiation Research Institute SPring-8" + }, + { + "author_name": "Koji Kato", + "author_inst": "Japan Synchrotron Radiation Research Institute SPring-8" + }, + { + "author_name": "Natsumi Hasegawa", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Kaito Aoki", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Yukiya Kurahashi", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Koichi Furukawa", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Mai Shinohara", + "author_inst": "Kobe university Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Tomoka Nakamura", + "author_inst": "kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Jun Arii", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Tatsuya Nagno", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + }, + { + "author_name": "Sachiko Nakamura", + "author_inst": "Hyogo Prefectural Kakogawa Medical Center" + }, + { + "author_name": "Shigeru Sano", + "author_inst": "Hyogo Prefectural Kakogawa Medical Center" + }, + { + "author_name": "Sachiyo Iwata", + "author_inst": "Hyogo Prefectural Kakogawa Medical Center" + }, + { + "author_name": "Yasuko Mori", + "author_inst": "Kobe University Graduate School of Medicine School of Medicine:" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.09.01.506266", "rel_title": "Neutrophil extracellular traps have auto-catabolic activity and produce mononucleosome-associated circulating DNA", @@ -196303,57 +198025,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.08.30.22279409", - "rel_title": "Racism and Racial Injustice During COVID-19: Impact on University Student Mental Health", - "rel_date": "2022-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.30.22279409", - "rel_abs": "The purpose of the study is to understand how undergraduate, graduate, and professional students were affected by the events of racial injustice and the COVID-19 pandemic. Data gathered from an online campus-wide survey administered during July and August 2020 indicated high levels of stress and rates of depression across all stages of training. A majority of these students also indicated that, while events around racism negatively impacted their mental health, such events did not affect students academic success as COVID-19 did. Although previous studies have demonstrated that student mental health has been negatively affected during COVID-19, this study shows that student mental health is also impacted by events driven by racism and racial injustice concurrent to the pandemic. In light of these findings, it is recommended that institutions adopt an intersectional approach toward addressing such contemporaneous stressors with initiatives that can adapt to multiple events simultaneously.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Laurence M. Boitet", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Claire Estep", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Lisa M. Schwiebert", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Kalani Upshaw", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Caro Wolfner", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Amy Hutson Chatham", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Sherilyn Garner", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Angela Stowe", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Robin Lanzi", - "author_inst": "University of Alabama at Birmingham" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.08.30.22279427", "rel_title": "A qualitative process evaluation using the behaviour change wheel approach: Did a whole genome sequence report form (SRF) used to reduce nosocomial SARS-CoV-2 within UK hospitals operate as anticipated?", @@ -197832,6 +199503,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.29.22279354", + "rel_title": "Coverage and correlates of COVID-19 vaccination among children aged 5-11 years in Alberta, Canada", + "rel_date": "2022-08-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.29.22279354", + "rel_abs": "Background and ObjectivesIn Alberta, Canada, the COVID-19 vaccination program for children aged 5-11 years opened on November 26, 2021. Our objectives were to determine the cumulative vaccine coverage, stratified by age, during the first seven months of vaccine availability, and investigate factors associated with vaccine uptake.\n\nMethodsThis retrospective cohort study used population-based administrative health data to assess COVID-19 vaccination coverage among children aged 5-11 years in Alberta, Canada. We determined cumulative vaccine coverage since the time of vaccine availability and used a modified Poisson regression to evaluate factors associated with vaccine uptake.\n\nResultsOf 377,753 eligible children, 43.8 % (n=165,429) received one or more doses of COVID-19 vaccine during the study period (11.2% received only one dose, while 32.5 % received 2 doses). Almost 90% of initial doses were received within the first two months of vaccine availability. Of those eligible for a second dose, only 75.1% (n=122,973) received it during the study time period. We found a step-wise relationship between increasing child age and higher vaccine coverage. Other factors associated with higher vaccine coverage included living in a neighborhood with higher income, in a more densely populated area, and in certain geographic health zones. Registration in a private school was associated with lower vaccine coverage.\n\nConclusionsMessaging around COVID-19 vaccine safety and need should be tailored to child age, rather than uniform across the 5-11 year age range. Opportunities for targeted vaccination interventions should be considered.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Shannon E MacDonald", + "author_inst": "University of Alberta" + }, + { + "author_name": "Laura Reifferscheid", + "author_inst": "University of Alberta" + }, + { + "author_name": "Yuba Raj Paudel", + "author_inst": "University of Alberta" + }, + { + "author_name": "JOAN ROBINSON", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.08.26.22279283", "rel_title": "An effective volunteer community-based COVID-19 response program: the Vashon, WA Medical Reserve Corp experience", @@ -197989,89 +199691,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.29.22279351", - "rel_title": "Insights into COVID-19 epidemiology and control from temporal changes in serial interval distributions in Hong Kong", - "rel_date": "2022-08-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.29.22279351", - "rel_abs": "The serial interval distribution is used to approximate the generation time distribution, an essential parameter to predict the effective reproductive number \"Rt\", a measure of transmissibility. However, serial interval distributions may change as an epidemic progresses rather than remaining constant. Here we show that serial intervals in Hong Kong varied over time, closely associated with the temporal variation in COVID-19 case profiles and public health and social measures that were implemented in response to surges in community transmission. Quantification of the variation over time in serial intervals led to improved estimation of Rt, and provided additional insights into the impact of public health measures on transmission of infections.\n\nOne-Sentence SummaryReal-time estimates of serial interval distributions can improve assessment of COVID-19 transmission dynamics and control.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Sheikh Taslim Ali", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Dongxuan Chen", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Wey Wen Lim", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Amy Yeung", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Dillon C. Adam", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Yiu Chung Lau", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Eric H. Y. Lau", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Jessica Y. Wong", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Jingyi Xiao", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Faith Ho", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Huizhi Gao", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Lin Wang", - "author_inst": "The University of Cambridge" - }, - { - "author_name": "Xiao-Ke Xu", - "author_inst": "Dalian Minzu University" - }, - { - "author_name": "Zhanwei Du", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Peng Wu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Gabriel M. Leung", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Benjamin J. Cowling", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.08.29.22279333", "rel_title": "A case-crossover study of the effect of vaccination on SARS-CoV-2 transmission relevant behaviours during a period of national lockdown in England and Wales", @@ -199730,6 +201349,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.26.22279242", + "rel_title": "A survey of patient and public perceptions and awareness of SARS-CoV-2-related risks among participants in India and South Africa", + "rel_date": "2022-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.26.22279242", + "rel_abs": "A cross-sectional survey was performed among the adult population of participating countries, India and South Africa. The purpose of this study was to explore perceptions and awareness of SARS-CoV-2-related risks in the relevant countries. The main outcome measures were the proportion of participants aware of SARS-CoV-2, and their perception of infection risks.\n\nSelf-administered questionnaires were used to collect data via a web- and paper-based survey over three months. For data capturing, Microsoft Excel was employed, and descriptive statistics used for presenting data. Pearsons Chi-squared test was used to assess relationships between variables, and a p-value less than 0.05 was considered significant.\n\nThere were 844 respondents (India: n=660, South Africa: n=184; response rate 87.6%), with a 61.1% vs 38.3% female to male ratio. Post-high-school or university education was the lowest qualification reported by most respondents in India (77.3%) and South Africa (79.3%). Sources of information about the pandemic were usually media and journal publications (73.2%), social media (64.6%), family and friends (47.7%) and government websites (46.2%). Most respondents correctly identified infection prevention measures (such as physical distancing, mask use), with 90.0% reporting improved hand hygiene practices since the pandemic. Hesitancy or refusal to accept the SARS-CoV-2 vaccine was reported among 17.9% and 50.9% of respondents in India and South Africa, respectively. Reasons cited included rushed vaccine development and the futility of vaccines for what respondents considered a self-limiting flu-like illness.\n\nRespondents identified public health promotion measures for SARS-CoV-2. Reported hesitancy to the up-take of SARS-CoV-2 vaccines was much higher in South Africa. Vaccination campaigns should consider robust public engagement and contextually fit communication strategies with multimodal, participatory online and offline initiatives to address public concerns, specifically towards vaccines developed for this pandemic and general vaccine hesitancy.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Oluchi N Mbamalu", + "author_inst": "University of Cape Town Faculty of Health Sciences" + }, + { + "author_name": "Surya Surendran", + "author_inst": "The George Institute for Global Health India" + }, + { + "author_name": "Vrinda Nampoothiri", + "author_inst": "Amrita Institute of Medical Sciences" + }, + { + "author_name": "Candice Bonaconsa", + "author_inst": "University of Cape Town Faculty of Health Sciences" + }, + { + "author_name": "Fabia Edathadathil", + "author_inst": "Amrita Institute of Medical Sciences" + }, + { + "author_name": "Nina Zhu", + "author_inst": "Imperial College London Faculty of Medicine - South Kensington Campus: Imperial College London Faculty of Medicine" + }, + { + "author_name": "Vanessa Carter", + "author_inst": "Health Communication and Social Media" + }, + { + "author_name": "Helen Lambert", + "author_inst": "University of Bristol Medical School" + }, + { + "author_name": "Carolyn Tarrant", + "author_inst": "University of Leicester Department of Health Sciences" + }, + { + "author_name": "Raheelah Ahmad", + "author_inst": "City University of London" + }, + { + "author_name": "Adrian Brink", + "author_inst": "University of Cape Town Faculty of Health Sciences" + }, + { + "author_name": "Ebrahim Steenkamp", + "author_inst": "University of Cape Town Department of Statistical Sciences" + }, + { + "author_name": "Alison Holmes", + "author_inst": "Imperial College London Faculty of Medicine - South Kensington Campus: Imperial College London Faculty of Medicine" + }, + { + "author_name": "Sanjeev Singh", + "author_inst": "Amrita Institute of Medical Sciences" + }, + { + "author_name": "Esmita Charani", + "author_inst": "Imperial College London Faculty of Medicine - South Kensington Campus: Imperial College London Faculty of Medicine" + }, + { + "author_name": "Marc Mendelson", + "author_inst": "University of Cape Town Faculty of Health Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.25.22279238", "rel_title": "Evaluation of Secondary Chemistry due to Disinfection of Indoor Air with Germicidal Ultraviolet Lamps", @@ -199915,141 +201613,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2022.08.26.505450", - "rel_title": "Characterization of SARS-CoV-2 Omicron BA.2.75 clinical isolates", - "rel_date": "2022-08-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.26.505450", - "rel_abs": "The prevalence of the Omicron subvariant BA.2.75 is rapidly increasing in India and Nepal. In addition, BA.2.75 has been detected in at least 34 other countries and is spreading globally. However, the virological features of BA.2.75 are largely unknown. Here, we evaluated the replicative ability and pathogenicity of BA.2.75 clinical isolates in Syrian hamsters. Although we found no substantial differences in weight change among hamsters infected with BA.2, BA.5, or BA.2.75, the replicative ability of BA.2.75 in the lungs was higher than that of BA.2 and BA.5. Of note, BA.2.75 caused focal viral pneumonia in hamsters, characterized by patchy inflammation interspersed in alveolar regions, which was not observed in BA.5-infected hamsters. Moreover, in competition assays, BA.2.75 replicated better than BA.5 in the lungs of hamsters. These results suggest that BA.2.75 can cause more severe respiratory disease than BA.5 and BA.2 and should be closely monitored.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Ryuta Uraki", - "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Shun Iida", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Peter J. Halfmann", - "author_inst": "Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison" - }, - { - "author_name": "Seiya Yamayoshi", - "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Yuichiro Hirata", - "author_inst": "Department of Pathology, National Institute of Infectious Diseases" - }, - { - "author_name": "Kiyoko Iwatsuki-Horimoto", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Maki Kiso", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Mutsumi Ito", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Yuri Furusawa", - "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Hiroshi Ueki", - "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Yuko Sakai-Tagawa", - "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Makoto Kuroda", - "author_inst": "Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison" - }, - { - "author_name": "Tadashi Maemura", - "author_inst": "Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison" - }, - { - "author_name": "Taksoo Kim", - "author_inst": "Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison" - }, - { - "author_name": "Sohtaro Mine", - "author_inst": "Department of Pathology, National Institute of Infectious Diseases" - }, - { - "author_name": "Noriko Kinoshita-Iwamoto", - "author_inst": "National Center for Global Health and Medicine: Kokuritsu Kenkyu Kaihatsu Hojin Kokuritsu Kokusai Iryo Kenkyu Center" - }, - { - "author_name": "Rong Li", - "author_inst": "Utah State University, College of Agriculture and Applied Sciences" - }, - { - "author_name": "Yanan Liu", - "author_inst": "Utah State University, College of Agriculture and Applied Sciences" - }, - { - "author_name": "Deanna Larson", - "author_inst": "Utah State University, College of Agriculture and Applied Sciences" - }, - { - "author_name": "Shuetsu Fukushi", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Shinji Watanabe", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Ken Maeda", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Zhongde Wang", - "author_inst": "Utah State University, College of Agriculture and Applied Sciences" - }, - { - "author_name": "Norio Ohmagari", - "author_inst": "National Center for Global Health and Medicine: Kokuritsu Kenkyu Kaihatsu Hojin Kokuritsu Kokusai Iryo Kenkyu Center" - }, - { - "author_name": "James Theiler", - "author_inst": "Space Data Science and Systems, Los Alamos National Laboratory" - }, - { - "author_name": "Will Fischer", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Bette Korber", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Masaki Imai", - "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Tadaki Suzuki", - "author_inst": "Department of Pathology, National Institute of Infectious Diseases" - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.08.26.505425", "rel_title": "Correlated substitutions reveal SARS-like coronaviruses recombine frequently with a diverse set of structured gene pools", @@ -201464,6 +203027,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.08.23.505031", + "rel_title": "New Insights into How JUUL Electronic Cigarette Aerosols and Aerosol Constituents Affect SARS-CoV-2 Infection of Human Bronchial Epithelial Cells", + "rel_date": "2022-08-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.23.505031", + "rel_abs": "BackgroundThe relationship between the use of tobacco products and SARS-CoV-2 infection is poorly understood and controversial. Most studies have been done with tobacco cigarettes, while few have examined the effect of electronic cigarettes (ECs) on SARS-CoV-2 infection. We tested the hypothesis that EC fluids and aerosols with high concentrations of nicotine promote SARS-COV-2 infection by increasing viral entry into human respiratory epithelial cells.\n\nMethodsResponses of BEAS-2B cells to authentic JUUL aerosols or their individual constituents (propylene glycol (PG)/vegetable glycerin (VG) and nicotine) were compared using three exposure platforms: submerged culture, air-liquid-interface (ALI) exposure in a cloud chamber, and ALI exposure in a Cultex(R) system, which produces authentic heated EC aerosols. SARS-CoV-2 infection machinery was assessed using immunohistochemistry and Western blotting. Specifically, the levels of the SARS-CoV-2 receptor ACE2 (angiotensin converting enzyme 2) and a spike modifying enzyme, TMPRSS2 (transmembrane serine protease 2), were evaluated. Following each exposure, lentivirus pseudoparticles with spike protein and a green-fluorescent reporter were used to test viral penetration and the susceptibility of BEAS-2B cells to infection.\n\nResultsNicotine, EC fluids, and authentic JUUL aerosols increased both ACE2 levels and TMPRSS2 activity, which in turn increased viral particle entry into cells. While most data were in good agreement across the three exposure platforms, cells were more responsive to treatments when exposed at the ALI in the Cultex system, even though the exposures were brief and intermittent. In the Cultex system, PG/VG, PG/VG/nicotine, and JUUL aerosols significantly increased infection above clean air controls. However, both the PG/VG and JUUL treatments were significantly lower than nicotine/PG/VG. PG/VG increased infection only in the Cultex(R) system, which produces heated aerosol.\n\nConclusionOur data are consistent with the conclusion that authentic JUUL aerosols or their individual constituents (nicotine or PG/VG) increase SARS-CoV-2 infection. The strong effect produced by nicotine was modulated in authentic JUUL aerosols, demonstrating the importance of studying mixtures and aerosols from actual EC products. These data support the idea that vaping increases the likelihood of contracting COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Rattapol Phandthong", + "author_inst": "University of California, Riverside" + }, + { + "author_name": "Man Wong", + "author_inst": "University of California, Riverside" + }, + { + "author_name": "Ann Song", + "author_inst": "University of California, Riverside" + }, + { + "author_name": "Teresa Martinez", + "author_inst": "University of California, Riverside" + }, + { + "author_name": "Prue Talbot", + "author_inst": "University of California, Riverside" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2022.08.24.22279160", "rel_title": "Comparing the Safety and Immunogenicity of homologous (Sputnik V) and heterologous (BNT162B2) COVID-19 prime-boost vaccination", @@ -201741,41 +203339,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.08.23.22279058", - "rel_title": "Knowledge, attitude, and practices of ward attendant and housekeeping staffs towards dead body care of COVID-19 patients at tertiary care hospital : A cross sectional study", - "rel_date": "2022-08-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.23.22279058", - "rel_abs": "BackgroundHealthcare workers worked untiringly during entire pandemic period and taken efforts to protect individuals, families and communities in adverse situations with stretched resources. Among health care workers role of ward attendant and housekeeping staffs have been very significant particularly in infection control practices and dead body management. Present studys aim is to gain an understanding of the knowledge, attitudes, and practices (KAP) of ward attendant and housekeeping staffs towards dead body management.\n\nMethodsHospital-based cross-sectional study design was conducted among ward attendant and housekeeping staffs working in COVID units. A total of 62 participants were selected using simple random sampling technique. Self-administered questionnaire was used to collect data. Binary logistic regression model was used to see association between outcome and independent variables.\n\nResultPresent study found mean knowledge, attitude and practice score of participants were 6.1, 49.9 and 12.28 indicates good knowledge, positive attitude and inappropriate practice towards dead body care. Study result also shows that odds of good knowledge were not significantly associated with demographic variables. However, the participants who didnt receive any training on dead body care were found to have positive attitude towards dead body care(AOR=3.90,95%CI=1.092-13.92), whereas gender (AOR=1.85,95%CI=.430-7.96), working experience in COVID units (AOR=99.5,95%CI=.913-98.8) and educational qualification (AOR=30.33,95%CI=1.5-577) were significantly associated with practice of dead body care of COVID-19 patients.\n\nConclusionThe study found that majority of participants were having good knowledge, positive attitude and inappropriate practice towards dead body care of COVID-19 patients. Hospital administration should conduct regular training of dead body care of COVID-19 patients for all the housekeeping staffs and ward attendant to minimise the risk of exposure to infections and better management of dead bodies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Girraj Saini", - "author_inst": "AIl India Institute of Medical, Sciences, Rishikesh" - }, - { - "author_name": "Prasan Kumar Panda", - "author_inst": "AIl India Institute of Medical, Sciences, Rishikesh" - }, - { - "author_name": "Maneesh Sharma", - "author_inst": "AIl India Institute of Medical, Sciences, Rishikesh" - }, - { - "author_name": "Mahendra Singh", - "author_inst": "AIl India Institute of Medical, Sciences, Rishikesh" - }, - { - "author_name": "Raviprakash Meshram", - "author_inst": "AIl India Institute of Medical, Sciences, Rishikesh" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.24.505060", "rel_title": "Predicting antiviral resistance mutations in SARS-CoV-2 main protease with computational and experimental screening", @@ -203346,6 +204909,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.21.22279044", + "rel_title": "SARS-CoV-2 IgM and IgG serology and clinical outcomes in COVID-19 patients", + "rel_date": "2022-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.21.22279044", + "rel_abs": "BackgroundThe SARS-CoV-2 virus has become pandemic for the last 2 years. Inflammatory response to the virus leads to organ dysfunction and death. Predicting the severity of inflammatory response helps in managing critical patients using serology tests IgG and IgM. We conducted a longitudinal study to correlate serum SARS-CoV-2 IgM and IgG serology with clinical outcomes in COVID-19 patients.\n\nMethodsWe analyzed patient data from March to December of 2020 for those who were admitted at AIIMS Rishikesh. Clinical and laboratory data of these patients were collected from the e-hospital portal and analysed. Correlation was seen with clinical outcomes and was assessed using MS Excel 2010 and SPSS software.\n\nResultsOut of 494 patients, the mean age of patients was 48.95 {+/-} 16.40 years and there were more male patients in the study (66.0%). The patients were classified into 4 groups; mild-moderate 328 (67.1%), severe 131 (26.8%) and critical 30 (6.1%). The mean duration from symptom onset to serology testing was 19.87 {+/-} 30.53 days. In-hospital mortality was observed in 25.1% patients. The seropositivity rate (i.e., either IgG or IgM >10 AU) was 50%. There was a significant difference between the 2 groups in terms of IgM Levels (AU/mL) (W = 33428.000, p = <0.001) and IgG Levels (AU/mL) (W = 39256.500, p = <0.001), with the median IgM/ IgG Levels (AU/mL) being highest in the RT-PCR-Positive group. There was no significant difference between the groups in terms of IgM Levels and IgG levels with all other clinical outcomes (disease severity, septic shock, Intensive care admission, mechanical ventilation and mortality).\n\nConclusionSerology (IgM and IgG) levels are high in RTPCR positive group compared to clinical COVID-19. However, serology cannot be useful for the prediction of disease outcomes except few situations. The study also highlights the importance of doing serology at a particular time as antibody titres vary with the duration of the disease.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Mohan S", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Pratap Kumar", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Prasan Kumar Panda", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Vikram Jain", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Rohit Raina", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Sarama Saha", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Vivekandan S", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Balram J Omar", + "author_inst": "AIIMS Rishikesh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.19.22278986", "rel_title": "Increased adverse events following third dose of BNT162b2/Pfizer vaccine in those with previous COVID-19, but not with concurrent influenza vaccine.", @@ -203511,61 +205121,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.08.19.22278966", - "rel_title": "Seasonal variations in social contact patterns in a rural population in north India: Implications for pandemic control", - "rel_date": "2022-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.19.22278966", - "rel_abs": "Social contact mixing patterns are critical to the transmission of communicable diseases and have been employed to model disease outbreaks including COVID-19. Nonetheless, there is a paucity of studies on contact mixing in low and middle-income countries such as India. Furthermore, mathematical models of disease outbreaks do not account for the temporal nature of social contacts. We conducted a longitudinal study of social contacts in rural north India across three seasons and analysed the temporal differences in contact patterns.\n\nA contact diary survey was performed across three seasons from October 2015-16, in which participants were queried on the number, duration, and characteristics of contacts that occurred on the previous day. A total of 8,421 responses from 3,052 respondents (49% females) recorded characteristics of 180,073 contacts. Respondents reported a significantly higher number and duration of contacts in the winter, followed by the summer and the monsoon season (Nemenyi post-hoc, p<0.001). Participants aged 0-9 years and 10-19 years of age reported the highest median number of contacts (16 (IQR 12-21), 17 (IQR 13-24) respectively) and were found to have the highest node centrality in the social network of the region (pageranks = 0.20, 0.17). Employed males across all age groups were found to have a higher number of contacts than unemployed males (Negative Binomial Regression: rate ratio 1.18, 95% CI: 1.05-1.31). A large proportion (>80%) of contacts that were reported in schools or on public transport involved physical contact.\n\nTo the best of our knowledge, our study is the first from India to show that contact mixing patterns vary by the time of the year and provides useful implications for pandemic control. Our results can be used to parameterize more accurate mathematical models for prediction of epidemiological trends of infections in rural India.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Sargun Nagpal", - "author_inst": "Ashoka University, Sonepat, Haryana" - }, - { - "author_name": "Rakesh Kumar", - "author_inst": "All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Riz Fernando Noronha", - "author_inst": "Ashoka University, Sonepat, Haryana" - }, - { - "author_name": "Supriya Kumar", - "author_inst": "Bill and Melinda Gates Foundation, Seattle, USA" - }, - { - "author_name": "Debayan Gupta", - "author_inst": "Ashoka University, Sonepat, Haryana" - }, - { - "author_name": "Ritvik Amarchand", - "author_inst": "All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Mudita Gosain", - "author_inst": "All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Hanspria Sharma", - "author_inst": "All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Gautam I. Menon", - "author_inst": "Ashoka University, Sonepat, Haryana" - }, - { - "author_name": "Anand Krishnan", - "author_inst": "All India Institute of Medical Sciences, New Delhi" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.08.19.22278993", "rel_title": "Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa", @@ -205124,6 +206679,45 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.08.17.504362", + "rel_title": "Ancestral lineage of SARS-CoV-2 is more stable in human biological fluids than Alpha, Beta and Omicron variants of concern", + "rel_date": "2022-08-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.17.504362", + "rel_abs": "SARS-CoV-2 is a zoonotic virus which was first identified in 2019, and has quickly spread worldwide. The virus is primarily transmitted through respiratory droplets from infected persons; however, the virus-laden excretions can contaminate surfaces which can serve as a potential source of infection. Since the beginning of the pandemic, SARS-CoV-2 has continued to evolve and accumulate mutations throughout its genome leading to the emergence of variants of concern (VOCs) which exhibit increased fitness, transmissibility, and/or virulence. However, the stability of SARS-CoV-2 VOCs in biological fluids has not been thoroughly investigated so far. The aim of this study was to determine and compare the stability of different SARS-CoV-2 strains in human biological fluids. Here, we demonstrate that the ancestral strain of Wuhan-like lineage A was more stable than the Alpha VOC B.1.1.7, and the Beta VOC B.1.351 strains in human liquid nasal mucus and sputum. In contrast, there was no difference in stability among the three strains in dried biological fluids. Furthermore, we also show that the Omicron VOC B.1.1.529 strain was less stable than the ancestral Wuhan-like strain in liquid nasal mucus. These studies provide insight into the effect of the molecular evolution of SARS-CoV-2 on environmental virus stability, which is important information for the development of countermeasures against SARS-CoV-2.\n\nImportanceGenetic evolution of SARS-CoV-2 leads to the continuous emergence of novel variants, posing a significant concern to global public health. Five of these variants have been classified so far into variants of concern (VOCs); Alpha, Beta, Gamma, Delta, and Omicron. Previous studies investigated the stability of SARS-CoV-2 under various conditions, but there is a gap of knowledge on the survival of SARS-CoV-2 VOCs in human biological fluids which are clinically relevant. Here, we present evidence that Alpha, Beta, and Omicron VOCs were less stable than the ancestral Wuhan-like strain in human biological fluids. Our findings highlight the potential risk of contaminated human biological fluids in SARS-CoV-2 transmission and contribute to the development of countermeasures against SARS-CoV-2.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Taeyong Kwon", + "author_inst": "Kansas State University" + }, + { + "author_name": "Natasha N Gaudreault", + "author_inst": "Kansas State University" + }, + { + "author_name": "David Meekins", + "author_inst": "Kansas State University" + }, + { + "author_name": "Chester McDowell", + "author_inst": "Kansas State Univeristy" + }, + { + "author_name": "Konner Cool", + "author_inst": "Kansas State University" + }, + { + "author_name": "Juergen A Richt", + "author_inst": "Kansas State University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.08.17.504313", "rel_title": "Epistasis lowers the genetic barrier to SARS-CoV-2 neutralizing antibody escape", @@ -205313,37 +206907,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.18.22278963", - "rel_title": "Relative contributions of vaccination and previous infection to population-level SARS-CoV-2 immunity over time: a simulation modelling study", - "rel_date": "2022-08-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.18.22278963", - "rel_abs": "Population-level immunity to SARS-CoV-2 directly impacts the incidence of COVID-19 morbidity and mortality. Understanding how this immunity is likely to change over time in the context of future vaccination schedules and emerging SARS-CoV-2 variants is critical to inform pandemic policy. This study simulates population-level COVID-19 immunity (including relative contributions of vaccination and previous infection) in Victoria, Australia over 18 months using an agent-based model and logistic regression equations that predict immunity and waning following vaccination and/or infection. Previous infection was found to drive most immunity against infection even with ongoing regular vaccination, however a greater proportion of overall immunity against mortality was accounted for by vaccination. Although previous infection appears to be driving a substantial component of population-level COVID-19 immunity currently, improved vaccines providing longer lasting (and better sterilizing) immunity are likely to be a critical component of the future pandemic response given the risks associated with SARS-CoV-2 infection.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Joshua Szanyi", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Tim Wilson", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Hassan Andrabi", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Tony Blakely", - "author_inst": "University of Melbourne" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.08.18.504053", "rel_title": "Single-cell RNA sequencing highlights a reduced function of natural killer and cytotoxic T cells in recovered COVID-19 pregnant women", @@ -206802,6 +208365,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.13.22278740", + "rel_title": "Demographic and Viral-Genetic Analyses of COVID-19 Severity in Bahrain Identify Local Risk Factors and a Protective Effect of Polymerase Mutations", + "rel_date": "2022-08-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.13.22278740", + "rel_abs": "A multitude of demographic, health, and genetic factors are associated with the risk of developing severe COVID-19 following infection by the SARS-CoV-2. There is a need to perform studies across human societies and to investigate the full spectrum of genetic variation of the virus. Using data from 869 COVID-19 patients in Bahrain between March 2020 and March 2021, we analyzed paired viral sequencing and non-genetic host data to understand host and viral determinants of severe COVID-19. We estimated the effects of demographic variables specific to the Bahrain population and found that the impact of health factors are largely consistent with other populations. To extend beyond the common variants of concern in the Spike protein analyzed by previous studies, we used a viral burden approach and detected a protective effect of low-frequency missense viral mutations in the RNA-dependent RNA polymerase (Pol) gene on disease severity. Our results contribute to the survey of severe COVID-19 in diverse populations and highlight the benefits of studying rare viral mutations.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Evan M Koch", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Justin Du", + "author_inst": "Yale University" + }, + { + "author_name": "Michelle Dressner", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Hashmeya Erahim Alwasti", + "author_inst": "Bahrain Ministry of Health" + }, + { + "author_name": "Zahra Al Taif", + "author_inst": "Bahrain Ministry of Health" + }, + { + "author_name": "Fatima Shehab", + "author_inst": "Bahrain Ministry of Health" + }, + { + "author_name": "Afaf Merza Mohamed", + "author_inst": "Bahrain Ministry of Health" + }, + { + "author_name": "Amani Alhajeri", + "author_inst": "Salmaniya Medical Complex" + }, + { + "author_name": "Amna Alawadhi", + "author_inst": "Salmaniya Medical Complex" + }, + { + "author_name": "Nabeel Almoamen", + "author_inst": "Salmaniya Medical Complex" + }, + { + "author_name": "Khulood Ashoor", + "author_inst": "Salmaniya Medical Complex" + }, + { + "author_name": "Sara Hasan", + "author_inst": "Salmaniya Medical Complex" + }, + { + "author_name": "Amjad Ghanem", + "author_inst": "Bahrain Ministry of Health" + }, + { + "author_name": "Alireza Haghighi", + "author_inst": "Brigham and Womens Hospital" + }, + { + "author_name": "Shamil Sunyaev", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Maha Farhat", + "author_inst": "Harvard Medical School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.12.22278726", "rel_title": "BNT162b2 induced neutralizing and non-neutralizing antibody functions against SARS-CoV-2 diminish with age", @@ -207003,53 +208645,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.08.16.504085", - "rel_title": "Synchronicity of viral shedding in molossid bat maternity colonies", - "rel_date": "2022-08-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.16.504085", - "rel_abs": "Infection dynamics in vertebrates are driven by biological and ecological processes. For bats, population structure and reproductive cycles have major effects on RNA virus transmission. On Reunion Island, previous studies have shown that parturition of pregnant females and aggregation of juvenile Reunion free-tailed bats (Mormopterus francoismoutoui) are associated to major increase in the prevalence of bats shedding viruses. The synchronicity of such shedding pulses, however, is yet to be assessed, between viruses but also maternity colonies. Based on 3422 fresh faeces collected every two to five weeks during four consecutive birthing seasons, we report the prevalence of bats shedding astroviruses (AstVs), coronaviruses (CoVs), and paramyxoviruses (PMVs) in two maternity colonies on Reunion Island. We found that the proportion of bats shedding viruses is highly influenced by sampling collection dates, and therefore by the seasonality of parturition. We highlight that virus shedding patterns are reproducible among years and colonies for CoVs and at a lesser extent for PMVs, but not for AstVs. We also report 1% of bats harbouring double infections, mostly CoVs and PMVs, but none shedding simultaneously AstVs, CoVs and PMVs.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Axel O.G. Hoarau", - "author_inst": "Universit\u00e9 de La R\u00e9union, Processus Infectieux en Milieu Insulaire Tropical, Inserm 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La R\u00e9union, France" - }, - { - "author_name": "Marie K\u00f6ster", - "author_inst": "Universit\u00e9 de La R\u00e9union, Processus Infectieux en Milieu Insulaire Tropical, Inserm 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La R\u00e9union, France" - }, - { - "author_name": "Muriel Dietrich", - "author_inst": "Universit\u00e9 de La R\u00e9union, Processus Infectieux en Milieu Insulaire Tropical, Inserm 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La R\u00e9union, France" - }, - { - "author_name": "Gildas Le Minter", - "author_inst": "Universit\u00e9 de La R\u00e9union, Processus Infectieux en Milieu Insulaire Tropical, Inserm 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La R\u00e9union, France" - }, - { - "author_name": "L\u00e9a Joffrin", - "author_inst": "Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium" - }, - { - "author_name": "Riana V. Ramanantsalama", - "author_inst": "Universit\u00e9 de La R\u00e9union, Processus Infectieux en Milieu Insulaire Tropical, Inserm 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La R\u00e9union, France" - }, - { - "author_name": "Patrick Mavingui", - "author_inst": "Universit\u00e9 de La R\u00e9union, Processus Infectieux en Milieu Insulaire Tropical, Inserm 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La R\u00e9union, France" - }, - { - "author_name": "Camille Lebarbenchon", - "author_inst": "Universit\u00e9 de La R\u00e9union, Processus Infectieux en Milieu Insulaire Tropical, Inserm 1187, CNRS 9192, IRD 249, Sainte-Clotilde, La R\u00e9union, France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "ecology" - }, { "rel_doi": "10.1101/2022.08.15.503946", "rel_title": "Collateral impacts of pandemic COVID-19 drive the nosocomial spread of antibiotic resistance", @@ -208648,6 +210243,177 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.08.08.22278550", + "rel_title": "Cohort Study Protocol of the Brazilian Collaborative Research Network on COVID-19: strengthening WHO global data", + "rel_date": "2022-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.08.22278550", + "rel_abs": "IntroductionWith the COVID-19 pandemic, hospitals in low-income countries were faced with a triple challenge. First, a large number of patients required hospitalization because of the infections more severe symptoms. Second, there was a lack of systematic and broad testing policies for early identification of cases. Third, there were weaknesses in the integration of information systems, which led to the need to search for available information from the hospital information systems. Accordingly, it is also important to state that relevant aspects of COVID-19s natural history had not yet been fully clarified. The aim of this research protocol is to present the strategies of a Brazilian network of hospitals to perform systematized data collection on COVID-19 through the World Health Organization (WHO) Platform.\n\nMethods and AnalysisThis is a multicenter project among Brazilian hospitals to provide data on COVID-19 through the WHO global platform, which integrates patient care information from different countries. From October 2020 to March 2021, a committee worked on defining a flowchart for this platform, specifying the variables of interest, data extraction standardization and analysis.\n\nEthics and DisseminationThis protocol was approved by the Research Ethics Committee (CEP) of the Research Coordinating Center of Brazil (CEP of the Hospital Nossa Senhora da Conceicao), on January 29, 2021, under approval No. 4.515.519 and by the National Research Ethics Commission (CONEP), on February 5, 2021, under approval No. 4.526.456. The project results will be explained in WHO reports and published in international peer-reviewed journals, and summaries will be provided to the funders of the study.\n\nStrengths and limitations of this studyAs the study involves a convenience and non-probabilistic sample of patients hospitalized in health units, it may not represent the population of patients with COVID-19 hospitalized in the country. However, the information generated by this research can serve as a basis for the development of maps of the evolution of SARS-CoV-2 infection and public policies to face pandemics. It is a study that uses secondary data, and therefore, information bias may occur, but on the other hand, it has a low cost and facilitates a population-based study with national coverage.\n\nArticle SummaryThis is a multicenter project among Brazilian hospitals to provide data on COVID-19 through the WHO global platform.\n\nIt is expected to deepen knowledge about the pandemic scenario and help hospital institutions to develop preventive measures, health service protocols and strengthen the training of teams in the existing complications.", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Fernando Anschau", + "author_inst": "Conceicao Hospitalar Group" + }, + { + "author_name": "Natalia Del' Angelo Aredes", + "author_inst": "Universidade Federal de Goias, Nursing School Goiania, Goias, BR" + }, + { + "author_name": "Ludovic Reveiz", + "author_inst": "Pan American Health Organization, DC, USA" + }, + { + "author_name": "Monica Padilla", + "author_inst": "Pan American Health Organization Brazil Brasilia, DF, BR" + }, + { + "author_name": "Rosane de Mendonca Gomes", + "author_inst": "Pan American Health Organization Brazil Brasilia, DF, BR" + }, + { + "author_name": "Wellington Mendes Carvalho", + "author_inst": "Pan American Health Organization Brazil Brasilia, DF, BR" + }, + { + "author_name": "Fernando Antonio Gomes Leles", + "author_inst": "Pan American Health Organization Brazil Brasilia, DF, BR" + }, + { + "author_name": "Fernanda Baeumle Reese", + "author_inst": "Complexo Hospitalar do Trabalhador Curitiba, PR, BR" + }, + { + "author_name": "Andre Hostilio Hubert", + "author_inst": "Complexo Hospitalar do Trabalhador Curitiba, Parana, BR" + }, + { + "author_name": "Elisandrea Sguario Kemper", + "author_inst": "Hospital da Crianca de Brasilia Distrito Federal, BR" + }, + { + "author_name": "Renilson Rehem de Souza", + "author_inst": "Hospital da Crianca de Brasilia, Distrito Federal, BR" + }, + { + "author_name": "Cristiane Feitosa Salviano", + "author_inst": "Hospital da Crianca de Brasilia, DF, BR" + }, + { + "author_name": "Hevelin Silveira e Silva", + "author_inst": "Hospital da Crianca de Brasilia, DF, BR" + }, + { + "author_name": "Eduardo Barbosa Coelho", + "author_inst": "Brazilian Company of Hospital Services Belo Horizonte, Minas Gerais, BR" + }, + { + "author_name": "Giuseppe Cesare Gatto", + "author_inst": "Brazilian Company of Hospital Services Belo Horizonte, Minas Gerais, BR" + }, + { + "author_name": "Rafael Freitas de Morais", + "author_inst": "Brazilian Company of Hospital Services Brasilia, Distrito Federal, BR" + }, + { + "author_name": "Leonardo Nunes Alegre", + "author_inst": "Brazilian Company of Hospital Services Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Rodrigo Citton Padilha dos Reis", + "author_inst": "Universidade Federal do Rio Grande do Sul, Graduate Program in Epidemiology Porto Alegre, RS, BR" + }, + { + "author_name": "Joaquim Francisco dos Santos Neto", + "author_inst": "Universidade Federal do Rio Grande do Sul, Graduate Program in Epidemiology Porto Alegre, RS, BR" + }, + { + "author_name": "Cesar Perdomo Purper", + "author_inst": "Grupo Hospitalar Conceicao, Gerencia de Ensino e Pesquisa Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Veridian Baldon dos Santos", + "author_inst": "Grupo Hospitalar Conceicao, Rio Grande do Sul, BR" + }, + { + "author_name": "Andressa Fontoura Garbini", + "author_inst": "Grupo Hospitalar Conceicao, Rio Grande do Sul, BR" + }, + { + "author_name": "Rafaela dos Santos Charao de Almeida,", + "author_inst": "Grupo Hospitalar Conceicao, Rio Grande do Sul, BR" + }, + { + "author_name": "Bruna Donida", + "author_inst": "Grupo Hospitalar Conceicao, Rio Grande do Sul, BR" + }, + { + "author_name": "Rogerio Farias Bitencourt", + "author_inst": "Grupo Hospitalar Conceicao, Gerencia de Ensino e Pesquisa Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Luciane Kopittke", + "author_inst": "Grupo Hospitalar Conceicao, Gerencia de Ensino e Pesquisa Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Fernanda Costa dos Santos", + "author_inst": "Grupo Hospitalar Conceicao Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Raquel Lutkmeier", + "author_inst": "Grupo Hospitalar Conceicao Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Daniela dos Reis Carazai", + "author_inst": "Grupo Hospitalar Conceicao Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Virginia Angelica Silveira Reis", + "author_inst": "Instituto de Saude e Gestao Hospitalar Fortaleza, CE, BR" + }, + { + "author_name": "Flavio Clemente Deulefeu,", + "author_inst": "Instituto de Saude e Gestao Hospitalar Fortaleza, CE, BR" + }, + { + "author_name": "Fernanda Gadelha Severino", + "author_inst": "Instituto de Saude e Gestao Hospitalar Fortaleza, CE, BR" + }, + { + "author_name": "Jose Gustavo da Costa Neto", + "author_inst": "Instituto de Saude e Gestao Hospitalar Fortaleza, CE, BR" + }, + { + "author_name": "Nirvania do Vale Carvalho", + "author_inst": "Health Department of the State of Piaui, Hospital Getulio Vargas Teresina, Piaui, BR" + }, + { + "author_name": "Andre Jamson Rocha de Andrade", + "author_inst": "Health Department of the State of Piaui, Hospital Getulio Vargas Teresina, Piaui, BR" + }, + { + "author_name": "Adriana Melo Teixeira", + "author_inst": "Brazilian Ministry of Health, Department of Hospital, Home, and Emergency Care (DAHU) of the Specialized Health Care Office (SAES) Brasilia, Distrito Federal, B" + }, + { + "author_name": "Olavo Braga Neto", + "author_inst": "Brazilian Ministry of Health, Department of Hospital, Home, and Emergency Care (DAHU) of the Specialized Health Care Office (SAES) Brasilia, Distrito Federal, B" + }, + { + "author_name": "Gabriel Cardozo Muller", + "author_inst": "Universidade Federal do Rio Grande do Sul, Graduate Program in Epidemiology Porto Alegre, RS, BR" + }, + { + "author_name": "Ricardo de Souza Kuchenbecker", + "author_inst": "Universidade Federal do Rio Grande do Sul, Graduate Program in Epidemiology Porto Alegre, RS, BR" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.08.05.22278487", "rel_title": "Excess mortality in Cyprus during the COVID-19 pandemic and its lack of association with vaccination rates", @@ -208773,145 +210539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, - { - "rel_doi": "10.1101/2022.08.10.503531", - "rel_title": "Development of highly potent non-covalent inhibitors of SARS-CoV-2 3CLpro", - "rel_date": "2022-08-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.10.503531", - "rel_abs": "The SARS-CoV-2 virus is the causal agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19). There is an urgent need for potent, specific antiviral compounds against SARS-CoV-2. The 3C-like protease (3CLpro) is an essential enzyme for the replication of SARS-CoV-2 and other coronaviruses, and thus is a target for coronavirus drug discovery. Nearly all inhibitors of coronavirus 3CLpro reported so far are covalent inhibitors. Here, we report the development of specific, non-covalent inhibitors of 3CLpro. The most potent one, WU-04, effectively blocks SARS-CoV-2 replications in human cells with EC50 values in the 10-nM range. WU-04 also inhibits the 3CLpro of SARS-CoV and MERS-CoV with high potency, indicating that it is a pan-inhibitor of coronavirus 3CLpro. WU-04 showed anti-SARS-CoV-2 activity similar to that of PF-07321332 (Nirmatrelvir) in K18-hACE2 mice when the same dose was administered orally. Thus, WU-04 is a promising drug candidate for coronavirus treatment.\n\nOne-Sentence SummaryA oral non-covalent inhibitor of 3C-like protease effectively inhibits SARS-CoV-2 replication.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Ningke Hou", - "author_inst": "Westlake University" - }, - { - "author_name": "Lei Shuai", - "author_inst": "Chinese Academy of Agricultural Sciences" - }, - { - "author_name": "Lijing Zhang", - "author_inst": "Westlake University" - }, - { - "author_name": "Xuping Xie", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Kaiming Tang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Yunkai Zhu", - "author_inst": "Fudan University" - }, - { - "author_name": "Yin Yu", - "author_inst": "Fudan University," - }, - { - "author_name": "Wenyi Zhang", - "author_inst": "Westlake University" - }, - { - "author_name": "Qiaozhu Tan", - "author_inst": "Westlake University" - }, - { - "author_name": "Gongxun Zhong", - "author_inst": "Chinese Academy of Agricultural Sciences" - }, - { - "author_name": "Zhiyuan Wen", - "author_inst": "Chinese Academy of Agricultural Sciences" - }, - { - "author_name": "Chong Wang", - "author_inst": "Chinese Academy of Agricultural Sciences" - }, - { - "author_name": "Xijun He", - "author_inst": "Chinese Academy of Agricultural Sciences" - }, - { - "author_name": "Hong Huo", - "author_inst": "Chinese Academy of Agricultural Sciences" - }, - { - "author_name": "Haishan Gao", - "author_inst": "Westlake University" - }, - { - "author_name": "You Xu", - "author_inst": "Westlake University" - }, - { - "author_name": "Jing Xue", - "author_inst": "Westlake University" - }, - { - "author_name": "Chen Peng", - "author_inst": "Westlake University" - }, - { - "author_name": "Jing Zou", - "author_inst": "University of Texas Medical Branch, Galveston" - }, - { - "author_name": "Craig Schindewolf", - "author_inst": "University of Texas Medical Branch, Galveston" - }, - { - "author_name": "Vineet Menachery", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Wenji Su", - "author_inst": "WuXi AppTec (Shanghai) Co., Ltd." - }, - { - "author_name": "Youlang Yuan", - "author_inst": "WuXi AppTec (Shanghai) Co., Ltd." - }, - { - "author_name": "Zuyuan Shen", - "author_inst": "WuXi AppTec (Shanghai) Co." - }, - { - "author_name": "Rong Zhang", - "author_inst": "Fudan University" - }, - { - "author_name": "Shuofeng Yuan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Hongtao Yu", - "author_inst": "Westlake University" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "University of Texas Medical Branch, Galveston" - }, - { - "author_name": "Zhigao Bu", - "author_inst": "Chinese Academy of Agricultural Sciences" - }, - { - "author_name": "Jing Huang", - "author_inst": "Westlake University" - }, - { - "author_name": "Qi Hu", - "author_inst": "Westlake University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.08.11.503553", "rel_title": "Nanomolar inhibition of SARS-CoV-2 infection by an unmodified peptide targeting the pre-hairpin intermediate of the spike protein", @@ -211038,6 +212665,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.08.08.503231", + "rel_title": "Vitamin B12 attenuates leukocyte inflammatory signature in COVID-19 via methyl-dependent changes in epigenetic marks", + "rel_date": "2022-08-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.08.503231", + "rel_abs": "COVID-19 induces chromatin remodeling in host immune cells, and it had previously been shown that vitamin B12 downregulates some inflammatory genes via methyl-dependent epigenetic mechanisms. In this work, whole blood cultures from moderate or severe COVID-19 patients were used to assess the potential of B12 as adjuvant drug. The vitamin normalized the expression of a panel of inflammatory genes still dysregulated in the leukocytes despite glucocorticoid therapy during hospitalization. B12 also increased the flux of the sulfur amino acid pathway, raising the bioavailability of methyl. Accordingly, B12-induced downregulation of CCL3 strongly and negatively correlated with the hypermethylation of CpGs in its regulatory regions. Transcriptome analysis revealed that B12 attenuates the effects of COVID-19 on most inflammation-related pathways affected by the disease. As far as we are aware, this is the first study to demonstrate that pharmacological modulation of epigenetic marks in leukocytes favorably regulates central components of COVID-19 physiopathology.\n\nTeaserB12 has great potential as an adjuvant drug for alleviating inflammation in COVID-19.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Vanessa C Silva", + "author_inst": "Universidade Federal de Sao Paulo" + }, + { + "author_name": "Marina S Oliveira", + "author_inst": "FIOCRUZ" + }, + { + "author_name": "Barbara V O Prado", + "author_inst": "Hospital Metropolitano Dr. Celio de Castro" + }, + { + "author_name": "Cristianne G Cardoso", + "author_inst": "Hospital Metropolitano Dr. Celio de Castro" + }, + { + "author_name": "Anna C M Salim", + "author_inst": "FIOCRUZ" + }, + { + "author_name": "Gloria R Franco", + "author_inst": "Universidade Federal de Minas Gerais" + }, + { + "author_name": "Saionara C Francisco", + "author_inst": "Hospital Metropolitano Dr. Celio de Castro" + }, + { + "author_name": "Roney S Coimbra", + "author_inst": "FIOCRUZ" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.08.09.503270", "rel_title": "Acetylsalicylic acid and Salicylic acid inhibit SARS-CoV-2 replication in precision-cut lung slices", @@ -211187,41 +212861,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.08.22278536", - "rel_title": "A study to assess the impact of cobas Liat point-of-care PCR assays (SARS-CoV-2 and Influenza A/B) on patient clinical management in the emergency department of the University of California at Davis Medical Center", - "rel_date": "2022-08-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.08.22278536", - "rel_abs": "BackgroundRapid detection of SARS-CoV-2 is crucial for reduction of transmission and clinical decision-making. The cobas(R) SARS-CoV-2 & Influenza A/B nucleic acid test for use on the cobas Liat(R) System is a rapid (20 minutes) point-of-care (POC) polymerase chain reaction (PCR) method.\n\nMethodsThis unblinded, pre-post study enrolled consecutive patients with symptoms/signs consistent with SARS-CoV-2 infection presenting to the University of California, Davis emergency department (ED). Outcomes following implementation of the cobas Liat SARS-CoV-2 & Influenza A/B test (intervention period: December 2020-May 2021) were compared with previous standard-of-care using centralized laboratory PCR methods (control period: April 2020-October 2020).\n\nResultsElectronic health records of 8879 symptomatic patients were analyzed, comprising 4339 and 4540 patient visits and 538 and 638 positive SARS-CoV-2 PCR test results in the control and intervention periods, respectively. Compared with the control period, turnaround time (TAT) was shorter in the intervention period (median 0.98 vs 12.3 hours; p<0.0001). ED length of stay (LOS) was generally longer in the intervention period compared with the control period, but for those SARS-CoV-2-negative who were admitted, ED LOS was shorter (median 12.53 vs 17.93 hours; p<0.0001). Overall, the rate of anti-infective prescribing was also lower in the intervention period than in the control period (antibiotics only: 38.11% vs 44.55%; p<0.0001 and antivirals only: 3.13% vs 0.94%; p<0.0001).\n\nConclusionThis real-world study confirms faster TAT with a POC PCR method in an emergency care setting and highlights the importance of rapid SARS-CoV-2 detection to aid patient management and inform treatment decisions.\n\nClinical RelevanceThis study reports data collected from a quasi-experimental pre-post study using the electronic health records of patients presenting to the emergency department (ED) of the University of California at Davis Medical Center with symptoms or signs consistent with SARS-CoV-2 infection during their ED visit. The primary objective of this study was to determine if implementation of the point-of-care (POC) cobas(R) Liat(R) SARS-CoV-2 & Influenza A/B test for use on the cobas Liat System reduced the diagnostic turnaround time and/or length of stay for ED patients with suspected SARS-CoV-2 infection compared with the previous standards of care (batch-wise diagnostic testing using the cobas 6800 System and on-demand urgent testing on the GenMark Dx(R) ePlex(R) system in a centralized clinical laboratory). Ultimately, these data help to inform how implementation of POC molecular testing methods impact patient management.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Larissa May", - "author_inst": "University of California Davis" - }, - { - "author_name": "Elissa Robbins", - "author_inst": "Roche Molecular Systems" - }, - { - "author_name": "Jesse A Canchola", - "author_inst": "Roche Molecular Systems" - }, - { - "author_name": "Kamal Chugh", - "author_inst": "Roche Molecular Systems" - }, - { - "author_name": "Nam K Tran", - "author_inst": "University of California Davis" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.08.22278490", "rel_title": "Effects of behavioral restrictions on COVID-19 spread", @@ -212992,6 +214631,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical ethics" }, + { + "rel_doi": "10.1101/2022.08.06.22278449", + "rel_title": "Severity Predictors of COVID-19 in SARS-CoV-2 Variant, Delta and Omicron Period; Single Center Study", + "rel_date": "2022-08-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.06.22278449", + "rel_abs": "BackgroundThe outcomes of coronavirus disease 2019 (COVID-19) treatment have improved due to vaccination and the establishment of better treatment regimens. However, the emergence of variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes COVID-19, and the corresponding changes in the characteristics of the disease present new challenges in patient management. This study aimed to analyze predictors of COVID-19 severity caused by the delta and omicron variants of SARS-CoV-2.\n\nMethodsWe retrospectively analyzed the data of patients who were admitted for COVID-19 at Yokohama City University Hospital from August 2021 to March 2022.\n\nResultsA total of 141 patients were included in this study. Of these, 91 had moderate COVID-19, whereas 50 had severe COVID-19. There were significant differences in sex, vaccination status, dyspnea, sore throat symptoms, and body mass index (BMI) (p <0.0001, p <0.001, p <0.001, p=0.02, p< 0.0001, respectively) between the moderate and severe COVID-19 groups. Regarding comorbidities, smoking habit and renal dysfunction were significantly different between the two groups (p=0.007 and p=0.01, respectively). Regarding laboratory data, only LDH level on the first day of hospitalization was significantly different between the two groups (p<0.001). Multiple logistic regression analysis revealed that time from the onset of COVID-19 to hospitalization, BMI, smoking habit, and LDH level were significantly different between the two groups (p<0.03, p=0.039, p=0.008, p<0.001, respectively). The cut-off value for the time from onset of COVID-19 to hospitalization was four days (sensitivity, 0.73; specificity, 0.70).\n\nConclusionsTime from the onset of COVID-19 to hospitalization is the most important factor in the prevention of the aggravation of COVID-19 caused by the delta and omicron SARS-CoV-2 variants. Appropriate medical management within four days after the onset of COVID-19 is essential for preventing the progression of COVID-19, especially in patients with smoking habits.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Fumihiro Ogawa", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Yasufumi Oi", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Hiroshi Honzawa", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Naho Misawa", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Tomoaki Takeda", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Yushi Kikuchi", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Ryosuke Fukui", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Katsushi Tanaka", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Daiki Kano", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Hideaki Kato", + "author_inst": "Yokohama City University Hospital, Infection prevention and control department" + }, + { + "author_name": "Takeru Abe", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Ichiro Takeuchi", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.07.499047", "rel_title": "Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir", @@ -213153,45 +214855,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.08.05.22278481", - "rel_title": "Two years of COVID-19 Pandemic: Framework of Health Interventions in a Brazilian City", - "rel_date": "2022-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.05.22278481", - "rel_abs": "The COVID-19 pandemic and its effects on public health have urgently demanded effective health policies to avoid the spread of COVID-19. Thus, public administrators have implemented non-pharmacological and pharmacological interventions to mitigate the pandemics impacts and strengthen health services. The aim of this ecological study is to describe the scenario of COVID-19 pandemic in a Brazilian city, during two years. This ecological study was carried out in Nova Friburgo, a Brazilian city, for 105 weeks (two years), from March 29, 2020 (week 1) to April 02, 2022 (week 105). Data on COVID-19 cases and COVID-19 deaths, occupation of COVID-19 exclusive beds in hospitals, community mobility, vaccination, government regulation on the opening of city establishments and city risk assessment were collected from public datasets. Four waves of COVID-19 cases and deaths were observed during this period. The first case occurred in week 1 and first death in week 3 of this study. The highest peaks of cases and deaths were observed during the third wave with 1,131 cases (week 54) and 47 deaths (week 55) and where the highest occupation of COVID-19 exclusive beds in local hospitals occurred. Interventions from more restrictive to more flexible, were implemented throughout this study, including lockdown and gradual return in economic and social strata levels. Vaccination began on week 43 and at the end of this study 89.91% of the total population was vaccinated with at least one dose, being 83.22% fully vaccinated. A deep description of several interventions used to avoid COVID-19 spread in a Brazilian city during two years of this pandemic can help promote better decision-making in the future while it exposes the challenges of conducting public health policies in a pandemic scenario.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Vanessa dos Santos Faioes", - "author_inst": "Universidade Federal Fluminense" - }, - { - "author_name": "Helvecio Cardoso Correa Povoa", - "author_inst": "Universidade Federal Fluminense" - }, - { - "author_name": "Bruna Alves Thurler", - "author_inst": "Universidade Federal Fluminense" - }, - { - "author_name": "Gabriela Ceccon Chianca", - "author_inst": "Universidade Estacio de Sa" - }, - { - "author_name": "Andrea Videira Assaf", - "author_inst": "Universidade Federal Fluminense" - }, - { - "author_name": "Natalia Lopes Pontes Povoa Iorio", - "author_inst": "Universidade Federal Fluminense" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.08.04.22278450", "rel_title": "COVID-19 rebound after Paxlovid treatment during Omicron BA.5 vs BA.2.12.1 subvariant predominance period", @@ -215238,6 +216901,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2022.08.03.22278363", + "rel_title": "Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is common in post-acute sequelae of SARS-CoV-2 infection (PASC): Results from a post-COVID-19 multidisciplinary clinic.", + "rel_date": "2022-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.03.22278363", + "rel_abs": "BackgroundThe global prevalence of PASC is estimated to be present in 0{middle dot}43 and based on the WHO estimation of 470 million worldwide COVID-19 infections, corresponds to around 200 million people experiencing long COVID symptoms. Despite this, its clinical features are not well defined.\n\nMethodsWe collected retrospective data from 140 patients with PASC in a post-COVID-19 clinic on demographics, risk factors, illness severity (graded as one-mild to five-severe), functional status, and 29 symptoms and principal component symptoms cluster analysis. The Institute of Medicine (IOM) 2015 criteria were used to determine the ME/CFS phenotype.\n\nFindingsThe median age was 47 years, 59{middle dot}0% were female; 49{middle dot}3% White, 17{middle dot}2% Hispanic, 14{middle dot}9% Asian, and 6{middle dot}7% Black. Only 12{middle dot}7% required hospitalization. Seventy-two (53{middle dot}5%) patients had no known comorbid conditions. Forty-five (33{middle dot}9%) were significantly debilitated. The median duration of symptoms was 285{middle dot}5 days, and the number of symptoms was 12. The most common symptoms were fatigue (86{middle dot}5%), post-exertional malaise (82{middle dot}8%), brain fog (81{middle dot}2%), unrefreshing sleep (76{middle dot}7%), and lethargy (74{middle dot}6%). Forty-three percent fit the criteria for ME/CFS.\n\nInterpretationsMost PASC patients evaluated at our clinic had no comorbid condition and were not hospitalized for acute COVID-19. One-third of patients experienced a severe decline in their functional status. About 43% had the ME/CFS subtype.\n\nFundingThe study did not received funding.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Hector Bonilla", + "author_inst": "Stanford University" + }, + { + "author_name": "Tom Quach", + "author_inst": "Stanford University" + }, + { + "author_name": "Anushri Tiwari", + "author_inst": "Stanford University" + }, + { + "author_name": "Andres Bonilla", + "author_inst": "University of Michigan" + }, + { + "author_name": "Mitchell G Miglis", + "author_inst": "Stanford University" + }, + { + "author_name": "Phillip Yang", + "author_inst": "Stanford University" + }, + { + "author_name": "Lauren Eggert", + "author_inst": "Stanford University" + }, + { + "author_name": "Husham Sharifi", + "author_inst": "Stanford University" + }, + { + "author_name": "Audra Horomanski", + "author_inst": "Stanford University" + }, + { + "author_name": "Aruna K Subramanian", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Liza Smirnoff", + "author_inst": "Stanford University" + }, + { + "author_name": "Norah Simpson", + "author_inst": "Stanford University" + }, + { + "author_name": "Houssam Halawi", + "author_inst": "Stanford University" + }, + { + "author_name": "Oliver Sum-Ping", + "author_inst": "Stanford University" + }, + { + "author_name": "Agnieszka Kalinowski", + "author_inst": "Stanford University" + }, + { + "author_name": "Zara Patel", + "author_inst": "Stanford University" + }, + { + "author_name": "Robert William Shafer", + "author_inst": "Stanford University" + }, + { + "author_name": "Linda Geng", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.03.22278386", "rel_title": "SARS-CoV-2 BA.4/5 Spike recognition and neutralization elicited after the third dose of mRNA vaccine", @@ -215455,57 +217205,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.08.03.502703", - "rel_title": "Double-dose mRNA vaccination to SARS-CoV-2 progressively increases recognition of variants-of-concern by Spike RBD-specific memory B cells", - "rel_date": "2022-08-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.03.502703", - "rel_abs": "BackgroundSARS-CoV-2 vaccination with BNT162b2 (Pfizer BioNTech) has been shown to be 95% effective.1 Double-dose vaccination generates high levels of spike-specific antibodies, memory B cells (Bmem) and T cells. However, variants of concern (VoC) with mutations in the spike Receptor Binding Domain (RBD) can evade antibody responses. Booster vaccinations improve antibody recognition of VoC, but it is unclear if this is due to higher total antibodies or their capacity to bind VoC. We here addressed the capacity of surface Ig on single Wuhan-specific Bmem after first and second dose BNT162b2 vaccination to recognize variant RBD.\n\nMethodsSamples were collected from 30 healthy COVID-19 naive individuals pre-BNT162b2 vaccination, 3 weeks post-dose 1 and 4-weeks post-dose 2. Plasma antibodies and Bmem were evaluated using recombinant RBD proteins of the Wuhan, Gamma and Delta strains.\n\nResultsAll individuals generated a robust antibody response to BNT162b2 vaccination with all participants producing neutralizing antibodies following dose 2. IgM+ and IgG+ RBD-specific Bmem were generated after one vaccine dose, and those expressing IgG1 increased in absolute number after dose 2. The majority of RBD-specific Bmem bound the Gamma and/or Delta variants, and this proportion significantly increased after the second dose.\n\nConclusionThe second dose of BNT162b2 increases the number of circulating Ig-class switched RBD-specific Bmem. Importantly, the second dose of vaccination is required for a high frequency of RBD-specific Bmem to recognize Gamma and Delta variants. This suggests that dose 2 not only increases the number of RBD-specific Bmem but also the affinity of the Bmem to overcome the point mutations in VoC.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Gemma E. Hartley", - "author_inst": "Monash University" - }, - { - "author_name": "Emily S.J. Edwards", - "author_inst": "Monash University" - }, - { - "author_name": "Nirupama Varese", - "author_inst": "Monash University" - }, - { - "author_name": "Irene Boo", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Pei M. Aui", - "author_inst": "Monash University" - }, - { - "author_name": "Scott J. Bornheimer", - "author_inst": "BD Biosciences" - }, - { - "author_name": "P. Mark Hogarth", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Heidi E. Drummer", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Menno C. van Zelm", - "author_inst": "Monash University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.08.04.502768", "rel_title": "A specific anti-IFITM2 antibody bars the way to SARS-CoV-2 entry into host cells.", @@ -216920,6 +218619,125 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.08.02.502439", + "rel_title": "Serological surveillance for wild rodent infection with SARS-CoV-2 in Europe", + "rel_date": "2022-08-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.02.502439", + "rel_abs": "We report serological surveillance for exposure to SARS-CoV-2 in 1,237 wild rodents and other small mammals across Europe. All samples were negative with the possible exception of one. Given the ongoing circulation of this virus in humans and potential host jumps, we suggest such surveillance be continued.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Vincent Bourret", + "author_inst": "University of Helsinki, INRAE" + }, + { + "author_name": "Lara Dutra", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Hussein Alburkat", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Sanna Maki", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Ella Lintunen", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Marine Wasniewski", + "author_inst": "ANSES" + }, + { + "author_name": "Ravi Kant", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Maciej Grzybek", + "author_inst": "Medical University of Gdansk" + }, + { + "author_name": "Vinaya Venkat", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Hayder Asad", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Julien Pradel", + "author_inst": "INRAE" + }, + { + "author_name": "Marie Bouilloud", + "author_inst": "IRD" + }, + { + "author_name": "Herwig Leirs", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Valeria Carolina Colombo", + "author_inst": "University of Antwerp, CONICET" + }, + { + "author_name": "Vincent Sluydts", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Peter Stuart", + "author_inst": "Munster Technological University" + }, + { + "author_name": "Andrew McManus", + "author_inst": "Munster Technological University" + }, + { + "author_name": "Jana A. Eccard", + "author_inst": "University of Potsdam" + }, + { + "author_name": "Jasmin Firozpoor", + "author_inst": "University of Potsdam" + }, + { + "author_name": "Christian Imholt", + "author_inst": "Julius Kuhn Institute" + }, + { + "author_name": "Joanna Nowicka", + "author_inst": "Medical University of Gdansk" + }, + { + "author_name": "Aleksander Goll", + "author_inst": "Medical University of Gdansk" + }, + { + "author_name": "Nathan Ranc", + "author_inst": "INRAE" + }, + { + "author_name": "Guillaume Castel", + "author_inst": "INRAE" + }, + { + "author_name": "Nathalie Charbonnel", + "author_inst": "INRAE" + }, + { + "author_name": "Tarja Sironen", + "author_inst": "University of Helsinki" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.08.02.502100", "rel_title": "NF-\u03baB inhibitor alpha has a cross-variant role during SARS-CoV-2 infection in ACE2-overexpressing human airway organoids", @@ -217173,41 +218991,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.08.02.502186", - "rel_title": "DNA Origami Presenting the Receptor Binding Domain of SARS-CoV-2 Elicit Robust Protective Immune Response", - "rel_date": "2022-08-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.02.502186", - "rel_abs": "Effective and safe vaccines are invaluable tools in the arsenal to fight infectious diseases. The rapid spreading of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible of the coronavirus disease 2019 pandemic has highlighted the need to develop methods for rapid and efficient vaccine development. DNA origami nanoparticles (DNA-NPs) presenting multiple antigens in prescribed nanoscale patterns have recently emerged as a safe, efficient, and easily scalable alternative for rational design of vaccines. Here, we are leveraging the unique properties of these DNA-NPs and demonstrate that precisely patterning ten copies of a reconstituted trimer of the receptor binding domain (RBD) of SARS-CoV-2 along with CpG adjuvants on the DNA-NPs is able to elicit a robust protective immunity against SARS-CoV-2 in a mouse model. Our results demonstrate the potential of our DNA-NP-based approach for developing safe and effective nanovaccines against infectious diseases.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Esra Oktay", - "author_inst": "George Mason University" - }, - { - "author_name": "Farhang Alem", - "author_inst": "George Mason University" - }, - { - "author_name": "Keziah Hernandez", - "author_inst": "George Mason University" - }, - { - "author_name": "Aarthi Narayanan", - "author_inst": "George Mason University" - }, - { - "author_name": "Remi Veneziano", - "author_inst": "George Mason University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2022.07.31.22278223", "rel_title": "Glasses Against transmission of SARS-CoV-2 in the community (GLASSY): a pragmatic randomized trial", @@ -218734,6 +220517,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.30.22278213", + "rel_title": "Higher Perceived Stress during the COVID-19 pandemic increased Menstrual Dysregulation and Menopause Symptoms", + "rel_date": "2022-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.30.22278213", + "rel_abs": "ObjectiveThe increased stress the globe has experienced with the COVID-19 pandemic has affected mental health, disproportionately affecting women. However, how perceived stress in the first year affected menstrual and menopausal symptoms has not yet been investigated.\n\nMethodsResidents in British Columbia, Canada, were surveyed online as part of the COVID-19 Rapid Evidence Study of a Provincial Population-Based Cohort for Gender and Sex (RESPPONSE). A subgroup (n=4171) who were assigned female sex at birth (age 25-69) and were surveyed within the first 6-12 months of the pandemic (August 2020-February 2021), prior to the widespread rollout of vaccines, were retrospectively asked if they noticed changes in their menstrual or menopausal symptoms, as well as completing validated measures of stress, depression, and anxiety.\n\nResultsWe found that 27.8% reported menstrual cycle disturbances and 6.7% reported increased menopause symptoms. Those who scored higher on perceived stress, depression, and anxiety scales were more likely to have reproductive cycle disturbances. Free text responses revealed that reasons for disturbances were perceived to be related to the pandemic.\n\nConclusionsThe COVID-19 pandemic has highlighted the need to research womens health issues, such as menstruation. Our data indicates that in the first year of the pandemic, almost a third of the menstruating population reported disturbances in their cycle, which is approximately two times higher than in non-pandemic situations and four times higher than any reported changes in menopausal symptoms across that first year of the pandemic.\n\nSummary SentencesWomen+ with higher anxiety, depression or perceived stress scores during the first year of the pandemic were more likely to have experienced menstrual cycle phase disturbance or menopausal status disruption. Younger women were particularly prone to disturbances in their reproductive cycles.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Romina Garcia de Leon", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Alexandra Baaske", + "author_inst": "Women's Health Research Institute" + }, + { + "author_name": "Arianne Albert", + "author_inst": "Women's Health Research Institute" + }, + { + "author_name": "Amy Booth", + "author_inst": "University of British Columbia" + }, + { + "author_name": "C. Sarai Racey", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Shanlea Gordon", + "author_inst": "Womens Health Research Institute" + }, + { + "author_name": "Laurie Smith", + "author_inst": "BC Cancer" + }, + { + "author_name": "Anna Gottschlich", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Manish Sadarangani", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Angela Kaida", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Gina Ogilvie", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Lori Brotto", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Liisa A.M Galea", + "author_inst": "University of British Columbia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "sexual and reproductive health" + }, { "rel_doi": "10.1101/2022.07.29.22278186", "rel_title": "Comparative effectiveness of BNT162b2 versus mRNA-1273 boosting in England: a cohort study in OpenSAFELY-TPP", @@ -218867,185 +220717,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2022.07.29.502029", - "rel_title": "A multispecific antibody confers pan-reactive SARS-CoV-2 neutralization and prevents immune escape", - "rel_date": "2022-07-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.29.502029", - "rel_abs": "Summary ParagraphDespite effective countermeasures, SARS-CoV-2 persists worldwide due to its ability to diversify and evade human immunity1. This evasion stems from amino-acid substitutions, particularly in the receptor-binding domain of the spike, that confer resistance to vaccines and antibodies 2-16. To constrain viral escape through resistance mutations, we combined antibody variable regions that recognize different receptor binding domain (RBD) sites17,18 into multispecific antibodies. Here, we describe multispecific antibodies, including a trispecific that prevented virus escape >3000-fold more potently than the most effective clinical antibody or mixtures of the parental antibodies. Despite being generated before the evolution of Omicron, this trispecific antibody potently neutralized all previous variants of concern and major Omicron variants, including the most recent BA.4/BA.5 strains at nanomolar concentrations. Negative stain electron microscopy revealed that synergistic neutralization was achieved by engaging different epitopes in specific orientations that facilitated inter-spike binding. An optimized trispecific antibody also protected Syrian hamsters against Omicron variants BA.1, BA.2 and BA.5, each of which uses different amino acid substitutions to mediate escape from therapeutic antibodies. Such multispecific antibodies decrease the likelihood of SARS-CoV-2 escape, simplify treatment, and maximize coverage, providing a strategy for universal antibody therapies that could help eliminate pandemic spread for this and other pathogens.", - "rel_num_authors": 41, - "rel_authors": [ - { - "author_name": "John Misasi", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Ronnie R. Wei", - "author_inst": "Modex Therapeutics Inc., an OPKO Health Company, Natick, MA 01760, USA" - }, - { - "author_name": "Lingshu Wang", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Amarendra Pegu", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Chih-Jen Wei", - "author_inst": "Modex Therapeutics Inc., an OPKO Health Company, Natick, MA 01760, USA" - }, - { - "author_name": "Olamide Oloniniyi", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Tongqing Zhou", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Juan I Moliva", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Bingchun Zhao", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Misook Choe", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Eun Sung Yang", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Yi Zhang", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Marika Boruszczak", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Man Chen", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Kwan Leung", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Juan Li", - "author_inst": "Modex Therapeutics Inc., an OPKO Health Company, Natick, MA 01760, USA." - }, - { - "author_name": "Zhi-Yong Yang", - "author_inst": "Modex Therapeutics Inc., an OPKO Health Company, Natick, MA 01760, USA" - }, - { - "author_name": "Hanne Andersen", - "author_inst": "Bioqual Inc" - }, - { - "author_name": "Kevin Carlton", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Sucheta Godbole", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Darcy R. Harris", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Amy R Henry", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Vera B. Ivleva", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Paula Lei", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Cuiping Liu", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Lindsay Longobardi", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Jonah S Merriam", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Danielle Nase", - "author_inst": "Bioqual, Inc., Rockville, MD 20850, USA." - }, - { - "author_name": "Adam S. Olia", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Laurent Pessaint", - "author_inst": "Bioqual, Inc., Rockville, MD 20850, USA." - }, - { - "author_name": "Maciel Porto", - "author_inst": "Bioqual, Inc., Rockville, MD 20850, USA." - }, - { - "author_name": "Wei Shi", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Jeremy J Wolff", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Daniel C Douek", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Mehul S Suthar", - "author_inst": "Department of Pediatrics, Emory Vaccine Center, Emory National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA." - }, - { - "author_name": "Jason Gall", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Richard A. Koup", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Peter D. Kwong", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "John R. Mascola", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Gary J. Nabel", - "author_inst": "Modex Therapeutics Inc., an OPKO Health Company, Natick, MA 01760, USA" - }, - { - "author_name": "Nancy J. Sullivan", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.07.29.502055", "rel_title": "Neutralization of SARS-CoV-2 Omicron sublineages by 4 doses of mRNA vaccine", @@ -220580,6 +222251,109 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.07.27.501719", + "rel_title": "Development of Equine Polyclonal Antibodies as a Broad-Spectrum Therapy Against SARS-CoV-2 Variants", + "rel_date": "2022-07-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.27.501719", + "rel_abs": "The Coronavirus disease 19 (COVID-19) pandemic has accumulated over 550 million confirmed cases and more than 6.34 million deaths worldwide. Although vaccinations has largely protected the population through the last two years, the effect of vaccination has been increasingly challenged by the emerging SARS-CoV-2 variants. Although several therapeutics including both monoclonal antibodies and small molecule drugs have been used clinically, high cost, viral escape mutations, and potential side effects have reduced their efficacy. There is an urgent need to develop a low cost treatment with wide-spectrum effect against the novel variants of SARS-CoV-2.\n\nHere we report a product of equine polyclonal antibodies that showed potential broad spectrum neutralization effect against the major variants of SARS-CoV-2. The equine polyclonal antibodies were generated by horse immunization with the receptor binding domain (RBD) of SARS-CoV-2 spike protein and purified from equine serum. A high binding affinity between the generated equine antibodies and the RBD was observed. Although designed against the RBD of the early wild type strain sequenced in 2020, the equine antibodies also showed a highly efficient neutralization capacity against the major variants of SARS-CoV-2, including the recent BA.2 Omicron variant (IC50 =1.867g/ml) in viral neutralization assay in Vero E6 cells using live virus cultured. The broad-spectrum neutralization capacity of the equine antibodies was further confirmed using pseudovirus neutralization assay covering the major SARS-CoV-2 variants including wild type, alpha, beta, delta, and omicron, showing effective neutralization against all the tested strains. Ex vivo reconstructed human respiratory organoids representing nasal, bronchial, and lung epitheliums were employed to test the treatment efficacy of the equine antibodies. Antibody treatment protected the human nasal, bronchial, and lung epithelial organoids against infection of the novel SARS-CoV-2 variants challenging public health, the Delta and Omicron BA.2 isolates, by reducing >95% of the viral load. The equine antibodies were further tested for potential side effects in a mouse model by inhalation and no significant pathological feature was observed.\n\nEquine antibodies, as a mature medical product, have been widely applied in the treatment of infectious diseases for more than a century, which limits the potential side effects and are capable of large scale production at a low cost. A cost-effective, wide-spectrum equine antibody therapy effective against the major SARS-CoV-2 variants can contribute as an affordable therapy to cover a large portion of the world population, and thus potentially reduce the transmission and mutation of SARS-CoV-2.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Shumin Liao", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China; The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China" + }, + { + "author_name": "Yunjiao He", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" + }, + { + "author_name": "Jing Qu", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Yue Shi", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" + }, + { + "author_name": "Yingzi Liu", + "author_inst": "Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, China; School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Keli Zhao", + "author_inst": "Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, China" + }, + { + "author_name": "Junhui Chen", + "author_inst": "Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, China" + }, + { + "author_name": "Yue Jing", + "author_inst": "Jiangxi Institute of Biological Products Co. Ltd., Jiangxi, China; Jiangxi Institute of Biological Products Shenzhen R&D Center Co. Ltd., Shenzhen, China; Haina" + }, + { + "author_name": "Clifton Kwang-Fu Shen", + "author_inst": "Jiangxi Institute of Biological Products Co. Ltd.Jiangxi; Jiangxi Institute of Biological Products Shenzhen R&D Center Co. Ltd., Shenzhen; Hainan Institute of P" + }, + { + "author_name": "Chong Ji", + "author_inst": "Jiangxi Institute of Biological Products Co. Ltd., Jiangxi, China; Jiangxi Institute of Biological Products Shenzhen R&D Center Co. Ltd., Shenzhen, China; Haina" + }, + { + "author_name": "Guxun Luo", + "author_inst": "Jiangxi Institute of Biological Products Co. Ltd., Jiangxi, China; Jiangxi Institute of Biological Products Shenzhen R&D Center Co. Ltd., Shenzhen, China; Haina" + }, + { + "author_name": "Xusheng Zhao", + "author_inst": "Jiangxi Institute of Biological Products Co. Ltd., Jiangxi, China; Jiangxi Institute of Biological Products Shenzhen R&D Center Co. Ltd., Shenzhen, China; Haina" + }, + { + "author_name": "Shuo Li", + "author_inst": "Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China; The Sixth Affiliated Hospital of Shenzhen University Health Science Cent" + }, + { + "author_name": "Yunping Fan", + "author_inst": "Department of Otolaryngology, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China" + }, + { + "author_name": "Ziquan Lv", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Shisong Fang", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Yaqing He", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Chunli Wu", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Renli Zhang", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Xuan Zou", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Peng Wang", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" + }, + { + "author_name": "Liang Li", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China; Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced T" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.07.27.501708", "rel_title": "Molecular basis for antiviral activity of pediatric neutralizing antibodies targeting SARS-CoV-2 Spike receptor binding domain", @@ -220829,45 +222603,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.07.27.22277642", - "rel_title": "Large-scale web scraping for problem gambling research: a case study of COVID-19 lockdown effects in Germany", - "rel_date": "2022-07-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.27.22277642", - "rel_abs": "The COVID-19 pandemic and the measures to prevent its spread have had a negative impact on substance use behaviour and posed a special threat for individuals at risk. Problem gambling is a major public health concern, and it is likely that the lockdown and social distancing measures have altered gambling behaviour, for instance shifting from land-based to online gambling. In this study, we used large-scale web scraping to analyse posting behaviour on a major German online gambling forum, gathering a database of more than 200k posts. We examined the relative usage of different subforums, i.e. terrestrial, online gambling and problem gambling sections, posting frequency, and changes in posting behaviour related to the casino closures that were part of the nationwide restrictions in Germany in 2020. There was a marked increase in the number of newly registered users during the first lockdown compared to the weeks prior to the lockdown, which may reflect a shift from terrestrial to online gambling. Further, there was an increase in the number of posts in the online gambling subforum with a concurrent decrease in the number of posts in the terrestrial gambling subforum. An analysis of user types revealed that a substantial number of users who posted in both the online and terrestrial forum contributed at least once to the problem gambling subforum. This subforum contained the longest posts, which were on average twice as long as the average post. Modelling the relationship between reply frequency and latency between initial posts and replies showed that the number of short-latency replies (i.e. replies posted within seven hours after the initial post) was substantially higher during the first lockdown compared to the preceding weeks. The increase during the first lockdown may reflect the general marked increase in screen time and/or usage of online platforms and media after the onset of the global COVID-19 pandemic. The analyses may help to identify lockdown-related effects on gambling behaviour. These potentially detrimental effects on mental health, including addiction and problem gambling, may require monitoring and special public health measures.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Elke Smith", - "author_inst": "Department of Psychology, Biological Psychology, University of Cologne" - }, - { - "author_name": "Simon Michalski", - "author_inst": "Department of Psychology, Biological Psychology, University of Cologne" - }, - { - "author_name": "Kilian H. K. Knauth", - "author_inst": "Department of Psychology, Biological Psychology, University of Cologne" - }, - { - "author_name": "Kai Kaspar", - "author_inst": "Department of Psychology, Social and Media Psychology, University of Cologne" - }, - { - "author_name": "Nils Reiter", - "author_inst": "Department of Digital Humanities, University of Cologne" - }, - { - "author_name": "Jan Peters", - "author_inst": "Department of Psychology, Biological Psychology, University of Cologne" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2022.07.26.501655", "rel_title": "High Frequencies of Phenotypically and Functionally Senescent and Exhausted CD56+CD57+PD-1+ Natural Killer Cells, SARS-CoV-2-Specific Memory CD4+ and CD8+ T cells Associated with Severe Disease in Unvaccinated COVID-19 Patients", @@ -222310,6 +224045,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.24.22277968", + "rel_title": "Effects of wearing FFP2 masks on SARS-CoV-2 infection rates in classrooms", + "rel_date": "2022-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.24.22277968", + "rel_abs": "ImportanceDifferent mitigation measures are mandated in schools worldwide to control the spread of SARS-CoV-2. The efficacy of most measures, however, has not been investigated thus far.\n\nObjectiveTo investigate the usefulness of FFP-2 masks in classrooms to prevent the spread of SARS-CoV-2.\n\nDesignA retrospective comparative cohort study of infection rates (evaluated by PCR screening in school) in students wearing FFP-2 masks continuously and students in sports classes with limited face mask use.\n\nSettingA single-center evaluation comparing classes (middle school: age 10-16 years, 4-year high school: age 14-20 years) with a high sports focus (SF), with regular classes during the Delta and Omicron waves (September 2021-April 2022).\n\nParticipantsIn total, 616 children/families were invited to participate in the comparative evaluation, and 614 (99.7%) followed this invitation by providing relevant information concerning their SARS-CoV-2 infection status. A total of 213 legal guardians (for children < 14 years) and 401 adolescents ([≥]14 years) reported SARS-CoV-2 infections during the 2021/22 school year.\n\nMain Outcomes and MeasuresA comparative analysis of cumulative SARS-CoV-2 infection rates in sports and non-sports classes (the 7-day classroom incidence of SARS-CoV-2 infections, and potential secondary infections among school classmates).\n\nResultsCumulative SARS-CoV-2 infection rates were clearly higher in sports classes (with limited mask use) than in non-sports classes (continuous mask use). After the relaxation of the mitigation measures, students in non-sports classes, however, showed a clear \"catch-up\" of infections, leading to a higher incidence of infections during this phase. By the end of the observation period (April 30, 2022), only a small difference in cumulative SARS-CoV-2 infection rates (p=0.037, {varphi}=0.09) was detected between classes with a sports focus and those without a sports focus.\n\nConclusions and RelevanceWearing FFP2 face masks reduces the risk of SARS-CoV-2 infection if strict mitigation measures are applied. Following the relaxation of strict measures, previously \"protected\" students show a significant \"catch-up\" infection rate. Thus, continuous face mask use postpones rather than avoids SARS-CoV-2 infection in many cases. Therefore, the advantage of reduced transmission must be carefully balanced against the disadvantages associated with mask wearing throughout schools.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Gerald Jarnig", + "author_inst": "Institute of Human Movement Science, Sport and Health, University of Graz, Graz, Austria" + }, + { + "author_name": "Reinhold Kerbl", + "author_inst": "Department of Pediatrics and Adolescent Medicine, LKH Hochsteiermark/Leoben, Austria" + }, + { + "author_name": "Mireille van Poppel", + "author_inst": "Institute of Human Movement Science, Sport and Health, University of Graz, Graz, Austria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.07.20.22277718", "rel_title": "Biomarkers and Outcomes in Hospitalized Covid-19 Patients: A Prospective Registry", @@ -222483,73 +224245,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2022.07.22.501163", - "rel_title": "Waning and boosting of functional humoral immunity to SARS-CoV-2", - "rel_date": "2022-07-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.22.501163", - "rel_abs": "Since the emergence of the SARS-CoV-2 virus, we have witnessed a revolution in vaccine development with the rapid emergence and deployment of both traditional and novel vaccine platforms. The inactivated CoronaVac vaccine and the mRNA-based Pfizer/BNT162b2 vaccine are among the most widely distributed vaccines, both demonstrating high, albeit variable, vaccine effectiveness against severe COVID-19 over time. Beyond the ability of the vaccines to generate neutralizing antibodies, antibodies can attenuate disease via their ability to recruit the cytotoxic and opsinophagocytic functions of the immune response. However, whether Fc-effector functions are induced differentially, wane with different kinetics, and are boostable, remains unknown. Here, using systems serology, we profiled the Fc-effector profiles induced by the CoronaVac and BNT162b2 vaccines, over time. Despite the significantly higher antibody functional responses induced by the BNT162b2 vaccine, CoronaVac responses waned more slowly, albeit still found at levels below those present in the systemic circulation of BNT162b2 immunized individuals. However, mRNA boosting of the CoronaVac vaccine responses resulted in the induction of significantly higher peak antibody functional responses with increased humoral breadth, including to Omicron. Collectively, the data presented here point to striking differences in vaccine platform-induced functional humoral immune responses, that wane with different kinetics, and can be functionally rescued and expanded with boosting.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Xin Tong", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Ryan P McNamara", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Maria J Avendano", - "author_inst": "School of Medicine, Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Eileen E Serrano", - "author_inst": "School of Medicine, Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Tamara Garcia-Salum", - "author_inst": "School of Medicine, Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Catalina Pardo-Roa", - "author_inst": "School of Medicine, Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Jorge Levican", - "author_inst": "School of Medicine, Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Estefany Poblete", - "author_inst": "School of Medicine, Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Erick Salinas", - "author_inst": "School of Medicine, Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Andres Munoz", - "author_inst": "School of Medicine, Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Arnoldo Riquelme", - "author_inst": "School of Medicine, Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Galit Alter", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Rafael A Medina", - "author_inst": "School of Medicine, Pontificia Universidad Catolica de Chile" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.07.23.501111", "rel_title": "McAN: an ultrafast haplotype network construction algorithm", @@ -224028,6 +225723,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.07.21.501010", + "rel_title": "Durability of the Neutralizing Antibody Response to mRNA Booster Vaccination Against SARS-CoV-2 BA.2.12.1 and BA.4/5 Variants", + "rel_date": "2022-07-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.21.501010", + "rel_abs": "The recent emergence of the SARS-CoV-2 BA.4/5 and BA.2.12.1 variants has led to rising COVID-19 case numbers and concerns over the continued efficacy of mRNA booster vaccination. Here we examine the durability of neutralizing antibody (nAb) responses against these SARS-CoV-2 Omicron subvariants in a cohort of health care workers 1-40 weeks after mRNA booster dose administration. Neutralizing antibody titers fell by [~]1.5-fold 4-6 months and by [~]2.5-fold 7-9 months after booster dose, with average nAb titers falling by 11-15% every 30 days, far more stable than two dose induced immunity. Notably, nAb titers from booster recipients against SARS-CoV-2 BA.1, BA.2.12.1, and BA.4/5 variants were [~]4.7-, 7.6-, and 13.4-fold lower than against the ancestral D614G spike. However, the rate of waning of booster dose immunity was comparable across variants. Importantly, individuals reporting prior infection with SARS-CoV-2 exhibited significantly higher nAb titers compared to those without breakthrough infection. Collectively, these results highlight the broad and stable neutralizing antibody response induced by mRNA booster dose administration, implicating a significant role of virus evolution to evade nAb specificity, versus waning humoral immunity, in increasing rates of breakthrough infection.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "PANKE QU", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Julia N. Faraone", + "author_inst": "The Ohio State University" + }, + { + "author_name": "John P. Evans", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Yi-Min Zheng", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Claire Carlin", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Gerard Lozanski", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Linda J. Saif", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Eugene M. Oltz", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Richard J. Gumina", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Shan-Lu Liu", + "author_inst": "The Ohio State University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.07.21.501023", "rel_title": "Learning from pre-pandemic data to forecast viral antibody escape", @@ -224209,69 +225959,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.07.21.22277831", - "rel_title": "COVID-19 vaccine effectiveness against mortality and risk of death from other causes after COVID-19 vaccination, the Netherlands, January 2021- January 2022", - "rel_date": "2022-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.21.22277831", - "rel_abs": "BackgroundWe aimed to estimate vaccine effectiveness (VE) against COVID-19 mortality, and to explore whether an increased risk of non-COVID-19 mortality exists in the weeks following a COVID-19 vaccine dose.\n\nMethodsNational registries of causes of death, COVID-19 vaccination, specialized health care and long-term care reimbursements were linked by a unique person identifier using data from 1 January 2021 to 31 January 2022. We used Cox regression with calendar time as underlying time scale to, firstly, estimate VE against COVID-19 mortality after primary and first booster vaccination, per month since vaccination and, secondly, estimate risk of non-COVID-19 mortality in the 5 or 8 weeks following a first, second or first booster dose, adjusting for birth year, sex, medical risk group and country of origin.\n\nResultsVE against COVID-19 mortality was >90% for all age groups two months after completion of the primary series. VE gradually decreased thereafter, to around 80% at 7-8 months post-primary series for most groups, and around 60% for elderly receiving a high level of long-term care and for people aged 90+ years. Following a first booster dose, the VE increased to >85% in all groups. The risk of non-COVID-19 mortality was lower or similar in the 5 or 8 weeks following a first dose compared to no vaccination, as well as following a second dose compared to one dose and a booster compared to two doses, for all age and long-term care groups.\n\nConclusionAt the population level, COVID-19 vaccination greatly reduced the risk of COVID-19 mortality and no increased risk of death from other causes was observed.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Brechje de Gier", - "author_inst": "RIVM" - }, - { - "author_name": "Liselotte van Asten", - "author_inst": "RIVM" - }, - { - "author_name": "Tjarda Boere", - "author_inst": "RIVM" - }, - { - "author_name": "Annika van Roon", - "author_inst": "RIVM" - }, - { - "author_name": "Caren van Roekel", - "author_inst": "RIVM" - }, - { - "author_name": "Joyce Pijpers", - "author_inst": "RIVM" - }, - { - "author_name": "Henri van Werkhoven", - "author_inst": "RIVM, Julius Center for Health Sciences and Primary Care" - }, - { - "author_name": "Caroline van den Ende", - "author_inst": "RIVM" - }, - { - "author_name": "Susan Hahn\u00e9", - "author_inst": "RIVM" - }, - { - "author_name": "Hester de Melker", - "author_inst": "RIVM" - }, - { - "author_name": "Mirjam Knol", - "author_inst": "RIVM" - }, - { - "author_name": "Susan van den Hof", - "author_inst": "RIVM" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.07.22.501169", "rel_title": "Synergism of interferon-beta with antiviral drugs against SARS-CoV-2 variants", @@ -225830,6 +227517,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.07.18.22277694", + "rel_title": "Determinants of healthcare employee preference to continue teleworking after the COVID-19 pandemic: a cross-sectional study using hierarchical regression", + "rel_date": "2022-07-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.18.22277694", + "rel_abs": "Employees post-pandemic telework preference is an important consideration for navigating post-pandemic work arrangements and can inform organizational planning and workforce management. A cross-sectional survey of employees (n=400, participation rate =36.4%) of a regional health authority who teleworked during the COVID-19 pandemic was conducted. The most common post-pandemic telework preference was all the time (52%) followed by over half but not all the time (32%) and less than half the time or not at all (16%). Using hierarchical multinomial logistic regression models and less than half the time or not at all as the reference outcome, being a provider of direct patient care and productivity while teleworking were strong determinants of post-pandemic telework preference while two or more weekly teleconference hours, work-life balance and having one or more people over five years of age in the home while teleworking were moderate determinants.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Andrea Marie Jones", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Jonathan Fan", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Leah Thomas-Olson", + "author_inst": "Fraser Health Authority" + }, + { + "author_name": "Wei Zhang", + "author_inst": "University of British Columbia/ Centre for Health Evaluation and Outcome Sciences" + }, + { + "author_name": "Christopher B McLeod", + "author_inst": "University of British Columbia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2022.07.19.22277747", "rel_title": "Cumulative incidence of SARS-CoV-2 infection in the general population of the Valencian Community (Spain) after the surge of the Omicron BA.1 variant", @@ -226103,69 +227825,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.07.19.500662", - "rel_title": "Persistence of SARS-CoV-2 neutralizing antibodies longer than 13 months in naturally-infected, captive white-tailed deer (Odocoileus virginianus), Texas", - "rel_date": "2022-07-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.19.500662", - "rel_abs": "After identifying a captive herd of white-tailed deer (WTD) in central Texas with >94% seroprevalence with SARS-CoV-2 neutralizing antibodies in September 2021, we worked retrospectively through archived serum samples of 21 deer and detected seroconversion of all animals between December 2020 and January 2021. We then collected prospective samples to conclude that the duration of persistence of neutralizing antibodies is at least 13 months for 19 (90.5%) of the animals, with two animals converting to seronegative after six and eight months. Antibody titers generally waned over this time frame, but three deer had a temporary 4 to 8-fold increases in PRNT titers over a month after seroconversion; anamnestic response cannot be ruled out.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Sarah Anne Hamer", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Chase M Nunez", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Christopher Roundy", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Wendy Tang", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Logan F Thomas", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Jack J Richison III", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Jamie Benn", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Lisa Auckland", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Terry Hensley", - "author_inst": "Texas A&M Veterinary Medical Diagnostic Laboratory" - }, - { - "author_name": "Walter E Cook", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Alex Pauvolid-Correa", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Gabriel Hamer", - "author_inst": "Texas A&M University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "zoology" - }, { "rel_doi": "10.1101/2022.07.15.22277688", "rel_title": "Loss of SARS-CoV-2 Seropositivity among Healthy Young Adults over Seven Months", @@ -227656,6 +229315,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.15.22277497", + "rel_title": "Global patterns and drivers of influenza decline during the COVID-19 pandemic", + "rel_date": "2022-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.15.22277497", + "rel_abs": "Influenza circulation declined during the COVID-19 pandemic. The timing and extent of decline and its association with interventions against COVID-19 were described for some regions. Here, we provide a global analysis of the influenza decline between March 2020 and September 2021 and investigate its potential drivers. We computed influenza change by country and trimester relative to the 2014-2019 period using the number of samples in the FluNet database. We used random forests to determine important predictors in a list of 20 covariates including demography, weather, pandemic preparedness, COVID-19 incidence, and COVID-19 pandemic response. With a regression tree we then classified observations according to these predictors. We found that influenza circulation decreased globally, with COVID-19 incidence and pandemic preparedness being the two most important predictors of this decrease. The regression tree showed interpretable groups of observations by country and trimester: Europe and North America clustered together in spring 2020, with limited influenza decline despite strong COVID-19 restrictions; in the period afterwards countries of temperate regions, with high pandemic preparedness, high COVID-19 incidence and stringent social restrictions grouped together having strong influenza decline. Conversely, countries in the tropics, with altogether low pandemic preparedness, low reported COVID-19 incidence and low strength of COVID-19 response showed low influenza decline overall. A final group singled out four \"zero-Covid\" countries, with the lowest residual influenza levels. The spatiotemporal decline of influenza during the COVID-19 pandemic was global, yet heterogeneous. The sociodemographic context and stage of the COVID-19 pandemic showed non-linear associations with this decline. Zero-Covid countries maintained the lowest levels of reduction with strict border controls and despite close-to-normal social activity. These results suggest that the resurgence of influenza could take equally diverse paths. It also emphasises the importance of influenza reseeding in driving countries seasonal influenza epidemics.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Francesco Bonacina", + "author_inst": "Sorbonne Universit\u00e9" + }, + { + "author_name": "Pierre-Yves Bo\u00eblle", + "author_inst": "Sorbonne Universit\u00e9" + }, + { + "author_name": "Vittoria Colizza", + "author_inst": "INSERM" + }, + { + "author_name": "Olivier Lopez", + "author_inst": "Sorbonne Universit\u00e9" + }, + { + "author_name": "Maud Thomas", + "author_inst": "Sorbonne Universit\u00e9" + }, + { + "author_name": "Chiara Poletto", + "author_inst": "INSERM and Sorbonne Universit\u00e9" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.16.22277705", "rel_title": "Attitudes toward COVID-19 pandemic among fully vaccinated individuals: evidence from Greece two years after the pandemic", @@ -227857,121 +229555,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.17.500346", - "rel_title": "Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform", - "rel_date": "2022-07-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.17.500346", - "rel_abs": "Reliable, easy-to-handle phenotypic screening platforms are needed for the identification of anti-SARS-CoV-2 compounds. Here, we present caspase 3/7 activity as a read-out for monitoring the replication of SARS-CoV-2 isolates from different variants, including a remdesivir-resistant strain, and of other coronaviruses in a broad range of cell culture models, independently of cytopathogenic effect formation. Compared to other cell culture models, the Caco-2 subline Caco-2-F03 displayed superior performance, as it possesses a stable SARS-CoV-2 susceptible phenotype and does not produce false-positive hits due to drug-induced phospholipidosis. A proof-of-concept screen of 1796 kinase inhibitors identified known and novel antiviral drug candidates including inhibitors of PHGDH, CLK-1, and CSF1R. The activity of the PHGDH inhibitor NCT-503 was further increased in combination with the HK2 inhibitor 2-deoxy-D-glucose, which is in clinical development for COVID-19. In conclusion, caspase 3/7 activity detection in SARS-CoV-2-infected Caco-2F03 cells provides a simple phenotypic high-throughput screening platform for SARS-CoV-2 drug candidates that reduces false positive hits.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Denisa Bojkova", - "author_inst": "Institute of Medical Virology" - }, - { - "author_name": "Philipp Reus", - "author_inst": "Goethe-University, Frankfurt am Main, Germany" - }, - { - "author_name": "Leona Panosch", - "author_inst": "Goethe-University, Frankfurt am Main, Germany" - }, - { - "author_name": "Marco Bechtel", - "author_inst": "Goethe-University, Frankfurt am Main, Germany" - }, - { - "author_name": "Tamara Rothenburger", - "author_inst": "Goethe-University" - }, - { - "author_name": "Joshua Kandler", - "author_inst": "Goethe-University" - }, - { - "author_name": "Annika Pfeiffer", - "author_inst": "Goethe-University, Frankfurt am Main, Germany" - }, - { - "author_name": "Julian UG Wagner", - "author_inst": "Goethe-University" - }, - { - "author_name": "Mariana Shumliakivska", - "author_inst": "Goethe-University" - }, - { - "author_name": "Stefanie Dimmeler", - "author_inst": "Goethe University Frankfurt" - }, - { - "author_name": "Ruth Olmer", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Ulrich Martin", - "author_inst": "-" - }, - { - "author_name": "Florian Vondran", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Tuna Toptan", - "author_inst": "Goethe-University" - }, - { - "author_name": "Florian Rothweiler", - "author_inst": "Goethe-University" - }, - { - "author_name": "Richard Zehner", - "author_inst": "Goethe-University" - }, - { - "author_name": "Holger Rabenau", - "author_inst": "Goethe-University" - }, - { - "author_name": "Karen L Osman", - "author_inst": "Public Health England" - }, - { - "author_name": "Steven T Pullan", - "author_inst": "Public Health England" - }, - { - "author_name": "Miles T Carroll", - "author_inst": "University of Oxford" - }, - { - "author_name": "Richard Stack", - "author_inst": "University of Kent" - }, - { - "author_name": "Sandra Ciesek", - "author_inst": "Goethe Universtiy Frankfurt" - }, - { - "author_name": "Mark N Wass", - "author_inst": "University of Kent" - }, - { - "author_name": "Martin Michaelis", - "author_inst": "University of Kent" - }, - { - "author_name": "Jindrich Cinatl Jr.", - "author_inst": "Klinikum der Goethe-Universitaet" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2022.07.15.500120", "rel_title": "Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq", @@ -229890,6 +231473,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.13.22277575", + "rel_title": "SARS-CoV-2 infections during Omicron (BA.1) dominant wave and subsequent population immunity in Gauteng, South Africa", + "rel_date": "2022-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.13.22277575", + "rel_abs": "BackgroundThe B.1.1.529 (Omicron BA.1) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global resurgence of coronavirus disease 2019 (Covid-19). The contribution of BA.1 infection to population immunity and its effect on subsequent resurgence of B.1.1.529 sub-lineages warrant investigation.\n\nMethodsWe conducted an epidemiologic survey to determine the sero-prevalence of SARS-CoV-2 IgG from March 1 to April 11, 2022, after the BA.1-dominant wave had subsided in Gauteng (South Africa), and prior to a resurgence of Covid-19 dominated by the BA.4 and BA.5 (BA.4/BA.5) sub-lineages. Population-based sampling included households in an earlier survey from October 22 to December 9, 2021 preceding the BA.1 dominant wave. Dried-blood-spot samples were quantitatively tested for IgG against SARS-CoV-2 spike protein and nucleocapsid protein. Epidemiologic trends in Gauteng for cases, hospitalizations, recorded deaths, and excess deaths were evaluated from the inception of the pandemic to the onset of the BA.1 dominant wave (pre-BA.1), during the BA.1 dominant wave, and for the BA.4/BA.5 dominant wave through June 6, 2022.\n\nResultsThe 7510 participants included 2420 with paired samples from the earlier survey. Despite only 26.7% (1995/7470) of individuals having received a Covid-19 vaccine, the overall sero-prevalence was 90.9% (95% confidence interval [CI], 90.2 to 91.5), including 89.5% in Covid-19 unvaccinated individuals. Sixty-four percent (95%CI, 61.8-65.9) of individuals with paired samples had serological evidence of SARS-CoV-2 infection during the BA.1 dominant wave. Of all cumulative recorded hospitalisations and deaths, 14.1% and 5.9% were contributed by the BA.1 dominant wave, and 5.1% and 1.6% by the BA.4/BA.5 dominant wave. The SARS-CoV-2 infection fatality risk was lower in the BA.1 compared with pre-BA.1 waves for recorded deaths (0.02% vs. 0.33%) and Covid-19 attributable deaths based on excess mortality estimates (0.03% vs. 0.67%).\n\nConclusionsGauteng province experienced high levels of infections in the BA.1 -dominant wave against a backdrop of high (73%) sero-prevalence. Covid-19 hospitalizations and deaths were further decoupled from infections during BA.4/BA.5 dominant wave than that observed during the BA.1 dominant wave.\n\n(Funded by the Bill and Melinda Gates Foundation.)", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Shabir Madhi", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Gaurav Kwatra", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Jonathan E. Myers", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Waasila Jassat", + "author_inst": "National institute for communicable diseases of South Africa" + }, + { + "author_name": "Nisha Dhar", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Christian K. Mukendi", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Lucille Blumberg", + "author_inst": "National institute for communicable diseases of South Africa" + }, + { + "author_name": "Richard Welch", + "author_inst": "National institute for communicable diseases of South Africa" + }, + { + "author_name": "Alane Izu", + "author_inst": "University of the Witwatersrand" + }, + { + "author_name": "Portia C. Mutevedzi", + "author_inst": "University of the Witwatersrand" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.14.22277647", "rel_title": "Estimating waning vaccine effectiveness from population-level surveillance data in multi-variant epidemics", @@ -229971,37 +231609,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.07.13.22277610", - "rel_title": "Bayesian Shrinkage Priors in Zero-Inflated and Negative Binomial Regression models with Real World Data Applications of COVID-19 Vaccine, and RNA-Seq", - "rel_date": "2022-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.13.22277610", - "rel_abs": "BackgroundCount data regression modeling has received much attention in several science fields in which the Poisson, Negative binomial, and Zero-Inflated models are some of the primary regression techniques. Negative binomial regression is applied to modeling count variables, usually when they are over-dispersed. A Poisson distribution is also utilized for counting data where the mean is equal to the variance. This situation is often unrealistic since the distribution of counts will usually have a variance that is not equal to its mean. Modeling it as Poisson distributed leads to ignoring under- or overdispersion, depending on if the variance is smaller or larger than the mean. Also, situations with outcomes having a larger number of zeros such as RNASeq data require Zero-inflated models. Variable selection through shrinkage priors has been a popular method to address the curse of dimensionality and achieve the identification of significant variables.\n\nMethodsWe present a unified Bayesian hierarchical framework that implements and compares shrinkage priors in negative-binomial and zero-inflated negative binomial regression models. The key feature is the representation of the likelihood by a Polya-Gamma data augmentation, which admits a natural integration with a family of shrinkage priors. We specifically focus on the Horseshoe, Dirichlet Laplace, and Double Pareto priors. Extensive simulation studies address the efficiency of the model and mean square errors are reported. Further, the models are applied to data sets such as the Covid-19 vaccine, and Covid-19 RNA-Seq data among others.\n\nResultsThe models are robust enough to address variable selection, and MSE decreases as the sample size increases, having lower errors in p > n cases. The noteworthy results showed that the adverse events of Covid-19 vaccines were dependent on age, recovery, medical history, and prior vaccination with a remarkable reduction in MSE of the fitted values. No. of publications of Ph.D. students were dependent on the no. of children, and the no. of articles in the last three years.\n\nConclusionsThe models are robust enough to conduct both variable selections and produce effective fit because of their high shrinkage property and applicability to a broad range of biometric and public health high dimensional problems.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Arinjita Bhattacharyya", - "author_inst": "University of Louisville" - }, - { - "author_name": "riten mitra", - "author_inst": "University of Louisville" - }, - { - "author_name": "Shesh Rai", - "author_inst": "University of Louisville" - }, - { - "author_name": "Subhadip Pal", - "author_inst": "University of Louisville" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.07.13.22277606", "rel_title": "Factors Associated with COVID-19 Breakthrough Infection in the Pre-Omicron Era Among Vaccinated Patients with Rheumatic Diseases: A Cohort Study", @@ -231572,6 +233179,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.10.22277467", + "rel_title": "Development of an Accurate and Rapid Antigen Assay for COVID-19 Diagnostics Using Saliva", + "rel_date": "2022-07-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.10.22277467", + "rel_abs": "The global outbreak of COVID-19 highlighted the need for rapid and accurate diagnostic testing to control the spread of this highly contagious disease (1-5). Here, we describe the nCoVega COVID-19 antigen rapid test ([~] 15min) that can detect the presence of the SARS-COV-2 virus particles from saliva sample on a portable device. The portable reader instrument, the Vega-200, has a small footprint and is designed for use at point of care settings. The test detects the fluorescence signal using wide-field illumination from antigen-antibody complexes captured on a special filter matrix (6). Results of this clinical evaluation of 183 subjects demonstrates that the nCoVega COVID-19 test performs at par with qRT-PCR tests (7) (gold standard) for both symptomatic and asymptomatic patients, with a strong inverse correlation between RFU (relative fluorescence units) and Ct counts (from RT-PCR) maintaining detection accuracy even at very low viral loads. The test has an analytical performance of 15.3 TCID50/mL, and 100% specificity for COVID-19 as compared to other human respiratory viruses, including other human coronaviruses. The working principle of this assay and test system can be used for developing other rapid, inexpensive antigen assays and it can offer an end-to-end, point-of-care solution to meet the continuous demand in tackling existing and emerging infectious diseases across the globe.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Camille Troup", + "author_inst": "Kaya17 Inc" + }, + { + "author_name": "Debnath Mukhopadhyay", + "author_inst": "Kaya17 Inc" + }, + { + "author_name": "Tania Chakrabarty", + "author_inst": "Kaya17 Inc" + }, + { + "author_name": "Anup Madan", + "author_inst": "Kaya17 Inc" + }, + { + "author_name": "Sri Satyanarayana", + "author_inst": "Kaya17, inc" + }, + { + "author_name": "Shreefal Mehta", + "author_inst": "Kaya17 Inc" + }, + { + "author_name": "Sulatha Dwarakanath", + "author_inst": "Kaya17 Inc" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.11.22277511", "rel_title": "Effect of Stay-at-Home Orders and Other COVID-Related Policies on Trauma Hospitalization Rates and Disparities in the United States: A Statewide Time-Series Analysis", @@ -231729,37 +233379,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.07.11.22277475", - "rel_title": "Type 1 and type 2 diabetes mellitus: Clinical outcomes due to COVID-19. Protocol of a systematic literature review", - "rel_date": "2022-07-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.11.22277475", - "rel_abs": "IntroductionDiabetes has been associated with an increased risk of complications in patients with COVID-19. Most studies do not differentiate between patients with type 1 and type 2 diabetes, which correspond to two pathophysiological distinct diseases that could represent different degrees of clinical compromise.\n\nObjectiveTo identify if there are differences in the clinical outcomes of patients with COVID-19 and diabetes (type 1 and type 2) compared to patients with COVID-19 without diabetes.\n\nMethodsObservational studies of patients with COVID-19 and diabetes (both type 1 and type 2) will be included without restriction of geographic region, gender or age, whose outcome is hospitalization, admission to intensive care unit or mortality compared to patients without diabetes. Two authors will independently perform selection, data extraction, and quality assessment, and a third reviewer will resolve discrepancies. The data will be synthesized regarding the sociodemographic and clinical characteristics of patients with diabetes and without diabetes accompanied by the measure of association for the outcomes. The data will be synthesized regarding the sociodemographic and clinical characteristics of patients with diabetes and without diabetes accompanied by the measure of association for the outcomes.\n\nExpected resultsUpdate the evidence regarding the risk of complications in diabetic patients with COVID-19 and in turn synthesize the information available regarding type 1 and type 2 diabetes mellitus, to provide keys to a better understanding of the pathophysiology of diabetics.\n\nSystematic review registryThis study was registered at the International Prospective Registry for Systematic Reviews (PROSPERO) - CRD42021231942.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Juan Pablo Perez Bedoya", - "author_inst": "Epidemiology Group. National Faculty of Public Health, University of Antioquia, Medellin, Colombia" - }, - { - "author_name": "Alejandro Mejia Munoz", - "author_inst": "Biology and control of infectious diseases group. Faculty of exact and natural sciences, University of Antioquia, Medellin, Colombia" - }, - { - "author_name": "Noel Christopher Barengo", - "author_inst": "Associate professor. Department of Translational Medicine, Herbert Wertheim College of Medicine & Department of Global Health, Robert Stempel College of Public " - }, - { - "author_name": "Paula Andrea Diaz Valencia", - "author_inst": "Epidemiology Group. National Faculty of Public Health, University of Antioquia, Medellin, Colombia" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.07.11.22277516", "rel_title": "Changes in General Practice use and costs with COVID-19 and telehealth initiatives", @@ -233634,6 +235253,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.05.22277189", + "rel_title": "Class switch towards non-inflammatory IgG isotypes after repeated SARS-CoV-2 mRNA vaccination", + "rel_date": "2022-07-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.05.22277189", + "rel_abs": "Repeated mRNA vaccinations are an efficient tool to combat the SARS-CoV-2 pandemic. High levels of neutralizing SARS-CoV-2-antibodies are an important component of vaccine-induced immunity. Shortly after the first or second mRNA vaccine dose, the IgG response mainly consists of the pro-inflammatory isotypes IgG1 and IgG3 and is driven by T helper (Th) 1 cells. Here, we report that several months after the second vaccination, SARS-CoV-2-specific antibodies were increasingly composed of non-inflammatory IgG2 and particularly IgG4, which were further boosted by a third mRNA vaccination and/or SARS-CoV-2 variant breakthrough infections. While IgG antibodies were affinity matured and of high neutralization capacity, the switch in constant domains caused changes in fragment crystallizable (Fc)-receptor mediated effector functions, including a decreased capacity to facilitate phagocytosis. IgG4 induction was neither induced by Th2 cells nor observed after homologous or heterologous SARS-CoV-2 vaccination with adenoviral vectors. In addition, IgG2- and IgG4-producing memory B cells were phenotypically indistinguishable from IgG1- or IgG3-producing cells. Since Fc-mediated effector functions are critical for antiviral immunity, the described class switch towards non-inflammatory IgG isotypes, which otherwise rarely occurs after vaccination or viral infection, may have consequences for the choice and timing of vaccination regimens using mRNA vaccines.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Pascal Irrgang", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Juliane Gerling", + "author_inst": "Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen," + }, + { + "author_name": "Katharina Kocher", + "author_inst": "Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlange" + }, + { + "author_name": "Dennis Lapuente", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Philipp Steininger", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Monika Wytopil", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Simon Sch\u00e4fer", + "author_inst": "Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen," + }, + { + "author_name": "Katharina Habenicht", + "author_inst": "Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen," + }, + { + "author_name": "Jahn Zhong", + "author_inst": "Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen," + }, + { + "author_name": "George Ssebyatika", + "author_inst": "Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany" + }, + { + "author_name": "Thomas Krey", + "author_inst": "Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany" + }, + { + "author_name": "Valeria Falcone", + "author_inst": "Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany" + }, + { + "author_name": "Christine Sch\u00fclein", + "author_inst": "Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlange" + }, + { + "author_name": "Antonia Sophia Peter", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Krystelle Nganou-Makamdop", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Hartmut Hengel", + "author_inst": "Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany" + }, + { + "author_name": "J\u00fcrgen Held", + "author_inst": "Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlange" + }, + { + "author_name": "Christian Bogdan", + "author_inst": "Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlange" + }, + { + "author_name": "Klaus \u00dcberla", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Kilian Schober", + "author_inst": "Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlange" + }, + { + "author_name": "Thomas H Winkler", + "author_inst": "Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen," + }, + { + "author_name": "Matthias Tenbusch", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.07.22277364", "rel_title": "Altered affinity to ACE2 and reduced Fc functional antibodies to SARS-CoV-2 RBD variants", @@ -233955,45 +235677,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.09.22277456", - "rel_title": "Examining the Impact of Increasing Vaccine Coverage and Nonpharmaceutical Interventions against Coronavirus Disease 2019 In Ghana using Mathematical Modeling", - "rel_date": "2022-07-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.09.22277456", - "rel_abs": "Seroprevalence studies assessing community exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Ghana concluded that population-level immunity remained low as of February 2021. Thus, it is important to demonstrate how increasing vaccine coverage reduces the economic and public health impacts associated with transmission of the novel coronavirus. To that end, this study used a Susceptible-Exposed-Presymptomatic-Symptomatic-Asymptomatic-Recovered-Dead-Vaccinated compartmental model to simulate coronavirus disease 2019 (COVID-19) transmission and the role of public health interventions in Ghana. The impact of increasing vaccination rate and decline in transmission rates due to nonpharmaceutical interventions (NPIs) on cumulative infections and deaths averted was explored under different scenarios. Latin hypercube sampling-partial rank correlation coefficient (LHS-PRCC) was used to investigate uncertainty and sensitivity of the outcomes to the parameters. Simulation results suggest that increasing the vaccination rate to achieve 50% coverage was associated with almost 30,000 deaths and 25 million infections averted. In comparison, a 50% decrease in the transmission coefficient was associated with about 50 million infections and 120,000 deaths averted. The LHS-PRCC results also found that cumulative infections and deaths averted were most sensitive to three model parameters: Transmission rate, vaccination rate, and waning immunity rate from infection. There is a need to increase vaccination coverage by ensuring an increased supply. Adherence to NPIs and increased vaccine uptake would successfully mitigate the impact of COVID-19 in Ghana.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sylvia Kesewaa Ofori", - "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health" - }, - { - "author_name": "Jessica S Schwind", - "author_inst": "Georgia Southern University Institute for Health Logistics and Analytics" - }, - { - "author_name": "Kelly L Sullivan", - "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health" - }, - { - "author_name": "Gerardo Chowell", - "author_inst": "Georgia State University School of Public Health" - }, - { - "author_name": "Benjamin J Cowling", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Isaac Chun-Hai Fung", - "author_inst": "Georgia Southern University Jiann-Ping Hsu College of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.07.09.22277458", "rel_title": "Modeling infections and deaths averted due to COVID-19 vaccination strategies in Ghana", @@ -235804,6 +237487,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.06.22277303", + "rel_title": "Quantifying the impact of vaccines and booster doses on COVID-19 in the U.S.", + "rel_date": "2022-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.06.22277303", + "rel_abs": "The COVID-19 pandemic continues to have a devastating impact on health systems and economies across the globe. Implementing public health measures in tandem with effective vaccination strategies have been instrumental in curtailing the burden of the pandemic. With the three vaccines authorized for use in the U.S. having varying efficacies and waning effects against major COVID-19 strains, understanding the impact of these vaccines on COVID-19 incidence and fatalities is critical. Here, we formulate and use mathematical models to assess the impact of vaccine type, vaccination and booster uptake, and waning of natural and vaccine-induced immunity on the incidence and fatalities of COVID-19 and to predict future trends of the disease in the U.S. when existing control measures are reinforced or relaxed. Results of the study show a 5, 1.8, and 2 times reduction in the reproduction number during the period in which vaccination, first booster, and second booster uptake started, respectively, compared to the previous period. Due to waning of vaccine-induced immunity, vaccinating up to 96% of the U.S. population might be required to attain herd immunity, if booster uptake is low. Additionally, vaccinating and boosting more people from the onset of vaccination and booster uptake, especially with mRNA vaccines (which confer superior protection than the Johnson & Johnson vaccine) would have led to a significant reduction in COVID-19 cases and deaths in the U.S. Furthermore, adopting natural immunity-boosting measures is important in fighting COVID-19 and transmission rate reduction measures such as mask-use are critical in combating COVID-19. The emergence of a more transmissible COVID-19 variant, or early relaxation of existing control measures can lead to a more devastating wave, especially if transmission rate reduction measures and vaccination are relaxed simultaneously, while chances of containing the pandemic are enhanced if both vaccination and transmission rate reduction measures are reinforced simultaneously. We conclude that maintaining or improving existing control measures and boosting with mRNA vaccines are critical in curtailing the burden of the pandemic in the U.S.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Calistus N. Ngonghala", + "author_inst": "Department of Mathematics, University of Florida, Gainesville, FL 32611, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA." + }, + { + "author_name": "Michael Asare-Baah", + "author_inst": "Department of Epidemiology, University of Florida, 2004 Mowry Road, Gainesville, FL 32610, USA; Emerging Pathogens Institute, University of Florida, Gainesville" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.02.22277181", "rel_title": "Integrative analysis of viral entry networks and clinical outcomes identifies a protective role for spironolactone in severe COVID-19", @@ -235985,81 +237691,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.04.22277230", - "rel_title": "SARS-CoV-2 seroprevalence among public school staff in Metro Vancouver after the first Omicron wave in British Columbia, Canada", - "rel_date": "2022-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.04.22277230", - "rel_abs": "ObjectiveTo determine the SARS-CoV-2 seroprevalence among school workers in the setting of full in-person schooling and the highly transmissible Omicron variants of concern.\n\nDesignCross-sectional study among school staff, comparing to period-, age-, sex- and postal code-weighted data from Canadian blood donors from the same community.\n\nSettingThree large school districts in the greater Vancouver metropolitan area, British Columbia, Canada, with serology sampling done between January 26, 2022 and April 8, 2022.\n\nParticipantsSchool staff actively working in the Vancouver, Richmond and Delta School Districts.\n\nMain outcome measureSARS-CoV-2 seroprevalence based on nucleocapsid (N)-protein testing, adjusted for the sensitivity and specificity of the assay.\n\nResultsA majority (65.8%) of the 1845 school staff enrolled reported close contact with a COVID-19 case outside the household. Of those, about half reported close contact with a COVID-19 case at school either in a student (51.5%) or co-worker (54.9%). In a representative sample of 1620 (87.8%) school staff, the adjusted seroprevalence was 26.5% [95%CrI: 23.9 - 29.3%]. This compared to an age, sex and residency area-weighted seroprevalence of 32.4% [95%CrI: 30.6 - 34.5%] among 7164 blood donors.\n\nConclusionDespite frequent COVID-19 exposures, the prevalence of SARS-CoV-2 infections among the staff of three main school districts in the Vancouver metropolitan area was no greater than a reference group of blood donors, even after the emergence of the more transmissible Omicron variant.\n\nWhat is already known on this subject?O_LIEarlier studies indicate that COVID-19 infection rates are not increased among school staff at previous stages of the pandemic compared to the community, yet controversy remains whether this will remain true after the emergence of the highly transmissible Omicron variant.\nC_LI\n\nWhat this study adds?O_LIDespite frequent COVID-19 exposures, this study identified no detectable increase in SARS-CoV-2 seroprevalence among school staff working in three metro Vancouver public school districts after the first Omicron wave in British Columbia, compared to a reference group of blood donors from the same age, sex and community area.\nC_LI", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Allison W Watts", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Louise C M\u00e2sse", - "author_inst": "University of British Columbia" - }, - { - "author_name": "David M Goldfarb", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Michael A Irvine", - "author_inst": "British Columbia Centre for Disease Control" - }, - { - "author_name": "Sarah Hutchison", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Lauren Muttucomaroe", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Bethany Poon", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Vilte Barakauskas", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Collette O'Reilly", - "author_inst": "Vancouver School District" - }, - { - "author_name": "Else S Bosman", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Frederic Reicherz", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Daniel Coombs", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Mark Pitblado", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Sheila O'Brien", - "author_inst": "Canadian Blood Services" - }, - { - "author_name": "Pascal M Lavoie", - "author_inst": "University of British Columbia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.04.22276207", "rel_title": "The association between diabetes and mortality among patients hospitalized with COVID-19: Cohort Study of Hospitalized Adults in Ontario, Canada and Copenhagen, Denmark", @@ -238766,6 +240397,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.03.22277196", + "rel_title": "Leveraging Serosurveillance and Postmortem Surveillance to Quantify the Impact of COVID-19 in Africa", + "rel_date": "2022-07-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.03.22277196", + "rel_abs": "BackgroundThe COVID-19 pandemic has had a devastating impact on global health, the magnitude of which appears to differ intercontinentally: for example, reports suggest 271,900 per million people have been infected in Europe versus 8,800 per million people in Africa. While Africa is the second largest continent by population, its reported COVID-19 cases comprise <3% of global cases. Although social, environmental, and environmental explanations have been proposed to clarify this discrepancy, systematic infection underascertainment may be equally responsible.\n\nMethodsWe seek to quantify magnitude of underascertainment in COVID-19s cumulative incidence in Africa. Using serosurveillance and postmortem surveillance, we constructed multiplicative factors estimating ratios of true infections to reported cases in African nations since March 2020.\n\nResultsMultiplicative factors derived from serology data - in a subset of 12 nations - suggested a range of COVID-19 reporting rates, from 1 in 630 infections reported in Kenya (May 2020) to 1 in 15 infections reported in South Africa (November 2021). The largest multiplicative factor, 3,795, corresponded to Malawi (June 2020), suggesting <0.05% of infections captured. A similar set of multiplicative factors for all nations derived from postmortem data points toward the same conclusion: reported COVID-19 cases are unrepresentative of true infections, suggesting a key reason for low case burden in many African nations is significant underdetection and underreporting.\n\nConclusionsWhile estimating COVID-19s exact burden is challenging, the multiplicative factors we present provide incidence curves reflecting likely-to-worst-case ranges of infection. Our results stress the need for expansive surveillance to allocate resources in areas experiencing severe discrepancies between reported cases, projected infections, and deaths.\n\nSummaryHere we present a range of estimates quantifying the extent of underascertainment of COVID-19 cumulative incidence in Africa. These estimates, constructed from serology and mortality data, suggest that systematic underdetection and underreporting may be contributing to the seemingly low burden of COVID-19 reported in Africa.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nicole Kogan", + "author_inst": "Harvard T. H. Chan School of Public Health | Northeastern University" + }, + { + "author_name": "Shae Gantt", + "author_inst": "Harvard T. H. Chan School of Public Health" + }, + { + "author_name": "David Swerdlow", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Cecile Viboud", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Muhammed Semakula", + "author_inst": "Rwanda Biomedical Centre" + }, + { + "author_name": "Marc Lipsitch", + "author_inst": "Harvard T. H. Chan School of Public Health | CDC" + }, + { + "author_name": "Mauricio Santillana", + "author_inst": "Northeastern University | Harvard T. H. Chan School of Public Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.29.498117", "rel_title": "COVID-19 Neuropathology: evidence for SARS-CoV-2 invasion of Human Brainstem Nuclei", @@ -239207,33 +240881,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.04.498661", - "rel_title": "Proteome dynamics of COVID-19 severity learnt by a graph convolutional network of multi-scale topology", - "rel_date": "2022-07-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.04.498661", - "rel_abs": "Many efforts have been recently done to characterise the molecular mechanisms of COVID-19 disease. These efforts resulted in a full structural identification of ACE2 as principal receptor of the Sars-CoV-2 spike protein in the cell. However, there are still important open questions related to other proteins involved in the progression of the disease. To this end, we have modelled the plasma proteome of 384 COVID patients. The model calibrated proteins measures at three time tags and make also use of the detailed clinical evaluation outcome of each patient after their hospital stay at day 28. Our analysis is able to discriminate severity of the disease by means of a metric based on available WHO scores of disease progression. Then, we identify by topological vectorisation those proteins shifting the most in their expression depending on that severity classification. Finally, the extracted topological invariants respect the protein expression at different times were used as base of a graph convolutional network. This model enabled the dynamical learning of the molecular interactions produced between the identified proteins.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Samy Gauthier", - "author_inst": "Universite Sorbonne Paris Nord, LAGA" - }, - { - "author_name": "Alexy Tran-Dinh", - "author_inst": "Universite de Paris, AP-HP, Hopital Bichat Claude Bernard, LVTS" - }, - { - "author_name": "Ian Morilla", - "author_inst": "Universit\u00e9 Sorbonne Paris Nord" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2022.07.03.498624", "rel_title": "Targeting C5aR1 signaling reduced neutrophil extracellular traps and ameliorates COVID-19 pathology", @@ -240804,6 +242451,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.07.01.22277163", + "rel_title": "Phase 2 randomised placebo-controlled trial of spironolactone and dexamethasone versus dexamethasone in COVID-19 hospitalised patients in Delhi", + "rel_date": "2022-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.01.22277163", + "rel_abs": "BackgroundIn this phase 2 randomised placebo-controlled clinical trial, we hypothesised that blocking mineralocorticoid receptors with spironolactone in patients with COVID-19 is safe and may reduce illness severity.\n\nMethodsHospitalised patients with confirmed COVID-19 were randomly allocated to low dose oral spironolactone (50mg day 1, then 25mg once daily for 21 days) or standard care in a 2:1 ratio. Both groups received dexamethasone 6mg for 10 days. Group allocation was blinded to the patient and research team. Primary outcomes were time to recovery, defined as the number of days until patients achieved WHO Ordinal Scale (OS) category [≤] 3, and the effect of spironolactone on aldosterone, D-dimer, angiotensin II and Von Willebrand Factor (VWF).\n\nResults120 patients were recruited in Delhi from 01 February to 30 April 2021. 74 were randomly assigned to spironolactone and dexamethasone (SpiroDex), and 46 to dexamethasone alone (Dex). There was no significant difference in the time to recovery between SpiroDex and Dex groups (SpiroDex median 4.5 days, Dex median 5.5 days, p = 0.055). SpiroDex patients had lower aldosterone levels on day 7 and lower D-dimer levels on days 4 and 7 (day 7 D-dimer mean SpiroDex 1.15{micro}g/mL, Dex 3.15 {micro}g/mL, p = 0.0004). There was no increase in adverse events in patients receiving SpiroDex. Post hoc analysis demonstrated reduced clinical deterioration (pre specified as escalating to WHO OS category >4) in the SpiroDex group vs Dex group (5.4% vs 19.6%).\n\nConclusionLow dose oral spironolactone in addition to dexamethasone was safe and reduced D-Dimer and aldosterone. Although time to recovery was not significantly reduced, fewer patients progressed to severe disease. Phase 3 randomised controlled trials with spironolactone should be considered.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Bharti Wadhwa", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" + }, + { + "author_name": "Vikas Malhotra", + "author_inst": "Department of ENT & Head and Neck Surgery, Maulana Azad Medical College & Associated Hospitals, New Delhi, India" + }, + { + "author_name": "Sukhyanti Kerai", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" + }, + { + "author_name": "Farah Husain", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" + }, + { + "author_name": "Nalini Bala Pandey", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" + }, + { + "author_name": "Kirti N Saxena", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" + }, + { + "author_name": "Vinay Singh", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" + }, + { + "author_name": "Tom Michael Quinn", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Feng Li", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Erin Gaughan", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Manu Shankar-Hari", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Bethany Mills", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Jean Antonelli", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Annya Bruce", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Keith Finlayson", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Anne Moore", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Kevin Dhaliwal", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Christopher Edwards", + "author_inst": "Imperial College, Hammersmith Campus, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2022.06.30.498338", "rel_title": "Transcriptional Profiles Analysis of COVID-19 and Malaria Patients Reveals Potential Biomarkers in Children", @@ -240929,49 +242663,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2022.06.29.22277065", - "rel_title": "Missing Americans: Early Death in the United States, 1933-2021", - "rel_date": "2022-06-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.29.22277065", - "rel_abs": "We assessed how many U.S. deaths would have been averted each year, 1933-2021, if U.S. age-specific mortality rates had equaled those of other wealthy nations. The annual number of excess deaths in the U.S. increased steadily beginning in the late 1970s, reaching 626,353 in 2019. Excess deaths surged during the COVID-19 pandemic. In 2021, there were 1,092,293 \"Missing Americans\" and 25 million years of life lost due to excess mortality relative to peer nations. In 2021, half of all deaths under 65 years and 91% of the increase in under-65 mortality since 2019 would have been avoided if the U.S. had the mortality rates of its peers. Black and Native Americans made up a disproportionate share of Missing Americans, although the majority were White.\n\nOne sentence summaryIn 2021, 1.1 million U.S. deaths - including 1 in 2 deaths under age 65 years - would have been averted if the U.S. had the mortality rates of other wealthy nations.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jacob Bor", - "author_inst": "Boston University" - }, - { - "author_name": "Andrew C Stokes", - "author_inst": "Boston University" - }, - { - "author_name": "Julia Raifman", - "author_inst": "Boston University" - }, - { - "author_name": "Atheendar Venkataramani", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Mary T Bassett", - "author_inst": "Harvard University" - }, - { - "author_name": "David Himmelstein", - "author_inst": "Hunter College (CUNY) and Cambridge Health Alliance" - }, - { - "author_name": "Steffie Woolhandler", - "author_inst": "Hunter College (CUNY) and Cambridge Health Alliance" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.29.498082", "rel_title": "Trapping virus-loaded aerosols using granular protein nanofibrils and iron oxyhydroxides nanoparticles", @@ -242478,6 +244169,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.29.22277010", + "rel_title": "Exploring the Role of Superspreading Events in SARS-CoV-2 Outbreaks", + "rel_date": "2022-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.29.22277010", + "rel_abs": "The novel coronavirus SARS-CoV-2 emerged in 2019 and subsequently spread throughout the world, causing over 529 million cases and 6 million deaths thus far. In this study, we formulate a continuous-time Markov chain model to investigate the influence of superspreading events (SSEs), defined here as public or social events that result in multiple infections over a short time span, on SARS-CoV-2 outbreak dynamics. Using Gillespies direct algorithm, we simulate a continuous-time Markov chain model for SARS-CoV-2 spread under multiple scenarios: first, with neither hospitalisation nor quarantine; second, with hospitalisation, quarantine, premature hospital discharge, and quarantine violation; and third, with hospitalisation and quarantine but neither premature hospital discharge nor quarantine violation. We also vary quarantine violation rates. Results indicate that, in most cases, SSE-dominated outbreaks are more variable but less severe than non-SSE-dominated outbreaks, though the most severe SSE-dominated outbreaks are more severe than the most severe non-SSE-dominated outbreaks. SSE-dominated outbreaks are outbreaks with relatively higher SSE rates. In all cases, SSE-dominated outbreaks are more sensitive to control measures, with premature hospital discharge and quarantine violation substantially reducing control measure effectiveness.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jordan Bramble", + "author_inst": "University of Kansas" + }, + { + "author_name": "Alexander Fulk", + "author_inst": "University of Kansas" + }, + { + "author_name": "Raul Saenz", + "author_inst": "University of Kansas Medical Center" + }, + { + "author_name": "Folashade Agusto", + "author_inst": "University of Kansas" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.06.27.497749", "rel_title": "The RNA demethylase FTO controls m6A marking on SARS-CoV-2 and classifies COVID-19 severity in patients", @@ -242715,41 +244437,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2022.06.27.22276976", - "rel_title": "Hand Dermatitis among Health Care Workers during the COVID-19 Pandemic: Prevalence, and Risk Factors", - "rel_date": "2022-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.27.22276976", - "rel_abs": "BackgroundHealth care workers (HCWs) need to perform new preventive measures to protect themselves and patients against ongoing COVID-19 transmission, which can increase the occurrence of hand dermatitis (HD) among them.\n\nObjectivesThis study aimed to investigate the prevalence of HD among HCWs and its possible risk factors in IRAN.\n\nMethodsA survey of 159 HCWS working in university hospitals was performed between August to September 2020. Research data were collected via the standardized Nordic Occupational Skin Questionnaire (NOSQ-2002).\n\nResultsThe prevalence of HD in the study population was 51.6%. Females had a 3.84 fold higher risk of HD than males (confidence interval (CI): 1.85-8). HCWs older than 40 years and those who aged 30-39 years had a 9.6 and 1.72 fold higher risk of HD than HCWs aged 20-29 years (CI: 2.6-35.7; CI: 0.87-3.4, respectively). A significant association was found between the prevalence of HD among HCWs and working hours per week, and wearing gloves (P<0.05).\n\nConclusionPossible risk factors for developing HD among HCWs are female gender and older age. Preventive measures for HD are needed for HCWs, especially during the COVID- 19 pandemic.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Omolbanin Motamed-Rezaei", - "author_inst": "Birjand University of Medical Sciences" - }, - { - "author_name": "Gholamreza Sharif-Zadeh", - "author_inst": "Birjand University of Medical Sciences" - }, - { - "author_name": "Hadis Rajabipour", - "author_inst": "Birjand University of Medical Sciences" - }, - { - "author_name": "Farnaz Jahani", - "author_inst": "Birjand University of Medical Sciences" - }, - { - "author_name": "Hamed Lotfi", - "author_inst": "Birjand University of Medical Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2022.06.28.22276985", "rel_title": "The effects of vaccination on the disease severity and factors for viral clearance and hospitalization in Omicron-infected patients: A retrospective observational cohort study from recent regional outbreaks in China", @@ -244308,6 +245995,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.24.22276852", + "rel_title": "Compliant citizens, defiant rebels or neither? Exploring changing COVID-19 vaccine attitudes and decisions in Bradford, UK: Findings from a follow-up qualitative study", + "rel_date": "2022-06-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.24.22276852", + "rel_abs": "BackgroundCOVID-19 vaccines have been the central pillar of the public health response to the pandemic, intended to enable us to live with Covid. It is important to understand COVID-19 vaccines attitudes and decisions in order to maximise uptake through an empathetic lens.\n\nObjectiveTo explore the factors that influenced peoples COVID-19 vaccines decisions and how attitudes towards the vaccines had changed in an eventful year.\n\nDesign and participantsThis is a follow up study that took place in Bradford, UK one year after the original study, between October 2021 and January 2022. In-depth phone interviews were conducted with 12 (of the 20 originally interviewed) people from different ethnic groups and areas of Bradford. Reflexive thematic analysis was conducted.\n\nResults11 of the 12 participants interviewed had received both doses of the COVID-19 vaccine and most intended to have a booster dose. Participants described a variety of reasons why they had decided to have the vaccines, including: feeling at increased risk at work; protecting family and others in their communities, unrestricted travel and being influenced by the vaccine decisions of family, friends and colleagues. All participants discussed ongoing interaction with COVID-19 misinformation and for some this meant they were uneasy about their decision to have the vaccine. They described feeling overloaded by and disengaged from COVID-19 information, which they often found contradictory and some felt mistrustful of the UK governments motives and decisions during the pandemic.\n\nConclusionsThe majority of participants had managed to navigate an overwhelming amount of circulating COVID-19 misinformation and chosen to have two or more COVID-19 vaccines, even if they had been previously said they were unsure. However, these decisions were complicated, and demonstrate the continuum of vaccine hesitancy and acceptance. This follow up study underlines that vaccine attitudes are changeable and contextual.\n\nPatient or Public ContributionThe original study was developed through a rapid community and stakeholder engagement process in 2020. Discussion with the Bradford Council Public Health team and the public through the Bradford COVID-19 Community Insights Group was undertaken in 2021 to identify important priorities for this follow up study.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Bridget Lockyer", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals Foundation Trust" + }, + { + "author_name": "Rachael H Moss", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals Foundation Trust" + }, + { + "author_name": "Charlotte Endacott", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals Foundation Trust" + }, + { + "author_name": "Shahid Islam", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals Foundation Trust" + }, + { + "author_name": "Laura Sheard", + "author_inst": "Bradford Teaching Hospitals Foundation Trust" + }, + { + "author_name": "- Bradford Institute for Health Research Covid-19 Scientific Advisory Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.06.22.22276744", "rel_title": "Vaccination saves lives: How do patients with chronic diseases and severe COVID-19 fare? Analysis from Indias National Clinical registry for COVID-19", @@ -244485,85 +246211,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, - { - "rel_doi": "10.1101/2022.06.27.22276938", - "rel_title": "Capturing the SARS-CoV-2 infection pyramid within the municipality of Rotterdam using longitudinal sewage surveillance", - "rel_date": "2022-06-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.27.22276938", - "rel_abs": "BackgroundDespite high vaccination rates in the Netherlands, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate. Longitudinal sewage monitoring was implemented along with the notification of cases as two parts of the surveillance pyramid to validate the use of sewage surveillance for monitoring SARS-CoV-2, as an early warning tool, and to measure the effect of interventions.\n\nMethodsSewage samples were collected from nine neighborhoods from September 2020 to November 2021, and compared with reported cases. Comparative analysis and modeling were performed to understand the correlation between wastewater and case trends.\n\nFindingsUsing high resolution sampling, normalization of wastewater SARS-CoV-2 concentrations and normalization of reported positive tests for testing delay and intensity, the incidence of reported positive tests could be modeled based on sewage data, and trends in both surveillance systems coincided. The high collinearity implied that high levels of viral shedding around the onset of disease largely determines SARS-CoV-2 levels in wastewater and the observed relation was independent of SARS-CoV-2 variants and vaccination levels.\n\nInterpretationWastewater surveillance can accurately display SARS-CoV-2 dynamics for small and large locations, and is sensitive enough to measure small variations in the number of infected individuals within or between neighborhoods. With the transition to a post-acute phase of the pandemic, continued sewage surveillance can help to keep sight on reemergence, but continued \"pyramid\" validation studies are needed to assess the predictive value of sewage surveillance with new variants.\n\nFundingHorizon H2020, Adessium Foundation, STOWA, TKI, Ministry of Health, Welfare and Sport", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Miranda de Graaf", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Jeroen Langeveld", - "author_inst": "Partners4urbanwater" - }, - { - "author_name": "Johan Post", - "author_inst": "Partners4urbanwater" - }, - { - "author_name": "Christian Carrizosa", - "author_inst": "Oslo University Hospital" - }, - { - "author_name": "Eelco Franz", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Ray W Izquierdo Lara", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Goffe Elsinga", - "author_inst": "KWR Water Research Institute" - }, - { - "author_name": "Leo Heijnen", - "author_inst": "KWR, Water Research Institute" - }, - { - "author_name": "Frederic Been", - "author_inst": "KWR Water Research Institute" - }, - { - "author_name": "Janko van Beek", - "author_inst": "Erasmus University Medical Center," - }, - { - "author_name": "Remy Schilderpoort", - "author_inst": "Partners4urbanwater" - }, - { - "author_name": "Rianne Vriend", - "author_inst": "Regional Public Health Service Rotterdam-Rijnmond" - }, - { - "author_name": "Ewout Fanoy", - "author_inst": "Regional Public Health Service Rotterdam-Rijnmond" - }, - { - "author_name": "Evelien I.T. de Schepper", - "author_inst": "Erasmus University Medical Center" - }, - { - "author_name": "Marion P.G. Koopmans", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Gertjan Medema", - "author_inst": "KWR Water Research Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.25.22276894", "rel_title": "Within-hotel transmission of SARS-CoV-2 during on-arrival quarantine in Hong Kong", @@ -245982,6 +247629,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.23.497376", + "rel_title": "Monitoring SARS-CoV-2 infection using a double reporter-expressing virus", + "rel_date": "2022-06-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.23.497376", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the highly contagious agent responsible for the coronavirus disease 2019 (COVID-19) pandemic. An essential requirement for understanding SARS-CoV-2 fundamental biology and the impact of anti-viral therapeutics are robust methods to detect for the presence of the virus in infected cells or animal models. Despite the development and successful generation of recombinant (r)SARS-CoV-2 expressing fluorescent or luciferase reporter genes, knowledge acquired from their use in in vitro assays and/or in live animals are limited to the properties of the fluorescent or luciferase reporter genes. Herein, for the first time, we engineered a replication-competent rSARS-CoV-2 that expresses both fluorescent (mCherry) and luciferase (Nluc) reporter genes (rSARS-CoV-2/mCherry-Nluc) to overcome limitations associated with the use of a single reporter gene. In cultured cells, rSARS-CoV-2/mCherry-Nluc displayed similar viral fitness as rSARS-CoV-2 expressing single reporter fluorescent and luciferase genes (rSARS-CoV-2/mCherry and rSARS-CoV-2/Nluc, respectively), or wild-type (WT) rSARS-CoV-2, while maintaining comparable expression levels of both reporter genes. In vivo, rSARS-CoV-2/mCherry-Nluc has similar pathogenicity in K18 human angiotensin converting enzyme 2 (hACE2) transgenic mice than rSARS-CoV-2 expressing individual reporter genes, or WT rSARS-CoV-2. Importantly, rSARS-CoV-2/mCherry-Nluc facilitates the assessment of viral infection and transmission in golden Syrian hamsters using in vivo imaging systems (IVIS). Altogether, this study demonstrates the feasibility of using this novel bireporter-expressing rSARS-CoV-2 for the study SARS-CoV-2 in vitro and in vivo.\n\nIMPORTANCEDespite the availability of vaccines and antivirals, the coronavirus disease 2019 (COVID-19) pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to ravage health care institutions worldwide. Previously, we have generated replication-competent recombinant (r)SARS-CoV-2 expressing fluorescent or luciferase reporter proteins to track viral infection in vitro and/or in vivo. However, these rSARS-CoV-2 are restricted to express only a single fluorescent or a luciferase reporter gene, limiting or preventing their use to specific in vitro assays and/or in vivo studies. To overcome this limitation, we have engineered a rSARS-CoV-2 expressing both fluorescent (mCherry) and luciferase (Nluc) genes and demonstrated its feasibility to study the biology of SARS-CoV-2 in vitro and/or in vivo, including the identification and characterization of neutralizing antibodies and/or antivirals. Using rodent models, we visualize SARS-CoV-2 infection and transmission through in vivo imaging systems (IVIS).", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Kevin Chiem", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jun-Gyu Park", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Desarey Morales Vasquez", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Richard K. Plemper", + "author_inst": "Georgia State University" + }, + { + "author_name": "Jordi B Torrelles", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "James Kobie", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Mark R Walter", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Chengjin Ye", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.06.23.497404", "rel_title": "The Functional Landscape of SARS-CoV-2 3CL Protease", @@ -246131,65 +247829,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.06.24.497526", - "rel_title": "In Vitro Evaluation and Mitigation of Niclosamide Liabilities as a COVID-19 Treatment.", - "rel_date": "2022-06-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.24.497526", - "rel_abs": "Niclosamide, an FDA-approved oral anthelmintic drug, has broad biological activity including anticancer, antibacterial, and antiviral properties. Niclosamide has also been identified as a potent inhibitor of SARS-CoV-2 infection in vitro, generating interest in its use for the treatment or prevention of COVID-19. Unfortunately, there are several potential issues with using niclosamide for COVID-19, including low bioavailability, significant polypharmacology, high cellular toxicity, and unknown efficacy against emerging SARS-CoV-2 variants of concern. In this study, we used high-content imaging-based immunofluorescence assays in two different cell models to assess these limitations and evaluate the potential for using niclosamide as a COVID-19 antiviral. We show that despite promising preliminary reports, the antiviral efficacy of niclosamide overlaps with its cytotoxicity giving it a poor in vitro selectivity index for anti-SARS-CoV-2 inhibition. We also show that niclosamide has significantly variable potency against the different SARS-CoV-2 variants of concern and is most potent against variants with enhanced cell-to-cell spread including B.1.1.7. Finally, we report the activity of 33 niclosamide analogs, several of which have reduced cytotoxicity and increased potency relative to niclosamide. A preliminary structure-activity relationship analysis reveals dependence on a protonophore for antiviral efficacy, which implicates nonspecific endolysosomal neutralization as a dominant mechanism of action. Further single-cell morphological profiling suggests niclosamide also inhibits viral entry and cell-to-cell spread by syncytia. Altogether, our results suggest that niclosamide is not an ideal candidate for the treatment of COVID-19, but that there is potential for developing improved analogs with higher clinical translational potential in the future.\n\nImportanceThere is still an urgent need for effective anti-SARS-CoV-2 therapeutics due to waning vaccine efficacy, the emergence of variants of concern, and limited efficacy of existing antivirals. One potential therapeutic option is niclosamide, an FDA approved anthelmintic compound that has shown promising anti-SARS-CoV-2 activity in cell-based assays. Unfortunately, there are significant barriers for the clinical utility of niclosamide as a COVID-19 therapeutic. Our work emphasizes these limitations by showing that niclosamide has high cytotoxicity at antiviral concentrations, variable potency against variants of concern, and significant polypharmacology as a result of its activity as a nonspecific protonophore. Some of these clinical limitations can be mitigated, however, through structural modifications to the niclosamide scaffold, which we demonstrate through a preliminary structure activity relationship analysis. Overall, we show that niclosamide is not a suitable candidate for the treatment of COVID-19, but that structural analogs with improved drug properties may have higher clinical-translational potential.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Jesse W. Wotring", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Sean M. McCarty", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Khadija Shafiq", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Charles J. Zhang", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Theophilus Nguyen", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Sophia R. Meyer", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Reid Fursmidt", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Carmen Mirabelli", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Martin C. Clasby", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Christiane E Wobus", - "author_inst": "University of Michigan" - }, - { - "author_name": "Jonathan Z Sexton", - "author_inst": "University of Michigan" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.06.24.496409", "rel_title": "A cell-based, spike protein binding assay highlights differences in antibody neutralising capacity for SARS-CoV-2 variants", @@ -247756,6 +249395,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.21.22276724", + "rel_title": "COVID-19 rebound after Paxlovid and Molnupiravir during January-June 2022", + "rel_date": "2022-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.21.22276724", + "rel_abs": "ImportanceRecent case reports document that some patients who were treated with Paxlovid experienced rebound COVID-19 infections and symptoms 2 to 8 days after completing a 5-day course of Paxlovid. The Centers for Disease Control and Prevention (CDC) has recently issued a Health Alert Network Health Advisory to update the public on the potential for COVID-19 rebound after Paxlovid treatments. However, the rates of COVID-19 rebound in a real-world population or whether rebound is unique to Paxlovid remains unknown.\n\nObjectivesTo examine the rates and relative risks of COVID-19 rebound in patients treated with Paxlovid or with Molnupiravir and to compare characteristics of patients who experienced COVID-19 rebound to those who did not.\n\nDesign, Setting, and ParticipantsRetrospective cohort study of electronic health records (EHRs) of 92 million patients from a multicenter and nationwide database in the US. The study population comprised 13,644 patients age [≥] 18 years who contracted COVID-19 between 1/1/2022-6/8/2022 and were treated with Paxlovid (n =11,270) or with Molnupiravir (n =2,374) within 5 days of their COVID-19 infection.\n\nExposuresPaxlovid or Molnupiravir.\n\nMain Outcomes and MeasuresThree types of COVID-19 rebound outcomes (COVID-19 infections, COVID-19 related symptoms, and hospitalizations) were examined. Hazard ratios and 95% confidence interval (CI) of 7-day and 30-day risk for COVID-19 rebound between patients treated with Paxlovid and patients treated with Molnupiravir were calculated before and after propensity-score matching.\n\nResultsThe 7-day and 30-day COVID-19 rebound rates after Paxlovid treatment were 3.53% and 5.40% for COVID-19 infection, 2.31% and 5.87% for COVID-19 symptoms, and 0.44% and 0.77% for hospitalizations. The 7-day and 30-day COVID-19 rebound rates after Molnupiravir treatment were 5.86% and 8.59% for COVID-19 infection, 3.75% and 8.21% for COVID-19 symptoms, and 0.84% and 1.39% for hospitalizations. After propensity-score matching, there were no significant differences in COVID-19 rebound risks between Paxlovid and Molnupiravir: infection (HR 0.90, 95% CI: 0.73-1.11), COVID-19 symptoms (HR: 1.03, 95% CI: 0.83-1.27), or hospitalizations (HR: 0.92, 95% CI: 0.56-1.55). Patients with COVID-19 rebound had significantly higher prevalence of underlying medical conditions than those without.\n\nConclusions and RelevanceCOVID-19 rebound occurred both after Paxlovid and Molnupiravir, especially in patients with underlying medical conditions. This indicates that COVID-19 rebound is not unique to Paxlovid and the risks were similar for Paxlovid and Molnupiravir. For both drugs the rates of COVID-19 rebound increased with time after treatments. Our results call for continuous surveillance of COVID-19 rebound after Paxlovid and Molnupiravir treatments. Studies are necessary to determine the mechanisms underlying COVID-19 rebounds and to test dosing and duration regimes that might prevent such rebounds in vulnerable patients.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lindsey Wang", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Nathan A Berger", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Pamela B Davis", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "David C Kaelber", + "author_inst": "MetroHealth" + }, + { + "author_name": "Nora Volkow", + "author_inst": "NIH/NIDA" + }, + { + "author_name": "Rong Xu", + "author_inst": "Case Western Reserve University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.21.22276660", "rel_title": "Evidence of recent Epstein-Barr virus reactivation in individuals experiencing Long COVID", @@ -247997,57 +249675,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.21.22276717", - "rel_title": "VirPool: Model-Based Estimation of SARS-CoV-2 Variant Proportions in Wastewater Samples", - "rel_date": "2022-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.21.22276717", - "rel_abs": "BackgroundThe genomes of SARS-CoV-2 are classified into variants, some of which are monitored as variants of concern (e.g. the delta variant B.1.617.2 or omicron variant B.1.1.529). Proportions of these variants in a population are typically estimated by large-scale sequencing of individual patient samples. Sequencing a mixture of SARS-CoV-2 RNA molecules from wastewater provides a cost-effective alternative, but requires methods for estimating variant proportions in a mixed sample.\n\nResultsWe propose a new method based on a probabilistic model of sequencing reads, capturing sequence diversity present within individual variants, as well as sequencing errors. The algorithm is implemented in an open source Python program called VirPool. We evaluated the accuracy of VirPool on several simulated and real sequencing data sets from both Illumina and nanopore sequencing platforms, including wastewater samples from Austria and France monitoring the onset of alpha and delta variants.\n\nConclusionsVirPool is a versatile tool for wastewater and other mixed-sample analysis that can handle both short- and long-read sequencing data. Our approach does not require pre-selection of characteristic mutations for variant profiles, it is able to use the entire length of reads instead of just the most informative positions, and can also capture haplotype dependencies within a single read.\n\nAvailabilityVirPool is an open source software available at https://github.com/fmfi-compbio/virpool.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Askar Gafurov", - "author_inst": "Comenius University in Bratislava" - }, - { - "author_name": "Andrej Balaz", - "author_inst": "Comenius University in Bratislava" - }, - { - "author_name": "Fabian Amman", - "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria" - }, - { - "author_name": "Kristina Borsova", - "author_inst": "Biomedical Research Center, Slovak Academy of Sciences" - }, - { - "author_name": "Viktoria Cabanova", - "author_inst": "Biomedical Research Center, Slovak Academy of Sciences" - }, - { - "author_name": "Boris Klempa", - "author_inst": "Biomedical Research Center, Slovak Academy of Sciences" - }, - { - "author_name": "Andreas Bergthaler", - "author_inst": "Medical University of Vienna" - }, - { - "author_name": "Tomas Vinar", - "author_inst": "Comenius University in Bratislava" - }, - { - "author_name": "Brona Brejova", - "author_inst": "Comenius University in Bratislava" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.20.22276645", "rel_title": "Leveraging serology testing to identify children at risk for post-acute sequelae of SARS-CoV-2 infection: An EHR-based cohort study from the RECOVER program", @@ -249706,6 +251333,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.06.20.22276596", + "rel_title": "Kinetics of neutralising antibodies against Omicron variant in Vietnamese healthcare workers after primary immunisation with ChAdOx1-S and booster with BNT162b2", + "rel_date": "2022-06-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.20.22276596", + "rel_abs": "We studied the development and persistence of neutralising antibodies against SARS-CoV-2 ancestral strain, and Delta and Omicron (BA.1 and BA.2) variants in Vietnamese healthcare workers (HCWs) up to 15 weeks after booster vaccination. We included 47 HCWs with different pre-existing immune statuses (group 1 (G1): n=21, and group 2 (G2): n=26 without and with prior breakthrough Delta variant infection, respectively). The study participants had completed primary immunisation with ChAdOx1-S and booster vaccination with BNT162b2. Neutralising antibodies were measured using a surrogate virus neutralisation assay. Of the 21 study participants in G1, neutralising antibodies against ancestral strain, Delta variant, BA.1 and BA.2 were (almost) abolished at month 8 after the second dose, but all had detectable neutralising antibodies to the study viruses at week two post booster dose. Of the 26 study participants in G2, neutralising antibody levels to BA.1 and BA.2 were significantly higher than those to the corresponding viruses measured at week 2 post breakthrough infection and before the booster dose. At week 15 post booster vaccination, neutralising antibodies to BA.1 and BA.2 dropped significantly, with more profound changes observed in those without breakthrough Delta variant infection. Booster vaccination enhanced neutralising activities against ancestral strain and Delta variant, as compared to those induced by primary vaccination. These responses were maintained at high levels for at least 15 weeks. Our findings emphasise the importance of the first booster dose in producing cross-neutralising antibodies against Omicron variant. A second booster dose might be needed to maintain long-term protection against Omicron variant.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Nguyen Van Vinh Chau", + "author_inst": "Department of Health, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Lam Anh Nguyet", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen Thanh Dung", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Vo Minh Quang", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen Thanh Truong", + "author_inst": "Tan Phu Hospital, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Le Mau Toan", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Le Manh Hung", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Dinh Nguyen Huy Man", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Dao Bach Khoa", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen Thanh Phong", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nghiem My Ngoc", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Huynh Phuong Thao", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Dinh Thi Bich Ty", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Pham Ba Thanh", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen Thi Han Ny", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Le Kim Thanh", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Cao Thu Thuy", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen To Anh", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen Thi Thu Hong", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Le Nguyen Truc Nhu", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Lam Minh Yen", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Guy Thwaites", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Tran Tan Thanh", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Le Van Tan", + "author_inst": "OUCRU-VN" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.14.22276397", "rel_title": "Association between Bisphosphonate use and COVID-19 related outcomes: a retrospective cohort study", @@ -249947,65 +251685,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.06.20.22276647", - "rel_title": "Natural and hybrid immunity following four COVID-19 waves in a South African cohort", - "rel_date": "2022-06-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.20.22276647", - "rel_abs": "BackgroundMore than half the global population has been exposed to SARS-CoV-2. Naturally induced immunity influences the outcome of subsequent exposure to variants and vaccine responses. We measured anti-spike IgG responses to explore the basis for this enhanced immunity.\n\nMethodsA prospective cohort study in a South African community through the ancestral/beta/delta/omicron SARS-CoV-2 waves. Health seeking behaviour/illness were recorded and post-wave serum samples probed for IgG to Spike (CoV2-S-IgG). To estimate protective CoV2-S-IgG threshold levels, logistic functions were fit to describe the correlation of CoV2-S-IgG measured before a wave and the probability for seroconversion/boosting thereafter for unvaccinated and vaccinated adults.\n\nFindingsDespite little disease, 176/339 (51{middle dot}9%) participants were seropositive following wave 1, rising to 74%, 89{middle dot}8% and 97{middle dot}3% after waves 2, 3 and 4 respectively. CoV2-S-IgG induced by natural exposure protected against subsequent SARS-CoV-2 infection with the greatest protection for beta and the least for omicron. Vaccination induced higher CoV2-S-IgG in seropositive compared to naive vaccinees. Amongst seropositive participants, proportions above the 50% protection against infection threshold were 69% (95% CrI: 62, 72) following 1 vaccine dose, 63% (95% CrI: 63, 75) following 2 doses and only 11% (95% CrI: 7, 14) in unvaccinated during the omicron wave.\n\nInterpretationNaturally induced CoV2-S-IgG do not achieve high enough levels to prevent omicron infection in most exposed individuals but are substantially boosted by vaccination leading to significant protection. A single vaccination in those with prior immunity is more immunogenic than 2 doses in a naive vaccinee and thus may provide adequate protection.\n\nFundingUK NIH GECO award (GEC111), Wellcome Trust Centre for Infectious Disease Research in Africa (CIDRI), Bill & Melinda Gates Foundation, USA (OPP1017641, OPP1017579) and NIH H3 Africa (U54HG009824, U01AI110466]. HZ is supported by the SA-MRC. MPN is supported by an Australian National Health and Medical Research Council Investigator Grant (APP1174455). BJQ is supported by a grant from the Bill and Melinda Gates Foundation (OPP1139859). Stefan Flasche is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (Grant number 208812/Z/17/Z).\n\nResearch in context\n\nEvidence before this studyNatural infection with ancestral SARS-CoV-2 virus provides partial protection against re-infection with the same and closely related SARS-CoV-2 variants, but higher rates of re-infection have been described with Omicron. In addition, vaccination against SARS-CoV2 provides relatively lower protection against symptomatic Omicron infection than for other variants. Hybrid immunity, a combination of immunity induced by natural infection and vaccination is of critical interest due to the high incidence of natural infection in many populations and increased availability of vaccination. Vaccination following infection may provide more robust immunity than either infection or vaccination alone, but there are limited data on the impact of hybrid immunity for protection against different variants or on the optimal vaccination strategy following natural infection.\n\nAdded value of this studyWe leveraged a unique South African birth cohort in a poor peri-urban area, to longitudinally investigate infection, illness and serological responses to natural exposure to SARS-CoV-2 over 4 waves of the pandemic in healthy mothers. We also investigated the impact of prior natural exposure on BNT162b2 mRNA vaccine responses. We used this information to derive estimates of levels of spike-specific IgG associated with protection for subsequent infection following natural or hybrid immunity. Despite little disease, most participants were seropositive with rates rising from 52% to 74%, 90% and 97% after waves 1, 2, 3 and 4 respectively. Antibodies to spike protein induced by natural exposure protected against subsequent infection with the greatest protection for beta and the least for omicron. Antibody levels following vaccination were significantly higher in those who were seropositive prior to vaccine, compared to those seronegative. Amongst seropositive participants, proportions above the 50% protection against infection threshold were 69% following 1 vaccine dose, 63% following 2 doses and only 11% in unvaccinated during the omicron wave. In those seropositive prior to vaccination no significant increase in antibody levels occurred after the 2nd dose of vaccine, unlike the increase in seronegative participants. A single dose of vaccine in seropositive individuals induced higher antibody concentrations than two doses in seronegative recipients.\n\nImplications of all the available evidenceNaturally induced spike antibodies do not achieve high enough levels to prevent omicron infection in most exposed individuals but are substantially boosted by vaccination leading to significant protection. A single vaccination in those with prior natural immunity is more immunogenic than 2 doses in seronegative people and may provide adequate protection against omicron and other variants. Vaccination programs in populations with high seroprevalence using a single vaccination as a primary strategy should be considered.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Heather J Zar", - "author_inst": "Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and SA-MRC Unit on Child & Adolescent Health, University of Cape Town, Ca" - }, - { - "author_name": "Rae MacGinty", - "author_inst": "Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, " - }, - { - "author_name": "Lesley Workman", - "author_inst": "Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, " - }, - { - "author_name": "Maresa Botha", - "author_inst": "Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, " - }, - { - "author_name": "Marina Johnson", - "author_inst": "Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London & Great Ormond Street Children's Hospital NHS Foundation Tru" - }, - { - "author_name": "Adam Hunt", - "author_inst": "Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London & Great Ormond Street Children's Hospital NHS Foundation Tru" - }, - { - "author_name": "Tiffany Burd", - "author_inst": "Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital and SA-MRC Unit on Child and Adolescent Health, University of Cape Town, " - }, - { - "author_name": "Mark P Nicol", - "author_inst": "Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia; Division of Medical Microbiology and Insti" - }, - { - "author_name": "Stefan Flasche", - "author_inst": "Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia" - }, - { - "author_name": "Billy J Quilty", - "author_inst": "Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia" - }, - { - "author_name": "David Goldblatt", - "author_inst": "Great Ormond Street Institute of Child Health Biomedical Research Centre, University College London & Great Ormond Street Children's Hospital NHS Foundation Tru" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.20.22276652", "rel_title": "A Bayesian hierarchical approach to account for reporting uncertainty, variants of concern and vaccination coverage when estimating the effects of non-pharmaceutical interventions on the spread of infectious diseases", @@ -251648,6 +253327,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.16.22276392", + "rel_title": "COVID-19 redux: clinical, virologic, and immunologic evaluation of clinical rebound after nirmatrelvir/ritonavir", + "rel_date": "2022-06-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.16.22276392", + "rel_abs": "Clinical rebound of COVID-19 after nirmatrelvir/ritonavir treatment has been reported. We performed clinical, virologic, and immune measurements in seven patients with symptomatic rebound, six after nirmatrelvir/ritonavir treatment and one without previous treatment. There was no evidence of severe disease or impaired antibody and T-cell responses in people with rebound symptoms.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Brian P Epling", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Joseph M Rocco", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Kristin L Boswell", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Elizabeth Laidlaw", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Frances Galindo", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Anela Kellogg", + "author_inst": "Leidos Biomedical Research" + }, + { + "author_name": "Sanchita Das", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Allison Roder", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Elodie Ghedin", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Allie Kreitman", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Robin L Dewar", + "author_inst": "Frederick National Laboratory" + }, + { + "author_name": "Sophie E. M. Kelly", + "author_inst": "National Institute of Biomedical Imaging and Bioengineering" + }, + { + "author_name": "Heather Kalish", + "author_inst": "National Institute of Biomedical Imaging and Bioengineering" + }, + { + "author_name": "Tauseef Rehman", + "author_inst": "Frederick National Laboratory" + }, + { + "author_name": "Jeroen Highbarger", + "author_inst": "Frederick National Laboratory" + }, + { + "author_name": "Adam Rupert", + "author_inst": "Frederick National Laboratory" + }, + { + "author_name": "Gregory Kocher", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Michael R Holbrook", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Andrea Lisco", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Maura Manion", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Richard A Koup", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Irini Sereti", + "author_inst": "National Institute of Allergy and Infectious Diseases" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.17.22276478", "rel_title": "The prevalence, incidence and longevity of antibodies against SARS-CoV-2 among primary healthcare providers in Belgium: a prospective cohort study with 12 months of follow-up", @@ -251845,53 +253627,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.06.17.496544", - "rel_title": "COVFlow: virus phylodynamics analyses from selected SARS-CoV-2 sequences", - "rel_date": "2022-06-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.17.496544", - "rel_abs": "Phylodynamic analyses can generate important and timely data to optimise public health response to SARS-CoV-2 outbreaks and epidemics. However, their implementation is hampered by the massive amount of sequence data and the difficulty to parameterise dedicated software packages. We introduce the COVFlow pipeline, accessible at https://gitlab.in2p3.fr/ete/CoV-flow, which allows a user to select sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) database according to user-specified criteria, to perform basic phylogenetic analyses, and to produce an XML file to be run in the Beast2 software package. We illustrate the potential of this tool by studying two sets of sequences from the Delta variant in two French regions. This pipeline can facilitate the use of virus sequence data at the local level, for instance, to track the dynamics of a particular lineage or variant in a region of interest.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Gonche Danesh", - "author_inst": "MIVEGEC, CNRS, IRD, Universite de Montpellier" - }, - { - "author_name": "Corentin Boennec", - "author_inst": "MIVEGEC, CNRS, IRD, Universite de Montpellier" - }, - { - "author_name": "Laura Verdurme", - "author_inst": "Laboratoire CERBA, France" - }, - { - "author_name": "Mathilde Roussel", - "author_inst": "Laboratoire CERBA, France" - }, - { - "author_name": "Sabine Trombert", - "author_inst": "Laboratoire CERBA, France" - }, - { - "author_name": "Benoit Visseaux", - "author_inst": "Laboratoire CERBA, France" - }, - { - "author_name": "Stephanie Haim-Boukobza", - "author_inst": "Laboratoire CERBA, France" - }, - { - "author_name": "Samuel Alizon", - "author_inst": "MIVEGEC, CNRS, IRD, Universite de Montpellier" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.06.15.22276423", "rel_title": "How acceptable is rapid whole genome sequencing for infectious disease management in hospitals? Perspectives of those involved in managing nosocomial SARS-CoV-2", @@ -253478,6 +255213,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2022.06.13.22276339", + "rel_title": "Effects of hydrometeorological and other factors on SARS-CoV-2 reproduction number in three contiguous countries of Tropical Andean South America: a spatiotemporally disaggregated time series analysis.", + "rel_date": "2022-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.13.22276339", + "rel_abs": "BackgroundThe COVID-19 pandemic has caused societal disruption globally and South America has been hit harder than other lower-income regions. This study modeled effects of 6 weather variables on district-level SARS-CoV-2 reproduction numbers (Rt) in three contiguous countries of Tropical Andean South America (Colombia, Ecuador, and Peru), adjusting for environmental, policy, healthcare infrastructural and other factors.\n\nMethodsDaily time-series data on SARS-CoV-2 infections were sourced from health authorities of the three countries at the smallest available administrative level. Rt values were calculated and merged by date and unit ID with variables from a Unified COVID-19 dataset and other publicly available sources for May - December 2020. Generalized additive mixed effects models were fitted.\n\nFindingsRelative humidity and solar radiation were inversely associated with SARS-CoV-2 Rt. Days with radiation above 1,000 KJ/m2 saw a 1.3%, and those with humidity above 50%, a 1.0% reduction in Rt. Transmission was highest in densely populated districts, and lowest in districts with poor healthcare access and on days with least population mobility. Temperature, region, aggregate government policy response and population age structure had little impact. The fully adjusted model explained 3.9% of Rt variance.\n\nInterpretationDry atmospheric conditions of low humidity increase, and higher solar radiation decrease district-level SARS-CoV-2 reproduction numbers, effects that are comparable in magnitude to population factors like lockdown compliance. Weather monitoring could be incorporated into disease surveillance and early warning systems in conjunction with more established risk indicators and surveillance measures.\n\nFundingNASAs Group on Earth Observations Work Programme (16-GEO16-0047).", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Josh M Colston", + "author_inst": "University of Virginia School of Medicine" + }, + { + "author_name": "Patrick Hinson", + "author_inst": "University of Virginia" + }, + { + "author_name": "Nhat-Lan H Nguyen", + "author_inst": "University of Virginia" + }, + { + "author_name": "Yen Ting Chen", + "author_inst": "Chi-Mei Medical Center" + }, + { + "author_name": "Hamada S. Badr", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Gaige H Kerr", + "author_inst": "George Washington University" + }, + { + "author_name": "Lauren Marie Gardner", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "David N Martin", + "author_inst": "University of Virginia School of Medicine" + }, + { + "author_name": "Antonio M Quispe", + "author_inst": "Universidad Continental" + }, + { + "author_name": "Francesca Schiaffino", + "author_inst": "Universidad Peruana Cayetano Heredia" + }, + { + "author_name": "Margaret N Kosek", + "author_inst": "University of Virginia" + }, + { + "author_name": "Benjamin F Zaitchik", + "author_inst": "Johns Hopkins University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.06.15.22276436", "rel_title": "Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron", @@ -253619,141 +255417,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2022.06.14.22276391", - "rel_title": "Factors associated with COVID-19 vaccine uptake in people with kidney disease: an OpenSAFELY cohort study", - "rel_date": "2022-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.14.22276391", - "rel_abs": "BackgroundKidney disease is a significant risk factor for COVID-19-related mortality. Achieving high COVID-19 vaccine coverage among people with kidney disease is therefore a public health priority.\n\nMethodsWith the approval of NHS England, we performed a retrospective cohort study using the OpenSAFELY-TPP platform. Individual-level routine clinical data from 24 million people in England were included. A cohort of individuals with stage 3-5 chronic kidney disease (CKD) or receiving renal replacement therapy (RRT) at the start of the COVID-19 vaccine roll-out was identified based on evidence of reduced estimated glomerular filtration rate or inclusion in the UK Renal Registry. Individual-level factors associated with vaccine uptake were explored via Cox proportional hazards models.\n\nResults948,845 people with stage 3-5 CKD or receiving RRT were included. Cumulative vaccine coverage as of 11th May 2022 was 97.5%, 97.0%, and 93.5% for doses 1, 2, and 3, respectively, and 61.1% among individuals with one or more indications for receipt of a fourth dose. Delayed 3-dose vaccine uptake was associated with non-White ethnicity, social deprivation, and severe mental illness - associations that were consistent across CKD stages and in RRT recipients. Similar associations were observed for 4-dose uptake, which was also delayed among care home residents.\n\nConclusionAlthough high primary and booster dose coverage has been achieved among people with kidney disease in England, key disparities in vaccine uptake remain across demographic groups. Identifying how to address these disparities remains a priority to reduce the risk of severe disease in this vulnerable patient group.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "- The OpenSAFELY Collaborative", - "author_inst": "-" - }, - { - "author_name": "Edward PK Parker", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK" - }, - { - "author_name": "John Tazare", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK" - }, - { - "author_name": "William J Hulme", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK" - }, - { - "author_name": "Christopher Bates", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK" - }, - { - "author_name": "Rupert Beale", - "author_inst": "The Francis Crick Institute, London, NW1 1AT, UK; UCL Department of Renal Medicine, Royal Free Hospital, London, UK" - }, - { - "author_name": "Edward J Carr", - "author_inst": "The Francis Crick Institute, London, NW1 1AT, UK" - }, - { - "author_name": "Jonathan Cockburn", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK" - }, - { - "author_name": "Helen J Curtis", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK" - }, - { - "author_name": "Louis Fisher", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK" - }, - { - "author_name": "Amelia CA Green", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK" - }, - { - "author_name": "Sam Harper", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK" - }, - { - "author_name": "Frank Hester", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK" - }, - { - "author_name": "Elsie MF Horne", - "author_inst": "Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK; NIHR Bristol Biomedical Research Centre, Bristol, UK" - }, - { - "author_name": "Fiona Loud", - "author_inst": "Kidney Care UK, Alton, UK" - }, - { - "author_name": "Susan Lyon", - "author_inst": "Patient Council, UK Kidney Association, Bristol, UK" - }, - { - "author_name": "Viyaasan Mahalingasivam", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK" - }, - { - "author_name": "Linda Nab", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK" - }, - { - "author_name": "John Parry", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX, UK" - }, - { - "author_name": "Shalini Santhakumaran", - "author_inst": "UK Renal Registry, Bristol, UK" - }, - { - "author_name": "Retha Steenkamp", - "author_inst": "UK Renal Registry, Bristol, UK" - }, - { - "author_name": "Jonathan AC Sterne", - "author_inst": "Population Health Sciences, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK; NIHR Bristol Biomedical Research Centre, Bristol, UK; H" - }, - { - "author_name": "Alex J Walker", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK" - }, - { - "author_name": "Elizabeth J Williamson", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK" - }, - { - "author_name": "Michelle Willicombe", - "author_inst": "Centre for Inflammatory Disease, Department of Immunology and Inflammation, Imperial College London, Hammersmith Campus, Du Cane Road London, W12 0NN, UK" - }, - { - "author_name": "Bang Zheng", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX2 6GG, UK" - }, - { - "author_name": "Dorothea Nitsch", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; UK Renal Registry, Bristol, UK" - }, - { - "author_name": "Laurie A Tomlinson", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.15.22276439", "rel_title": "Prevalence and severity of symptoms 3 months after infection with SARS-CoV-2 compared to test-negative and population controls in the Netherlands", @@ -255672,6 +257335,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.09.22276030", + "rel_title": "Immunogenicity and safety of coadministration of COVID-19 and influenza vaccination among healthcare workers", + "rel_date": "2022-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.09.22276030", + "rel_abs": "BackgroundA third dose of COVID-19 vaccination ( COVID booster vaccination) has become established as an important measure to strengthen the immune response against SARS-CoV-2. In contrast, seasonal influenza vaccination has been an important infection prevention measure for years, especially among highly exposed healthcare workers (HCWs). Coadministration of vaccines against COVID-19 and seasonal influenza could be an efficient strategy to protect HCWs from two major viral respiratory infections. Yet, the immunogenicity and safety of coadministration remains to be evaluated.\n\nMethodsThis study examines the differences in Anti-SARS-CoV-2-Spike IgG antibody formation as well as side effects based on a digital questionnaire after a third COVID-19 vaccination with or without coadministration of a seasonal quadrivalent influenza vaccine (Influvac Tetra vaccine 2021/2022). 1,231 HCWs were recruited who received a mRNA-based booster COVID-19 vaccination (mRNA-1273 or BNT162b2mRNA) after basic immunisation with BNT162b2mRNA twice. Anti-SARS-CoV-2-Spike IgG levels were determined at least 14 days after vaccination by SERION ELISA agile SARS-CoV-2 IgG.\n\nFindingsAnti-SARS-CoV-2-Spike IgG concentrations were by 25{middle dot}4% lower in individuals with coadministration of the seasonal quadrivalent influenza vaccination than without (p<0{middle dot}01). There was no statistically significant difference in the reported side effects. The concentration of Anti-SARS-CoV-2-Spike IgG was higher in HCWs who had received the influenza vaccine concomitantly with mRNA-1273 than with BNT162b2mRNA as third COVID-19 vaccine (p<0{middle dot}0001).\n\nInterpretationCoadministration of the seasonal quadrivalent influenza vaccine significantly limits the levels in Anti-SARS-CoV-2-Spike IgG levels, with a more restricted elevation in case of a BNT162b2mRNA booster vaccination compared with mRNA-1273 vaccine. The reduced humoral immune response in case of coadministration needs to be considered in seasonal vaccination recommendations, although the consequences of lower Anti-SARS-CoV-2-Spike IgG levels for the protection against SARS-CoV-2 infection and severe COVID-19 disease course are currently unknown. An augmented mRNA-based COVID-19 vaccine dosage may compensate for the restricted immunogenicity in case of coadministration.\n\nFundingThis study was funded by the Federal Ministry for Education and Science (BMBF) through a grant provided to the University Hospital of Wuerzburg by the Network University Medicine on COVID-19 (B-FAST, grant-No 01KX2021) as well as by the Free State of Bavaria with COVID-research funds provided to the University of Wuerzburg, Germany. Nils Petri is supported by the German Research Foundation (DFG) funded scholarship UNION CVD.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSFor evaluation of the previously published evidence, PubMed and medRxiv were searched for the terms \"influenza vaccination\", \"influenza vaccine\", \"influenza\", \"flu\", \"seasonality\", combined with \"coadministration\", \"concomitant\", \"COVID-19 vaccination\", \"COVID-19 vaccine\", \"SARS-CoV-2\", in title or abstract, published between 1st of January 2020 and 18th of May 2022.\n\nTo date, it is unclear if coadministration of COVID-19 and influenza vaccine is effective and safe, particularly in the cohort of healthcare workers (HCWs) as key public health stakeholders. For the subunit COVID-19 vaccine NVX-CoV2373, an impairment of Anti-SARS-CoV-2-Spike IgG levels has been shown in individuals coadministered with a seasonal influenza vaccine. The two previously published studies on coadministration of a mRNA-based COVID-19 and a seasonal quadrivalent influenza vaccine have reported a restriction of humoral Anti-SARS-CoV-2-Spike immune response in the coadministration group. These examinations were conducted with limited correspondence to real-life conditions and in smaller cohorts. Additionally, these former studies do not consider the important aspect of side effects as a possible direct effect of the prevention measure on the availability of public health care in combination with Anti-SARS-CoV-2-Spike IgG levels. In summary, the humoral immunogenicity and side effects of a coadministered third COVID-19 and a seasonal influenza vaccine are still unclear and the limited available data is not transferable to the general public.\n\nAdded value of this studyWe performed the first large-scale real-life evaluation of humoral immunogenicity and side effects of COVID-19 and influenza vaccine coadministration in HCWs. Anti-SARS-CoV-2-Spike IgG levels were significantly lower in the coadministered cohort compared to the not coadministered control group, stratified by third COVID-19 vaccine (BNT162b2mRNA or mRNA-1273). Anti-SARS-CoV-2-Spike IgG post-vaccine elevation was lower among BNT162b2mRNA vaccinated HCWs than in those vaccinated with mRNA-1273 as a third COVID-19 vaccination. The influence of the seasonal quadrivalent influenza vaccine is evaluated in a cohort including 1,231 HCWs in total, covering a broad age range. Coadministration did not lead to an increase in side effects, which is a central requirement for considering the option of coadministration, given the role of HCWs as key personnel in maintaining health care capacities.\n\nImplications of all the available evidenceOur data suggest, that coadministration of third mRNA-based COVID-19 and quadrivalent seasonal influenza vaccine is safe and immunogenic, although it leads to a slightly reduced Anti-SARS-CoV-2-Spike antibody formation. While the clinical impact of the observed reduction in humoral Anti-SARS-CoV-2-Spike immune response for protection against SARS-CoV-2 infection and severe COVID-19 disease is still unclear, influenza vaccination remains an important infection prevention measure, especially among highly exposed HCWs. The coadministration does not increase side effects but may improve vaccination rate. A higher-dosed mRNA-based COVID-19 vaccine may compensate for the restricted immunogenicity in case of seasonal influenza vaccine coadministration. Our results will support the development of public health recommendations for coadministration of COVID-19 and influence vaccines in anticipation of the imminent infection waves in the coming winter season.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Isabell Wagenh\u00e4user", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Julia Reusch", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Alexander Gabel", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Anna H\u00f6hn", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Thi\u00ean-Tr\u00ed L\u00e2m", + "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Giovanni Almanzar", + "author_inst": "Paediatric Rheumatology/Special Immunology, Department of Paediatrics, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Martina Prelog", + "author_inst": "Paediatric Rheumatology/Special Immunology, Department of Paediatrics, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Lukas B. Krone", + "author_inst": "Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK; University Hospital of Psychiatry and Psychotherapy, University of Bern, Bern," + }, + { + "author_name": "Anna Frey", + "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Alexandra Schubert-Unkmeir", + "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Lars D\u00f6lken", + "author_inst": "Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Stefan Frantz", + "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Oliver Kurzai", + "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg; Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knoell-I" + }, + { + "author_name": "Ulrich Vogel", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg; Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg," + }, + { + "author_name": "Nils Petri", + "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Manuel Krone", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg; Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg," + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.09.22276150", "rel_title": "Antigen test swabs are comparable to nasopharyngeal swabs for sequencing of SARS-CoV-2", @@ -255921,61 +257663,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.13.22276244", - "rel_title": "Association of Lung Fibrotic Changes and Cardiological Dysfunction with Hypertension in Long COVID-19 cohort", - "rel_date": "2022-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.13.22276244", - "rel_abs": "BackgroundLong COVID-19 symptoms appeared in many COVID-19 survivors. However, the prevalence and symptoms associated with long COVID and its comorbidities have not been established.\n\nMethodsBetween May and September 2020, we included 312 patients with post-COVID-19 from 21 primary care centers if they had any persistent symptoms for at least three months from the first onset of the disease. On the 6 months follow up, their lung function was assessed by CT and spirometry, whereas cardiac function was assessed by electrocardiogram (ECG), Holter ECG, Echocardiography, and 24-hour blood pressure monitoring. A six-minute test (6MWT) was conducted on 308 participants during the follow-up visit. All participants were given a questionnaire with items on demographic information, current complaints, comorbidities, and medications, and Chalder Fatigue Scale (CFS) questionnaire. Statistical analysis was done using R vs. 4.1.2. Two-group comparison of continuous variables was performed using a T-test for normally distributed data, and the Mann-Whitney Wilcoxon test, ANOVA, and Kruskal-Wallis tests were applied for multiple comparisons following with Tukey and Dunn tests as post-hoc methods. Hochberg p-value adjustment was used to reduce the false discovery rate during multiple comparisons. Categorical variables were analyzed with Fishers Exact test.\n\nResultsOf 312 persons investigated, there was no significant gender difference between post-COVID-19 clinical manifestations except for memory dysfunction and anxiety, more prevalent among female participants. Chalder Fatigue Score [≥]4 was predominant in female participants (243, 78%). 39 (12.5%) participants reported having type 2 diabetes mellitus, and 158 (50.64%) had hypertension.\n\nAmong the tested parameters, those positively correlated with comorbid conditions include age, BMI, D-dimers, NT-proBNP, C-reactive protein, neutrophils, fasting glucose, and HbA1c; hypertension also shows three associations that were not found in patients when examining the role of diabetes: increased hemoglobin, fibrinogen, and ferritin. 24-hour blood pressure monitoring revealed significantly higher systolic and diastolic blood pressure, left ventricular hypertrophy, and elevated NT-proBNP in participants with hypertension and subjects with type 2 diabetes. Left ventricular diastolic dysfunction is more frequently present in patients with hypertension.\n\nChest CT was conducted on 227 (72.8%) participants 5.8{+/-}0.9 months after the onset of COVID-19. The most common registered CT abnormality was chronic bronchitis (198, 87.2%), followed by fibrotic changes in (83, 36.6%) and mediastinal lymphadenopathy (23, 10.1%).\n\nImmunological test results showed that SARS-CoV19 IgG antibodies were present in 241 subjects (77.2%), and SARS-CoV19 IgM antibodies were present in 9 subjects (2.88%).\n\nConclusionsOur study provides valuable clues for long-term post-sequelae in a cohort of the Long COVID-19 subjects. We demonstrated a strong association of signs of cardiac dysfunction, lung fibrotic changes, increased hemoglobin, fibrinogen, and ferritin with hypertension but not with other comorbidities. Our results are of importance for understanding the Long Covid-19 syndrome.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ainur Tauekelova", - "author_inst": "National Research Cardiac Surgery Center" - }, - { - "author_name": "Zhanar Kalila", - "author_inst": "National Research Cardiac Surgery Center" - }, - { - "author_name": "Akerke Bakhtiyar", - "author_inst": "National Research Cardiac Surgery Center" - }, - { - "author_name": "Zarina Sautbayeva", - "author_inst": "School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan" - }, - { - "author_name": "Polina Len", - "author_inst": "School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan" - }, - { - "author_name": "Aliya Sailybayeva", - "author_inst": "National Research Cardiac Surgery Center" - }, - { - "author_name": "Sadyk Khamitov", - "author_inst": "National Research Cardiac Surgery Center" - }, - { - "author_name": "Nazira Kadroldinova", - "author_inst": "School of Medicine, Nazarbayev University, Nur-Sultan, Kazakhstan" - }, - { - "author_name": "Natasha S. Barteneva", - "author_inst": "School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan" - }, - { - "author_name": "Makhabbat Bekbossynova", - "author_inst": "National Research Cardiac Surgery Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.10.22276249", "rel_title": "Radiographic Assessment of Lung Edema (RALE) Scores are Highly Reproducible and Prognostic of Clinical Outcomes for Inpatients with COVID-19", @@ -257578,6 +259265,109 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.06.12.495779", + "rel_title": "An attenuated vaccinia vaccine encoding the SARS-CoV-2 spike protein elicits broad and durable immune responses, and protects cynomolgus macaques and human ACE2 transgenic mice from SARS-CoV-2 and its variants", + "rel_date": "2022-06-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.12.495779", + "rel_abs": "As long as the coronavirus disease 2019 (COVID-19) pandemic continues, new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with altered antigenicity will emerge. The development of vaccines that elicit robust, broad, and durable protection against SARS-CoV-2 variants is urgently needed. We have developed a vaccine (rDIs-S) consisting of the attenuated vaccinia virus DIs strain platform carrying the SARS-CoV-2 S gene. rDIs-S induced neutralizing antibody and T-lymphocyte responses in cynomolgus macaques and human angiotensin converting enzyme 2 (hACE2) transgenic mice, and showed broad protection against SARS-CoV-2 isolates ranging from the early-pandemic strain (WK-521) to the recent Omicron BA. 1 variant (TY38-839). Using a tandem mass tag (TMT) -based quantitative proteomic analysis of lung homogenates from hACE2 transgenic mice, we found that, among mice subjected to challenge infection with WK-521, vaccination with rDIs-S prevented protein expression related to the severe pathogenic effects of SARS-CoV-2 infection (tissue destruction, inflammation, coagulation, fibrosis, and angiogenesis) and restored protein expression related to immune responses (antigen presentation and cellular response to stress). Furthermore, long-term studies in mice showed that rDIs-S maintains S protein-specific antibody titers for at least 6 months after a 1st vaccination. Thus, rDIs-S appears to provide broad and durable protective immunity against SARS-CoV-2, including current and possibly future variants.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Hirohito Ishigaki", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Fumihiko Yasui", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Misako Nakayama", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Akinori Endo", + "author_inst": "Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Naoki Yamamoto", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Kenzaburo Yamaji", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Cong Thanh Nguyen", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Yoshinori Kitagawa", + "author_inst": "Division of Microbiology and Infectious Diseases, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Takahiro Sanada", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Tomoko Honda", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Tsubasa Munakata", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Masahiko Higa", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Sakiko Toyama", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Risa Kono", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Asako Takagi", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Yusuke Matsumoto", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Kaori Hayashi", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Masanori Shiohara", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Koji Ishii", + "author_inst": "Department of Quality Assurance and Radiological Protection, National Institute of Infectious Diseases" + }, + { + "author_name": "Yasushi Saeki", + "author_inst": "Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Yasushi Itoh", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Michinori Kohara", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.06.13.495912", "rel_title": "Accurate and Fast Clade Assignment via Deep Learning and Frequency Chaos Game Representation", @@ -257671,45 +259461,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.06.12.495841", - "rel_title": "Structure of SARS-CoV-2 M protein in lipid nanodiscs", - "rel_date": "2022-06-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.12.495841", - "rel_abs": "SARS-CoV-2 encodes four structural proteins incorporated into virions, spike (S), envelope (E), nucleocapsid (N), and membrane (M). M plays an essential role in viral assembly by organizing other structural proteins through physical interactions and directing them to sites of viral budding. As the most abundant protein in the viral envelope and a target of patient antibodies, M is a compelling target for vaccines and therapeutics. Still, the structure of M and molecular basis for its role in virion formation are unknown. Here, we present the cryo-EM structure of SARS-CoV-2 M in lipid nanodiscs to 3.5 [A] resolution. M forms a 50 kDa homodimer that is structurally related to the SARS-CoV-2 ORF3a viroporin, suggesting a shared ancestral origin. Structural comparisons reveal how intersubunit gaps create a small, enclosed pocket in M and large open cavity in ORF3a, consistent with a structural role and ion channel activity, respectively. M displays a strikingly electropositive cytosolic surface that may be important for interactions with N, S, and viral RNA. Molecular dynamics simulations show a high degree of structural rigidity and support a role for M homodimers in scaffolding viral assembly. Together, these results provide insight into roles for M in coronavirus assembly and structure.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kimberly A. Dolan", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Mandira Dutta", - "author_inst": "The University of Chicago" - }, - { - "author_name": "David M Kern", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Abhay Kotecha", - "author_inst": "Thermo Fisher Scientific" - }, - { - "author_name": "Gregory A Voth", - "author_inst": "University of Chicago" - }, - { - "author_name": "Stephen G Brohawn", - "author_inst": "University of California Berkeley" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.06.13.22276358", "rel_title": "Alterations in the Nasopharyngeal Microbiome Associated with SARS-CoV-2 Infection Status and Disease Severity", @@ -259156,6 +260907,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.06.07.495170", + "rel_title": "Single-cell Multi-omics Integration for Unpaired Data by a Siamese Network with Graph-based Contrastive Loss", + "rel_date": "2022-06-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.07.495170", + "rel_abs": "Single-cell omics technology is being rapidly developed to measure the epigenome, genome, and transcriptome across a range of cell types. However, integrating omics data from different modalities is still challenging. Here, we propose a variation of the Siamese neural network framework called MinNet, which is trained to integrate multi-omics data on the single-cell resolution by utilizing graph-based contrastive loss. By training the model and testing it on several benchmark datasets, we showed its accuracy and generalizability in integrating scRNA-seq with scATAC-seq, and scRNA-seq with epitopes data. Further evaluation demonstrated our models unique capacity in removing the batch effect, which is a common problem in actual practice. To show how the integration impacts downstream analysis, we established model-based smoothing and cis-regulatory element inferring method and validated it with external pcHi-C evidence. Finally, the framework was applied to a COVID-19 dataset to compensate the original work with integration-based analysis, showing its necessity in single-cell multi-omics research.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Chaozhong Liu", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Linhua Wang", + "author_inst": "Baylor College of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.06.07.495149", "rel_title": "SARS-CoV-2 spike protein induces long-term TLR4-mediated synapse and cognitive loss recapitulating Post-COVID syndrome", @@ -259413,45 +261187,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.07.22276117", - "rel_title": "Safety of the fourth COVID-19 BNT162b2 mRNA (second booster) vaccine", - "rel_date": "2022-06-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.07.22276117", - "rel_abs": "COVID-19 remains a global concern due to vaccine protection waning and the emergence of immuneevasive variants. While the effectiveness of a second booster vaccine dose (i.e., fourth inoculation) is well proven, its safety has yet to be fully understood, and vaccine compliance remains low. We conducted a prospective observational study to compare the short-term effects of the first and second BNT162b2 mRNA COVID-19 vaccine booster doses. 2,019 participants received smartwatches and filled in a daily questionnaire on systemic reactions to the vaccine. We found substantial changes from baseline levels in the 72 hours post-vaccination with the second booster in both self-reported and physiological reactions measured by the smartwatches. However, no significant difference in reactions was observed between the first and second boosters. We also found that participants who experienced more severe reactions to the first booster tended to likewise experience more severe reactions to the second booster. Our work supports the safety of the second booster from both subjective (self-reported questionnaires) and objective (physiological measurements) perspectives.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Matan Yechezkel", - "author_inst": "Tel Aviv university" - }, - { - "author_name": "Merav Mofaz", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Tal Patalon", - "author_inst": "Maccabi Healthcare Services" - }, - { - "author_name": "Sivan Gazit", - "author_inst": "Maccabi Healthcare Services" - }, - { - "author_name": "Erez Shmueli", - "author_inst": "Tel-Aviv University" - }, - { - "author_name": "Dan Yamin", - "author_inst": "Tel Aviv University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.07.22276055", "rel_title": "Development of a COVID-19 warning system for neighborhood-scale wastewater-based epidemiology in low incidence situations", @@ -261270,6 +263005,41 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.06.05.494856", + "rel_title": "A uniquely stable trimeric model of SARS-CoV-2 spike transmembrane domain", + "rel_date": "2022-06-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.05.494856", + "rel_abs": "The spike (S) protein of SARS-CoV-2 effectuates membrane fusion and virus entry into target cells. Its transmembrane domain (TMD) represents a homotrimer of -helices anchoring the spike in the viral envelope. Although S-protein models available to date include the TMD, its precise configuration was given brief consideration. Understanding viral fusion entails realistic TMD models, while no reliable approaches towards predicting the 3D structure of transmembrane (TM) trimers exist. Here, we propose a comprehensive computational framework to model the spike TMD (S-TMD) based solely on its primary structure. First, we performed amino acid sequence pattern matching and compared molecular hydrophobicity potential (MHP) distribution on the helix surface against TM homotrimers with known 3D structures and thus selected the TMD of the tumour necrosis factor receptor 1 (TNFR-1) for subsequent template-based modelling. We then iteratively built an all-atom homotrimer model of S-TMD based on \"dynamic MHP portraits\" and residue variability motifs. In this model each helix possessed two overlapping interfaces interacting with either of the remaining helices, which include conservative residues I1216, F1220, I1227, M1229, and M1233. Finally, the stability of this and several alternative models (including a recent NMR structure) and a set of mutant forms was tested in all-atom molecular dynamics (MD) simulations in a POPC bilayer mimicking the viral envelope membrane. Unlike other configurations, our model trimer remained extraordinarily tightly packed over a microsecond-range MD and retained its stability when palmitoylated in accordance with experimental data. Palmitoylation had no significant impact on the TMD conformation nor the way in which the lipid bilayer was perturbed in the presence of the trimer. Overall, the resulting model of S-TMD conforms to known basic principles of TM helix packing and will be further used to explore the complex machinery of membrane fusion from a broader perspective beyond the TMD.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Elena T. Aliper", + "author_inst": "MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia" + }, + { + "author_name": "Nikolay A. Krylov", + "author_inst": "MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia" + }, + { + "author_name": "Dmitry E. Nolde", + "author_inst": "MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia" + }, + { + "author_name": "Anton A. Polyansky", + "author_inst": "Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria" + }, + { + "author_name": "Roman G. Efremov", + "author_inst": "MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.06.05.493249", "rel_title": "Pathogen-Host Adhesion between SARS-CoV-2 S Proteins from Different Variants and Human ACE2 Probed at Single-Molecule and Single-Cell Levels", @@ -261407,53 +263177,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2022.06.02.494559", - "rel_title": "Zooanthroponotic transmission of SARS-CoV-2 and host-specific viral mutations revealed by genome-wide phylogenetic analysis", - "rel_date": "2022-06-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.02.494559", - "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a generalist virus, infecting and evolving in numerous mammals, including captive and companion animals, free-ranging wildlife, and humans. Transmission among non-human species poses a risk for the establishment of SARS-CoV-2 reservoirs, makes eradication difficult, and provides the virus with opportunities for new evolutionary trajectories, including selection of adaptive mutations and emergence of new variant lineages. Here we use publicly available viral genome sequences and phylogenetic analysis to systematically investigate transmission of SARS-CoV-2 between human and non-human species and to identify mutations associated with each species. We found the highest frequency of animal-to-human transmission from mink, compared with lower transmission from other sampled species (cat, dog, and deer). Although inferred transmission events could be limited by sampling biases, our results provide a useful baseline for further studies. Using genome-wide association studies, no single nucleotide variants (SNVs) were significantly associated with cats and dogs, potentially due to small sample sizes. However, we identified three SNVs statistically associated with mink and 26 with deer. Of these SNVs, [~][2/3] were plausibly introduced into these animal species from local human populations, while the remaining [~][1/3] were more likely derived in animal populations and are thus top candidates for experimental studies of species-specific adaptation. Together, our results highlight the importance of studying animal-associated SARS-CoV-2 mutations to assess their potential impact on human and animal health.\n\nImportanceSARS-CoV-2, the causative agent of COVID-19, can infect many animal species, making eradication difficult because it can be reseeded from different reservoirs. When viruses replicate in different species, they may be faced with different evolutionary pressures and acquire new mutations, with unknown consequences for transmission and virulence in humans. Here we analyzed SARS-CoV-2 genome sequences from cats, dogs, deer, and mink to estimate transmission between each of these species and humans. We found several transmission events from humans to each animal, but relatively few detectable transmissions from animals back to humans, with the exception of mink. We also identified three mutations more likely to be found in mink than humans, and 26 in deer. These mutations could help the virus adapt to life in these different species. Ongoing surveillance of SARS-CoV-2 from animals will be important to understand their potential impacts on both human and animal health.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sana Naderi", - "author_inst": "McGill University" - }, - { - "author_name": "Peter E Chen", - "author_inst": "University of Montreal" - }, - { - "author_name": "Carmen Lia Murall", - "author_inst": "McGill University" - }, - { - "author_name": "Raphael Poujol", - "author_inst": "Montreal Heart Institute" - }, - { - "author_name": "Susanne A Kraemer", - "author_inst": "McGill University" - }, - { - "author_name": "Bradley S Pickering", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Selena M Sagan", - "author_inst": "McGill University" - }, - { - "author_name": "B. Jesse Shapiro", - "author_inst": "McGill University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2022.06.04.22275993", "rel_title": "Modelling Lockdown Effects on Controlling the Spread of COVID-19", @@ -263040,6 +264763,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.06.03.22275964", + "rel_title": "Indian Female Migrants Face Greater Barriers to Post-Covid Recovery than Males: Evidence from a Panel Study", + "rel_date": "2022-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.03.22275964", + "rel_abs": "BackgroundIndias abrupt nationwide Covid-19 lockdown internally displaced millions of urban migrants, who made arduous journeys to distant rural homes. Documenting their labor market reintegration is a critical aspect of understanding the economic costs of the pandemic for Indias poor. In a country marked by low and declining female labor force participation, identifying gender gaps in labor market reintegration - as a marker of both womens vulnerability at times of crisis and setbacks in womens agency - is especially important. Yet most studies of pandemic-displaced Indian migrants are small, rely on highly selected convenience samples, and lack a gender focus.\n\nMethodsBeginning in April 2020 we enrolled roughly 4,600 displaced migrants who had returned to two of Indias poorest states into a panel survey, which tracked enrollees through July 2021. Survey respondents were randomly selected from the states official databases of return migrants, with sampling stratified by state and gender. 85 percent of enrollees (3,950) were working in urban areas prior to the pandemic. Our analysis focuses on a balanced panel of 1,780 workers who were interviewed three times through July 2021, considering labor market re-entry, earnings, and measures of vulnerability by gender.\n\nFindingsBoth men and women struggle to remigrate - by July 2021 (over a year after the nationwide lockdown ended), no more than 63 percent (95% CI [60,66]) of men and 55 percent [51,59] of women had left their home villages since returning. Initially, returning migrants transition from non-agricultural urban employment into agriculture and unemployment in rural areas. Alongside, incomes plummet, with both genders earning roughly 17 percent of their pre-lockdown incomes in July 2020. Remigration is critical to regaining income - male re-migrants report earnings on par with their pre-lockdown incomes by January 2021, while men remaining in rural areas earn only 23 percent [19,27] of their pre-pandemic income. Remigration benefits women to a lesser extent - female remigrants regain no more than 65 percent [57,73] of their pre-pandemic income at any point. This contrast reflects significantly higher rates of unemployment among women, both among those remaining in rural areas (9 percentage points [6,13] higher than men across waves) and among those who remigrate (13 percentage points [9,17] higher than men across waves). As a result, we observe gender gaps in well-being: female migrants were 7 percentage points [4,10] more likely to report reduced consumption of essential goods and fare 6 percentage points [4,7] worse on a food security index.\n\nInterpretationReturn migrants of both genders experienced persistent hardships for over a year after the initial pandemic lockdown. Female migrants fare worse, driven by both lower rates of remigration and lower rates of labor market re-entry both inside and outside home villages. Some women drop out of the labor force entirely, but most unemployed report seeking or being available to work. In short, pandemic-induced labor market displacement has far-reaching, long-term consequences for migrant workers, especially women.\n\nFundingSurvey costs were funded by research grants from IZA/FCDO Gender, Growth, and Labour Markets in Low Income Countries Programme, J-PAL Jobs and Opportunity Initiative, and the Evidence-based Measures of Empowerment for Research on Gender Equality (EMERGE) program at University of California San Diego. Funders had no role in study design, study implementation, data analysis, or manuscript preparation.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSMost research documenting the experience of displaced domestic migrants during the pandemic is focused on difficulties faced in returning to their home villages and the immediate consequences of this displacement. Existing evidence has found high levels of short-run economic and psychological distress, especially among women and children, and under-coverage of government programs designed to ease the lockdowns sudden economic shock.\n\nAdded value of this studyThis study contributes to existing literature by surveying a large sample of male and female workers, designed to be broadly representative of returned migrants in two of Indias poorest states. Our work takes a longer-term view, tracking study participants efforts to remigrate and reintegrate into the labor force over 15 months. We document sustained difficulties attaining pre-pandemic levels of income and consumption insecurity, especially among women, who struggle even after remigrating.\n\nImplications of all the available evidenceTaken as a whole, the evidence underscores that displaced Indian migrants are a vulnerable and underserved social group, who have faced (and will likely continue to face) lasting negative effects of the Covid-19 pandemic. Displaced migrants - and especially women - would likely benefit from programs designed to facilitate re-entry into urban labor markets; wrap around services that address other effects of the pandemic (e.g. psychological distress) may be particularly valuable.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jenna Allard", + "author_inst": "MacMillan Center, Yale University" + }, + { + "author_name": "Maulik Jagnani", + "author_inst": "University of Colorado Denver" + }, + { + "author_name": "Yusuf Neggers", + "author_inst": "University of Michigan" + }, + { + "author_name": "Rohini Pande", + "author_inst": "Economic Growth Center, Yale University" + }, + { + "author_name": "Simone Schaner", + "author_inst": "Center for Economic and Social Research, University of Southern California" + }, + { + "author_name": "Charity Troyer Moore", + "author_inst": "MacMillan Center, Yale University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.06.02.22275918", "rel_title": "Delays in COVID-19 Diagnosis and Hospitalization and Outcomes -- New York City, New York, USA, October 2020-November 2021", @@ -263237,57 +264999,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.02.494552", - "rel_title": "Age exacerbates SARS-CoV-2-induced blood-brain barrier leakage and neuropsychiatric dysfunction", - "rel_date": "2022-06-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.02.494552", - "rel_abs": "Respiratory infection with SARS-CoV-2 causes systemic vascular inflammation and cognitive impairment. We sought to identify the underlying mechanisms mediating vascular dysfunction and inflammation following mild respiratory SARS-CoV-2 infection. To this end, we conduced unbiased transcriptional analysis to identify brain endothelial cell signaling pathways dysregulated by SARS-CoV-2 in vivo. This analysis revealed significant suppression of Wnt/{beta}-catenin signaling, a critical regulator of blood brain barrier integrity. We therefore hypothesized that enhancing cerebrovascular Wnt/{beta}-catenin activity would offer protection against BBB permeability, neuroinflammation, and neurological signs in acute infection. Indeed, we found that delivery of cerebrovascular-targeted, engineered Wnt7a ligands protected blood brain barrier integrity, reduced T cell infiltration of the brain, and reduced microglial activation in SARS-CoV-2 infection. Importantly, this therapeutic strategy also mitigated SARS-CoV-2 induced deficits in the novel object recognition assay for learning and memory and the pole descent task for bradykinesia. These observations suggest that enhancement of Wnt/{beta}-catenin signaling or its downstream effectors could be potential interventional strategies for restoring cognitive health following acute viral infections.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Troy N Trevino", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Avital B Fogel", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Jacob Class", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Mark A Sanborn", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Benoit Vanhollebeke", - "author_inst": "ULB Neuroscience Institute" - }, - { - "author_name": "Jalees Rehman", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Leon M. Tai", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Justin ME Richner", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Sarah E Lutz", - "author_inst": "University of Illinois at Chicago" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2022.05.31.22275010", "rel_title": "Homologous and heterologous boosting of the ChAdOx1-S1-S COVID-19 vaccine with the SCB-2019 vaccine candidate: a randomized, observer-blinded, controlled, phase 2 study", @@ -264890,6 +266601,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.05.31.22274501", + "rel_title": "Severe acute respiratory syndrome coronavirus 2 breakthrough infections in healthcare workers vaccinees with BNT162b2 (Pfizer-BioNtech) in Bogota, Colombia", + "rel_date": "2022-06-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.31.22274501", + "rel_abs": "The healthcare workers are considered as a high-risk group for infection with SARS-CoV-2, so they were included in the first stage of the National Plan for Vaccination against COVID-19 in Colombia.\n\nAn ongoing prospective cohort study to evaluate immune response to vaccination included 490 workers from health institutions in Bogota, Colombia, vaccinated between March and June 2021 with BNT162b2 (Pfizer-BioNtech). Multiple samples were collected during a follow-up period of 6 months after immunization. We report cases of asymptomatic and symptomatic SARS-CoV-2 infections detected in this cohort. For each participant demographic data, vaccination dates, results for SARS-CoV-2 RT-PCR, and detection of antibody (IgG) tests during the follow-up period were collected.\n\nSARS-CoV-2 infection was detected in 38 (7.7 %) volunteers. Of these, 81.6% had a positive RT-PCR for SARS-CoV-2, and 18.4% were confirmed by detection of IgG anti-SARS-CoV-2 nucleoprotein; 76.3% of infections occurred after 7 days of second dose. A total of 57.9% of the cases were asymptomatic. No hospitalizations or deaths were registered. When infection occurred, 81.6% of infected participants had presence of IgG anti-S antibodies. In 12 samples in which genomic characterization was achieved, 83.4% corresponded to the variant Mu, 8.3% Gamma, and 8.3% Delta.\n\nAll findings agree with other reports in different studies that show the benefit of COVID-19 vaccines, protecting specially against severe disease but not against infection or re-infection.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Pilar Tavera-Rodriguez", + "author_inst": "Instituto Nacional de Salud Colombia" + }, + { + "author_name": "Juliana Barbosa-Ramirez", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Andrea Bermudez-Forero", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Diego Prada-Cardozo", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Jhonnatan Reales-Gonzalez", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Dioselina Pelaez-Carvajal", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Diana Malo-Sanchez", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Maria-Ximena Meneses-Gil", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Marcela Mercado-Reyes", + "author_inst": "Instituto Nacional de Salud" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.31.22275746", "rel_title": "Symptom variation, correlations, and relationship to physical activity in Long Covid: intensive longitudinal study", @@ -265023,41 +266785,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.06.01.22275872", - "rel_title": "Artificial intelligence tool for the study of COVID-19 microdroplet spread across the human diameter and airborne space", - "rel_date": "2022-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.01.22275872", - "rel_abs": "The 2019 novel coronavirus (SARS-COV2 / COVID-19), with a point of origin in Wuhan, China, has spread rapidly all over the world. It turned into a raging pandemic wrecking havoc on health care facilities, world economy and affecting everyones life to date. With every new variant, rate of transmission, spread of infections and the number of cases continues to rise at an international level and scale. There are limited reliable researches that study microdroplets spread and transmissions from human sneeze or cough in the airborne space. In this paper, we propose an intelligent technique to visualize, detect, measure the distance of the spread in a real-world settings of microdroplet transmissions in airborne space, called \"COVNET45\". In this paper, we investigate the microdroplet transmission and validate the measurements accuracy compared to published researches, by examining several microscopic and visual images taken to investigate the novel coronavirus (SARS-COV2 / COVID-19). The ultimate contribution is to calculate the spread of the microdroplets measurements precisely with graphical presentation.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Heshami H. Alsaadi", - "author_inst": "Zayed University" - }, - { - "author_name": "Monther Aldwairi", - "author_inst": "Zayed University" - }, - { - "author_name": "Faten Yasin", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Sandra C. P. Cachinho", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Abdullah Hussein", - "author_inst": "Rochester Institute of Technology - Dubai Campus" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.06.01.22275786", "rel_title": "U.S. CDC support to international SARS-CoV-2 seroprevalence surveys, May 2020-February 2022", @@ -266512,6 +268239,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.05.29.22275277", + "rel_title": "Investigation of a SARS-CoV-2 outbreak in a Texas summer camp resulting from a single introduction", + "rel_date": "2022-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.29.22275277", + "rel_abs": "SARS-CoV-2 is the etiological agent responsible for the COVID-19 pandemic. It is estimated that only 10 aerosol-borne virus particles are sufficient to establish a secondary infection with SARS-CoV-2. However, the dispersal pattern of SARS-CoV-2 is highly variable and only 10- 20% of cases are responsible for up 80% of secondary infections. The heterogeneous nature of SARS-CoV-2 transmission suggests that super-spreader events play an important role in viral transmission. Super-spreader events occur when a single person is responsible for an unusually high number of secondary infections due to a combination of biological, environmental, and/or behavioral factors. While super-spreader events have been identified as a significant factor driving SARS-CoV-2 transmission, epidemiologic studies have consistently shown that education settings do not play a major role in community transmission. However, an outbreak of SARS-CoV-2 was recently reported among 186 children (aged 10-17) and adults (aged 18 +) after attending an overnight summer camp in Texas in June 2021. To understand the transmission dynamics of the outbreak, RNA was isolated from 36 nasopharyngeal swabs collected from patients that attended the camp and 19 control patients with no known connection to the outbreak. Genome sequencing on the Oxford Nanopore platform was performed using the ARTIC approaches for library preparation and bioinformatic analysis. SARS-CoV-2 amplicons were produced from all RNA samples and >70% of the viral genome was successfully reconstructed with >10X coverage for 46 samples. Phylogenetic methods were used to estimate the transmission history and suggested that the outbreak was the result of a single introduction. We also found evidence for secondary transmission from campers to the community. Together, these findings demonstrate that super-spreader events may occur during large gatherings of children.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Daniele Michele Swetnam", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Rojelio Elias Alvarado", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Stephanea Sotcheff", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Brooke M Mitchell", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Allan McConnell", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Rafael R.G. Machado", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Nehad Saada", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Florence P Haseltine", + "author_inst": "University of Texas at Arlington" + }, + { + "author_name": "Sara Maknojia", + "author_inst": "Galveston County Health District" + }, + { + "author_name": "Anajane Smith", + "author_inst": "University of Texas at Arlington" + }, + { + "author_name": "Ping Ren", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Philip Keiser", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Scott Weaver", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Andrew L Routh", + "author_inst": "University of Texas Medical Branch" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.29.22275262", "rel_title": "Incidence of Post-Covid Syndrome and Associated Symptoms in Outpatient Care in Bavaria, Germany", @@ -266661,29 +268459,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.05.29.493871", - "rel_title": "Genome similarities between human-derived and mink-derived SARS-CoV-2 make mink a potential reservoir of the virus", - "rel_date": "2022-05-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.29.493871", - "rel_abs": "The SARS-CoV-2 has RNA as the genome, which makes the virus more prone to mutations. Occasionally, mutations help a virus to cross the species barrier. The SARS-CoV-2 infection to humans and minks (Neovison vison) are examples of zoonotic spillover. Many studies have been published on the analysis of human-derived SARS-CoV-2, here we performed mutation analysis on the minks-derived SARS-CoV-2 genome sequences. We analyzed all available full-length mink derived SARS-CoV-2 genome sequences on GISAID (214 from Netherlands and 133 from Denmark). We found that the mutation pattern in the Netherlands and Denmark derived samples were different. Out of a total of 201 mutations, we found in this study, only 13 mutations were common in the Netherlands and Denmark derived samples. We found 4 mutations prevailed in the Netherlands and Denmark mink derived samples and these 4 mutations are also reported to prevail in human-derived SARS-CoV-2.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Mohammad Khalid", - "author_inst": "College of Pharmacy" - }, - { - "author_name": "Yousef Al-ebini", - "author_inst": "King Khalid University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2022.05.26.22275649", "rel_title": "Governance is key to controlling SARS-CoV-2's vaccine resistance", @@ -268222,6 +269997,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.27.493682", + "rel_title": "Structural basis of a two-antibody cocktail exhibiting highly potent and broadly neutralizing activities against SARS-CoV-2 variants including diverse Omicron sublineages", + "rel_date": "2022-05-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.27.493682", + "rel_abs": "SARS-CoV-2 variants of concern (VOCs), especially the latest Omicron, have exhibited severe antibody evasion. Broadly neutralizing antibodies with high potency against Omicron are urgently needed for understanding working mechanisms and developing therapeutic agents. In this study, we characterized previously reported F61, which was isolated from convalescent patients infected with prototype SARS-CoV-2, as a broadly neutralizing antibody against all VOCs including Omicron BA.1, BA.1.1, BA.2, BA.3 and BA.4 sublineages by utilizing antigen binding and cell infection assays. We also identified and characterized another broadly neutralizing antibody D2 with epitope distinct from that of F61. More importantly, we showed that a combination of F61 with D2 exhibited synergy in neutralization and protecting mice from SARS-CoV-2 Delta and Omicron BA.1 variants. Cryo-EM structures of the spike-F61 and spike-D2 binary complexes revealed the distinct epitopes of F61 and D2 at atomic level and the structural basis for neutralization. Cryo-EM structure of the Omicron-spike-F61-D2 ternary complex provides further structural insights into the synergy between F61 and D2. These results collectively indicated F61 and F61-D2 cocktail as promising therapeutic antibodies for combating SARS-CoV-2 variants including diverse Omicron sublineages.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Xiaoman Li", + "author_inst": "The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Bio" + }, + { + "author_name": "Yongbing Pan", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Qiangling Yin", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Zejun Wang", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Sisi Shan", + "author_inst": "NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Ts" + }, + { + "author_name": "Laixing Zhang", + "author_inst": "The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Bio" + }, + { + "author_name": "Jinfang Yu", + "author_inst": "The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Bio" + }, + { + "author_name": "Yuanyuan Qu", + "author_inst": "Institution of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518107, China" + }, + { + "author_name": "Lina Sun", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Fang Gui", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Jia Lu", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Zhaofei Jing", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Wei Wu", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Tao Huang", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Xuanling Shi", + "author_inst": "NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Ts" + }, + { + "author_name": "Jiandong Li", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Xinguo Li", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Dexin Li", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Shiwen Wang", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Maojun Yang", + "author_inst": "The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Bio" + }, + { + "author_name": "Linqi Zhang", + "author_inst": "NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Ts" + }, + { + "author_name": "Kai Duan", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Mifang Liang", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Xiaoming Yang", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Xinquan Wang", + "author_inst": "The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Bio" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.05.27.493400", "rel_title": "The Glycan-Specificity of the Pineapple Lectin AcmJRL and its Carbohydrate-Dependent Binding of the SARS-CoV-2 Spike Protein", @@ -268375,53 +270265,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.05.26.22275639", - "rel_title": "Protection against Omicron conferred by mRNA primary vaccine series, boosters, and prior infection", - "rel_date": "2022-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.26.22275639", - "rel_abs": "BO_SCPLOWACKGROUNDC_SCPLOWPrisons and jails are high-risk settings for Covid-19 transmission, morbidity, and mortality. We evaluate protection conferred by prior infection and vaccination against the SARS-CoV-2 Omicron variant within the California state prison system.\n\nMO_SCPLOWETHODSC_SCPLOWWe employed a test-negative design to match resident and staff cases during the Omicron wave (December 24, 2021--April 14, 2022) to controls according to a cases test-week as well as demographic, clinical, and carceral characteristics. We estimated protection against infection using conditional logistic regression, with exposure status defined by vaccination, stratified by number of mRNA doses received, and prior infection, stratified by periods before or during Delta variant predominance.\n\nRO_SCPLOWESULTSC_SCPLOWWe matched 15,783 resident and 8,539 staff cases to 180,169 resident and 90,409 staff controls. Among cases, 29.7% and 2.2% were infected before or during the emergence of the Delta variant, respectively; 30.6% and 36.3% were vaccinated with two or three doses, respectively. Estimated protection from Omicron infection for two and three doses were 14.9% (95% Confidence Interval [CI], 12.3--19.7%) and 43.2% (42.2--47.4%) for those without known prior infections, 47.8% (95% CI, 46.6--52.8%) and 61.3% (95% CI, 60.7--64.8%) for those infected before the emergence of Delta, and 73.1% (95% CI, 69.8--80.1%) and 86.8% (95% CI, 82.1--92.7) for those infected during the period of Delta predominance.\n\nCO_SCPLOWONCLUSIONC_SCPLOWA third mRNA dose provided significant, additional protection over two doses, including among individuals with prior infection. Our findings suggest that vaccination should remain a priority--even in settings with high levels of transmission and prior infection.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Elizabeth T Chin", - "author_inst": "Stanford University" - }, - { - "author_name": "David Leidner", - "author_inst": "California Department of Corrections and Rehabilitation" - }, - { - "author_name": "Lauren Lamson", - "author_inst": "Stanford University" - }, - { - "author_name": "Kimberley Lucas", - "author_inst": "California Correctional Health Care Services" - }, - { - "author_name": "David M Studdert", - "author_inst": "Stanford University" - }, - { - "author_name": "Jeremy D Goldhaber-Fiebert", - "author_inst": "Stanford University" - }, - { - "author_name": "Jason R Andrews", - "author_inst": "Stanford University" - }, - { - "author_name": "Joshua A Salomon", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.26.22275279", "rel_title": "Shared within-host SARS-CoV-2 variation in households", @@ -270592,6 +272435,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.05.26.493529", + "rel_title": "The emergence of variants with increased fitness accelerates the slowdown of genome sequence heterogeneity in the SARS CoV 2 coronavirus", + "rel_date": "2022-05-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.26.493529", + "rel_abs": "Since the outbreak of the COVID-19 pandemic, the SARS-CoV-2 coronavirus has accumulated an important amount of genetic and genomic variability through mutation and recombination events. To test evolutionary trends that could inform us on the adaptive process of the virus to its human host, we summarize all this sequence variability by computing the Sequence Compositional Complexity (SCC) in more than 23,000 high-quality coronavirus genome sequences from across the globe, covering the period spanning from the start of the pandemic in December 2019 to March 2022. In early samples, we found no statistical support for any trend in SCC values over time, although the virus as a whole appears to evolve faster than Brownian Motion expectation. However, in samples taken after the first Variant of Concern (VoC) with higher transmissibility (Alpha) emerges, and controlling for phylogenetic and sampling effects, we were able to detect a statistically significant trend for decreased SCC values over time. SARS-CoV-2 evolution towards lower values of genome heterogeneity is further intensified by the emergence of successive, widespread VoCs. Concomitantly to the temporal reduction in SCC, its absolute evolutionary rate kept increasing toward the present, meaning that the SCC decrease itself accelerated over time. As compared to Alpha or Delta variants, the currently dominant VoC, Omicron, shows much stronger trends in both SCC values and rates over time. These results indicate that the increases in fitness of variant genomes associated to a higher transmissibility leads to a reduction of their genome sequence heterogeneity, thus explaining the general slowdown of SCC along with the pandemic course.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jos\u00e9 L. Oliver", + "author_inst": "Professor of Genetics, Facultad de Ciencias, Universidad de Granada, Spain" + }, + { + "author_name": "Pedro Bernaola-Galv\u00e1n", + "author_inst": "Professor of Applied Physics, E.T.S. de Ingenieria de Telecomunicacion, Universidad de Malaga, Spain" + }, + { + "author_name": "Francisco Perfectti", + "author_inst": "Professor of Genetics, Grupo de Genetica Evolutiva, Departamento de Genetica and Research Unit Modeling Nature Evoflor, Unidad Asociada al CSIC, Universidad de" + }, + { + "author_name": "Cristina G\u00f3mez-Mart\u00edn", + "author_inst": "Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, Amsterdam, Netherlands" + }, + { + "author_name": "Pasquale Raia", + "author_inst": "Dip.to DiSTAR, Napoli Universita di Napoli Federico II, Dipartimento di Scienze della Terra, dell Ambiente e delle Risorse, Italy" + }, + { + "author_name": "Miguel Verd\u00fa", + "author_inst": "Centro de Investigaciones sobre Desertificacion, Consejo Superior de Investigaciones Cientificas (CSIC), University of Valencia and Generalitat Valenciana, 4611" + }, + { + "author_name": "Andr\u00e9s Moya", + "author_inst": "Professor of Genetics, University of Valencia Chair, Institutional Professorship FISABIO - University of Valencia, Spain" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2022.05.21.22275421", "rel_title": "Analysis of the genetic diversity of SARS-CoV-2 genomes carrying the Omicron B.1.1.529 mutation", @@ -270745,61 +272631,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.22.22275422", - "rel_title": "SARS-CoV-2 NSP3, NSP4 and NSP6 mutations and Epistasis during the pandemic in the world: Evolutionary Trends and Natural Selections in Six Continents", - "rel_date": "2022-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.22.22275422", - "rel_abs": "BackgroundThe Coronavirus 2019 (COVID-19) was named by the World Health Organization (WHO) due to its rapid transmittable potential and high mortality rate. Based on the critical role of None Structural Proteins (NSP), NSP3, NSP4, and NSP6 in COVID-19, this study attempts to investigate the superior natural selection mutations and Epistasis among these none structural proteins.\n\nMethodsApproximately 6.5 million SARS-CoV-2 protein sequences of each NSP3, NSP4, and NSP6 nonstructural protein were analyzed from January 2020 to January 2022. Python programming language was utilized to preprocess and apply inclusion criteria on the FASTA file to prepare a list of suitable samples. NSP3, NSP4, and NSP6 were aligned to the reference sequence to compare and identify mutation patterns categorized based on frequency, geographical zone distribution, and date. To discover epistasis situations, linear regression between mutation frequency and date among candidate genes was performed to determine correlations.\n\nResultsThe rate of NSP3, NSP4, and NSP6 mutations in divided geographical areas was different. Based on continental studies, P1228L (54.48%), P1469S (54.41%), and A488S (53.86%) mutations in NSP3, T492I (54.84%), and V167L (52.81%) in NSP4 and T77A (69.85%) mutation in NSP6 increased over time, especially in recent months. For NSP3, Europe had the highest P1228L, P1469S, and A488S mutations. For NSP4, Oceania had the highest T492I and V167L mutations, and for NSP6, Europe had the highest T77A mutation. Hot spot regions for NSP3, NSP4, and NSP6 were 1358 to 1552 AA, 150 to 200 AA, and 58 to 87 AA, respectively. Our results showed a significant correlation and co-occurrence between NSP3, NSP4, and NSP6 mutations.\n\nConclusionWe conclude that the effect of mutations on virus stability and replication can be predicted by examining the amino acid changes of P1228L, P1469S, A488S, T492I, V167L and T77A mutations. Also, these mutations can possibly be effective on the function of proteins and their targets in the host cell.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Haniyeh Fooladinezhad", - "author_inst": "Department of genetics, Faculty of sciences Shahrekord branch Islamic Azad University, Shahrekord, Iran." - }, - { - "author_name": "Maryamsadat Shahidi", - "author_inst": "Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran." - }, - { - "author_name": "Mohammadamin Mahmanzar", - "author_inst": "Department of Bioinformatics, Kish International Campus University of Tehran, Kish, Iran" - }, - { - "author_name": "Bahar Mahdavi", - "author_inst": "Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran" - }, - { - "author_name": "Samaneh Tokhanbigli", - "author_inst": "Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Ira" - }, - { - "author_name": "Mahsa Mollapour Sisakht", - "author_inst": "ErasmusMC" - }, - { - "author_name": "Bahman Moradi", - "author_inst": "Department of biology,faculty of sciences, Shahid Bahonar University of Kerman, Iran" - }, - { - "author_name": "Mohamad Reza Ganjalikhany", - "author_inst": "Department of Cell and Molecular Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran" - }, - { - "author_name": "Karim Rahimian", - "author_inst": "Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran." - }, - { - "author_name": "Mazdak Ganjalikhani-Hakemi", - "author_inst": "Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.22.22275183", "rel_title": "SARS-CoV-2 Booster Effect and Waning Immunity in Hemodialysis Patients", @@ -272494,6 +274325,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.20.22275407", + "rel_title": "Social divisions and risk perception can drive divergent epidemic dynamics and large second and third waves", + "rel_date": "2022-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.20.22275407", + "rel_abs": "During infectious disease outbreaks, individuals may adopt protective measures like vaccination and physical distancing in response to awareness of disease burden. Prior work showed how feedback between epidemic intensity and awareness-based behavior shapes disease dynamics (e.g., producing plateaus and oscillations). These models often overlook social divisions, where population subgroups may be disproportionately impacted by a disease and more responsive to the effects of disease within their group. We hypothesize that socially divided awareness-based behavior could fundamentally alter epidemic dynamics and shift disease burden between groups.\n\nWe develop a compartmental model of disease transmission in a population split into two groups to explore the impacts of awareness separation (relatively greater in-versus out-group awareness of epidemic severity) and mixing separation (relatively greater in-versus out-group contact rates). Protective measures are adopted based on awareness of recent disease-linked mortality. Using simulations, we show that groups that are more separated in awareness have smaller differences in mortality. Fatigue-driven abandonment of protective behavior can drive additional infection waves that can even exceed the size of the initial wave, particularly if uniform awareness drives early protection in one group, leaving that group largely susceptible to future infection. Finally, vaccine or infection-acquired immunity that is more protective against transmission and mortality may indirectly lead to more infections by reducing perceived risk of infection, and thereby reducing vaccine uptake. The dynamics of awareness-driven protective behavior, including relatively greater awareness of epidemic conditions in ones own group, can dramatically impact protective behavior uptake and the course of epidemics.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Mallory J Harris", + "author_inst": "Biology Department, Stanford University, Stanford, CA 94301" + }, + { + "author_name": "Erin A. Mordecai", + "author_inst": "Biology Department, Stanford University, Stanford, CA 94301" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.22.22275417", "rel_title": "Comparative effectiveness of sotrovimab and molnupiravir for prevention of severe COVID-19 outcomes in non-hospitalised patients: an observational cohort study using the OpenSAFELY platform", @@ -272759,69 +274613,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.05.20.22275319", - "rel_title": "Low testing rates limit the ability of genomic surveillance programs to monitor SARS-CoV-2 variants: a mathematical modelling study", - "rel_date": "2022-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.20.22275319", - "rel_abs": "The first step in SARS-CoV-2 genomic surveillance is testing to identify infected people. However, global testing rates are falling as we emerge from the acute health emergency and remain low in many low- and middle-income countries (LMICs) (mean = 27 tests/100,000 people/day). We simulated COVID-19 epidemics in a prototypical LMIC to investigate how testing rates, sampling strategies, and sequencing proportions jointly impact surveillance outcomes and showed that low testing rates and spatiotemporal biases delay time-to-detection of new variants by weeks-to-months and can lead to unreliable estimates of variant prevalence even when the proportion of samples sequenced is increased. Accordingly, investments in wider access to diagnostics to support testing rates of [~]100 tests/100,000 people/day could enable more timely detection of new variants and reliable estimates of variant prevalence. The performance of global SARS-CoV-2 genomic surveillance programs is fundamentally limited by access to diagnostic testing.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Alvin X. Han", - "author_inst": "Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands" - }, - { - "author_name": "Amy Toporowski", - "author_inst": "Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland" - }, - { - "author_name": "Jilian A. Sacks", - "author_inst": "Department of Epidemic and Pandemic Preparedness and Prevention, Emergency Preparedness Programme, World Health Organization, Geneva, Switzerland" - }, - { - "author_name": "Mark Perkins", - "author_inst": "Department of Epidemic and Pandemic Preparedness and Prevention, Emergency Preparedness Programme, World Health Organization, Geneva, Switzerland" - }, - { - "author_name": "Sylvie Briand", - "author_inst": "Department of Epidemic and Pandemic Preparedness and Prevention, Emergency Preparedness Programme, World Health Organization, Geneva, Switzerland" - }, - { - "author_name": "Maria van Kerkhove", - "author_inst": "Department of Epidemic and Pandemic Preparedness and Prevention, Emergency Preparedness Programme, World Health Organization, Geneva, Switzerland" - }, - { - "author_name": "Emma Hannay", - "author_inst": "Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland" - }, - { - "author_name": "Sergio Carmona", - "author_inst": "Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland" - }, - { - "author_name": "Bill Rodriguez", - "author_inst": "Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland" - }, - { - "author_name": "Edyth Parker", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Brooke E. Nichols", - "author_inst": "Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands" - }, - { - "author_name": "Colin A. Russell", - "author_inst": "Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.05.20.22275409", "rel_title": "A Mesoscale Agent Based Modeling Framework For Flow-mediated Infection Transmission In Indoor Occupied Spaces", @@ -274652,6 +276443,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.05.18.22275283", + "rel_title": "BNT162b2 induces robust cross-variant SARS-CoV-2 immunity in children", + "rel_date": "2022-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.18.22275283", + "rel_abs": "Currently available mRNA vaccines are extremely safe and effective to prevent severe SARS-CoV-2 infections. However, the emergence of novel variants of concerns has highlighted the importance of high population-based vaccine rates to effectively suppress viral transmission and breakthrough infections. While initially left out from vaccine efforts, children have become one of the most affected age groups and are key targets to stop community and household spread. Antibodies are central for vaccine induced protection and emerging data points to the importance of additional Fc effector functions like opsononophagocytosis or cytotoxicity, particularly in the context of variants of concern that escape neutralizing antibodies. Here, we observed delayed induction and reduced magnitude of vaccine induced antibody titers in children 5-11 years receiving two doses of the age recommended 10 g dose of the Pfizer SARS-CoV-2 BNT162b2 vaccine compared to adolescents (12-15 years) or adults receiving the 30 g dose. Conversely, children mounted equivalent or more robust neutralization and opsonophagocytic functions at peak immunogenicity, pointing to a qualitatively more robust humoral functional response in children. Moreover, broad cross-variants of concern responses were observed across children, with enhanced IgM and parallel IgG cross-reactivity to variants of concern (VOCs) in children compared to adults. Collectively, these data argue that despite the lower magnitude of the BNT162b2 induced antibody response in children, vaccine induced immunity in children target VOCs broadly and exhibit enhanced functionality that may contribute to attenuation of disease.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yannic C Bartsch", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Jessica W Chen", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Jaewon Kang", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Madeline D Burns", + "author_inst": "Massachusetts General Hospital Department of Pediatrics" + }, + { + "author_name": "Kerri J St.Denis", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Maegan L Sheehan", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Jameson P Davis", + "author_inst": "Massachusetts General Hospital Department of Pediatrics" + }, + { + "author_name": "Alejandro B Balazs", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Lael M Yonker", + "author_inst": "Massachusetts General Hospital Department of Pediatrics" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.18.22275240", "rel_title": "Exploring barriers and facilitators to physical activity during the COVID-19 pandemic: a qualitative study", @@ -274841,37 +276687,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.05.20.22275397", - "rel_title": "Comorbidities and sociodemographic factors on COVID-19 fatalities", - "rel_date": "2022-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.20.22275397", - "rel_abs": "IntroductionPrevious studies have evaluated comorbidities and sociodemographic factors individually or by type but not comprehensively. This study aims to analyze the influence of a wide variety of factors in a single study to better understand the big picture of their effects on case-fatalities.\n\nMethodsCounty-level comorbidities, social determinants of health such as income and race, measures of preventive healthcare, age, education level, average household size, population density, and political voting patterns were all evaluated on a national and regional basis. Analysis was performed through Generalized Additive Models and adjusted by CCVI.\n\nResultsFactors associated with reducing COVID-19 case fatality rates were mostly sociodemographic factors such as age, education and income, and preventive health measures. Obesity, minimal leisurely activity, binge drinking, and higher rates of individuals taking high blood pressure medication were associated with increased case fatality rate in a county. Political leaning influences case case-fatality rates. Regional trends showed contrasting effects where larger household size was protective in the Midwest, yet harmful in Northeast. Notably, higher rates of respiratory comorbidities such as asthma and COPD diagnosis were associated with reduced case-fatality rates in the Northeast. Increased rates of CKD within counties were often the strongest predictor of increased case-fatality rates for several regions.\n\nConclusionOur findings highlight the importance of considering the full context when evaluating contributing factors to case-fatality rates. The spectrum of factors identified in this study must be analyzed in the context of one another and not in isolation.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jacob Gerken", - "author_inst": "Rocky Vista University" - }, - { - "author_name": "Demi Zapata", - "author_inst": "Rocky Vista University" - }, - { - "author_name": "Daniel Kuivinen", - "author_inst": "Rocky Vista University" - }, - { - "author_name": "Isain Zapata", - "author_inst": "Rocky Vista University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.05.20.22275380", "rel_title": "The negative impact of COVID-19 on working memory revealed using a rapid online quiz", @@ -276530,6 +278345,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.05.14.22275075", + "rel_title": "Self-medication practices and associated factors among COVID-19 recovered patients to prevent future infections: A web-based survey in Bangladesh", + "rel_date": "2022-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.14.22275075", + "rel_abs": "BackgroundHuman health is largely affected by self-medication in both ways, adversely and favorably, as evidenced by the COVID-19 pandemic. The fear of spreading COVID-19 among health workers and hospital environments has led many Bangladeshi people to practice self-medicate for as a preventive strategy against this disease. Consequently, this practice entails an improper and injudicious use of medicine to cure self-recognized symptoms. To date, the COVID-19 has no effective treatment. The lack of a cure for COVID-19 and the continual progression of the diseases in educational settings induce a substantial population to practice self-medication. Therefore a study of self-medication practices is necessary for the framework of the pandemic. This study aimed to estimate the prevalence and factors associated with self-medication to prevent or manage future COVID-19 infections among recovered COVID-19 patients.\n\nMethodsThis cross-sectional study was conducted from September 2020 to February 2021 using an e-survey along with 360 participants. Data were collected using a pre-tested self-reported questionnaire. Descriptive statistics and correlations analysis were performed in the study.\n\nResultsAmong 360 participants, males were 69.7%, and females 30.3%. The prevalence of self-medication is 11%, and monthly family income, residence, education, occupation, and previous history of SM are the associated factors. Among the participants, 29.7% use antibiotics, and 30% use herbal products or drugs as medication.\n\nConclusionThe present study found SMP is moderately prevalent among COVID-19 recovered patients. To minimize the rate of SMP, adequate health care access systems and public education should be introduced, and media & community should be engaged in rational use of medication.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Md. Safaet Hossain Sujan", + "author_inst": "Department of Public Health and Informatics, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh" + }, + { + "author_name": "Atefehsadat Haghighathoseini", + "author_inst": "Department of Health Administration and Policy, George Mason University" + }, + { + "author_name": "Rafia Tasnim", + "author_inst": "Department of Public Health and Informatics, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh; Centre for Advanced Research Excellence in Public Health, " + }, + { + "author_name": "Md. Saiful Islam", + "author_inst": "Department of Public Health and Informatics, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh" + }, + { + "author_name": "Sarif Mahammad Salauddin", + "author_inst": "Sir Salimullah Medical College, Dhaka-1212, Bangladesh" + }, + { + "author_name": "Mohammad Mohiuddin Hasan", + "author_inst": "Hospital Services Management, DGHS, Mohakhali, Dhaka-1212, Bangladesh" + }, + { + "author_name": "Muhammad Ramiz Uddin", + "author_inst": "Department of Chemistry and Biochemistry, The university of Oklahoma, Norman, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.17.22275154", "rel_title": "COVID-19 booster dose antibody response in pregnant, lactating, and nonpregnant women", @@ -276707,61 +278565,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.16.22274315", - "rel_title": "Clinical validation of 3D-printed nasopharyngeal and oropharyngeal swabs for SARS-CoV-2 RT-PCR", - "rel_date": "2022-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.16.22274315", - "rel_abs": "Due to limited access to commercially available flocked nasopharyngeal (NP) and oropharyngeal (OP) swabs during the SARS-COV-2 pandemic, we have evaluated the sensitivity of 3D-printed swabs compared to commercial swabs in a clinical setting. We included 35 subjects with known exposure to SARS-CoV-2. Participants were tested with commercial and prototype NP/OP swab pairs 8 and 22 days after exposure. At day 8, the sensitivity of the prototype was 96% for NP-samples (CI 81-99%) and 91% for OP-samples (CI 72-97%). The sensitivity of the commercial swab was 92% for NP-samples (CI 76-98%) and 91% for OP-samples (CI 72-97%). At day 22, the sensitivities of the commercial swab were 100% for NP-samples (CI 82-100%) and OP-samples (CI 77-100%), whereas sensitivity of the prototype was 61% for NP-samples (CI 39-80%) and 54% for OP-samples (CI 29-77%). In conclusion, the prototype might be an alternative to commercial swabs when used early in the course of infection.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "\u00c5se Garl\u00f8v Riis", - "author_inst": "Division of Medicine, Stavanger University Hospital, Stavanger, Norway" - }, - { - "author_name": "Tonje Merethe R\u00f8ssland", - "author_inst": "Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway" - }, - { - "author_name": "Iren H\u00f8yland L\u00f6hr", - "author_inst": "Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway" - }, - { - "author_name": "Ingvild Dalen", - "author_inst": "Department of Research, Section of Biostatistics (I.D.), Stavanger University Hospital Stavanger, Norway" - }, - { - "author_name": "Lars K\u00e5re Kleppe", - "author_inst": "Division of Medicine, Stavanger University Hospital, Stavanger, Norway" - }, - { - "author_name": "Jon Sundal", - "author_inst": "Division of Medicine, Stavanger University Hospital, Stavanger, Norway" - }, - { - "author_name": "\u00c5se Berg", - "author_inst": "Division of Medicine, Stavanger University Hospital, Stavanger, Norway" - }, - { - "author_name": "May Sissel Vadla", - "author_inst": "Faculty of health science, University of Stavanger, Norway and Municipality of Randaberg, Stavanger, Norway." - }, - { - "author_name": "Ole Bernt Lenning", - "author_inst": "Research Department, Stavanger University Hospital, Stavanger, Norway and Municipality of Randaberg, Stavanger, Norway." - }, - { - "author_name": "Heidi Syre", - "author_inst": "Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.13.22275049", "rel_title": "Assessment of the humoral response to the homologous Gam-COVID-Vac (Sputnik V) or heterologous Sputnik V/mRNA-1273 (Moderna) vaccination against SARS-CoV-2 in dialysis patients.", @@ -278132,6 +279935,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.05.17.22275027", + "rel_title": "A Randomized Phase 2/3 Study of Ensitrelvir, a Novel Oral SARS-CoV-2 3C-like Protease Inhibitor, in Japanese Patients With Mild-to-Moderate COVID-19 or Asymptomatic SARS-CoV-2 Infection: Results of the Phase 2a Part", + "rel_date": "2022-05-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.17.22275027", + "rel_abs": "For the treatment of coronavirus disease 2019 (COVID-19), antiviral agents that can achieve rapid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reduction are warranted. This double-blind, phase 2a part of a phase 2/3 study assessed the efficacy and safety of ensitrelvir, a novel oral SARS-CoV-2 3C-like protease inhibitor, in Japanese patients with mild-to-moderate COVID-19 or asymptomatic SARS-CoV-2 infection. Sixty-nine patients enrolled from 56 sites were randomized (1:1:1) to orally receive 5-day ensitrelvir fumaric acid (375 mg on day 1 followed by 125 mg daily or 750 mg on day 1 followed by 250 mg daily) or placebo and followed up until day 28. The primary outcome was change from baseline in SARS-CoV-2 viral titer. A total of 16, 14, and 17 patients in the ensitrelvir 125 mg, ensitrelvir 250 mg, and placebo groups, respectively, were included in the intention-to-treat population (mean age: 38.8, 40.4, and 38.0 years, respectively). On day 4, the change from baseline in SARS-CoV-2 viral titer (log10 50% tissue culture infectious dose/mL) in patients with positive viral titer and viral RNA at baseline was greater with ensitrelvir 125 mg (mean [standard deviation], -2.42 [1.42]; P = 0.0712) and 250 mg (-2.81 [1.21]; P = 0.0083) versus placebo (-1.54 [0.74]), and ensitrelvir treatment reduced SARS-CoV-2 RNA by -1.4 to -1.5 log10 copies/mL versus placebo. All adverse events were mild to moderate. Ensitrelvir treatment demonstrated rapid SARS-CoV-2 clearance and was well tolerated in patients with mild-to-moderate COVID-19 or asymptomatic SARS-CoV-2 infection (Japan Registry of Clinical Trials identifier: jRCT2031210350).", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Hiroshi Mukae", + "author_inst": "Nagasaki University Graduate School of Biomedical Sciences" + }, + { + "author_name": "Hiroshi Yotsuyanagi", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Yohei Doi", + "author_inst": "University of Pittsburgh School of Medicine/Fujita Health University School of Medicine" + }, + { + "author_name": "Takumi Imamura", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Takuhiro Sonoyama", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Takahiro Fukuhara", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Genki Ichihashi", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Takao Sanaki", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Keiko Baba", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Yosuke Takeda", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Yuko Tsuge", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Takeki Uehara", + "author_inst": "Shionogi & Co., Ltd." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.16.22275163", "rel_title": "Performance and validation of an adaptable multiplex assay for detection of serologic response to SARS-CoV-2 infection or vaccination.", @@ -278337,29 +280207,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.17.22275205", - "rel_title": "A hybrid approach to predict COVID-19 cases using neural networks and inverse problem", - "rel_date": "2022-05-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.17.22275205", - "rel_abs": "We derive a novel hybrid approach, a combination of neural networks and inverse problem, in order to forecast COVID-19 cases, and more generally any infectious disease. For this purpose, we extract a second order nonlinear differential equation for the total confirmed cases from a SIR-like model. That differential equation is the key factor of the present study. The neural network and inverse problems are used to compute the trial functions for total cases and the model parameters, respectively. The number of suspected and infected individuals can be found using the trial function of total confirmed cases. We divide the time domain into two parts, training interval (first 365/395 days) and test interval (first 366 to 395/ 396 to 450 days), and train the neural networks on the preassigned training zones. To examine the efficiency and effectiveness, we apply the proposed method to Canada, and use the Canadian publicly available database to estimate the parameters of the trial function involved with total cases. The trial functions of model parameters show that the basic reproduction number was closed to unity over a wide range, the first from 100 to 365 days of the current pandemic in Canada. The proposed prediction models, based on influence of previous time and social economic policy, show excellent agreement with the data. The test results revel that the single path prediction can forecast a period of 30 days, and forecasting using previous social and economical situation can forecast a range of 55 days.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Subhendu Paul", - "author_inst": "Carleton University" - }, - { - "author_name": "Emmanuel Lorin", - "author_inst": "Carleton University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.16.22275165", "rel_title": "Severity of dental caries in New York City children receiving school-based prevention and the role of SARS-Cov-2: Results from the CariedAway pragmatic trial", @@ -279834,6 +281681,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2022.05.14.491911", + "rel_title": "SARS-CoV-2 Omicron Variant Wave in India: Advent, Phylogeny and Evolution", + "rel_date": "2022-05-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.14.491911", + "rel_abs": "SARS-CoV-2 evolution has continued to generate variants, responsible for new pandemic waves locally and globally. Varying disease presentation and severity has been ascribed to inherent variant characteristics and vaccine immunity. This study analyzed genomic data from 305 whole genome sequences from SARS-CoV-2 patients before and through the third wave in India. Delta variant was responsible for disease in patients without comorbidity(97%), while Omicron BA.2 caused disease primarily in those with comorbidity(77%). Tissue adaptation studies brought forth higher propensity of Omicron variants to bronchial tissue than lung, contrary to observation in Delta variants from Delhi. Study of codon usage pattern distinguished the prevalent variants, clustering them separately, Omicron BA.2 isolated in February grouped away from December strains, and all BA.2 after December acquired a new mutation S959P in ORF1b (44.3% of BA.2 in the study) indicating ongoing evolution. Loss of critical spike mutations in Omicron BA.2 and gain of immune evasion mutations including G142D, reported in Delta but absent in BA.1, and S371F instead of S371L in BA.1 could possibly be due to evolutionary trade-off and explain very brief period of BA.1 in December 2021, followed by complete replacement by BA.2.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Urvashi B Singh", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Sushanta Deb", + "author_inst": "All India institute of medical sciences" + }, + { + "author_name": "Rama Chaudhry", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Kiran Bala", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Lata Rani", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Ritu Gupta", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Lata Kumari", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Jawed Ahmed", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Sudesh Gaurav", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Sowjanya Perumalla", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Md. Nizam", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Anwita Mishra", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "J. Stephenraj", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Jyoti Shukla", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Deepika Bhardwaj", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Jamshed Nayer", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Praveen Aggarwal", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Madhulika Kabra", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Vineet Ahuja", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Subrata Sinha", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Randeep Guleria", + "author_inst": "All India Institute of Medical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2022.05.13.491763", "rel_title": "AI-based search for convergently expanding, advantageous mutations in SARS-CoV-2 by focusing on oligonucleotide frequencies", @@ -279947,37 +281893,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.05.16.22275128", - "rel_title": "School Reopening Simulations with COVID-19 Agent-based Model for the Philippine Regions", - "rel_date": "2022-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.16.22275128", - "rel_abs": "Schools have been closed in the Philippines since March 2020 due to the COVID-19 pandemic. In 2022, the government already allowed a pilot run of limited in-person classes in low-risk areas. With such development, the present paper aims to explore the question \"Is it safe to reopen schools with the current vaccination coverage?\" We used an age-stratified COVID-19 agent-based model coupled with social contact probabilities to simulate school reopening and vaccination scenarios in the 17 regions of the country. Through these simulations, we found downtick points for infections and deaths--the vaccination coverage at which we do not expect increases in infections and deaths should schools reopen. We then calculated the School Reopening Viability (SRV) of the regions and visualized these scores with a stop-go map for school reopening. Simulation results suggest that all regions except Regions 7, 9, BARMM, and 13 can already reopen schools without the fear of upticks in infections nor deaths. These regions have lower vaccination coverages relative to the rest of the country, especially against the case of Luzon which has the highest vaccination coverage. We recommend that the areas of concern ramp up their vaccination efforts before reopening schools. At the same time, behavioral factors (mask-wearing, physical distancing, hand-washing) and disease resistance factors (healthy living habits) shall be enforced once schools reopen. Finally, school reopening shall be gradual to ensure the crafting of data-driven (hospital utilization, positivity rate) policies.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Vena Pearl Bongolan", - "author_inst": "University of the Philippines, Diliman" - }, - { - "author_name": "Nico Andrew Francisco", - "author_inst": "University of the Philippines, Diliman" - }, - { - "author_name": "Martin Thomas Saliba", - "author_inst": "University of the Philippines, Diliman" - }, - { - "author_name": "Jimuel N. Celeste Jr.", - "author_inst": "University of the Philippines, Diliman" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.16.491949", "rel_title": "Human Surfactant Protein D Facilitates SARS-CoV-2 Pseudotype Binding and Entry in DC-SIGN Expressing Cells, and Downregulates Spike protein Induced Inflammation", @@ -281404,6 +283319,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.05.10.491351", + "rel_title": "The SARS-CoV-2 Spike Protein Activates the Epidermal Growth Factor Receptor-Mediated Signaling", + "rel_date": "2022-05-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.10.491351", + "rel_abs": "ObjectivesThe coronavirus disease-19 (COVID-19) pandemic is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At the molecular and cellular levels, the SARS-Cov-2 uses its envelope glycoprotein, the spike S protein, to infect the target cells in the lungs via binding with their transmembrane receptor, the angiotensin-converting enzyme 2 (ACE2). Here, we wanted to invesitgate if other molecular targets and pathways may be used by SARS-Cov-2.\n\nMethodsWe investigated the possibility for the spike 1 S protein and its receptor-binding domain (RBD) to target the epidermal growth factor receptor (EGFR) and its downstream signaling pathway in vitro using the lung cancer cell line (A549 cells). Protein expression and phosphorylation was examined upon cell treatment with the recombinant full spike 1 S protein or RBD.\n\nResultsWe demonstrate for the first time the activation of EGFR by the Spike 1 protein associated with the phosphorylation of the canonical ERK1/2 and AKT kinases and an increase of survivin expression controlling the survival pathway.\n\nConclusionsOur study suggests the putative implication of EGFR and its related signaling pathways in SARS-CoV-2 infectivity and Covid-19 pathology. This may open new perspectives in the treatment of Covid-19 patients by targeting EGFR.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Abdulrasheed Palakkott", + "author_inst": "The United Arab Emirates University" + }, + { + "author_name": "Aysha Alneyadi", + "author_inst": "The United Arab Emirates University" + }, + { + "author_name": "Khalid Muhammad", + "author_inst": "The United Arab Emirates University" + }, + { + "author_name": "Eid H Ali", + "author_inst": "Qatar University" + }, + { + "author_name": "Khaled Amiri", + "author_inst": "The United Arab Emirates University" + }, + { + "author_name": "Mohammed Akli Ayoub", + "author_inst": "The United Arab Emirates University" + }, + { + "author_name": "Rabah Iratni", + "author_inst": "The United Arab Emirates University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2022.05.12.491597", "rel_title": "Delivery of Circular mRNA via Degradable Lipid Nanoparticles against SARS-COV-2 Delta Variant", @@ -281537,41 +283495,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.05.09.491227", - "rel_title": "Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern", - "rel_date": "2022-05-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.09.491227", - "rel_abs": "The emergence of Variants of Concern (VOCs) of SARS-CoV-2 with increased transmissibility, immune evasion properties, and virulence poses a great challenge to public health. Despite unprecedented efforts to increase genomic surveillance, fundamental facts about the evolutionary origins of VOCs remain largely unknown. One major uncertainty is whether the VOCs evolved during transmission chains of many acute infections or during long-term infections within single individuals. We test the consistency of these two possible paths with the observed dynamics, focusing on the clustered emergence of the first three VOCs, Alpha, Beta, and Gamma, in late 2020, following a period of relative evolutionary stasis. We consider a range of possible fitness landscapes, in which the VOC phenotypes could be the result of single mutations, multiple mutations that each contribute additively to increasing viral fitness, or epistatic interactions among multiple mutations that do not individually increase viral fitness--a \"fitness plateau\". Our results suggest that the timing and dynamics of the VOC emergence, together with the observed number of mutations in VOC lineages, are in best agreement with the VOC phenotype requiring multiple mutations and VOCs having evolved within single individuals with long-term infections.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mahan Ghafari", - "author_inst": "University of Oxford" - }, - { - "author_name": "Qihan Liu", - "author_inst": "Emory University" - }, - { - "author_name": "Arushi Dhillon", - "author_inst": "Emory University" - }, - { - "author_name": "Aris Katzourakis", - "author_inst": "University of Oxford" - }, - { - "author_name": "Daniel Weissman", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2022.05.09.491254", "rel_title": "Three-dose vaccination-induced immune responses protect against SARS-CoV-2 Omicron-BA.2", @@ -283438,6 +285361,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.05.09.22274714", + "rel_title": "Mental-health before and during the COVID-19 pandemic in adults with neurodevelopmental disorders.", + "rel_date": "2022-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.09.22274714", + "rel_abs": "The COVID-19 pandemic negatively impacted mental health globally. Individuals with neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD), are at elevated risk of mental health difficulties. Therefore, we investigated the impact of the pandemic on anxiety, depression and mental wellbeing in adults with NDDs using longitudinal data from the Avon Longitudinal Study of Parents and Children study (n=3,058). Mental health data were collected pre-pandemic (age 21-25) and at three timepoints during the pandemic (ages 27-28) using the Short Mood and Feelings Questionnaire, Generalised Anxiety Disorder Assessment-7, and Warwick Edinburgh Mental Wellbeing Scale. ADHD and ASD were defined using validated cut-points of the Strengths and Difficulties Questionnaire and Autism Spectrum Quotient, self-reported at age 25. We used multi-level mixed-effects models to investigate changes in mental health in those with ADHD and ASD compared to those without. Prevalences of depression, anxiety and poor mental wellbeing were higher at all timepoints (pre-pandemic and during pandemic) in those with ADHD and ASD compared to those without. Anxiety increased to a greater extent in those with ADHD ({beta}=0.8 [0.2,1.4], p=0.01) and ASD ({beta}=1.2 [-0.1,2.5], p=0.07), while depression symptoms decreased, particularly in females with ASD ({beta}=-3.1 [-4.6,-1.5], p=0.0001). On average, mental wellbeing decreased in all, but to a lesser extent in those with ADHD ({beta}=1.3 [0.2,2.5], p=0.03) and females with ASD ({beta}=3.0 [0.2,5.9], p=0.04). To conclude, anxiety disproportionately increased in adults with NDDs during the pandemic, however, the related lockdowns may have provided a protective environment for depressive symptoms in the same individuals.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Amy Shakeshaft", + "author_inst": "Cardiff University" + }, + { + "author_name": "Rachel Blakey", + "author_inst": "University of Bristol" + }, + { + "author_name": "Alex Siu Fung Kwong", + "author_inst": "University of Bristol" + }, + { + "author_name": "Lucy Riglin", + "author_inst": "Cardiff University" + }, + { + "author_name": "George Davey Smith", + "author_inst": "University of Bristol" + }, + { + "author_name": "Evie Stergiakouli", + "author_inst": "University of Bristol" + }, + { + "author_name": "Kate Tilling", + "author_inst": "University of Bristol" + }, + { + "author_name": "Anita Thapar", + "author_inst": "Cardiff University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.05.10.22272976", "rel_title": "Have the COVID-19 Pandemic and Lockdown Affected Children's Mental Health in Long Term? A Repeated Cross-Sectional Study.", @@ -283699,33 +285669,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2022.05.09.22274863", - "rel_title": "Comparison of pandemic excess mortality in 2020-2021 across different empirical calculations", - "rel_date": "2022-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.09.22274863", - "rel_abs": "Different modeling approaches can be used to calculate excess deaths for the COVID-19 pandemic period. We compared 6 calculations of excess deaths (4 previously published and two new ones that we performed with and without age-adjustment) for 2020-2021. With each approach, we calculated excess deaths metrics and the ratio R of excess deaths over recorded COVID-19 deaths. The main analysis focused on 33 high-income countries with weekly deaths in the Human Mortality Database (HMD at mortality.org) and reliable death registration. Secondary analyses compared calculations for other countries, whenever available. Across the 33 high-income countries, excess deaths were 2.0-2.8 million without age-adjustment, and 1.6-2.1 million with age-adjustment with large differences across countries. In our analyses after age-adjustment, 8 of 33 countries had no overall excess deaths; there was a death deficit in children; and 0.478 million (29.7%) of the excess deaths were in people <65 years old. In countries like France, Germany, Italy, and Spain excess death estimates differed 2 to 4-fold between highest and lowest figures. The R values range exceeded 0.3 in all 33 countries. In 16 of 33 countries, the range of R exceeded 1. In 25 of 33 countries some calculations suggest R>1 (excess deaths exceeding COVID-19 deaths) while others suggest R<1 (excess deaths smaller than COVID-19 deaths). Inferred data from 4 evaluations for 42 countries and from 3 evaluations for another 98 countries are very tenuous Estimates of excess deaths are analysis-dependent and age-adjustment is important to consider. Excess deaths may be lower than previously calculated.\n\nSIGNIFICANCE STATEMENTExcess deaths are a key metric for assessing the impact of a pandemic. They reflect the composite impact of deaths from infection, from indirect pandemic effects, and from the measures taken. Different modeling approaches can be used to calculate excess deaths for the COVID-19 pandemic. Here, we compare four previous calculations of excess deaths and two new ones that we performed with and without adjusting for changing age structure in the estimation. Proper age-adjustment results in substantial reduction in estimates of excess deaths for 2020-2021. While results from different calculation methods are correlated, the absolute differences in estimated excess deaths are very high in most countries. Extrapolations to countries without reliable death registration is extremely tenuous.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Michael Levitt", - "author_inst": "Stanford School of Medicine" - }, - { - "author_name": "Fracesco Zonta", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China" - }, - { - "author_name": "John P.A. Ioannidis", - "author_inst": "Departments of Medicine, of Epidemiology and Population Health, of Biomedical Data Science, and of Statistics, and Meta-Research Innovation Center at Stanford (" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.05.10.22274919", "rel_title": "Too much to mask: determinants of sustained adherence to COVID-19 preventive measures among older Syrian refugees in Lebanon", @@ -285220,6 +287163,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2022.05.06.22274782", + "rel_title": "Post-acute health care burden after SARS-CoV-2 infection: A retrospective cohort study among 530,892 adults", + "rel_date": "2022-05-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.06.22274782", + "rel_abs": "ImportanceThe SARS-CoV-2 pandemic portends a significant increase in health care use related to post-acute COVID sequelae, but the magnitude is not known.\n\nObjectiveTo assess the burden of post-acute health care use after a positive versus negative polymerase chain reaction (PCR) test for SARS-CoV-2.\n\nDesign, Setting, and ParticipantsRetrospective cohort study of community-dwelling adults January 1, 2020 to March 31, 2021 in Ontario, Canada, using linked population-based health data. Follow-up began 56 days after PCR testing.\n\nExposuresIndividuals with a positive SARS-CoV-2 PCR test were matched 1:1 to individuals who tested negative based on hospitalization, test date, public health unit, sex, and a propensity score of socio-demographic and clinical characteristics.\n\nMain Outcomes and MeasuresThe health care utilization rate was the number of outpatient clinical encounters, homecare encounters, emergency department visits, days hospitalized, and days in long-term care per person-year. Mean health care utilization for test-positive versus negative individuals was compared using negative binomial regression, and rates at 95th and 99th percentiles were compared. Outcomes were also stratified by sex.\n\nResultsAmong 530,232 unique, matched individuals, mean age was 44 years (sd 17), 51% were female, and 0.6% had received [≥]1 COVID-19 vaccine dose. The mean rate of health care utilization was 11% higher in test-positive individuals (RR 1.11, 95% confidence interval [CI] 1.10-1.13). At the 95th percentile, test-positive individuals had 2.1 (95% CI 1.5-2.6) more health care encounters per person-year, and at the 99th percentile 71.9 (95% CI 57.6-83.2) more health care encounters per person-year. At the 95th percentile, test-positive women had 3.8 (95% CI 2.8-4.8) more health care encounters per person-year while there was no difference for men. At the 99th percentile, test-positive women had 76.7 (95% CI 56.3-89.6) more encounters per person-year, compared to 37.6 (95% CI 16.7-64.3) per person-year for men.\n\nConclusions and RelevancePost-acute health care utilization after a positive SARS-CoV-2 PCR test is significantly higher compared to matched test-negative individuals. Given the number of infections worldwide, this translates to a tremendous increase in use of health care resources. Stakeholders can use these findings to prepare for health care demand associated with long COVID.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSHow does the burden of health care use [≥]56 days after a positive SARS-CoV-2 polymerase chain reaction (PCR) test compare to matched individuals who tested negative?\n\nFindingsAfter accounting for multiple factors, the mean burden of post-acute health care use was 11% higher among those who tested positive, with higher rates of outpatient encounters, days hospitalized, and days in long-term care. Rates of homecare use were higher for test-positive women but lower for men.\n\nFor perspective, for every day in January 2022 with 100,000 or more infections, this translates to an estimated 72,000 additional post-acute health care encounters per year for the 1% of people who experienced the most severe complications of SARS-CoV-2; among those in the top 50% of health care use, this translates to 245,000 additional health care encounters per year. This increase will occur in the context of an ongoing pandemic and, in many health care systems, a depleted workforce and backlogs of care. Unless addressed, this increase is likely to exacerbate existing health inequities.\n\nMeaningGiven the large number of people infected, stakeholders can use these findings to plan for health care use associated with long COVID.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Candace D McNaughton", + "author_inst": "ICES, Sunnybrook Research Institute, and University of Toronto" + }, + { + "author_name": "Peter C Augstin", + "author_inst": "ICES, Sunnybrook Research Institute, Institute of Health Policy, Management and Evaluation, University of Toronto" + }, + { + "author_name": "Atul Sivaswamy", + "author_inst": "ICES" + }, + { + "author_name": "Jiming Fang", + "author_inst": "ICES" + }, + { + "author_name": "Husam Abdel-Qadir", + "author_inst": "ICES, Institute of Health Policy, Management and Evaluation, University of Toronto, Peter Munk Cardiac Centre, Toronto General Hospital, Division of Cardiology," + }, + { + "author_name": "Nick Daneman", + "author_inst": "ICES, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, University of Toronto" + }, + { + "author_name": "Jacob Allan Udell", + "author_inst": "Women's College Hospital" + }, + { + "author_name": "Walter Wodchis", + "author_inst": "ICES, Sunnybrook Research Institute" + }, + { + "author_name": "Ivona Mostarac", + "author_inst": "Sunnybrook Research Institute" + }, + { + "author_name": "Clare L Atzema", + "author_inst": "ICES, Sunnybrook Research Institute, Institute of Health Policy, Management and Evaluation, University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.05.22273234", "rel_title": "Changes in English medication safety indicators throughout the COVID-19 pandemic: a federated analysis of 57 million patients' primary care records in situ using OpenSAFELY", @@ -285465,41 +287463,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2022.05.05.22274731", - "rel_title": "Deep learning identified genetic variants associated with COVID-19 related mortality", - "rel_date": "2022-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.05.22274731", - "rel_abs": "Analysis of host genetic components provides insights into the susceptibility and response to viral infection such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19). To reveal genetic determinants of susceptibility to COVID-19 related mortality, we train a deep learning model to identify groups of genetic variants and their interactions that contribute to the COVID-19 related mortality risk using the UK Biobank data. We refer to such groups of variants as super variants. We identify 15 super variants with various levels of significance as susceptibility loci for COVID-19 mortality. Specifically, we identify a super variant (OR=1.594, p=5.47x10-9) on Chromosome 7 that consists of the minor allele of rs76398985, rs6943608, rs2052130, 7:150989011_CT_C, rs118033050 and rs12540488. We also discover a super variant (OR=1.353, p=2.87x10-8) on Chromosome 5 that contains rs12517344, rs72733036, rs190052994, rs34723029, rs72734818, 5:9305797_GTA_G and rs180899355.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Zihuan Liu", - "author_inst": "Yale University" - }, - { - "author_name": "Wei Dai", - "author_inst": "Yale University" - }, - { - "author_name": "Shiying Wang", - "author_inst": "Yale University" - }, - { - "author_name": "Yisha Yao", - "author_inst": "Yale University" - }, - { - "author_name": "Heping Zhang", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.04.22274681", "rel_title": "Longitudinal analysis reveals elevation then sustained higher expression of autoantibodies for six months after SARS-CoV-2 infection", @@ -286930,6 +288893,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.05.02.22274456", + "rel_title": "Change in stroke presentations during COVID-19 pandemic in South-Western Sydney.", + "rel_date": "2022-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.02.22274456", + "rel_abs": "BackgroundAustralia managed relatively well during the global COVID-19 pandemic owing to our swift mandated public health response. During the NSW lockdown restrictions, we noted a decrease in acute stroke presentations at our institution, similar to what was subsequently reported worldwide.\n\nAimsWe aimed to test our hypothesis that (i) the true numbers of ischaemic strokes did not change, however patients were presenting later and (ii) the proportion of TIAs decreased.\n\nMethodsWe conducted a retrospective audit of all stroke and TIA presentations in 2020 and compared these with data from 2019. We collected information about stroke subtype, severity, time from stroke/TIA onset to presentation and acute reperfusion therapies.\n\nResultsBetween January-February and April-March 2020, there was a 15% drop in acute stroke presentations (128 vs. 109). In the same period \"stroke mimic\" presentations dropped by 22%. The proportion of patients attending the emergency department within 4.5hrs was only 36% compared with 48% over the similar period in 2019.\n\nConclusionsAlthough the raw numbers of ischemic stroke presentations remained stable during NSW Covid lockdown, the proportion of patients presenting within time window for acute reperfusion therapies fell. The number of TIAs similarly fell suggesting COVID-19 discouraged patients from presenting to hospital which placed them at higher risk of disabling stroke. The opportunity cost of lockdown restrictions on stroke outcome should be considered in future policy directives.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "James Thomas", + "author_inst": "Liverpool Hospital" + }, + { + "author_name": "Dennis Cordato", + "author_inst": "Liverpool Hospital" + }, + { + "author_name": "David Manser", + "author_inst": "Liverpool Hospital" + }, + { + "author_name": "Paul M Middleton", + "author_inst": "Liverpool Hospital" + }, + { + "author_name": "Cecilia Cappelen-Smith", + "author_inst": "Liverpool Hospital" + }, + { + "author_name": "Alan McDougall", + "author_inst": "Liverpool Hospital" + }, + { + "author_name": "Peter Thomas", + "author_inst": "Liverpool Hospital" + }, + { + "author_name": "Nicholas Moore", + "author_inst": "Liverpool Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2022.05.04.22274657", "rel_title": "Have infection control and prevention measures resulted in any adverse outcomes for care home and domiciliary care residents and staff?", @@ -287175,85 +289185,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.03.22274622", - "rel_title": "SARS-CoV-2 neutralizing antibodies in Chile after a vaccination campaign with five different schemes", - "rel_date": "2022-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.03.22274622", - "rel_abs": "Using levels of neutralizing antibodies (nAbs), we evaluate the successful Chilean SARS-CoV-2 vaccine campaign, which combines technologies and heterologous boosters. In 120 randomly selected seropositive individuals from a population-based study, we conclude that the booster dose, regardless of vaccine technology or natural infection, and mRNA vaccines significantly improve nAbs response.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Ximena Aguilera", - "author_inst": "Universidad del Desarrollo" - }, - { - "author_name": "Juan Hormazabal", - "author_inst": "Universidad del Desarrollo" - }, - { - "author_name": "Cecilia Vial", - "author_inst": "Universidad del Desarrollo" - }, - { - "author_name": "Lina Jimena Cortes", - "author_inst": "Universidad del Desarrollo" - }, - { - "author_name": "Claudia W. Gonzalez", - "author_inst": "Universidad del Desarrollo" - }, - { - "author_name": "Paola Rubilar", - "author_inst": "Universidad del Desarrollo" - }, - { - "author_name": "Mauricio Apablaza", - "author_inst": "Universidad del Desarrollo" - }, - { - "author_name": "Muriel Ramirez-Santana", - "author_inst": "Universidad Catolica del Norte, Coquimbo" - }, - { - "author_name": "Gloria Icaza", - "author_inst": "Universidad de Talca" - }, - { - "author_name": "Loreto Nunez-Franz", - "author_inst": "Universidad de Talca" - }, - { - "author_name": "Carla Castillo-Laborde", - "author_inst": "Universidad del Desarrollo" - }, - { - "author_name": "Carolina Ramirez-Riffo", - "author_inst": "Universidad del Desarrollo" - }, - { - "author_name": "Claudia Perez", - "author_inst": "Universidad del Desarrollo" - }, - { - "author_name": "Ruben Quezada-Gaete", - "author_inst": "Universidad Catolica del Norte, Coquimbo" - }, - { - "author_name": "Macarena Said", - "author_inst": "Universidad de Talca" - }, - { - "author_name": "Pablo Vial", - "author_inst": "Universidad del Desarrollo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.03.22274395", "rel_title": "Development and evaluation of low-volume tests to detect and characterise antibodies to SARS-CoV-2", @@ -289100,6 +291031,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.05.01.490203", + "rel_title": "SARS-CoV-2 Main Protease: a Kinetic Approach", + "rel_date": "2022-05-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.01.490203", + "rel_abs": "In this article, I present a new model of the interaction of the main protease (Mpro) from SARS-CoV-2 virus with its substrate. The reaction scheme used to describe this mechanism is an extension of the well-known Michaelis-Menten model proposed in 1913 by Leonor Michaelis and Maud Menten [1]. The model I present here takes into account that one Mpro enzyme monomer interacts with another Mpro monomer in the presence of the substrate, leading to the formation of an enzyme dimer bound to one substrate molecule. Indeed, this dimer is formed by the sequentially binding of one Mpro enzyme monomer to one molecule of substrate, followed by another Mpro enzyme monomer binding to this Mpro-substrate complex. This reaction mechanism is also known in the literature as substrate-induced dimerization [3]. Starting from this new reaction scheme established for this catalytic mechanism, I derived a mathematical expression describing the catalytic rate of the active Mpro enzyme dimer as a function of the substrate concentration [S]. The plot corresponding to this substrate-induced dimerization reaction shows a function f ([S]) that is not monotonic, i.e. not strictly increasing or decreasing, but with a second derivative initially negative and then becoming positive after having passed the Vmax point. This is typically a type of curve showing a phenomenon like the one of substrate inhibition (for instance, inhibition by excess-substrate [7]). The graphical representation of this process shows an interesting behaviour: from zero M/s, the reaction rate increases progressively, similar to the kind of curve described by the Michaelis-Menten model. However, after having reached its maximum catalytic rate, Vmax, the reaction rate decreases progressively as we continue to increase the substrate concentration. I propose an explanation to this interesting behavior. At the moment where Vcat is maximum, we can assume that, in theory, every single substrate molecule in solution is bound to two enzyme monomers (i.e. to one active dimer). The catalytic rate is thus theoretically maximized. At the time where the reaction rate begins to decrease, we observe a new phenomenon that appears: the enzyme monomers begin to be \"diluted\" in the solution containing the excess substrate. The dimers begin to dissociate and to bind increasingly to the substrate as inactive monomers instead of active dimers. Hence, it is more and more unlikely for the enzyme monomers to sequentially bind twice to the same substrate molecule (here, [E] << [S]). Thus, at this stage, the substrate-induced dimerization occurs less often. At the limit, when the substrate is in high excess, there is virtually no more dimerization which occurs. This is one example of excess-substrate inhibition. Furthermore, after having established this fact, I wanted to see if this catalytic behavior was also observed in vitro. Therefore, I conducted an experiment where I measured the catalytic rate of the Mpro dimer for different substrate concentrations. The properties of my substrate construct were such, that I could determine the catalytic rate of the enzyme dimer by directly measuring the spectrophotometric absorbance of the cleaved substrate at{lambda} = 405 nm. The results show explicitly -- within a margin of error -- that the overall shape of the experimental curve looks like the one of the theoretical curve. I thus conclude that the biochemical behavior of the Mpro in vitro follows a new path when it is in contact with its substrate: an excess substrate concentration decreases the activity of the enzyme by the phenomenon of a type of excess-substrate inhibition. This finding could open a new door in the discovery of drugs directed against the Mpro enzyme of the SARS-CoV-2 virus, acting on the inhibition by excess-substrate of the Mpro enzyme, this protein being a key component in the metabolism of the virus. Furthermore, I have established that the maximum of the fitted curve, Vmax, depends only on [E]T and not on [S]. [Formula] exhibits the same dependence pattern. Therefore, if I keep [E]T close to zero, the catalytic rate of the enzyme will also be greatly reduced, which can be understood intuitively. Finally, if we dilute the enzyme sufficiently in the host cell by injecting a suitably high concentration of the octapeptide substrate AVLQSGFR (an inhibitor of the original substrate), this artificial substrate will bind to the \"intermediate\" dimer from the polypeptide and prevent the precursor Mpro from auto-cleaving and dimerizing due to the \"distorted key\" effect of the octapeptide on the \"intermediate\" dimer. The precursor peptide Mpro will auto-cleave to a lesser extent than in the absence of the artificial octapeptide and thus the concentration of the total enzyme [E]T will be lowered in the cell. It would therefore be possible to control the virulence of the virus by adjusting the concentration of the artificial inhibitory octapeptide. However, this is only speculation and has yet to be verified in practice.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Thierry Rebetez", + "author_inst": "ETHZ" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.04.30.489997", "rel_title": "BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection", @@ -289417,61 +291367,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.05.02.22274436", - "rel_title": "Omicron infection induces low-level, narrow-range SARS-CoV-2 neutralizing activity", - "rel_date": "2022-05-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.02.22274436", - "rel_abs": "BackgroundThe rapid worldwide spread of the mildly pathogenic SARS-CoV-2 Omicron variant has led to the suggestion that it will induce levels of collective immunity that will help putting an end to the COVID19 pandemics.\n\nMethodsConvalescent serums from non-hospitalized individuals previously infected with Alpha, Delta or Omicron BA.1 SARS-CoV-2 or subjected to a full mRNA vaccine regimen were evaluated for their ability to neutralize a broad panel of SARS-CoV-2 variants.\n\nFindingsPrior vaccination or infection with the Alpha or to a lesser extent Delta strains conferred robust neutralizing titers against most variants, albeit more weakly against Beta and even more Omicron. In contrast, Omicron convalescent serums only displayed low level of neutralization activity against the cognate virus and were unable to neutralize other SARS-CoV-2 variants.\n\nInterpretationModerately symptomatic Omicron infection is only poorly immunogenic and does not represent a substitute for vaccination.\n\nFundingEPFL COVID Fund; private foundation advised by CARIGEST SA; Private Foundation of the Geneva University Hospitals; General Directorate of Health of the canton of Geneva, the Swiss Federal Office of Public Health.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Priscilla Turelli", - "author_inst": "EPFL, School of Life Sciences; Switzerland" - }, - { - "author_name": "Maria Eugenia Zaballa", - "author_inst": "Geneva University Hospitals, Switzerland" - }, - { - "author_name": "Charlene Raclot", - "author_inst": "EPFL, School of Life Sciences, Switzerland" - }, - { - "author_name": "Craig Fenwick", - "author_inst": "Lausanne University Hospital" - }, - { - "author_name": "Laurent Kaiser", - "author_inst": "University of Geneva Hospitals" - }, - { - "author_name": "Isabella Eckerle", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Giuseppe Pantaleo", - "author_inst": "Lausanne University Hospital" - }, - { - "author_name": "Idris Guessous", - "author_inst": "Faculty of Medicine, University of Geneva" - }, - { - "author_name": "Silvia Stringhini", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Didier Trono", - "author_inst": "EPFL, School of Life Sciences; Switzerland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.01.22274406", "rel_title": "Continued Emergence and Evolution of Omicron in South Africa: New BA.4 and BA.5 lineages", @@ -291138,6 +293033,105 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2022.04.28.489942", + "rel_title": "Immediate myeloid depot for SARS-CoV-2 in the human lung", + "rel_date": "2022-04-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.28.489942", + "rel_abs": "In the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, considerable focus has been placed on a model of viral entry into host epithelial populations, with a separate focus upon the responding immune system dysfunction that exacerbates or causes disease. We developed a precision-cut lung slice model to investigate very early host-viral pathogenesis and found that SARS-CoV-2 had a rapid and specific tropism for myeloid populations in the human lung. Infection of alveolar macrophages was partially dependent upon their expression of ACE2, and the infections were productive for amplifying virus, both findings which were in contrast with their neutralization of another pandemic virus, Influenza A virus (IAV). Compared to IAV, SARS-CoV-2 was extremely poor at inducing interferon-stimulated genes in infected myeloid cells, providing a window of opportunity for modest titers to amplify within these cells. Endotracheal aspirate samples from humans with the acute respiratory distress syndrome (ARDS) from COVID-19 confirmed the lung slice findings, revealing a persistent myeloid depot. In the early phase of SARS-CoV-2 infection, myeloid cells may provide a safe harbor for the virus with minimal immune stimulatory cues being generated, resulting in effective viral colonization and quenching of the immune system.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Melia Magnen", + "author_inst": "UCSF" + }, + { + "author_name": "Ran You", + "author_inst": "UCSF" + }, + { + "author_name": "Arjun A Rao", + "author_inst": "UCSF" + }, + { + "author_name": "Ryan T Davis", + "author_inst": "UCSF" + }, + { + "author_name": "Lauren Rodriguez", + "author_inst": "UCSF" + }, + { + "author_name": "Camille R Simoneau", + "author_inst": "UCSF" + }, + { + "author_name": "Lisiena Hysenaj", + "author_inst": "UCSF" + }, + { + "author_name": "Kenneth H Hu", + "author_inst": "UCSF" + }, + { + "author_name": "- The UCSF COMET Consortium", + "author_inst": "-" + }, + { + "author_name": "Christina Love", + "author_inst": "UCSF" + }, + { + "author_name": "Prescott G Woodruff", + "author_inst": "UCSF" + }, + { + "author_name": "David J Erle", + "author_inst": "UCSF" + }, + { + "author_name": "Carolyn M Hendrickson", + "author_inst": "UCSF" + }, + { + "author_name": "Carolyn S Calfee", + "author_inst": "UCSF" + }, + { + "author_name": "Michael A Matthay", + "author_inst": "UCSF" + }, + { + "author_name": "Jeroen P Roose", + "author_inst": "UCSF" + }, + { + "author_name": "Anita Sil", + "author_inst": "UCSF" + }, + { + "author_name": "Melanie Ott", + "author_inst": "UCSF" + }, + { + "author_name": "Charles R Langelier", + "author_inst": "UCSF" + }, + { + "author_name": "Matthew F Krummel", + "author_inst": "UCSF" + }, + { + "author_name": "Mark R Looney", + "author_inst": "UCSF" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.04.26.22274264", "rel_title": "Pilot study on the use of low molecular weight heparins in the prevention of thromboembolic disease during pregnancy and puerperium.", @@ -291287,41 +293281,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.25.22274276", - "rel_title": "Exploring U.S. food system workers' intentions to work while ill during the early COVID-19 pandemic: a national survey analysis", - "rel_date": "2022-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.25.22274276", - "rel_abs": "BackgroundWhile \"stay at home\" orders were in effect during early phases of the COVID-19 pandemic, many U.S. food workers attended in-person work, charged with maintaining operation of the national food supply chain. Anecdotal evidence suggests that many U.S. food system workers encountered barriers to staying home despite symptomatic COVID-19 illness.\n\nMethodsWe conducted a national, cross-sectional, online survey between July 31 to October 2, 2020, among 2,535 respondents. We used multivariable regression and free-text analyses to explore factors associated with U.S. food system workers intentions to attend work while ill (i.e., presenteeism intentions) during the first four to six months of the COVID-19 pandemic.\n\nResultsOverall, 8.8% of workers surveyed reported intentions to attend work while symptomatic with COVID-19 disease. Almost half of respondents (41.1%) reported low or very low household food security. Workers reporting a high workplace safety climate score were half as likely to report presenteeism intentions (adjusted odds ratio [aOR] 0.52, 95% confidence interval (CI) 0.37, 0.75) relative to those reporting low scores. Workers reporting low (aOR 2.06, 95% CI 1.35, 3.13) or very low (aOR 2.31, 95% CI 1.50, 3.13) levels of household food security had twice the odds of reporting presenteeism intentions relative to those reporting high/marginal food security.\n\nConclusionsOur findings suggest that workplace culture and safety climate could enable employees to feel like they can take leave when sick during a pandemic, which is critical to individual health and prevention of workplace disease transmission. However, the pressure experienced by food workers to work when ill, especially by those experiencing food insecurity, themselves, underscores the need for strategies which address these vulnerabilities and empower food workers to make health-protective decisions.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Caitlin A Ceryes", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Jackie Agnew", - "author_inst": "Johns Hopkins School of Public Health" - }, - { - "author_name": "Andrea L. Wirtz", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Daniel Barnett", - "author_inst": "Johns Hopkins School of Public Health" - }, - { - "author_name": "Roni A Neff", - "author_inst": "Johns Hopkins School of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2022.04.25.22274285", "rel_title": "Evaluating diagnostic accuracies of Panbio\u2122 COVID-19 rapid antigen test and RT-PCR for the detection of SARS-CoV-2 in Addis Ababa, Ethiopia using Bayesian Latent-Class Models (BLCM)", @@ -293092,6 +295051,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.04.28.489850", + "rel_title": "GM-CSF-activated human dendritic cells promote type1 T follicular helper cells (Tfh1) polarization in a CD40-dependent manner", + "rel_date": "2022-04-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.28.489850", + "rel_abs": "T follicular helper (Tfh) cells are specialized CD4+ T cells that regulate humoral immunity by providing B cell help. Tfh1 sub-population was recently identified and associated with severity in infection and autoimmune diseases. The cellular and molecular requirements to induce human Tfh1 differentiation are unknown. Our work investigated the role of human dendritic cells (DC) in promoting Tfh1 differentiation and their physiopathological implication in mycobacterium tuberculosis and mild COVID-19 infection.\n\nActivated human blood CD1c+ DC were cocultured with allogeneic naive CD4+ T cells. Single-cell RNA sequencing was then used alongside protein validation to define the induced Tfh lineage. DC signature and correlation with Tfh1 cells in infected patients was established through bioinformatic analysis.\n\nOur results show that GM-CSF-activated DC drove the differentiation of Tfh1 cells, displaying typical Tfh molecular features, including 1) high levels of PD-1, CXCR5, and ICOS expression; 2) BCL6 and TBET co-expression; 3) IL-21 and IFN-{gamma} secretion. Mechanistically, GM-CSF triggered the emergence of two distinct DC sub-populations defined by their differential expression of CD40 and ICOS-ligand (ICOS-L), and distinct phenotype, morphology, transcriptomic signature, and function. We showed that Tfh1 differentiation was efficiently and specifically induced by CD40highICOS-Llow DC in a CD40-dependent manner. Tfh1 cells were positively associated with a CD40highICOS-LLow DC signature in patients with latent mycobacterium tuberculosis and mild COVID-19 infection.\n\nOur study uncovers a novel CD40-dependent human Tfh1 axis. Immunotherapy modulation of Tfh1 activity might contribute to control diseases where Tfh1 are known to play a key role, such as infections.\n\nSignificance StatementDendritic cells (DC) play a central role in triggering the adaptive immune response due to their T cell priming functions. Among different T cell subsets, it is still not clear how human type1 T follicular helper cells (Tfh1) differentiate. Tfh1 cells are implicated in several physiopathological conditions, including infections. Here we show that GM-CSF induces diversification of human DC. Only CD40highICOS-LLow DC were able to drive Tfh1 cell differentiation. We found that CD40highICOS-LLow DC signature was associated to Tfh1 cells in mycobacterium tuberculosis and COVID-19 patients. Our data reveal a previously undescribed pathway leading to human Tfh1 cell differentiation and highlight the importance of GM-CSF and CD40 as potential targets for the design of anti-infective therapies.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Sarantis Korniotis", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis, F-75010, Paris, France" + }, + { + "author_name": "Melissa Saichi", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis" + }, + { + "author_name": "Coline Trichot", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis" + }, + { + "author_name": "Caroline Hoffmann", + "author_inst": "Institut Curie, INSERM U932 Research Unit, Immunity and Cancer, F-75005 Paris, France" + }, + { + "author_name": "Elise Amblard", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis" + }, + { + "author_name": "Annick Viguier", + "author_inst": "Institut Curie, INSERM U932 Research Unit, Immunity and Cancer, F-75005 Paris, France" + }, + { + "author_name": "Sophie Grondin", + "author_inst": "Institut Curie, INSERM U932 Research Unit, Immunity and Cancer, F-75005 Paris, France" + }, + { + "author_name": "Floriane Noel", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis" + }, + { + "author_name": "Hamid Mattoo", + "author_inst": "Immunology and Inflammation Therapeutic Area, Sanofi, Cambridge MA, USA" + }, + { + "author_name": "Vassili Soumelis", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.04.28.489772", "rel_title": "Structural and functional characteristics of SARS-CoV-2 Omicron subvariant BA.2 spike", @@ -293369,25 +295383,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, - { - "rel_doi": "10.1101/2022.04.28.489618", - "rel_title": "A Pan-Coronavirus Vaccine Candidate: Nine Amino Acid Substitutions in the ORF1ab Gene Attenuate 99% of 365 Unique Coronaviruses: A Comparative Effectiveness Research Study", - "rel_date": "2022-04-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.28.489618", - "rel_abs": "BackgroundThe COVID-19 pandemic has been a watershed event. Industry and governments have reacted, investing over US$105 billion in vaccine research.1 The Holy Grail is a universal, pan-coronavirus, vaccine to protect humankind from future SARS-CoV-2 variants and the thousands of similar coronaviruses with pandemic potential.2 This paper proposes a new vaccine candidate that appears to attenuate the SARS-Cov-2 coronavirus variants to render it safe to use as a vaccine. Moreover, these results indicate it may be efficacious against 99% of 365 coronaviruses. This research model is wet-dry-wet; it originated in genomic sequencing laboratories, evolved to computational modeling, and the candidate result now require validation back in a wet lab.\n\nObjectivesThis studys purpose was to test the hypothesis that machine learning applied to sequenced coronaviruses genomes could identify which amino acid substitutions likely attenuate the viruses to produce a safe and effective pan-coronavirus vaccine candidate. This candidate is now eligible to be pre-clinically then clinically tested and proven. If validated, it would constitute a traditional attenuated virus vaccine to protect against hundreds of coronaviruses, including the many future variants of SARS-CoV-2 predicted from continuously recombining in unvaccinated populations and spreading by modern mass travel.\n\nMethodsUsing machine learning, this was an in silico comparative effectiveness research study on trinucleotide functions in nonstructural proteins of 365 novel coronavirus genomes. Sequences of 7,097 codons in the ORF1ab gene were collected from 65 global locations infecting 68 species and reported to the US National Institute of Health. The data were proprietarily transformed twice to enable machine learning ingestion, mapping, and interpretation. The set of 2,590,405 data points was randomly divided into three cohorts: 255 (70%) observations for training; and two cohorts of 55 (15%) observations each for testing. Machine learning models were trained in the statistical programming language R and compared to identify which mixture of the 7.097 x 1023 possible amino-acid-location combinations would attenuate SARS-CoV-2 and other coronaviruses that have infected humans.\n\nResultsContests of machine-learning algorithms identified nine amino-acid point substitutions in the ORF1ab gene that likely attenuate 98.98% of 365 (361) novel coronaviruses. Notably, seven substitutions are for the amino acid alanine. Most of the locations (5 of 9) are in nonstructural proteins (NSPs) 2 and 3. The substitutions are alanine to (1) valine at codon 4273; (2) leucine at codon 5077; (3) phenylalanine at codon 2001; (4) leucine at codon 372; (5) proline at codon 354; (6) phenylalanine at codon 2811; (7) phenylalanine at codon 4703; (8) leucine to serine at codon 2333; and, (9) threonine to alanine at codon 5131.\n\nConclusionsThe primary outcome is a new, highly promising, pan-coronavirus vaccine candidate based on nine amino-acid substitutions in the ORF1ab gene. The secondary outcome was evidence that sequences of wet-dry lab collaborations - here machine learning analysis of viral genomes informing codon functions -- may discover new broader and more stable vaccines candidates more quickly and inexpensively than traditional methods.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Eric Luellen", - "author_inst": "Bioinformatix" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "synthetic biology" - }, { "rel_doi": "10.1101/2022.04.27.22274334", "rel_title": "Mortality among healthcare workers in Indonesia during 18 months of COVID-19", @@ -294802,6 +296797,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.23.22274192", + "rel_title": "Excess all-cause mortality across counties in the United States, March 2020 to December 2021", + "rel_date": "2022-04-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.23.22274192", + "rel_abs": "Excess mortality is the difference between expected and observed mortality in a given period and has emerged as a leading measure of the overall impact of the Covid-19 pandemic that is not biased by differences in testing or cause-of-death assignment. Spatially and temporally granular estimates of excess mortality are needed to understand which areas have been most impacted by the pandemic, evaluate exacerbating and mitigating factors, and inform response efforts, including allocating resources to affected communities. We estimated all-cause excess mortality for the United States from March 2020 through February 2022 by county and month using a Bayesian hierarchical model trained on data from 2015 to 2019. An estimated 1,159,580 excess deaths occurred during the first two years of the pandemic (first: 620,872; second: 538,708). Overall, excess mortality decreased in large metropolitan counties, but increased in nonmetro counties, between the first and second years of the pandemic. Despite the initial concentration of mortality in large metropolitan Northeast counties, beginning in February 2021, nonmetro South counties had the highest cumulative relative excess mortality. These results highlight the need for investments in rural health as the pandemics disproportionate impact on rural areas continues to grow.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Eugenio Paglino", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Dielle J. Lundberg", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Zhenwei Zhou", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Joe A. Wasserman", + "author_inst": "RTI International" + }, + { + "author_name": "Rafeya Raquib", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Anneliese N. Luck", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Katherine Hempstead", + "author_inst": "The Robert Wood Johnson Foundation" + }, + { + "author_name": "Jacob Bor", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Samuel H. Preston", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Irma T. Elo", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Andrew C. Stokes", + "author_inst": "Boston University School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.22.22274058", "rel_title": "Coronavirus and incomes: the COVID-19 pandemic dynamics in Africa in February 2022", @@ -294995,41 +297049,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.04.24.489298", - "rel_title": "Anti-SARS-Cov-2 S-RBD IgG formed after BNT162b2 vaccination can bind C1q and activate complement", - "rel_date": "2022-04-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.24.489298", - "rel_abs": "IntroductionActivation of the classical complement pathway through C1q binding to immunoglobulins (Ig) contributes to pathogen neutralization, thus, the ability of Ig produced after vaccination to bind C1q could affect vaccine efficacy. In this study, we investigated C1q binding and subsequent complement activation by anti-spike (S) protein receptor-binding domain (RBD) specific antibodies produced following vaccination with either the mRNA vaccine BNT162b2 or the inactivated vaccine BBIBP-CorV.\n\nMethodsSerum samples were collected in the period July 2021-March 2022. Participants demographic data, type of vaccine, date of vaccination, as well as adverse effects of the vaccine were recorded. The serum samples were incubated with S protein RBD-coated plates. Levels of human IgG, IgM, and C1q, that were bound to the plate, as well as formed C5b-9, were compared between different groups of participants.\n\nResultsA total of 151 samples were collected from vaccinated (n=116) and non-vaccinated (n=35) participants. Participants who received either one or two doses of BNT162b2 formed higher levels of anti-RBD IgG than participants who received BBIBP-CorV. The anti-RBD IgG formed following either vaccine bound C1q, but significantly more C1q binding was observed in participants who received BNT162b2. Subsequently, C5b-9 formation was significantly higher in participants who received BNT162b2, while no significant difference in C5b-9 formation was found between the non-vaccinated and BBIBP-CorV groups. Formation of C5b-9 was strongly correlated to C1q binding, additionally, the ratio of formed C5b-9/ bound C1q was significantly higher in the BNT162b2 group.\n\nConclusionAnti-RBD IgG formed following vaccination can bind C1q with subsequent complement activation, the degree of terminal complement pathway activation differed between vaccines, which could play a role in in the protection offered by COVID-19 vaccines. Further investigation into the correlation between vaccine protection and the ability of vaccine generated antibodies to activate complement is required.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Anas H. A. Abu-Humaidan", - "author_inst": "Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan" - }, - { - "author_name": "Fatima M Ahmad", - "author_inst": "Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan. Department of the Clinical " - }, - { - "author_name": "Dima Awajan", - "author_inst": "Department of Clinical Pharmacy and Therapeutics, Applied Science Private University, Amman 11931, Jordan" - }, - { - "author_name": "Rabaa Jarrar", - "author_inst": "Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan" - }, - { - "author_name": "Nader Alaridah", - "author_inst": "Department of Pathology, Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.04.25.489472", "rel_title": "Targeted genomic sequencing with probe capture for discovery and surveillance of coronaviruses in bats", @@ -296560,6 +298579,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.21.22274155", + "rel_title": "Usage and awareness of antiviral medications for COVID-19", + "rel_date": "2022-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.21.22274155", + "rel_abs": "We surveyed people that recently tested positive for SARS-CoV-2 to assess the frequency and correlates of early treatment seeking behavior. Among high risk respondents, 66.0% were aware of treatment for COVID-19 and 36.3% had sought treatment, however only 1.7% reported use of an antiviral for SARS-CoV-2 infection. More public outreach is needed to raise awareness of the benefits of treatment for COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Noah Kojima", + "author_inst": "UCLA" + }, + { + "author_name": "Jeffrey D Klausner", + "author_inst": "USC" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.21.22274082", "rel_title": "COVID-19 patients share common, corticosteroid-independent features of impaired host immunity to pathogenic molds", @@ -296749,45 +298791,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.21.22274140", - "rel_title": "Snotwatch COVID-Toes: An ecological study of chilblains and COVID-19 diagnoses in Victoria, Australia", - "rel_date": "2022-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.21.22274140", - "rel_abs": "BackgroundThe COVID-19 pandemic has caused widespread illness with varying clinical manifestations. One less-commonly-reported presentation of COVID-19 infection is chilblain-like lesions.\n\nAimsWe conducted an ecological analysis of chilblain presentations in comparison with confirmed and suspected COVID-19 infections in a primary care setting to establish that a relationship exists between the two.\n\nStudy DesignOur study collated data from three Primary Health Networks across Victoria, Australia, from 2017-2021, to understand patterns of chilblain presentations prior to and throughout the pandemic. Using a zero-inflated negative binomial regression analysis, we estimated the relationship between local minimum temperature, COVID-19 infections and the frequency of chilblain presentations.\n\nResultsWe found a 5.72 risk ratio of chilblain incidence in relation to COVID-19 infections and a 3.23 risk ratio associated with suspected COVID-19 infections. COVID-19 infections were also more strongly associated with chilblain presentations in 0-16-year-olds throughout the pandemic in Victoria.\n\nConclusionOur study statistically demonstrates that chilblains are significantly associated with COVID-19 infections in a primary care setting. This has major implications for clinicians aiming to diagnose COVID-19 infections or determine the cause of a presentation of chilblains. Additionally, we demonstrate the utility of large-scale primary care data and its potential application to monitoring the spread of COVID-19 infections across the state, supporting current epidemiological efforts for COVID-19 tracking.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Rana Sawires", - "author_inst": "Monash University" - }, - { - "author_name": "Christopher Pearce", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Michael Fahey", - "author_inst": "Monash Health" - }, - { - "author_name": "Hazel Clothier", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Karina Gardner", - "author_inst": "University of Newcastle" - }, - { - "author_name": "Jim Buttery", - "author_inst": "Murdoch Children's Research Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.19.22274044", "rel_title": "The statistical analysis of daily data associated with different parameters of the New Coronavirus COVID-19 pandemic in Georgia and their monthly interval prediction from January 1, 2022 to March 31, 2022", @@ -299998,6 +302001,77 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.04.20.488873", + "rel_title": "Uncovering the structural flexibility of SARS-CoV-2 glycoprotein spike variants", + "rel_date": "2022-04-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.20.488873", + "rel_abs": "The severe acute respiratory syndrome CoV-2 rapidly spread worldwide, causing a pandemic. After a period of evolutionary stasis, a set of SARS-CoV-2 mutations has arisen in the spike, the leading glycoprotein at the viral envelope and the primary antigenic candidate for vaccines against the 2019 CoV disease (COVID-19). Here, we present comparative biochemical data of the glycosylated full-length ancestral and D614G spike together with three other highly transmissible strains classified by the World Health Organization as variants of concern (VOC): beta, gamma, and delta. By showing that only D614G early variant has less hydrophobic surface exposure and trimer persistence at mid-temperatures, we place D614G with features that support a model of temporary fitness advantage for virus spillover worldwide. Further, during the SARS-CoV-2 adaptation, the spike accumulates alterations leading to less structural rigidity. The decreased trimer stability observed for the ancestral and the gamma strain and the presence of D614G uncoupled conformations mean higher ACE-2 affinities when compared to the beta and delta strains. Mapping the energetic landscape and flexibility of spike variants is necessary to improve vaccine development.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Hiam R. S. Arruda", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Tulio M. Lima", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Renata G. F. Alvim", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Fernanda B. A. Victorio", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Daniel P. B. Abreu", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Federico F. Marsili", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Karen D. Cruz", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Patricia Sosa-Acosta", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Mauricio Quinones-Vega", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Jessica S. Guedes", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "F\u00e1bio C. S. Nogueira", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Jerson L. Silva", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Leda R. Castilho", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Guilherme A. P. de Oliveira", + "author_inst": "Federal University of Rio de Janeiro" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.04.20.22274061", "rel_title": "Vaccine effectiveness against SARS-CoV-2 infection and COVID-19-related hospitalization with the Alpha, Delta and Omicron SARS-CoV-2 variants: a nationwide Danish cohort study", @@ -300219,41 +302293,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2022.04.13.22272869", - "rel_title": "Estimating the risk of hospitalisation and death in England's remaining unvaccinated population", - "rel_date": "2022-04-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.13.22272869", - "rel_abs": "The roll-out of COVID-19 vaccines in the England has generally been very good - with over 80% of over 12s having received two doses of vaccine by the start of February 2022, and 67% having received a further booster dose. Despite this, there is a small section of the population who remain unvaccinated, either due to lack of access, hesitancy or resistant to vaccination. In this report we estimate that, during 2021, there were approximately 3,500 deaths in unvaccinated people, who could otherwise have reasonably been expected to receive a vaccination. Further, we show that if all of the remaining unvaccinated population in England were to become infected (or reinfected) with the Omicron variant of COVID-19, we would expect to see approximately 11,700 further deaths and 29,600 hospitalisations. These number could fall to 5,300 and 19,600 respectively, if all but the most vaccine resistant individuals become fully vaccinated.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Joseph Shingleton", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Steven Dyke", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Brodie F Walker", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Archie Herrick", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Thomas Finnie", - "author_inst": "United Kingdom Health Security Agency" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.04.14.22273870", "rel_title": "Methadone overdoses increased 48% during the COVID-19 epidemic", @@ -301616,6 +303655,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2022.04.14.22273868", + "rel_title": "Effectiveness of Four Vaccines in Preventing SARS-CoV-2 Infection in Kazakhstan", + "rel_date": "2022-04-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.14.22273868", + "rel_abs": "BACKGROUNDIn February 2021 Kazakhstan began offering COVID-19 vaccines to adults. Breakthrough SARS-CoV-2 infections raised concerns about real-world vaccine effectiveness. We aimed to evaluate effectiveness of four vaccines against SARS-CoV-2 infection.\n\nMETHODSWe conducted a retrospective cohort analysis among adults in Almaty using aggregated vaccination data and individual-level breakthrough COVID-19 cases ([≥]14 days from 2nd dose) using national surveillance data. We ran time-adjusted Cox-proportional-hazards model with sensitivity analysis accounting for varying entry into vaccinated cohort to assess vaccine effectiveness for each vaccine (measured as 1-adjusted hazard ratios) using the unvaccinated population as reference (N=565,390). We separately calculated daily cumulative hazards for COVID-19 breakthrough among vaccinated persons by age and vaccine month.\n\nRESULTSFrom February 22 to Sept 1, 2021 in Almaty, 747,558 (57%) adults were fully vaccinated (received 2 doses) and 108,324 COVID-19 cases (11,472 breakthrough) were registered. Vaccine effectiveness against infection was 78% (sensitivity estimates: 74-82%) for QazVac, 77% (72- 81%) for Sputnik V, 71% (69-72%) for Hayat-Vax, and 69% (64-72%) for CoronaVac. Among vaccinated persons, the 90-day follow-up cumulative hazard for breakthrough infection was 2.2%. Cumulative hazard was 2.9% among people aged [≥]60 years versus 1.9% among persons aged 18-39 years (p<0.001), and 1.2% for people vaccinated in February-May versus 3.3% in June-August (p<0.001).\n\nCONCLUSIONOur analysis demonstrates high effectiveness of COVID-19 vaccines against infection in Almaty similar to other observational studies. Higher cumulative hazard of breakthrough among people >60 years of age and during variant surges warrants targeted booster vaccination campaigns.\n\nWhat is already known on this topicO_LIPlenty of data are published on effectiveness of mRNA vaccines; however, these vaccines were not widely available in many low- and middle-income countries in 2021.\nC_LIO_LIThere are no real-world effectiveness studies on several vaccines available in the Central Asia region, including QazVac vaccine, an inactivated vaccine developed by Kazakhstan.\nC_LIO_LIUnderstanding how these vaccines are performing outside of clinical trials is critical for the COVID-19 response and lack of published data can contribute to vaccine hesitancy.\nC_LI\n\nWhat this study addsO_LIOur study demonstrated that at the population-level the four vaccines against COVID-19 used in Kazakhstan were effective at preventing SARS-CoV-2 infection.\nC_LIO_LIVaccination reduced the risk of infection by 76% and prevented over 100,000 cases of SARS-CoV-2 infection in Almaty, the countrys most populous city.\nC_LIO_LIThis is also the first study that demonstrated high vaccine effectiveness in real-world conditions of QazVac, developed in Kazakhstan.\nC_LI\n\nHow this study might affect research, practice or policyO_LIPolicy makers in Kazakhstan and the Central Asia region need data on vaccines provided in the region to update evidence-based vaccine guidelines for different populations.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Dilyara NABIROVA", + "author_inst": "U.S. Centers for Disease Control and Prevention, Central Asia Regional Office" + }, + { + "author_name": "Roberta Horth", + "author_inst": "U.S. Centers for Disease Control and Prevention, Central Asia Regional Office" + }, + { + "author_name": "Manar Smagul", + "author_inst": "Scientific and practical center of sanitary-epidemiological examination and monitoring, branch of the National Center for Public Health, Almaty, Kazakhstan" + }, + { + "author_name": "Gaukhar Nukenova", + "author_inst": "Scientific and practical center of sanitary-epidemiological examination and monitoring, branch of the National Center for Public Health, Almaty, Kazakhstan" + }, + { + "author_name": "Aizhan Yesmagambetova", + "author_inst": "Ministry of Healthcare of the Republic of Kazakhstan" + }, + { + "author_name": "Daniel Singer", + "author_inst": "U.S. Centers for Disease Control and Prevention, Central Asia Regional Office" + }, + { + "author_name": "Alden Henderson", + "author_inst": "U.S. Centers for Disease Control and Prevention, Atlanta, USA" + }, + { + "author_name": "Alexey Tsoy", + "author_inst": "Ministry of Healthcare of the Republic of Kazakhstan" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.13.22273837", "rel_title": "How did the COVID-19 Pandemic impact self-reported cancer screening rates in 12 Midwestern states?", @@ -301865,49 +303951,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.18.488660", - "rel_title": "Modeling COVID-19 disease biology to identify drug treatment candidates", - "rel_date": "2022-04-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.18.488660", - "rel_abs": "Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Currently, there are a limited number of effective treatments. A variety of drugs that have been approved for other diseases are being tested for the treatment of COVID-19, and thus far only remdesevir, dexamethasone, baricitinib, tofacitinib, tocilizumab, and sarilumab have been recommended by the National Institutes of Health (NIH) COVID-19 Treatment Guidelines Panel for the therapeutic management of hospitalized adults with COVID-19. Using a disease biology modeling approach, we constructed a protein-protein interactome network based on COVID-19- associated genes/proteins described in research literature together with known protein-protein interactions in epithelial cells. Phenotype and disease enrichment analysis of the COVID-19 disease biology model demonstrated strong statistical enrichments consistent with patients clinical presentation. The model was used to interrogate host biological response induced by SARS-CoV-2 and identify COVID-19 drug treatment candidates that may inform on drugs currently being evaluated or provide insight into possible targets for potential new therapeutic agents. We focused on cancer drugs as they are often used to control inflammation, inhibit cell division, and modulate the host microenvironment to control the disease. From the top 30 COVID-19 drug candidates, twelve have a role as an antineoplastic agent, seven of which are approved for human use. Altogether, nearly 40% of the drugs identified by our model have been identified by others for COVID-19 clinical trials. Disease biology modeling incorporating disease-associated genes/proteins discussed in the research literature together with known molecular interactions in relevant cell types is a useful method to better understand disease biology and identify potentially effective therapeutic interventions.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Walter J Jessen", - "author_inst": "LabCorp: Laboratory Corporation of America Holdings" - }, - { - "author_name": "Stefan Diaz Gaisenband", - "author_inst": "LabCorp: Laboratory Corporation of America Holdings" - }, - { - "author_name": "M\u2019Lissa Quintanilla", - "author_inst": "LabCorp: Laboratory Corporation of America Holdings" - }, - { - "author_name": "Sadiq Lula", - "author_inst": "LabCorp: Laboratory Corporation of America Holdings" - }, - { - "author_name": "Patrick McLeroth", - "author_inst": "LabCorp: Laboratory Corporation of America Holdings" - }, - { - "author_name": "Adam Sullivan", - "author_inst": "LabCorp: Laboratory Corporation of America Holdings" - }, - { - "author_name": "Stanley Letovsky", - "author_inst": "LabCorp: Laboratory Corporation of America Holdings" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2022.04.12.22273760", "rel_title": "Admissions to a large tertiary care hospital and Omicron BA.1 and BA.2 SARS-CoV-2 PCR positivity: primary, contributing, or incidental COVID-19", @@ -303318,6 +305361,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.18.22273970", + "rel_title": "A comparative analysis of pediatric mental health-related emergency department utilization in Montreal, Canada before and during the COVID-19 pandemic", + "rel_date": "2022-04-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.18.22273970", + "rel_abs": "BackgroundReports on longitudinal trends in mental health-related (MHR) emergency department (ED) utilization spanning the pre- and post-pandemic periods are lacking, along with evidence comparing healthcare services utilization by sociodemographic subgroups. The aim of this study was to evaluate COVID-19-associated changes in MHR ED utilization among youth overall and by age, sex, and socioeconomic status (SES).\n\nMethodsThis retrospective cross-sectional study analyzed MHR ED utilization before and during the COVID-19 pandemic at a large urban pediatric tertiary care hospital in Montreal, Canada. All ED visits for children (5-11 years) and adolescents (12-17 years) between April 1, 2016 and November 30, 2021 were included. The main outcome was the monthly count of MHR ED visits. Pre-pandemic and pandemic periods were compared using an interrupted time series design. The effect of seasonality (in months), age (in years), sex (male or female), and SES (low, average, high) were compared using a generalized additive model.\n\nResultsThere were a total of 437,147 ED visits (204,215 unique patients) during the five-year study period of which 9,748 (5.8%) were MHR visits (7,686 unique patients). We observed an increase of 69% (95% CI, +53% to +85%; p = .001) in the mean monthly count of MHR ED visits during the pandemic period, which remained significant after adjusting for seasonality (44% increase, 95% CI, +38% to +51%; p = .001). The chance of presenting for a MHR ED visit increased non-linearly with age. There were increased odds of presenting for a MHR ED visit among girls between the pre-pandemic and pandemic periods (OR 1.42, 95% CI 1.29-1.56). No difference by SES group during and before the COVID-19 pandemic was found (OR 1.01, 95% CI 0.89-1.15 [low]; OR 1.09, 95% CI 0.96-1.25 [high]).\n\nConclusionsOur study shows important increases in MHR ED utilization among youth, and especially among girls, during the first 20 months of the COVID-19 pandemic, highlighting the need for sustained, targeted and scalable mental health resources to support youth mental health during the current and future crises.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Gabrielle Beaudry", + "author_inst": "Department of Psychiatry, University of Oxford, Oxford (UK)" + }, + { + "author_name": "Olivier Drouin", + "author_inst": "Sainte-Justine Hospital Research Center, Montreal, Quebec (Canada)" + }, + { + "author_name": "Jocelyn Gravel", + "author_inst": "Sainte-Justine Hospital Research Center, Montreal, Quebec (Canada)" + }, + { + "author_name": "Anna Smyrnova", + "author_inst": "Sainte-Justine Hospital Research Center, Montreal, Quebec (Canada)" + }, + { + "author_name": "Andreas Bender", + "author_inst": "Department of Statistics, LMU Munich, Munich (Germany)" + }, + { + "author_name": "Massimiliano Orri", + "author_inst": "McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec (Canada)" + }, + { + "author_name": "Marie-Claude Geoffroy", + "author_inst": "McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec (Canada)" + }, + { + "author_name": "Nicholas Chadi", + "author_inst": "Sainte-Justine Hospital Research Center, Montreal, Quebec (Canada)" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.04.15.22273460", "rel_title": "Coronavirus infection in neonates: Neurodevelopmental outcomes at 18 months of age", @@ -303607,129 +305697,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.07.22273558", - "rel_title": "Safety and effectiveness of RBD-specific polyclonal equine F(ab')2 fragments for the treatment of hospitalized patients with severe Covid-19 disease: a retrospective cohort study.", - "rel_date": "2022-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.07.22273558", - "rel_abs": "Passive immunotherapy has been evaluated as a therapeutic alternative for patients with COVID-19 disease. Equine polyclonal immunotherapy for COVID-19 (EPIC) showed adequate safety and potential efficacy in a clinical trial setting and obtained emergency use authorization in Argentina. We studied its utility in a real world setting with a larger population.\n\nMethodsWe conducted a retrospective cohort study at \"Hospital de Campana Escuela-Hogar\" in Corrientes, Argentina, to assess safety and effectiveness of EPIC in hospitalized adults with severe COVID-19 pneumonia. Primary endpoints were 28-days all-cause mortality and safety. Mortality and improvement in modified WHO clinical scale at 14 and 21 days were secondary endpoints. Potential confounder adjustment was made by logistic regression weighted by the inverse of the probability of receiving the treatment (IPTW) and doubly robust approach.\n\nResultsClinical records of 395 exposed (EPIC) and 446 non-exposed (Controls) patients admitted between November 2020 and April 2021 were analyzed. Median age was 58 years and 56.8% were males. Mortality at 28 days was 15.7% (EPIC) vs. 21.5% (Control). After IPTW adjustment the OR was 0.66 (95 % CI: 0.46 - 0.96), P= 0.03. The effect was more evident in the subgroup who received two EPIC doses (complete treatment, n=379), OR: 0.58 (95% CI 0.39 to 0.85), P=0.005. Overall and serious adverse events were not significantly different between groups.\n\nImportanceIn this retrospective cohort study, EPIC showed adequate safety and effectiveness in the treatment of hospitalized patients with severe SARS-CoV-2 disease.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Diego H Farizano Salazar", - "author_inst": "Hospital de Campa\u00f1a Escuela Hogar" - }, - { - "author_name": "Fernando Achinelli", - "author_inst": "Hospital de Campa\u00f1a Escuela Hogar" - }, - { - "author_name": "Mariana Colonna", - "author_inst": "Inmunova S.A." - }, - { - "author_name": "Luc\u00eda P\u00e9rez", - "author_inst": "Departamento de Investigaci\u00f3n, Hospital Italiano de Buenos Aires" - }, - { - "author_name": "Anal\u00eda A Gim\u00e9nez", - "author_inst": "Hospital de Campa\u00f1a Escuela Hogar" - }, - { - "author_name": "Mar\u00eda A Ojeda", - "author_inst": "Hospital de Campa\u00f1a Escuela Hogar" - }, - { - "author_name": "Susana N Miranda Puente", - "author_inst": "Hospital de Campa\u00f1a Escuela Hogar" - }, - { - "author_name": "L\u00eda S\u00e1nchez Negrete", - "author_inst": "Hospital de Campa\u00f1a Escuela Hogar" - }, - { - "author_name": "Florencia Ca\u00f1ete", - "author_inst": "Hospital de Campa\u00f1a Escuela Hogar" - }, - { - "author_name": "Ornela I Martelotte Ibarra", - "author_inst": "Hospital de Campa\u00f1a Escuela Hogar" - }, - { - "author_name": "Santiago Sanguineti", - "author_inst": "Inmunova S.A." - }, - { - "author_name": "Linus Spatz", - "author_inst": "Inmunova S.A." - }, - { - "author_name": "Fernando A Goldbaum", - "author_inst": "Inmunova S.A." - }, - { - "author_name": "Carolina Massa", - "author_inst": "Inmunova S.A." - }, - { - "author_name": "Marta Rivas", - "author_inst": "Inmunova S.A." - }, - { - "author_name": "Mariana Pichel", - "author_inst": "Inmunova S.A." - }, - { - "author_name": "Yanina Hiriart", - "author_inst": "Inmunova S.A." - }, - { - "author_name": "Vanesa Zylberman", - "author_inst": "Inmunova S.A." - }, - { - "author_name": "Sandra Gallego", - "author_inst": "InViV-CONICET, Universidad Nacional de C\u00f3rdoba" - }, - { - "author_name": "Brenda Konigheim", - "author_inst": "InViV-CONICET, Universidad Nacional de C\u00f3rdoba" - }, - { - "author_name": "Francisco Fern\u00e1ndez", - "author_inst": "Laboratorio Elea Phoenix S.A." - }, - { - "author_name": "Mat\u00edas Deprati", - "author_inst": "Laboratorio Elea Phoenix S.A." - }, - { - "author_name": "Ian Roubicek", - "author_inst": "Inmunova S.A." - }, - { - "author_name": "Diego H Giunta", - "author_inst": "Departamento de Investigaci\u00f3n, Hospital Italiano de Buenos Aires" - }, - { - "author_name": "Esteban Nannini", - "author_inst": "Departamento de Enfermedades Infecciosas, Sanatorio Brit\u00e1nico" - }, - { - "author_name": "Gustavo Lopardo", - "author_inst": "Hospital Municipal Dr. Bernardo Houssay" - }, - { - "author_name": "Waldo H Belloso", - "author_inst": "Departamento de Investigaci\u00f3n, Hospital Italiano de Buenos Aires" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.15.22273914", "rel_title": "mRNA-1273 but not BNT162b2 induces antibodies against polyethylene glycol (PEG) contained in mRNA-based vaccine formulations", @@ -304960,6 +306927,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.11.22273702", + "rel_title": "Making maternity and neonatal care personalised in the COVID-19 pandemic: results from the Babies Born Better Survey in the UK and the Netherlands", + "rel_date": "2022-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.11.22273702", + "rel_abs": "Structured abstractO_ST_ABSBackgroundC_ST_ABSThe COVID-19 pandemic had a severe impact on womens birth experiences. To date, there are no studies that use both quantitative and qualitative data to compare womens birth experiences before and during the pandemic, across more than one country.\n\nAimTo examine womens birth experiences during the COVID-19 pandemic and to compare the experiences of women who gave birth in the United Kingdom (UK) or the Netherlands (NL) either before or during the pandemic.\n\nMethodThis study is based on analyses of quantitative and qualitative data from the online Babies Born Better survey. Responses recorded by women giving birth in the UK and the NL between June and December 2020 have been used, encompassing women who gave birth between 2017 and 2020. Quantitative data were analysed descriptively, and chi-squared tests were performed to compare women who gave birth pre- versus during pandemic and separately by country. Qualitative data was analysed by inductive thematic analysis.\n\nFindingsRespondents in both the UK and the NL who gave birth during the pandemic were as likely, or, if they had a self-reported above average standard of life, more likely to rate their labour and birth experience positively when compared to women who gave birth pre-pandemic. This was despite the fact that those labouring in the pandemic reported less support and choice. Two potential explanatory themes emerged from the qualitative data: respondents had lower expectations during the pandemic, and they appreciated that care providers tried hard to personalise care.\n\nConclusionOur study implies that many women labouring during the COVID-19 pandemic experienced restrictions, but their experience was mitigated by staff actions. However, personalised care should not be maintained by the good will of care providers, but should be a priority in maternity care policy to benefit all service users equitably.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Lauri M.M. van den Berg", + "author_inst": "Amsterdam UMC Locatie VUmc" + }, + { + "author_name": "Naseerah Akooji", + "author_inst": "University of Central Lancashire" + }, + { + "author_name": "Gill Thomson", + "author_inst": "University of Central Lancashire" + }, + { + "author_name": "Ank de Jonge", + "author_inst": "Amsterdam UMC Locatie VUmc" + }, + { + "author_name": "Marie-Clare Balaam", + "author_inst": "University of Central Lancashire" + }, + { + "author_name": "Anastasia Topalidou", + "author_inst": "University of Central Lancashire" + }, + { + "author_name": "Soo Downe", + "author_inst": "University of Central Lancashire" + }, + { + "author_name": "the ASPIRE COVID-19 research team", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2022.04.15.22273412", "rel_title": "COVID-19 vaccine effectiveness against SARS-CoV-2 infection in the United States prior to the Delta and Omicron-associated surges: a retrospective cohort study of repeat blood donors", @@ -305117,37 +307131,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.15.22273881", - "rel_title": "Can We Really Trust the Findings of the COVID-19 Research? Quality Assessment of Randomized Controlled Trials Published on COVID-19", - "rel_date": "2022-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.15.22273881", - "rel_abs": "ObjectiveTo evaluate the quality of randomized controlled trials (RCTs) published on Coronavirus Disease-19 (COVID-19) and to investigate the reasons behind compromising the quality, if found.\n\nMethodsA systematic literature search was performed in PubMed, Google Scholar, and Cochrane CENTRAL to identify the Randomized Controlled Trails published on Coronavirus Disease-19 between 1st Dec 2019 to 31st Aug 2021. Research articles met with study criteria were included in the study. Assessment of quality of randomized controlled trials was done using modified Jadad scale.\n\nResults21,259 records of randomized controlled trials were identified through database searching, out of which 90 randomized controlled trials were included in the study and, 34 (37.8%) were of high-quality, 46 (51.1%) were of moderate quality, and 10 (11.1 %) were of low-quality studies. There were 40 (44.4%), 38 (42.2%), and 12 (13.3%) randomized controlled trials published in the early, middle, and late terms with Jadad score 5.12{+/-}1.67, 5.34{+/-}1.32, and 5.68{+/-}1.50 respectively (P=0.52). When comparing the blinding status, appropriate blinding, and methods to evaluate adverse events in randomized controlled trials with modified Jadad score, a significant difference was observed (P<0.001). A significant moderate positive correlation was found between the impact factor of the journal and the modified Jadad scale score (R2= 0.48, P<0.001).\n\nConclusionFindings from our study indicate that accelerated publication of Coronavirus Disease-19 researches along with the fast-track review process has resulted in lowering study quality scores. With the emergence of stronger evidence, Coronavirus Disease-19 clinical studies with lower methodological quality should be revisited.\n\nImpacts on practiceO_LIThere have been numerous sacrifices and tragedies in the clinical response to covid-19. Revising the quality of randomized controlled trials published on COVID-19 as we enter the third wave of the pandemic and beyond, will improve the evidence-based practice of medications for clinical pharmacy services.\nC_LIO_LICOVID-19 Patients will benefit from evidence-based pharmaceutical care through reduced drug-related problems.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Athira S Joshy", - "author_inst": "National Institute of Pharmaceutical Education and Research (NIPER), Guwahati" - }, - { - "author_name": "Christy Thomas", - "author_inst": "National Institute of Pharmaceutical Education and Research (NIPER), Guwahati" - }, - { - "author_name": "Saphal Surendran", - "author_inst": "National Institute of Pharmaceutical Education and Research (NIPER), Guwahati" - }, - { - "author_name": "Krishna Undela", - "author_inst": "National Institute of Pharmaceutical Education and Research (NIPER),Guwahati" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.15.22273859", "rel_title": "Effectiveness of ChAdOx1 nCoV-19 Corona Virus Vaccine (CovishieldTM) in preventing SARS-CoV2 infection, Chennai, Tamil Nadu, India, 2021", @@ -306582,6 +308565,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.12.22273804", + "rel_title": "Nowcasting and Forecasting COVID-19 Waves: The Recursive and Stochastic Nature of Transmission", + "rel_date": "2022-04-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.12.22273804", + "rel_abs": "We propose a parsimonious, yet effective, susceptible-exposed-infected-removed-type model that incorporates the time change in the transmission and death rates. The model is calibrated by Tikhonov-type regularization from official reports from New York City (NYC), Chicago, the State of Sao Paulo, in Brazil, and British Columbia, in Canada. To forecast, we propose different ways to extend the transmission parameter, considering its estimated values. The forecast accuracy is then evaluated using real data from the above referred places. All the techniques accurately provided forecast scenarios for periods 15 days long. One of the models effectively predicted the magnitude of the four waves of infections in NYC, including the one caused by the Omicron variant for periods of 45 days long using out-of-sample data.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.12.22273761", "rel_title": "Multiplex RT-qPCR assay (N200) to detect and estimate prevalence of multiple SARS-CoV-2 Variants of Concern in wastewater", @@ -306811,41 +308808,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.04.12.488092", - "rel_title": "SARS-CoV-2 Delta breakthrough infections in vaccinated patients", - "rel_date": "2022-04-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.12.488092", - "rel_abs": "The continuous emergence of SARS-CoV-2 variants with increased transmission and immune evasion has caused breakthrough infections in vaccinated population. It is important to determine the threshold of neutralizing antibody titers that permit breakthrough infections. Here we tested the neutralization titers of vaccinated patients who contracted Delta variant. All 75 patients with Delta breakthrough infections exhibited neutralization titers (NT50) of less than 70. Among the breakthrough patients, 76%, 18.7%, and 5.3% of them had the NT50 ranges of <20, 20-50, and 50-69, respectively. These clinical laboratory results have implications in vaccine strategy and public health policy.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jing Zou", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Xuping Xie", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Mingru Liu", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Ping Ren", - "author_inst": "University of Texas Medical Branch" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.04.12.488075", "rel_title": "Structural and biochemical mechanism for increased infectivity and immune evasion of Omicron BA.1 and BA.2 variants and their mouse origins", @@ -308365,6 +310327,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.07.22273561", + "rel_title": "The effect of the COVID-19 lockdown on mental health care use in South Africa: an interrupted time series analysis", + "rel_date": "2022-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.07.22273561", + "rel_abs": "AimsIn March 2020, South Africa introduced a lockdown in response to the COVID-19 pandemic, entailing the suspension of all non-essential activities and a complete ban of tobacco and alcohol sales. We studied the effect of the lockdown on mental health care utilisation rates in private-sector care in South Africa.\n\nMethodsWe did an interrupted time series analysis using insurance claims from January 1, 2017, to June 1, 2020 of beneficiaries 18 years or older from a large private sector medical aid scheme. We calculated weekly outpatient consultation and hospital admission rates for organic mental disorders, substance use disorders, serious mental disorders, depression, anxiety, other mental disorders, any mental disorder, and alcohol withdrawal syndrome. We calculated adjusted odds ratios (OR) for the effect of the lockdown on weekly outpatient consultation and hospital admission rates and the weekly change in rates during the lockdown until June 1, 2020.\n\nResults710,367 persons were followed up for a median of 153 weeks. Hospital admission rates (OR 0.38; 95% CI 0.33-0.44) and outpatient consultation rates (OR 0.74; 95% CI 0.63-0.87) for any mental disorder decreased substantially after the lockdown and did not recover to pre-lockdown levels until June 1, 2020. Health care utilisation rates for alcohol withdrawal syndrome doubled after the introduction of the lockdown, but the statistical uncertainty around the estimates was large (OR 2.24; 95% CI 0.69-7.24).\n\nConclusionsReduced mental health care contact rates during the COVID-19 lockdown likely reflect a substantial unmet need for mental health services with potential long-term consequences for mental health patients and their families. Steps to ensure access and continuity of mental health services during future lockdowns should be considered.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Anja Elisabeth Wettstein", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Switzerland and Graduate School for Health Sciences, University of Bern, Switzerland" + }, + { + "author_name": "Mpho Tlali", + "author_inst": "Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa" + }, + { + "author_name": "John A Joska", + "author_inst": "HIV Mental Health Research Unit, Department of Psychiatry and Mental Health, Neuroscience Institute, Cape Town, South Africa" + }, + { + "author_name": "Morna Cornell", + "author_inst": "Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa" + }, + { + "author_name": "Veronika W Skrivankova", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + }, + { + "author_name": "Soraya Seedat", + "author_inst": "Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa" + }, + { + "author_name": "Johannes P Mouton", + "author_inst": "Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa and Division of Clinical Pharmacology, Department of M" + }, + { + "author_name": "Leigh L van den Heuvel", + "author_inst": "Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa" + }, + { + "author_name": "Nicola Maxwell", + "author_inst": "Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa" + }, + { + "author_name": "Mary-Ann Davies", + "author_inst": "Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa" + }, + { + "author_name": "Gary Maartens", + "author_inst": "Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa" + }, + { + "author_name": "Matthias Egger", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Centre for Infectious Disease Epidemiology and Research, University of Cape " + }, + { + "author_name": "Andreas D Haas", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.07.22273593", "rel_title": "Inequities in COVID-19 vaccine and booster coverage across Massachusetts ZIP codes: large gaps persist after the 2021/22 Omicron wave", @@ -308498,29 +310527,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.11.487924", - "rel_title": "Independent acquisition of short insertions at the RIR1 site in the spike N-terminal domain of the SARS-CoV-2 BA.2 lineage", - "rel_date": "2022-04-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.11.487924", - "rel_abs": "Although the SARS-CoV-2 variants BA.1 and BA.2 share over 30 non-synonymous substitutions in the spike glycoprotein, they show several unique mutations that were likely acquired after the split between these two major omicron lineages. One of the most intriguing mutations associated with BA.1 is the presence of the inserted tripeptide Glu-Pro-Glu within the N-terminal domain. While the functional implications of this insertion are still unclear, several other SARS-CoV-2 lineages had previously independently acquired similarly short insertions at the very same site, named RIR1. We have previously identified this site, located approximately between codon 212 and codon 216, as a hotspot of insertions, which usually involve small nucleotide sequences including three or four codons.\n\nHere we show that similar insertion events have independently occurred at least 13 times in early 2022 within the BA.2 lineage, being occasionally associated with significant community transmission. One of these omicron sublineages, characterized by a Ser-Gly-Arg insertion in position 212, is responsible of over 2% of all SARS-CoV-2 cases recorded in Denmark, as of early April 2022. Molecular surveillance data highlight a slow but steady growth compared with the parental BA.2 lineage in all Danish regions, suggesting that the RIR1 insertion may confer a selective advantage. We report the identification of other currently circulating BA.2 sublineages showing similar insertions, whose spread should be therefore carefully monitored in the upcoming months.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Samuele Greco", - "author_inst": "University of Trieste" - }, - { - "author_name": "Marco Gerdol", - "author_inst": "University of Trieste" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2022.04.10.486823", "rel_title": "Subtyping of major SARS-CoV-2 variants reveals different transmission dynamics", @@ -309883,6 +311889,89 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.04.07.487520", + "rel_title": "Hippo Signaling Pathway Activation during SARS-CoV-2 Infection Contributes to Host Antiviral Response", + "rel_date": "2022-04-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.07.487520", + "rel_abs": "SARS-CoV-2, responsible for the COVID-19 pandemic, causes respiratory failure and damage to multiple organ systems. The emergence of viral variants poses a risk of vaccine failures and prolongation of the pandemic. However, our understanding of the molecular basis of SARS-CoV-2 infection and subsequent COVID-19 pathophysiology is limited. In this study, we have uncovered a critical role for the evolutionarily conserved Hippo signaling pathway in COVID-19 pathogenesis. Given the complexity of COVID-19 associated cell injury and immunopathogenesis processes, we investigated Hippo pathway dynamics in SARS-CoV-2 infection by utilizing COVID-19 lung samples, and human cell models based on pluripotent stem cell-derived cardiomyocytes (PSC-CMs) and human primary lung air-liquid interface (ALI) cultures. SARS-CoV-2 infection caused activation of the Hippo signaling pathway in COVID-19 lung and in vitro cultures. Both parental and Delta variant of concern (VOC) strains induced Hippo pathway. The chemical inhibition and gene knockdown of upstream kinases MST1/2 and LATS1 resulted in significantly enhanced SARS-CoV-2 replication, indicating antiviral roles. Verteporfin a pharmacological inhibitor of the Hippo pathway downstream transactivator, YAP, significantly reduced virus replication. These results delineate a direct antiviral role for Hippo signaling in SARS-CoV-2 infection and the potential for this pathway to be pharmacologically targeted to treat COVID-19.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Gustavo Garcia Jr.", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Yijie Wang", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Joseph Ignatius Irudayam", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Arjit Vijey Jeyachandran", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Sebastian Castillo Cario", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Chandani Sen", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Shen Li", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Yunfeng Li", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Ashok Kumar", + "author_inst": "Wayne State University" + }, + { + "author_name": "Karin Nielsen-Saines", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Samuel W. French", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Priya S. Shah", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Kouki Morizono", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Brigitte Gomperts", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Arjun Deb", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Arunachalam Ramaiah", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Vaithilingaraja Arumugaswami", + "author_inst": "University of California, Los Angeles" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.04.07.487528", "rel_title": "Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike", @@ -310124,65 +312213,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.04.08.487674", - "rel_title": "NVX-CoV2373 vaccination induces functional SARS-CoV-2-specific CD4+ and CD8+ T cell responses", - "rel_date": "2022-04-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.08.487674", - "rel_abs": "NVX-CoV2373 is an adjuvanted recombinant full-length SARS-CoV-2 spike trimer protein vaccine demonstrated to be protective against COVID-19 in efficacy trials. Here we demonstrate that vaccinated subjects made CD4+ T cell responses after one and two doses of NVX-CoV2373, and a subset of individuals made CD8+ T cell responses. Characterization of the vaccine-elicited CD8+T cells demonstrated IFN{gamma} production. Characterization of the vaccine-elicited CD4+ T cells revealed both circulating T follicular helper cells (cTFH) and TH1 cells (IFN{gamma}, TNF, and IL-2) were detectable within 7 days of the primary immunization. Spike-specific CD4+ T cells were correlated with the magnitude of the later SARS-CoV-2 neutralizing antibody titers, indicating that robust generation of CD4+ T cells, capable of supporting humoral immune responses, may be a key characteristic of NVX-CoV2373 which utilizes Matrix-M adjuvant.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Carolyn Rydyznski Moderbacher", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Christina Kim", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Jose Mateus", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Joyce Plested", - "author_inst": "Novavax, Inc" - }, - { - "author_name": "Mingzhu Zhu", - "author_inst": "Novavax, Inc" - }, - { - "author_name": "Shane Cloney-Clark", - "author_inst": "Novavax, Inc" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute For Immunology" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Louis Fries", - "author_inst": "Novavax, Inc" - }, - { - "author_name": "Gregory Glenn", - "author_inst": "Novavax, Inc" - }, - { - "author_name": "Shane Crotty", - "author_inst": "La Jolla Institute For Immunology (LJI)" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.04.06.22272747", "rel_title": "Longitudinal lung function assessment of patients hospitalised with COVID-19 using 1H and 129Xe lung MRI", @@ -311865,6 +313895,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.06.22273080", + "rel_title": "Serious underlying medical conditions and COVID-19 vaccine hesitancy.", + "rel_date": "2022-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.06.22273080", + "rel_abs": "ObjectiveTo examine vaccine uptake, hesitancy and explanatory factors amongst people with serious and/or chronic health conditions, including the impact of underlying disease on attitudes to vaccination.\n\nDesignCross-sectional survey.\n\nSettingTen Australian health services.\n\nParticipants4683 patients (3560 cancer, 842 diabetes and 281 multiple sclerosis) receiving care at the health services participated in the 42-item survey, between June 30 to October 5, 2021.\n\nMain outcome measuresSociodemographic and disease-related characteristics, COVID-19 vaccine uptake, and the scores of three validated scales which measured vaccine hesitancy and vaccine-related beliefs generally and specific to the participants disease, including the Oxford COVID-19 Vaccine Hesitancy Scale, the Oxford COVID-19 Vaccine Confidence and Complacency Scale and the Disease Influenced Vaccine Acceptance Scale. Multivariable logistic regression was used to determine the associations between scale scores and vaccine uptake.\n\nResultsOf all participants, 81.5% reported having at least one COVID-19 vaccine. Unvaccinated status was associated with younger age, female sex, lower education and income, English as a second language, and residence in regional areas (all p<0.05). Unvaccinated participants were more likely to report greater vaccine hesitancy and more negative perceptions toward vaccines (all p<0.05). Disease-related vaccine concerns were associated with unvaccinated status and hesitancy, including greater complacency about COVID-19 infection, and concerns relating to vaccine efficacy and impact on their disease and/or treatment (all p<0.05).\n\nConclusionsDisease-specific concerns impact COVID-19 vaccine-related behaviours and beliefs in people with serious and/or chronic health conditions. This highlights the need to develop targeted strategies and education about COVID-19 vaccination to support medically vulnerable populations and health professionals.\n\nTrial registrationACTRN12621001467820", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Daphne Day", + "author_inst": "Monash Health" + }, + { + "author_name": "Lisa Grech", + "author_inst": "Monash University" + }, + { + "author_name": "Mike Nguyen", + "author_inst": "Monash Health" + }, + { + "author_name": "Nathan Bain", + "author_inst": "Monash Health" + }, + { + "author_name": "Alastair Kwok", + "author_inst": "Monash Health" + }, + { + "author_name": "Sam Harris", + "author_inst": "Bendigo Health" + }, + { + "author_name": "Hieu Chau", + "author_inst": "Latrobe Regional Hospital" + }, + { + "author_name": "Bryan Chan", + "author_inst": "Sunshine Coast Hospital and Health Service" + }, + { + "author_name": "Richard Blennerhassett", + "author_inst": "Central Coast Haematology" + }, + { + "author_name": "Louise Nott", + "author_inst": "Icon Cancer Centre Hobart" + }, + { + "author_name": "Nada Hamad", + "author_inst": "St Vincent's Hospital Sydney" + }, + { + "author_name": "Annette Tognela", + "author_inst": "Campbelltown Hospital" + }, + { + "author_name": "David Hoffman", + "author_inst": "Dr David Hoffman" + }, + { + "author_name": "Amelia McCartney", + "author_inst": "Monash Health" + }, + { + "author_name": "Kate Webber", + "author_inst": "Monash Health" + }, + { + "author_name": "Jennifer Wong", + "author_inst": "Monash Health" + }, + { + "author_name": "Craig Underhill", + "author_inst": "Border Medical Oncology" + }, + { + "author_name": "Brett Sillars", + "author_inst": "Sunshine Coast Hospital and Health Service" + }, + { + "author_name": "Antony Winkel", + "author_inst": "Sunshine Coast Hospital and Health Service" + }, + { + "author_name": "Mark Savage", + "author_inst": "Bendigo Health" + }, + { + "author_name": "Bao Sheng Loe", + "author_inst": "Cambridge University" + }, + { + "author_name": "Daniel Freeman", + "author_inst": "University of Oxford" + }, + { + "author_name": "Eva Segelov", + "author_inst": "Monash Health" + }, + { + "author_name": "- CANVACCS, DIABVACCS, and MSVACCS investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.06.22273512", "rel_title": "Pandemic-EBT and grab-and-go school Meals: Costs, reach, and benefits of two approaches to keep children fed during school closures due to COVID-19", @@ -311994,29 +314135,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.03.22273345", - "rel_title": "Racial/Ethnic, Biomedical, and Sociodemographic Risk Factors for COVID-19 Positivity and Hospitalization in the San Francisco Bay Area", - "rel_date": "2022-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.03.22273345", - "rel_abs": "BACKGROUNDThe COVID-19 pandemic has uncovered clinically meaningful racial/ethnic disparities in COVID-19-related health outcomes. Current understanding of the basis for such an observation remains incomplete, with both biomedical and social/contextual variables proposed as potential factors.\n\nPURPOSEUsing a logistic regression model, we examined the relative contributions of race/ethnicity, biomedical, and socioeconomic factors to COVID-19 test positivity and hospitalization rates in a large academic health care system in the San Francisco Bay Area prior to the advent of vaccination and other pharmaceutical interventions for COVID-19.\n\nRESULTSWhereas socioeconomic factors, particularly those contributing to increased social vulnerability, were associated with test positivity for COVID-19, biomedical factors and disease co-morbidities were the major factors associated with increased risk of COVID-19 hospitalization. Hispanic individuals had a higher rate of COVID-19 positivity, while Asian persons had higher rates of COVID-19 hospitalization. Diabetes was an important risk factor for COVID-19 hospitalization, particularly among Asian patients, for whom diabetes tended to be more frequently undiagnosed and higher in severity.\n\nCONCLUSIONSWe observed that biomedical, racial/ethnic, and socioeconomic factors all contributed in varying but distinct ways to COVID-19 test positivity and hospitalization rates in a large, multiracial, socioeconomically diverse metropolitan area of the United States. The impact of a number of these factors differed according to race/ethnicity. Improving over-all COVID-19 health outcomes and addressing racial and ethnic disparities in COVID-19 out-comes will likely require a comprehensive approach that incorporates strategies that target both individual-specific and group contextual factors.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Wendy K. Tam Cho", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "David G. Hwang", - "author_inst": "University of California San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.05.487240", "rel_title": "Vascular inflammation exposes perivascular cells to SARS-CoV-2 infection", @@ -313519,6 +315637,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2022.03.29.22273148", + "rel_title": "Modeling behavior change and underreporting in the early phase of COVID-19 pandemic in Metro Manila, Philippines", + "rel_date": "2022-04-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.29.22273148", + "rel_abs": "IntroductionAt the start of the pandemic, the Philippine capital Metro Manila was placed under a strict lockdown termed Enhanced Community Quarantine (ECQ). When ECQ was eased to General Community Quarantine (GCQ) after three months, healthcare systems were soon faced with a surge of COVID-19 cases, putting most facilities at high or critical risk and prompting a return to a stricter policy.\n\nMethodsWe developed a mathematical model considering behavior changes and underreporting to represent the first major epidemic wave in Metro Manila. Key parameters were fitted to the cumulative cases in the capital from March to September 2020. A bi-objective optimization problem was formulated that allows easing of restrictions at an earlier time and minimizes the necessary additional beds to ensure sufficient capacity in healthcare facilities once ECQ was lifted.\n\nResultsIf behavior was changed one to four weeks earlier before GCQ, then the cumulative number of cases can be reduced by up to 55% and the peak delayed by up to four weeks. Increasing the reporting ratio during ECQ threefold may increase the reported cases by 23% but can reduce the total cases, including the unreported, by 61% on June 2020. If GCQ began on May 28, 2020, 48 beds should have been added per day to keep the capacity only at high-risk (75% occupancy). Among the optimal solutions, the peak of cases is lowest if ECQ was lifted on May 20, 2020 and with at least 56 additional beds per day.\n\nConclusionSince infectious diseases are likely to reemerge, the formulated model can be used as a decision support tool to improve existing policies and plan effective strategies that can minimize the socioeconomic impact of strict lockdown measures and ensure adequate healthcare capacity.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Victoria May P. Mendoza", + "author_inst": "Institute of Mathematics, University of the Philippines Diliman" + }, + { + "author_name": "Renier Mendoza", + "author_inst": "Institute of Mathematics, University of the Philippines Diliman" + }, + { + "author_name": "Youngsuk Ko", + "author_inst": "Department of Mathematics, Konkuk University" + }, + { + "author_name": "Jongmin Lee", + "author_inst": "Department of Mathematics, Konkuk University" + }, + { + "author_name": "Eunok Jung", + "author_inst": "Department of Mathematics, Konkuk University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.04.03.22273370", "rel_title": "Automated method to extract and purify RNA from wastewater enables more sensitive detection of SARS-CoV-2 markers in community sewersheds", @@ -313684,65 +315837,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.03.29.22272960", - "rel_title": "Nonutility of procalcitonin for diagnosing bacterial pneumonia in COVID-19", - "rel_date": "2022-04-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.29.22272960", - "rel_abs": "Patients hospitalized with COVID-19 are at significant risk for superimposed bacterial pneumonia. However, diagnosing superinfection is challenging due to its clinical resemblance to severe COVID-19. We therefore evaluated whether the immune biomarker, procalcitonin, could facilitate the diagnosis of bacterial superinfection. To do so, we identified 185 patients with severe COVID-19 who underwent lower respiratory culture; 85 had superinfection. Receiver operating characteristic curve analysis showed that procalcitonin at the time of culture was incapable of distinguishing patients with bacterial infection (AUC, 0.52). We conclude that static measurement of procalcitonin does not aid in the diagnosis of superinfection in severe COVID-19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Avi J Cohen", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Laura R Glick", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Seohyuk Lee", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Yukiko Kunitomo", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Derek A Tsang", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Sarah Pitafi", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Patricia Valda Toro", - "author_inst": "University of California San Francisco School of Medicine" - }, - { - "author_name": "Ethan Zhang", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Rupak Datta", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Charles S Dela Cruz", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Samir Gautam", - "author_inst": "Yale School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.03.31.22273072", "rel_title": "Cardiovascular diseases worsen the maternal prognosis of COVID-19", @@ -315553,6 +317647,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2022.04.02.22273333", + "rel_title": "High rate of BA.1, BA.1.1 and BA.2 in triple vaccinated", + "rel_date": "2022-04-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.02.22273333", + "rel_abs": "BackgroundBooster vaccine doses offer protection against severe COVID-19 caused by omicron but are less effective against infection. Characteristics such as serological correlates of protection, viral abundance, and clearance of omicron infection in triple vaccinated individuals are scarce.\n\nMethodsWe conducted a 4-week twice-weekly SARS-CoV-2 qPCR screening shortly after an mRNA vaccine booster in 368 healthcare workers. Spike-specific IgG levels and neutralization titers were determined at study start. qPCR-positive participants were sampled repeatedly for two weeks and monitored for symptoms.\n\nResultIn total 81 (cumulative incidence 22%) omicron infections were detected, divided between BA.1, BA.1.1 and BA.2. Increasing post-booster antibody titers were protective against infection (p<0.05), linked to reduced viral load (p<0.01) and time to viral clearance (p<0.05). Only 10% of infected participants remained asymptomatic through the course of their infection. Viral load peaked at day 3 and live virus could be detected for up to 9 days after first PCR-positive sample. Presence of symptoms correlated to elevated viral load (p<0.0001), but despite resolution of symptoms most participants showed Ct levels <30 at day 9. No significant differences were observed for viral load and time to viral clearance between BA.1, BA.1.1 and BA.2 infected individuals.\n\nConclusionWe report a high incidence of omicron infection despite recent booster vaccination in triple vaccinated individuals. Increasing levels of vaccine-induced spike-specific WT antibodies entail increased protection against infection and reduce viral load if infected. High viral load and secretion of live virus for up to nine days may facilitate transmission in a triple vaccinated population.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Ulrika Marking", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Sebastian Havervall", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Nina Greilert Norin", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Oscar Bladh", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Wanda Christ", + "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Max Gordon", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Henry Ng", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Kim Blom", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Mia Phillipson", + "author_inst": "Department of Medical Cell Biology and SciLifeLab, Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Sara Mangsbo", + "author_inst": "Department of Pharmacy and SciLifeLab, Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Anna Smed-Sorensen", + "author_inst": "Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden." + }, + { + "author_name": "Peter Nilsson", + "author_inst": "Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Sophia Hober", + "author_inst": "Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Mikael Aberg", + "author_inst": "Department of Medical Sciences, Clinical Chemistry and SciLifeLab, Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Jonas Klingstrom", + "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Charlotte Thalin", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.31.22273111", "rel_title": "Predictors of all-cause mortality among patients hospitalized with influenza, respiratory syncytial virus, or SARS-CoV-2", @@ -315670,25 +317843,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, - { - "rel_doi": "10.1101/2022.04.02.22273341", - "rel_title": "Variation in National COVID-19 Mortality Rates Across Asian Subgroups in the United States, 2020", - "rel_date": "2022-04-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.02.22273341", - "rel_abs": "Provisional U.S. national COVID-19 mortality data for the year 2020 analyzed by the CDC in March 2021 indicated that non-Hispanic Asians fared markedly better overall than other racial/ethnic minority groups-and marginally better than non-Hispanic Whites-in terms of age-adjusted mortality rates. However, Asians in the United States are composed of diverse array of origin subgroups with highly varying social, economic, and environmental experiences, which influence health outcomes. As such, lumping all Asians together into a single category can mask meaningful health disparities among more vulnerable Asian subgroups. To date, there has not been a national-level analysis of COVID-19 mortality outcomes between Asian subgroups. Utilizing final multiple cause of death data for 2020 and population projections from the U.S. Census Bureaus Current Population Survey Annual Social and Economic Supplement for 2020, crude and age-adjusted national COVID-19 mortality rates, both overall and stratified by sex, were calculated for the six major single-race Asian origin subgroups (Asian Indian, Chinese, Filipino, Japanese, Korean, and Vietnamese) and a catch-all seventh category that comprises the remaining Asian subgroups (Other Asians), contrasting them to the corresponding mortality rates of other racial/ethnic groups. A substantially more nuanced picture emerges when disaggregating Asians into its diverse origin subgroups and stratifying by sex, with Filipino males and Asian males outside of the six major Asian subgroups in particular experiencing markedly higher age-adjusted mortality rates than their White male counterparts, whether comparisons were restricted to their non-Hispanic subsets or not. During the COVID-19 pandemic and in the post-pandemic recovery, it is imperative not to overlook the health needs of vulnerable Asian populations. Public health strategies to mitigate the effects of COVID-19 must avoid viewing Asians as a monolithic entity and recognize the heterogeneous risk profiles within the U.S. Asian population.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Jay J Xu", - "author_inst": "University of California, Los Angeles" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.03.26.22272727", "rel_title": "Association of Mass Distribution of Rapid Antigen Tests and SARS-CoV-2 Prevalence: Results from NIH-CDC funded Say Yes! Covid Test program in Michigan", @@ -317199,6 +319353,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2022.03.31.22273262", + "rel_title": "Emulation of epidemics via Bluetooth-based virtual safe virus spread: experimental setup, software, and data", + "rel_date": "2022-04-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.31.22273262", + "rel_abs": "We describe an experimental setup and a currently running experiment for evaluating how physical interactions over time and between individuals affect the spread of epidemics. Our experiment involves the voluntary use of the Safe Blues Android app by participants at The University of Auckland (UoA) City Campus in New Zealand. The app spreads multiple virtual safe virus strands via Bluetooth depending on the social and physical proximity of the subjects. The evolution of the virtual epidemics is recorded as they spread through the population. The data is presented as a real-time (and historical) dashboard. A simulation model is applied to calibrate strand parameters. Participants locations are not recorded, but participants are rewarded based on the duration of participation within a geofenced area, and aggregate participation numbers serve as part of the data. Once the experiment is complete, the data will be made available as an open-source anonymized dataset.\n\nThis paper outlines the experimental setup, software, subject-recruitment practices, ethical considerations, and dataset description. The paper also highlights current experimental results in view of the lockdown that started in New Zealand at 23:59 on August 17, 2021. The experiment was initially planned in the New Zealand environment, expected to be free of COVID and lockdowns after 2020. However, a COVID Delta strain lockdown shuffled the cards and the experiment is currently extended into 2022.\n\nAuthor summaryIn this paper, we describe the Safe Blues Android app experimental setup and a currently running experiment at the University of Auckland City Campus. This experiment is designed to evaluate how physical interactions over time and between individuals affect the spread of epidemics.\n\nThe Safe Blues app spreads multiple virtual safe virus strands via Bluetooth based on the subjects unobserved social and physical proximity. The app does not record the participants locations, but participants are rewarded based on the duration of participation within a geofenced area, and aggregate participation numbers serve as part of the data. When the experiment is finished, the data will be released as an open-source anonymized dataset.\n\nThe experimental setup, software, subject recruitment practices, ethical considerations, and dataset description are all described in this paper. In addition, we present our current experimental results in view of the lockdown that started in New Zealand at 23:59 on August 17, 2021. The information we provide here may be useful to other teams planning similar experiments in the future.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Azam Asanjarani", + "author_inst": "The University of Auckland" + }, + { + "author_name": "Aminath Shausan", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Keng Chew", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Thomas Graham", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Kirsty R. Short", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Yoni Nazarathy", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Shane G. Henderson", + "author_inst": "Cornell University" + }, + { + "author_name": "Hermanus M. Jansen", + "author_inst": "Delft University of Technology" + }, + { + "author_name": "Peter G. Taylor", + "author_inst": "The University of melbourne" + }, + { + "author_name": "Aapeli Vuorinen", + "author_inst": "Columbia University" + }, + { + "author_name": "Yuvraj Yadav", + "author_inst": "Indian Institute of Technology Delhi" + }, + { + "author_name": "Ilze Ziedins", + "author_inst": "The University of Auckland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2022.04.01.22273291", "rel_title": "Metabolic alkalosis and mortality in COVID-19", @@ -317420,33 +319637,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.01.22273305", - "rel_title": "Long-term psychological consequences of long Covid: a propensity score matching analysis comparing trajectories of depression and anxiety symptoms before and after contracting long Covid vs short Covid", - "rel_date": "2022-04-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.01.22273305", - "rel_abs": "BackgroundThere is a growing global awareness of the psychological consequences of long Covid, supported by emerging empirical evidence. However, the mergence and long-term trajectories of psychological symptoms following the infection are still unclear.\n\nAimsTo examine when psychological symptoms first emerge following the infection with SARS-CoV-2, and the long-term trajectories of psychological symptoms comparing long and short Covid groups.\n\nMethodsWe analysed longitudinal data from the UCL Covid-19 Social Study (March 2020-November 2021). We included data from adults living in England who reported contracting SARS-CoV-2 by November 2021 (N=3,115). Of these, 15.9% reported having had long Covid (N=495). They were matched to participants who had short Covid using propensity score matching on a variety of demographic, socioeconomic and health covariates (N=962, n=13,325) and data were further analysed using growth curve modelling.\n\nResultsDepressive and anxiety symptoms increased immediately following the onset of infection in both long and short Covid groups. But the long Covid group had substantially greater initial increases in depressive symptoms and heightened levels over 22 months follow-up. Initial increases in anxiety were not significantly different between groups, but only the short Covid group experienced an improvement in anxiety over follow-up, leading to widening differences between groups.\n\nConclusionsThe findings shed light on the psychobiological pathways involved in the development of psychological symptoms relating to long Covid. The results highlight the need for monitoring of mental health and provision of adequate support to be interwoven with diagnosis and treatment of the physical consequences of long Covid.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Steptoe", - "author_inst": "University College London" - }, - { - "author_name": "Feifei Bu", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2022.04.01.22273296", "rel_title": "Uptake of COVID-19 vaccines among pregnant women: a systematic review and meta-analysis", @@ -319129,6 +321319,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.03.31.22273226", + "rel_title": "Cross-talk between red blood cells and plasma influences blood flow and omics phenotypes in severe COVID-19", + "rel_date": "2022-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.31.22273226", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and can affect multiple organs, among which is the circulatory system. Inflammation and mortality risk markers were previously detected in COVID-19 plasma and red blood cells (RBCs) metabolic and proteomic profiles. Additionally, biophysical properties, such as deformability, were found to be changed during the infection. Based on such data, we aim to better characterize RBC functions in COVID-19. We evaluate the flow properties of RBCs in severe COVID-19 patients admitted to the intensive care unit by using in vitro microfluidic techniques and automated methods, including artificial neural networks, for an unbiased RBC analysis. We find strong flow and RBC shape impairment in COVID-19 samples and demonstrate that such changes are reversible upon suspension of COVID-19 RBCs in healthy plasma. Vice versa, healthy RBCs immediately resemble COVID-19 RBCs when suspended in COVID-19 plasma. Proteomics and metabolomics analyses allow us to detect the effect of plasma exchanges on both plasma and RBCs and demonstrate a new role of RBCs in maintaining plasma equilibria at the expense of their flow properties. Our findings provide a framework for further investigations of clinical relevance for therapies against COVID-19 and possibly other infectious diseases.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Steffen M. Recktenwald", + "author_inst": "Saarland University" + }, + { + "author_name": "Greta Simionato", + "author_inst": "Saarland University" + }, + { + "author_name": "Marcelle G.M. Lopes", + "author_inst": "Cysmic GmbH" + }, + { + "author_name": "Fabia Gamboni", + "author_inst": "University of Colorado Denver" + }, + { + "author_name": "Monika Dzieciatkowska", + "author_inst": "University of Colorado Denver" + }, + { + "author_name": "Patrick Meybohm", + "author_inst": "University Hospital Wuerzburg" + }, + { + "author_name": "Kai Zacharowski", + "author_inst": "University Hospital Frankfurt" + }, + { + "author_name": "Andreas von Knethen", + "author_inst": "University Hospital Frankfurt" + }, + { + "author_name": "Christian Wagner", + "author_inst": "saarland University" + }, + { + "author_name": "Lars Kaestner", + "author_inst": "Saarland University" + }, + { + "author_name": "Angelo D'Alessandro", + "author_inst": "University of Colorado Denver" + }, + { + "author_name": "Stephan Quint", + "author_inst": "Cysmic GmbH" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2022.03.30.22273206", "rel_title": "Remdesivir for the treatment of hospitalised patients with COVID-19: final results from the DisCoVeRy randomised, controlled, open-label trial", @@ -319598,61 +321851,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.03.30.486403", - "rel_title": "SARS-CoV-2 accessory protein ORF8 decreases antibody-dependent cellular cytotoxicity", - "rel_date": "2022-03-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.30.486403", - "rel_abs": "SARS-CoV-2 Spike glycoprotein is the major target of host neutralizing antibodies and the most changing viral protein in the continuously emerging SARS-CoV-2 variants as a result of frequent viral evasion from host antibody responses. In addition, SARS-CoV-2 encodes multiple accessory proteins that modulate host antiviral immunity by different mechanisms. Among all SARS-CoV-2 accessory proteins, ORF8 is rapidly evolving and a deletion in this protein has been linked to milder disease. Here, we studied the effect of ORF8 on peripheral blood mononuclear cells (PBMC). Specifically, we found that ORF8 can bind monocytes as well as NK cells. Strikingly, ORF8 binds CD16a (Fc{gamma}RIIIA) with nanomolar affinity and decreases the overall level of CD16 at the surface of monocytes and, to a lesser extent, NK cells. Strikingly, this decrease significantly reduces the capacity of PBMCs and particularly monocytes to mediate antibody-dependent cellular cytotoxicity (ADCC). Overall, our data identifies a new immune-evasion activity used by SARS-CoV-2 to escape humoral responses.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Guillaume Beaudoin-Bussieres", - "author_inst": "CRCHUM" - }, - { - "author_name": "Ariana Arduini", - "author_inst": "McGill" - }, - { - "author_name": "Catherine Bourassa", - "author_inst": "CRCHUM" - }, - { - "author_name": "Halima Medjahed", - "author_inst": "CRCHUM" - }, - { - "author_name": "Gabrielle Gendron-Lepage", - "author_inst": "CRCHUM" - }, - { - "author_name": "Jonathan Richard", - "author_inst": "CRCHUM" - }, - { - "author_name": "Qinghua Pan", - "author_inst": "McGill" - }, - { - "author_name": "Zhen Wang", - "author_inst": "McGill" - }, - { - "author_name": "Chen Liang", - "author_inst": "McGill" - }, - { - "author_name": "Andres Finzi", - "author_inst": "CRCHUM" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.03.30.486356", "rel_title": "Differential gene expression profiling reveals potential biomarkers and pharmacological compounds against SARS-CoV-2: insights from machine learning and bioinformatics approaches", @@ -321739,6 +323937,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2022.03.29.486173", + "rel_title": "A mosaic-type trimeric RBD-based COVID-19 vaccine candidate induces potent neutralization against Omicron and other SARS-CoV-2 variants", + "rel_date": "2022-03-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.29.486173", + "rel_abs": "Large-scale populations in the world have been vaccinated with COVID-19 vaccines, however, breakthrough infections of SARS-CoV-2 are still growing rapidly due to the emergence of immune-evasive variants, especially Omicron. It is urgent to develop effective broad-spectrum vaccines to better control the pandemic of these variants. Here, we present a mosaic-type trimeric form of spike receptor-binding domain (mos-tri-RBD) as a broad-spectrum vaccine candidate, which carries the key mutations from Omicron and other circulating variants. Tests in rats showed that the designed mos-tri-RBD, whether used alone or as a booster shot, elicited potent cross-neutralizing antibodies against not only Omicron but also other immune-evasive variants. Neutralizing antibody titers induced by mos-tri-RBD were substantially higher than those elicited by homo-tri-RBD (containing homologous RBDs from prototype strain) or the inactivated vaccine BBIBP-CorV. Our study indicates that mos-tri-RBD is highly immunogenic, which may serve as a broad-spectrum vaccine candidate in combating SARS-CoV-2 variants including Omicron.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Jing Zhang", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Zi Bo Han", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Yu Liang", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Xue Feng Zhang", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Yu Qin Jin", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Li Fang Du", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Shuai Shao", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Hui Wang", + "author_inst": "Beijing Institute of Biological Products Company Limited" + }, + { + "author_name": "Jun Wei Hou", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Ke Xu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC)" + }, + { + "author_name": "Ze Hua Lei", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Zhao Ming Liu", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Jin Zhang", + "author_inst": "Beijing Institute of Biological Products Company Limited" + }, + { + "author_name": "Ya Nan Hou", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Ning Liu", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Fu Jie Shen", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Jin Juan Wu", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Xiang Zheng", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Xin Yu Li", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Xin Li", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Wei Jin Huang", + "author_inst": "National Institute for Food and Drug Control (NIFDC)" + }, + { + "author_name": "Gui Zhen Wu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC)" + }, + { + "author_name": "Ji Guo Su", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Qi Ming Li", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.29.486253", "rel_title": "Discovery of a druggable copper-signaling pathway that drives cell plasticity and inflammation", @@ -322156,37 +324465,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.03.29.486282", - "rel_title": "Repeated ethanol exposure and withdrawal alters ACE2 expression in discrete brain regions: Implications for SARS-CoV-2 infection", - "rel_date": "2022-03-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.29.486282", - "rel_abs": "Emerging evidence suggests that people with alcohol use disorders are at higher risk for SARS-CoV-2. SARS-CoV-2 engages angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) receptors for cellular entry. While ACE2 and TMPRSS2 genes are upregulated in the cortex of alcohol-dependent individuals, information on expression in specific brain regions and neural populations implicated in SARS-CoV-2 neuroinvasion, particularly monoaminergic neurons, is limited. We sought to clarify how chronic alcohol exposure affects ACE2 and TMPRSS2 expression in monoaminergic brainstem circuits and other putative SARS-CoV-2 entry points. C57BL/6J mice were exposed to chronic intermittent ethanol (CIE) vapor for 4 weeks and brains were examined using immunofluorescence. We observed increased ACE2 levels in the olfactory bulb and hypothalamus following CIE, which are known to mediate SARS-CoV-2 neuroinvasion. Total ACE2 immunoreactivity was also elevated in the raphe magnus (RMG), raphe obscurus (ROB), and locus coeruleus (LC), while in the dorsal raphe nucleus (DRN), ROB, and LC we observed increased colocalization of ACE2 with monoaminergic neurons. ACE2 also increased in the periaqueductal gray (PAG) and decreased in the amygdala. Whereas ACE2 was detected in most brain regions, TMPRSS2 was only detected in the olfactory bulb and DRN but was not significantly altered after CIE. Our results suggest that previous alcohol exposure may increase the risk of SARS-CoV-2 neuroinvasion and render brain circuits involved in cardiovascular and respiratory function as well as emotional processing more vulnerable to infection, making adverse outcomes more likely. Additional studies are needed to define a direct link between alcohol use and COVID-19 infection.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Nagalakshmi Balasubramanian", - "author_inst": "University of Iowa" - }, - { - "author_name": "Thomas D James", - "author_inst": "University of Iowa" - }, - { - "author_name": "Selvakumar Govindhasamy Pushpavathi", - "author_inst": "University of Iowa" - }, - { - "author_name": "Catherine A Marcinkiewcz", - "author_inst": "University of Iowa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2022.03.29.486190", "rel_title": "CD169-mediated restrictive SARS-CoV-2 infection of macrophages induces pro-inflammatory responses", @@ -324309,6 +326587,145 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.03.23.485509", + "rel_title": "Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq", + "rel_date": "2022-03-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.23.485509", + "rel_abs": "Phage Immunoprecipitation-Sequencing (PhIP-Seq) allows for unbiased, proteome-wide autoantibody discovery across a variety of disease settings, with identification of disease-specific autoantigens providing new insight into previously poorly understood forms of immune dysregulation. Despite several successful implementations of PhIP-Seq for autoantigen discovery, including our previous work (Vazquez et al. 2020), current protocols are inherently difficult to scale to accommodate large cohorts of cases and importantly, healthy controls. Here, we develop and validate a high throughput extension of PhIP-seq in various etiologies of autoimmune and inflammatory diseases, including APS1, IPEX, RAG1/2 deficiency, Kawasaki Disease (KD), Multisystem Inflammatory Syndrome in Children (MIS-C), and finally, mild and severe forms of COVID19. We demonstrate that these scaled datasets enable machine-learning approaches that result in robust prediction of disease status, as well as the ability to detect both known and novel autoantigens, such as PDYN in APS1 patients, and intestinally expressed proteins BEST4 and BTNL8 in IPEX patients. Remarkably, BEST4 antibodies were also found in 2 patients with RAG1/2 deficiency, one of whom had very early onset IBD. Scaled PhIP-Seq examination of both MIS-C and KD demonstrated rare, overlapping antigens, including CGNL1, as well as several strongly enriched putative pneumonia-associated antigens in severe COVID19, including the endosomal protein EEA1. Together, scaled PhIP-Seq provides a valuable tool for broadly assessing both rare and common autoantigen overlap between autoimmune diseases of varying origins and etiologies.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Sara E Vazquez", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Sabrina A Mann", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Aaron Bodansky", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Andrew F Kung", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Zoe Quandt", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Elise M N Ferr\u00e9", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Nils Landegren", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Daniel Eriksson", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Paul Bastard", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Shen-Ying Zhang", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Jamin Liu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Anthea Mitchell", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Caleigh Mandel-Brehm", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Brenda Miao", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Gavin Sowa", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kelsey Zorn", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alice Y Chan", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Chisato Shimizu", + "author_inst": "UC San Diego Health System" + }, + { + "author_name": "Adriana Tremoulet", + "author_inst": "UC San Diego Health System" + }, + { + "author_name": "Kara Lynch", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Michael R Wilson", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Olle K\u00e4mpe", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Kerry Dobbs", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Ottavia M Delmonte", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Luigi D Notarangelo", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Jane C Burns", + "author_inst": "UC San Diego Health System" + }, + { + "author_name": "Jean-Laurent Casanova", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Michail S Lionakis", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Troy R Torgerson", + "author_inst": "Allen Institute for Immunology" + }, + { + "author_name": "Mark S Anderson", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Joseph L DeRisi", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.24.485734", "rel_title": "SARS-CoV-2 harnesses host translational shutoff and autophagy to optimize virus yields: The role of the envelope (E) protein", @@ -324418,29 +326835,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.23.22272819", - "rel_title": "Vaccine Adverse Event Reporting System (VAERS): Evaluation of 31 Years of Reports and Pandemics' Impact", - "rel_date": "2022-03-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.23.22272819", - "rel_abs": "BackgroundVaccine adverse event reporting system (VAERS) was established in the United States (U.S.) as an early warning system with a main purpose of collecting postmarketing adverse events following immunizations (AEFIs) reports to monitor the vaccine safety and to mitigate the risks from vaccines. During the coronavirus diseases 2019 (COVID-19) pandemic, VAERS got more attention as its important role in monitoring the safety of the vaccines. Thus, the aim of this study was to investigate VAERS patterns, reported AEFIs, adverse events of special interest (AESIs), impact of different pandemics since its inception, and surveillance rate of serious vs nonserious AEFIs.\n\nMethodsThis was an observational study using VARES data from 2/7/1990 to 12/11/2021. Patterns of reports over years were first described, followed by a comparison of reports statistics per year. Furthermore, a comparison of incidents (death, ER visits, etc.) statistics over years, in addition to statistics of each vaccine were calculated. Moreover, each incidents statistics for each vaccine were calculated and top vaccines were reported. Finally, survival analysis utilizing cox regression was done, in addition to AESIs distribution stratified by age groups and gender. All analyses were conducted using R (Version 1.4.1717) and Excel for Microsoft 365.\n\nResultsThere were 1,396,280 domestic and 346,210 non-domestic reports during 1990-2021, including 228 vaccines. For both domestic and non-domestic reports, year of 2021 had the highest reporting rate (48.52% and 70.33%), in addition a notable changes in AEFIs patterns were recorded during 1991, 1998, 2000, 2006, 2009, 2011, and 2017. AEFIs were as follow: deaths (1.00% and 4.08%), ER or doctor visits (13.37% and 2.27%), hospitalizations (5.84% and 27.78%), lethal threat (1.42% and 4.38%), and disabilities (1.4% and 7.96%). Pyrexia was the top reported symptom during the past 31 years, except for 2021 where headache was the top one. COVID-19 vaccines namely Moderna, Pfizer-Biontech, and Janssen were the top 3 reported vaccines with headache, pyrexia, and fatigue as the top associated AEFIs. Followed by Zoster, Seasonal Influenza, Pneumococcal, and Human papillomavirus vaccines. Myocarditis or Pericarditis were the top reported AESIs (26.95% and 25.84%). Male (HR:1.15, 1.14 - 1.16) for domestic (HR:1.23, 1.22 -1.25) for nondomestic have a higher probability of having serious AEFIs. In addition, age group [≤] 5 years old in domestic and >84 years old in nondomestic have a higher probability of having AEFIs compared to other age groups.\n\nConclusionsThe large data available in VARES make it a useful tool for detecting and monitoring vaccine AEFIs. However, its usability relies on understating the limitations of this surveillance system, the impact of governmental regulations, availability of vaccines, and public health recommendations on the reporting rate.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ohoud Almadani", - "author_inst": "Saudi Food and Drug Authority" - }, - { - "author_name": "Thamir M Alshammari", - "author_inst": "King Saud University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.24.22272884", "rel_title": "COVID-19 outcomes associated with clinical and demographic characteristics in patients hospitalized with severe and critical disease in Peshawar", @@ -325691,6 +328085,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.24.22272835", + "rel_title": "Relative Effectiveness of Four Doses Compared to Three Dose of the BNT162b2 Vaccine in Israel", + "rel_date": "2022-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.24.22272835", + "rel_abs": "ObjectivesThe rapid spread of the Omicron variant (B.1.1.529) alongside evidence of a relatively rapid waning of the third dose prompted Israel to administer a fourth dose of the BNT162b2 vaccine on January 2022. Thus far, sufficient real-world evidence demonstrating the effectiveness of a fourth dose against infection and severe COVID-19 are lacking. This study examined the short-term effectiveness of a fourth dose compared to three doses over the span of 10 weeks.\n\nDesignA retrospective test-negative case-control study, performing both a matched analysis and an unmatched multiple-tests analysis.\n\nSettingNationally centralized database of Maccabi Healthcare Services (MHS), an Israeli national health fund that covers 2.5 million people.\n\nParticipantsThe study population included 97,499 MHS members aged 60 or older who were eligible to receive a fourth vaccine dose and performed at least one PCR test during the study period. Of them, 27,876 received the fourth dose and 69,623 received only three doses.\n\nMain outcomes and measuresAnalyses focused on the period from January 10, 2022 (7 days after the fourth dose was first administered to eligible individuals) to March 13, 2022, an Omicron-dominant period in Israel. We evaluated two SARS-CoV-2-related outcomes: (1) breakthrough infection, defined as a positive PCR test performed 7 or more days after inoculation with the BNT162b2 vaccine; and (2) breakthrough infection resulting in a severe disease, defined as COVID-19-related hospitalization or COVID-19 associated mortality.\n\nResultsA fourth dose provided considerable additional protection against both SARS-CoV-2 infection and severe disease relative to three doses of the vaccine. However, vaccine effectiveness against infection varied over time, peaking during the third week with a VE of 64% (95% CI: 62.0%-65.9%) and declining to 29.2% (95% CI: 17.7%-39.1%) by the end of the 10-week follow-up period. Unlike VE against infection, the relative effectiveness of a fourth dose against severe COVID-19 was maintained at high level (>73%) throughout the 9-week follow-up period. Importantly, severe disease was a relatively rare event, occurring in <1% of both fourth dose and third dose only recipients.\n\nConclusionsA fourth dose of the BNT162b2 vaccine provided considerable additional protection against both SARS-CoV-2 infection and severe disease relative to three doses of the vaccine. However, effectiveness of the fourth dose against infection wanes sooner than that of the third dose.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sivan Gazit", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Yaki Saciuk", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Galit Perez", + "author_inst": "Maccabi health care servises" + }, + { + "author_name": "Asaf Peretz", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Virginia E. Pitzer", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Tal Patalon", + "author_inst": "Maccabi Healthcare Services" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.03.24.22272892", "rel_title": "The modified COVID-19 Yorkshire Rehabilitation Scale (C19-YRSm) patient-reported outcome measure for Long Covid or Post-COVID syndrome", @@ -325908,53 +328341,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.03.24.485618", - "rel_title": "Improved And Optimized Drug Repurposing For The SARS-CoV-2 Pandemic", - "rel_date": "2022-03-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.24.485618", - "rel_abs": "The active global SARS-CoV-2 pandemic caused more than 426 million cases and 5.8 million deaths worldwide. The development of completely new drugs for such a novel disease is a challenging, time intensive process. Despite researchers around the world working on this task, no effective treatments have been developed yet. This emphasizes the importance of drug repurposing, where treatments are found among existing drugs that are meant for different diseases. A common approach to this is based on knowledge graphs, that condense relationships between entities like drugs, diseases and genes. Graph neural networks (GNNs) can then be used for the task at hand by predicting links in such knowledge graphs. Expanding on state-of-the-art GNN research, Doshi et al. recently developed the Dr-COVID model. We further extend their work using additional output interpretation strategies. The best aggregation strategy derives a top-100 ranking of 8,070 candidate drugs, 32 of which are currently being tested in COVID-19-related clinical trials. Moreover, we present an alternative application for the model, the generation of additional candidates based on a given pre-selection of drug candidates using collaborative filtering. In addition, we improved the implementation of the Dr-COVID model by significantly shortening the inference and pre-processing time by exploiting data-parallelism. As drug repurposing is a task that requires high computation and memory resources, we further accelerate the post-processing phase using a new emerging hardware -- we propose a new approach to leverage the use of high-capacity Non-Volatile Memory for aggregate drug ranking.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Davis Issac", - "author_inst": "Universitat Potsdam" - }, - { - "author_name": "Sarel Cohen", - "author_inst": "Hasso Plattner Institute" - }, - { - "author_name": "Moshik Hershcovitch", - "author_inst": "IBM Research" - }, - { - "author_name": "Martin Taraz", - "author_inst": "Hasso Plattner Institute" - }, - { - "author_name": "Otto Ki\u00dfig", - "author_inst": "Hasso Plattner Institute" - }, - { - "author_name": "Daniel Waddington", - "author_inst": "IBM Research" - }, - { - "author_name": "Peter Chin", - "author_inst": "Boston University" - }, - { - "author_name": "Tobias Friedrich", - "author_inst": "Hasso Plattner Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.03.20.22272549", "rel_title": "Viral load dynamics of SARS-CoV-2 Delta and Omicron variants following multiple vaccine doses and previous infection", @@ -327689,6 +330075,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.23.22272804", + "rel_title": "Waning effectiveness of BNT162b2 and ChAdOx1 COVID-19 vaccines over six months since second dose: a cohort study using linked electronic health records", + "rel_date": "2022-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.23.22272804", + "rel_abs": "BackgroundThe rate at which COVID-19 vaccine effectiveness wanes over time is crucial for vaccination policies, but is incompletely understood with conflicting results from different studies.\n\nMethodsThis cohort study, using the OpenSAFELY-TPP database and approved by NHS England, included individuals without prior SARS-CoV-2 infection assigned to vaccines priority groups 2-12 defined by the UK Joint Committee on Vaccination and Immunisation. We compared individuals who had received two doses of BNT162b2 or ChAdOx1 with unvaccinated individuals during six 4-week comparison periods, separately for subgroups aged 65+ years; 16-64 years and clinically vulnerable; 40-64 years and 18-39 years. We used Cox regression, stratified by first dose eligibility and geographical region and controlled for calendar time, to estimate adjusted hazard ratios (aHRs) comparing vaccinated with unvaccinated individuals, and quantified waning vaccine effectiveness as ratios of aHRs per-4-week period. The outcomes were COVID-19 hospitalisation, COVID-19 death, positive SARS-CoV-2 test, and non-COVID-19 death.\n\nFindingsThe BNT162b2, ChAdOx1 and unvaccinated groups comprised 1,773,970, 2,961,011 and 2,433,988 individuals, respectively. Waning of vaccine effectiveness was similar across outcomes and vaccine brands: e.g. in the 65+ years subgroup ratios of aHRs versus unvaccinated for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test ranged from 1.23 (95% CI 1.15-1.32) to 1.27 (1.20-1.34) for BNT162b2 and 1.16 (0.98-1.37) to 1.20 (1.14-1.27) for ChAdOx1. Despite waning, rates of COVID-19 hospitalisation and COVID-19 death were substantially lower among vaccinated individuals compared to unvaccinated individuals up to 26 weeks after second dose, with estimated aHRs <0.20 (>80% vaccine effectiveness) for BNT162b2, and <0.26 (>74%) for ChAdOx1. By weeks 23-26, rates of SARS-CoV-2 infection in fully vaccinated individuals were similar to or higher than those in unvaccinated individuals: aHRs ranged from 0.85 (0.78-0.92) to 1.53 (1.07-2.18) for BNT162b2, and 1.21 (1.13-1.30) to 1.99 (1.94-2.05) for ChAdOx1.\n\nInterpretationThe rate at which estimated vaccine effectiveness waned was strikingly consistent for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test, and similar across subgroups defined by age and clinical vulnerability. If sustained to outcomes of infection with the Omicron variant and to booster vaccination, these findings will facilitate scheduling of booster vaccination doses.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Elsie MF Horne", + "author_inst": "University of Bristol" + }, + { + "author_name": "William J Hulme", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Ruth H Keogh", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Tom M Palmer", + "author_inst": "University of Bristol" + }, + { + "author_name": "Elizabeth J Williamson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Edward PK Parker", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Amelia Green", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Venexia Walker", + "author_inst": "University of Bristol" + }, + { + "author_name": "Alex J Walker", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Helen Curtis", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Louis Fisher", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Brian MacKenna", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Richard Croker", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Lisa Hopcroft", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Robin Y Park", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Jon Massey", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Jessica Morely", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Amir Mehrkar", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Sebastian Bacon", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "David Evans", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Peter Inglesby", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Caroline E Morton", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "George Hickman", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Simon Davy", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Tom Ward", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Iain Dillingham", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Ben Goldacre", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Miguel A Hernan", + "author_inst": "Harvard University" + }, + { + "author_name": "Jonathan AC Sterne", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.21.22272358", "rel_title": "Undiagnosed COVID-19 in households with a child with mitochondrial disease", @@ -327850,105 +330367,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.21.22272490", - "rel_title": "Early detection of SARS-CoV-2 variants using traveler-based genomic surveillance at four US airports, September 2021- January 2022", - "rel_date": "2022-03-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.21.22272490", - "rel_abs": "We enrolled arriving international air travelers in SARS-CoV-2 genomic surveillance, using molecular testing of pooled nasal swabs, and sequencing positive samples for viral lineage. Traveler-based genomic surveillance provided early warning variant detection; we reported the first U.S. Omicron BA.2 and first BA.3 in North America, weeks before next reported detection.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Renee D. Wegrzyn", - "author_inst": "Ginkgo Bioworks, Inc., Boston, Massachusetts" - }, - { - "author_name": "Grace D. Appiah", - "author_inst": "Centers for Disease Control and Prevention (CDC)" - }, - { - "author_name": "Robert Morfino,", - "author_inst": "Ginkgo Bioworks, Inc., Boston, Massachusetts" - }, - { - "author_name": "Scott R. Milford", - "author_inst": "XpresSpa Group, Inc., New York, New York" - }, - { - "author_name": "Allison Taylor Walker", - "author_inst": "Centers for Disease Control and Prevention (CDC)" - }, - { - "author_name": "Ezra T. Ernst", - "author_inst": "XpresSpa Group, Inc., New York, New York" - }, - { - "author_name": "William W. Darrow", - "author_inst": "XpresSpa Group, Inc., New York, New York" - }, - { - "author_name": "Siayo Lisa Li", - "author_inst": "Ginkgo Bioworks, Inc., Boston, Massachusetts" - }, - { - "author_name": "Keith Robison", - "author_inst": "Ginkgo Bioworks, Inc., Boston, Massachusetts" - }, - { - "author_name": "Duncan MacCannell", - "author_inst": "Office of Advanced Molecular Detection, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Geor" - }, - { - "author_name": "Dongjuan Dai", - "author_inst": "Ginkgo Bioworks, Inc., Boston, Massachusetts" - }, - { - "author_name": "Brintha P. Girinathan", - "author_inst": "Ginkgo Bioworks, Inc., Boston, Massachusetts" - }, - { - "author_name": "Allison L. Hicks", - "author_inst": "Ginkgo Bioworks, Inc., Boston, Massachusetts" - }, - { - "author_name": "Bryan Cosca", - "author_inst": "Ginkgo Bioworks, Inc., Boston, Massachusetts" - }, - { - "author_name": "Gabrielle Woronoff", - "author_inst": "Ginkgo Bioworks, Inc., Boston, Massachusetts" - }, - { - "author_name": "Alex M. Plocik", - "author_inst": "Ginkgo Bioworks, Inc., Boston, Massachusetts" - }, - { - "author_name": "Birgitte B. Simen", - "author_inst": "Ginkgo Bioworks, Inc., Boston, Massachusetts" - }, - { - "author_name": "Leah Moriarty", - "author_inst": "Division of Parasitic Diseases and Malaria, Centers for Disease Control and Prevention, Atlanta, GA" - }, - { - "author_name": "Sarah Anne J. Guagliardo", - "author_inst": "Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, GA" - }, - { - "author_name": "Martin S. Cetron", - "author_inst": "Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, GA" - }, - { - "author_name": "Cindy R. Friedman", - "author_inst": "Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, Atlanta, GA" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.22.22272770", "rel_title": "Long-term symptoms after SARS-CoV-2 infection in a cohort of hospital employees: duration and predictive factors", @@ -329391,6 +331809,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.21.485157", + "rel_title": "Stability and expression of SARS-CoV-2 spike-protein mutations", + "rel_date": "2022-03-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.21.485157", + "rel_abs": "Protein fold stability likely plays a role in SARS-CoV-2 S-protein evolution, together with ACE2 binding and antibody evasion. While few thermodynamic stability data are available for S-protein mutants, many systematic experimental data exist for their expression. In this paper, we explore whether such expression levels relate to the thermodynamic stability of the mutants. We studied mutation-induced SARS-CoV-2 S-protein fold stability, as computed by three very distinct methods and eight different protein structures to account for method- and structure-dependencies. For all methods and structures used (24 comparisons), computed stability changes correlate significantly (99% confidence level) with experimental yeast expression from the literature, such that higher expression is associated with relatively higher fold stability. Also significant, albeit weaker, correlations were seen for ACE2 binding. The effect of thermodynamic fold stability may be direct or a correlate of amino acid or site properties, notably the solvent exposure of the site. Correlation between computed stability and experimental expression and ACE2 binding suggests that functional properties of the SARS-CoV-2 S-protein mutant space are largely determined by a few simple features, due to underlying correlations. Our study lends promise to the development of computational tools that may ideally aid in understanding and predicting SARS-CoV-2 S-protein evolution.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kristoffer T Baek", + "author_inst": "Technical University of Denmark" + }, + { + "author_name": "Rukmankesh Mehra", + "author_inst": "Indian Institute of Technology Bhilai" + }, + { + "author_name": "Kasper Planeta Kepp", + "author_inst": "Technical University of Denmark" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.03.20.485044", "rel_title": "Robust and durable prophylactic protection conferred by RNA interference in preclinical models of SARS-CoV-2", @@ -329740,41 +332185,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.03.18.22272605", - "rel_title": "Medical students' crisis-induced stress and the association with social support", - "rel_date": "2022-03-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.18.22272605", - "rel_abs": "BackgroundMedical schools are challenged to guard student wellbeing due to the potential negative impact of the COVID-19 outbreak on top of the already high prevalence of mental distress. Whereas social support is generally associated with less crisis-induced stress, it is unknown whether this applies to medical students during the COVID-19 outbreak.\n\nObjectivesThe impact of the COVID-19 outbreak on perceived stress of medical students was assessed by comparing their perceived stress levels during the outbreak to both their own baseline and the previous cohorts pre-COVID-19 stress levels. Then, the association between social support and COVID-19 induced stress was assessed.\n\nMethodsDutch Year-1 medical students of cohort 2019 (n=99) completed the 14-item Perceived Stress Scale (PSS-14) at two time points: baseline (pre-COVID-19) and final measurement (COVID-19). Social support - emotional-informational support and club membership - was assessed during the final measurement. PSS and social support scores were compared to similar measurements of cohort 2018 (n=196). Students baseline stress levels, gender and study performance were controlled for when comparing two cohorts.\n\nResultsStress levels did not differ statistically significant between both pre-COVID-19 measurements of cohort 2018 and baseline cohort 2019. During the COVID-19 outbreak, cohort 2019 showed significantly higher stress levels compared to baseline (paired t-test: t=6.07, p<.001) and compared to cohort 2018 (linear regression: B=4.186, p<.001). Only during the COVID-19 outbreak, higher levels of social support - i.e. emotional-informational support (B=-0.75, p<.001) and club membership (B=-3.68, p<.01) - were associated with lower levels of stress.\n\nConclusionsDuring the COVID-19 outbreak, the perceived stress of medical students was higher - especially for students with lower levels of social support. Our results suggest that medical schools should optimize social support to minimize crisis-induced stress.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Vera M.A. Broks", - "author_inst": "Institute of Medical Education Research Rotterdam, Erasmus MC University Medical Centre Rotterdam, the Netherlands" - }, - { - "author_name": "Karen M. Stegers-Jager", - "author_inst": "Institute of Medical Education Research Rotterdam, Erasmus MC University Medical Centre Rotterdam, the Netherlands" - }, - { - "author_name": "Jeroen van der Waal", - "author_inst": "Department of Public Administration and Sociology, Erasmus University Rotterdam, Rotterdam, the Netherlands" - }, - { - "author_name": "Walter W. van den Broek", - "author_inst": "Institute of Medical Education Research Rotterdam, Erasmus MC University Medical Centre Rotterdam, the Netherlands" - }, - { - "author_name": "Andrea M Woltman", - "author_inst": "Institute of Medical Education Research Rotterdam, Erasmus MC University Medical Centre Rotterdam, the Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2022.03.18.22272601", "rel_title": "Use of an extended KDIGO definition to diagnose acute kidney injury in patients with COVID-19: A multinational study of the ISARIC cohort", @@ -331625,6 +334035,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.16.22272527", + "rel_title": "Severe Acute Respiratory Coronavirus-2 Antibody and T cell response after a third vaccine dose in hemodialysis patients compared with healthy controls", + "rel_date": "2022-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.16.22272527", + "rel_abs": "1.Hemodialysis patients (HD patients) have a high health risk from Severe Acute Respiratory Coronavirus-2 (SARS-CoV-2) infection. In this study, we assess the impact of a third vaccine dose (3D) on antibody levels and T cell response in HD patients and compare the results to those of a healthy control group.\n\nWe conducted a prospective cohort study consisting of 60 HD patients and 65 healthy controls. All of them received two doses of the Comirnaty mRNA vaccine and a third mRNA vaccine dose (Spikevax or Comirnaty). The SARS-CoV-2 S antibody response in all participants was measured 6 months after the second vaccine dose and 6 to 8 weeks after administration of the 3D. We also assessed INF-{gamma} secretion 6-8 weeks after the 3D in 24 healthy controls, 17 HD patients with a normal and 20 HD patients with a low or no antibody response after the second dose. The groups were compared using univariate quantile regressions and multiple analyses. The adverse effects of vaccines were assessed via a questionnaire.\n\nAfter the 3D, the SARS-CoV-2-specific antibody and INF-{gamma} titers of most HD patients were comparable to those of healthy controls. A subgroup of HD patients who had shown a diminished antibody response after the first two vaccine doses developed a significantly lower antibody and INF-{gamma} response compared to responder HD patients and controls, even after the 3D. A new strategy is needed to protect this patient group from severe COVID-19 infection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Benedikt Simon", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Harald Rubey", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Martin Gromann", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Astrid Knop-Voelkerer", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Boris Hemedi", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Sonja Zehetmayer", + "author_inst": "MedUni Wien" + }, + { + "author_name": "Bernhard Kirsch", + "author_inst": "LK Mistelbach" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2022.03.17.22272589", "rel_title": "A multiplexed Cas13-based assay with point-of-care attributes for simultaneous COVID-19 diagnosis and variant surveillance", @@ -331826,69 +334279,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.03.17.484817", - "rel_title": "Potent and specific human monoclonal antibodies against SARS-CoV-2 Omicron variant by rapid mRNA immunization of humanized mice", - "rel_date": "2022-03-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.17.484817", - "rel_abs": "The Omicron variant (B.1.1.529) of SARS-CoV-2 rapidly becomes dominant globally. Its extensive mutations confer severe efficacy reduction to most of existing antibodies or vaccines. Here, we developed RAMIHM, a highly efficient strategy to generate fully human monoclonal antibodies (mAbs), directly applied it with Omicron-mRNA immunization, and isolated three potent and specific clones against Omicron. Rapid mRNA immunization elicited strong anti-Omicron antibody response in humanized mice, along with broader anti-coronavirus activity. Customized single cell BCR sequencing mapped the clonal repertoires. Top-ranked clones collectively from peripheral blood, plasma B and memory B cell populations showed high rate of Omicron-specificity (93.3%) from RAMIHM-scBCRseq. Clone-screening identified three highly potent neutralizing antibodies that have low nanomolar affinity for Omicron RBD, and low ng/mL level IC50 in neutralization, more potent than majority of currently approved or authorized clinical RBD-targeting mAbs. These lead mAbs are fully human and ready for downstream IND-enabling and/or translational studies.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Ping Ren", - "author_inst": "Yale University" - }, - { - "author_name": "Lei Peng", - "author_inst": "Yale University" - }, - { - "author_name": "Zhenhao Fang", - "author_inst": "Yale University" - }, - { - "author_name": "Kazushi Suzuki", - "author_inst": "Yale University" - }, - { - "author_name": "Paul A Renauer", - "author_inst": "Yale University" - }, - { - "author_name": "Qianqian Lin", - "author_inst": "Yale University" - }, - { - "author_name": "Meizhu Bai", - "author_inst": "Yale University" - }, - { - "author_name": "Luojia Yang", - "author_inst": "Yale University" - }, - { - "author_name": "Tongqing Li", - "author_inst": "Yale University" - }, - { - "author_name": "Paul Clark", - "author_inst": "Yale University" - }, - { - "author_name": "Daryl Klein", - "author_inst": "Yale University" - }, - { - "author_name": "Sidi Chen", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2022.03.17.484786", "rel_title": "Prime-boost vaccinations with two serologically distinct chimpanzee adenovirus vectors expressing SARS-CoV-2 spike or nucleocapsid tested in a hamster COVID-19 model", @@ -333547,6 +335937,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2022.03.14.22272342", + "rel_title": "Tongue Coating in COVID-19 Patients: A Case-Control Study", + "rel_date": "2022-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.14.22272342", + "rel_abs": "It has been suggested that COVID-19 patients have distinct tongue features, which may help to monitor the development of their condition. To determine if there was any specific tongue coating feature in COVID-19, this study investigated the difference in tongue coating between COVID-19 subjects and subjects with other acute inflammatory diseases characterized by fever. Tongue images taken with smartphones from three age-matched groups, namely, COVID group (n=92), non-COVID febrile group (n=92), and normal control group (n=92), were analyzed by two blinded raters according to a tongue coating scoring scheme, which assessed the levels of thick fur, slimy or greasy fur, discolored fur and composite index of tongue coating. Compared with control, significant increases in all coating indexes were found in the COVID group (P<0.001), as well as in the non-COVID febrile group (P<0.001). However, no difference was observed between COVID and non-COVID febrile groups for all coating indexes measured. In COVID-19 subjects, their scores of coating indexes had weak but significant correlations with certain inflammatory biomarkers, including WBC and neutrophil - lymphocyte ratio. It is concluded that COVID-19 subjects have pathological tongue coating patterns that are associated with inflammatory responses, and these coating patterns can help to indicate the direction of disease development.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Zhi Chun Wang", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Xi Hong Cai", + "author_inst": "The Third Affiliated Hospital of Guangzhou University of Chinese Medicine" + }, + { + "author_name": "Jeremy Chan", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Yi Yi Chan", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Xiaotong Chen", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Ching Wan Cheng", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Donghui Huang", + "author_inst": "Guangdong Provincial Hospital of Traditional Chinese Medicine" + }, + { + "author_name": "Luqi Huang", + "author_inst": "China Academy of Chinese Medical Sciences" + }, + { + "author_name": "Bei-ni Lao", + "author_inst": "Second Clinical Medical College of Guangzhou University of Chinese Medicine: The Second Affiliated Hospital of Guangzhou University of Chinese Medicine" + }, + { + "author_name": "Xu-sheng Liu", + "author_inst": "Guangdong Hospital of Traditional Chinese Medicine: Guangdong Provincial Hospital of Traditional Chinese Medicine" + }, + { + "author_name": "Aiping Lyu", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Wenliang Lv", + "author_inst": "China Academy of Chinese Medical Sciences" + }, + { + "author_name": "Huixian Wang", + "author_inst": "Guangdong Provincial Hospital of Traditional Chinese Medicine" + }, + { + "author_name": "Helen Zhang", + "author_inst": "Hong Kong Northern District Hospital" + }, + { + "author_name": "Xuebin Zhang", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Shi Ping Zhang", + "author_inst": "Hong Kong Baptist University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.17.22272535", "rel_title": "Comparison of the 2021 COVID-19 'Roadmap' Projections against Public Health Data", @@ -333732,61 +336201,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.17.484640", - "rel_title": "Long-term T cell perturbations and waning antibody levels in individuals needing hospitalization for COVID-19", - "rel_date": "2022-03-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.17.484640", - "rel_abs": "COVID-19 is being extensively studied, and much remains unknown regarding the long-term consequences of the disease on immune cells. The different arms of the immune system are interlinked, with humoral responses and the production of high-affinity antibodies being largely dependent on T cell immunity. Here, we longitudinally explored the effect COVID-19 has on T cell populations and the virus-specific T cells, as well as neutralizing antibody responses, for 6-7 months following hospitalization. The CD8+ TEMRA and exhausted CD57+CD8+ T cells were markedly affected with elevated levels that lasted long into convalescence. Further, markers associated with T-cell activation were upregulated at the inclusion, and in the case of CD69+CD4+ T cells this lasted all through the study duration. The levels of T cells expressing negative immune checkpoint molecules were increased in COVID-19 patients and sustained for a prolonged duration following recovery. Within 2-3 weeks after symptom onset, all COVID-19 patients developed anti-nucleocapsid IgG and spike-neutralizing IgG as well as SARS-CoV-2-specific T cell responses. In addition, we found alterations in follicular T helper (TFH) cell populations, such as enhanced TFH-TH2 following recovery from COVID-19. Our study revealed significant and long-term alterations in T cell populations and key events associated with COVID-19 pathogenesis.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Melissa Govender", - "author_inst": "Linkoping University" - }, - { - "author_name": "Francis R Hopkins", - "author_inst": "Linkoping University" - }, - { - "author_name": "Robin Goransson", - "author_inst": "Linkoping University" - }, - { - "author_name": "Cecilia Svanberg", - "author_inst": "Linkoping University" - }, - { - "author_name": "Shankar Esaki Muthu", - "author_inst": "Central University of Tamil Nadu" - }, - { - "author_name": "Maria Hjorth", - "author_inst": "Linkoping University" - }, - { - "author_name": "Asa Nilsdotter Augustinsson", - "author_inst": "Linkoping University" - }, - { - "author_name": "Johanna Sjowall", - "author_inst": "Linkoping University" - }, - { - "author_name": "Sofia Nystrom", - "author_inst": "Linkoping University" - }, - { - "author_name": "Marie Larsson", - "author_inst": "Linkoping University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.03.16.484099", "rel_title": "The effect of waning on antibody levels and memory B cell recall following SARS-CoV-2 infection or vaccination", @@ -335233,6 +337647,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.14.22272368", + "rel_title": "Area-level social and structural inequalities determine mortality related to COVID-19 diagnosis in Ontario, Canada: a population-based explanatory modeling study of 11.8 million people", + "rel_date": "2022-03-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.14.22272368", + "rel_abs": "ImportanceSocial determinants of health (SDOH) play an important role in COVID-19 outcomes. More research is needed to quantify this relationship and understand the underlying mechanisms.\n\nObjectivesTo examine differential patterns in COVID-19-related mortality by area-level SDOH accounting for confounders; and to compare these patterns to those for non-COVID-19 mortality, and COVID-19 case fatality (COVID-19-related death among those diagnosed).\n\nDesign, setting, and participantsPopulation-based retrospective cohort study including all community living individuals aged 20 years or older residing in Ontario, Canada, as of March 1, 2020 who were followed through to March 2, 2021.\n\nExposureSDOH variables derived from the 2016 Canada Census at the dissemination area-level including: median household income; educational attainment; proportion of essential workers, racialized groups, recent immigrants, apartment buildings, and high-density housing; and average household size.\n\nMain outcomes and measuresCOVID-19-related death was defined as death within 30 days following, or 7 days prior to a positive SARS-CoV-2 test. Cause-specific hazard models were employed to examine the associations between SDOH and COVID-19-related mortality, treating non-COVID-19 mortality as a competing risk.\n\nResultsOf 11,810,255 individuals included, 3,880 (0.03%) died related to COVID-19 and 88,107 (0.75%) died without a positive test. After accounting for demographics, baseline health, and other SDOH, the following SDOH were associated with increased hazard of COVID-19-related death (hazard ratios [95% confidence intervals]) comparing the most to least vulnerable group): lower income (1.30[1.09-1.54]), lower educational attainment (1.27[1.10-1.47]), higher proportion essential workers (1.28[1.10-1.50]), higher proportion racialized groups (1.42[1.16-1.73]), higher proportion apartment buildings (1.25[1.11-1.41]), and larger vs. medium household size (1.30[1.13-1.48]). In comparison, areas with higher proportion racialized groups were associated with a lower hazard of non-COVID-19 mortality (0.88[0.85-0.92]). With the exception of income, SDOH were not independently associated with COVID-19 case fatality.\n\nConclusions and relevanceArea-level social and structural inequalities determine COVID-19-related mortality after accounting for individual demographic and clinical factors. COVID-19 has reversed the pattern of lower non-COVID-19 mortality by racialized groups. Pandemic responses should include prioritized and community-tailored intervention strategies to address SDOH that mechanistically underpin disproportionate acquisition and transmission risks and shape barriers to the reach of, and access to prevention interventions.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSAre area-level social determinants of health factors independently associated with coronavirus disease 2019 (COVID-19)-related mortality after accounting for demographics and clinical factors?\n\nFindingsIn this population-based cohort study including 11.8 million adults residing in Ontario, Canada and 3,880 COVID-19-related death occurred between Mar 1, 2020 and Mar 2, 2021, we found that areas characterized by lower SES (including lower income, lower educational attainment, and higher proportion essential workers), greater ethnic diversity, more apartment buildings, and larger vs. medium household size were associated with increased hazard of COVID-19-related mortality compared to their counterparts, even after accounting for individual-level demographics, baseline health, and other area-level SDOH.\n\nMeaningPandemic responses should include prioritized and community-tailored intervention strategies to address SDOH that mechanistically underpin inequalities in acquisition and transmission risks, and in the reach of, and access to prevention interventions.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Linwei Wang", + "author_inst": "Unity Health Toronto" + }, + { + "author_name": "Andrew Calzavara", + "author_inst": "ICES" + }, + { + "author_name": "Stefan Baral", + "author_inst": "JHSPH" + }, + { + "author_name": "Janet Smylie", + "author_inst": "University of Toronto" + }, + { + "author_name": "Adrienne K Chan", + "author_inst": "University of Toronto" + }, + { + "author_name": "Beate Sander", + "author_inst": "University Health Network" + }, + { + "author_name": "Peter C Austin", + "author_inst": "ICES" + }, + { + "author_name": "Jeff C Kwong", + "author_inst": "ICES" + }, + { + "author_name": "Sharmistha Mishra", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.14.22272359", "rel_title": "Biomarkers Selection for Population Normalization in SARS-CoV-2 Wastewater-based Epidemiology", @@ -335430,85 +337895,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.15.22272371", - "rel_title": "Neutralizing responses in fully vaccinated with BNT162b2, CoronaVac, ChAdOx1, and Ad26.COV2.S against SARS-CoV-2 lineages in Colombia, 2020-2021", - "rel_date": "2022-03-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.15.22272371", - "rel_abs": "BackgroundBy March 2022, around 34 million people in Colombia had received a complete scheme of vaccines against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) including, mRNA-based vaccines, viral vectored coronavirus vaccines, or the inactivated whole virus vaccine. However, as several SARS-CoV-2 variants of concern (VOC) and interest (VOI) co-circulate in the country, determining the resistance level to vaccine-elicited neutralizing antibodies (nAbs) is useful to improve the efficacy of COVID-19 vaccination programs.\n\nMethodsMicroneutralization assays with the most prevalent SARS-CoV-2 lineages in Colombia during 2020-2021 were performed using serum samples from immunologically naive individuals between 9 and 13 weeks after receiving complete regimens of CoronaVac, BNT162b2, ChAdOx1, or Ad26.COV2.S. The mean neutralization titer (MN50) was calculated by the Reed-Muench method and used to determine differences in vaccine-elicited nAbs against the SARS-CoV-2 lineages B.1.111, P.1 (Gamma), B.1.621 (Mu), and AY.25.1 (Delta).\n\nResultsThe most administered vaccines in the country, BNT162b2 and CoronaVac, elicited significantly different nAb responses against Mu, as the GMTs were 75.7 and 5.9-fold lower relative to the control lineage (B.1.111), while for Delta were 15.8 and 1.1-fold lower, respectively. In contrast, nAb responses against Mu and Delta were comparable between ChAd0x1-s and Ad26.COV2.S as the GMTs remained around 5 to 7-fold lower relative to B.1.111.\n\nConclusionsThe emergence of SARS-CoV-2 variants in Colombia with a significant capacity to escape from vaccine-elicited nAbs indicates that a booster dose is highly recommended. Furthermore, other non-pharmacological measures should be retained in the vaccinated population.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Diego Alejandro Alvarez-Diaz", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Ana Luisa Munoz", - "author_inst": "Fundacion Banco Nacional de Sangre Hemolife" - }, - { - "author_name": "Maria T Herrera", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Pilar Tavera", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Katherine Laiton-Donato", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Carlos Franco-Munoz", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Hector Ruiz-Moreno", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Dioselina Pelaez-Carvajal", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Alejandra Munoz-Suarez", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Marisol Galindo", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Jhonnatan Reales-Gonzalez", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Jenssy D Catama", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Beatriz H De Arco", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Tatiana Cobos", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Edgar J. Arias-Ramirez", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Marcela Mercado-Reyes", - "author_inst": "Instituto Nacional de Salud" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.15.484018", "rel_title": "Dynamic single-cell RNA sequencing reveals BCG vaccination curtails SARS-CoV-2 induced disease severity and lung inflammation", @@ -337055,6 +339441,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.03.10.22272123", + "rel_title": "Polymorphism in IFNAR contributes to glucocorticoid response and outcome in ARDS and COVID-19", + "rel_date": "2022-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.10.22272123", + "rel_abs": "The use of glucocorticoids has given contradictory results for treating acute respiratory distress syndrome (ARDS). Here we report a novel disease association of a SNP rs9984273, which is situated in the interferon alpha/beta receptor (IFNAR2) gene in an area corresponding to a binding motif of the glucocorticoid receptor (GR). The minor allele of SNP rs9984273 associates with higher IFNAR expression, lower IFN-gamma and IL-6 levels and less severe form of coronavirus diseases (COVID-19) according to the COVID-19 Host Genetics Initiative database, and better outcome in interferon (IFN) beta treated patients with ARDS. Thus, the distribution of this SNP within clinical study arms may explain the contradictory results of multiple ARDS studies and outcomes in COVID-19 concerning type I IFN signalling and glucocorticoids.\n\nOne-Sentence SummarySingle nucleotide polymorphism in interferon receptor contributes to corticosteroid response and outcome in ARDS and COVID-19", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Juho Jalkanen", + "author_inst": "Faron Pharmaceuticals" + }, + { + "author_name": "Sofia Khan", + "author_inst": "University of Turku" + }, + { + "author_name": "Kati Elima", + "author_inst": "University of Turku" + }, + { + "author_name": "Teppo Huttunen", + "author_inst": "Estimates" + }, + { + "author_name": "Ning Wang", + "author_inst": "University of Turku" + }, + { + "author_name": "Maija Hollmen", + "author_inst": "University of Turku" + }, + { + "author_name": "Laura Elo", + "author_inst": "University of Turku" + }, + { + "author_name": "Sirpa Jalkanen", + "author_inst": "University of Turku" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2022.03.10.22272237", "rel_title": "Long COVID in Children and Adolescents: A Systematic Review and Meta-analyses.", @@ -337168,65 +339601,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.10.22272196", - "rel_title": "Milder disease trajectory among COVID-19 patients hospitalised with the SARS-CoV-2 Omicron variant compared with the Delta variant in Norway", - "rel_date": "2022-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.10.22272196", - "rel_abs": "Using individual-level national registry data, we conducted a cohort study to estimate differences in the length of hospital stay, and risk of admission to an intensive care unit and in-hospital death among patients infected with the SARS-CoV-2 Omicron variant, compared to patients infected with Delta variant in Norway. We included 409 (38%) patients infected with Omicron and 666 (62%) infected with Delta who were hospitalised with COVID-19 as the main cause of hospitalisation between 6 December 2021 and 6 February 2022. Omicron patients had a 48% lower risk of intensive care admission (aHR: 0.52, 95%CI: 0.34-0.80) and a 56% lower risk of in-hospital death (aHR: 0.44, 95%CI: 0.24-0.79) compared to Delta patients. Omicron patients had a shorter length of stay (with or without ICU stay) compared to Delta patients in the age groups from 18-79 years and those who had at least completed their primary vaccination. This supports growing evidence of reduced disease severity among hospitalised Omicron patients compared with Delta patients.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Jeanette Stalcrantz", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Kristoffersen Braten Anja", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Hakon Boas", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Lamprini Veneti", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Elina Marjukka Seppala", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Nina Aasand", - "author_inst": "Norwegian Institute of PublicHealth" - }, - { - "author_name": "Olav Hungnes", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Reidar Kvale", - "author_inst": "Haukeland University Hospital" - }, - { - "author_name": "Karoline Bragstad", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Eirik Alnes Buanes", - "author_inst": "Haukeland University Hospital" - }, - { - "author_name": "Robert Neil Whittaker", - "author_inst": "Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.10.22272177", "rel_title": "The Omicron SARS-CoV-2 epidemic in England during February 2022", @@ -338913,6 +341287,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2022.03.09.22272113", + "rel_title": "Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination", + "rel_date": "2022-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.09.22272113", + "rel_abs": "Between November 2021 and February 2022, SARS-CoV-2 Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events. We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant. We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5-end of the viral genome was from the Delta genome, and the 3-end from Omicron including the majority of the spike protein gene, though the breakpoints were different. Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared to the circulating Omicron lineages.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Alexandre Bolze", + "author_inst": "Helix" + }, + { + "author_name": "Tracy Basler", + "author_inst": "Helix" + }, + { + "author_name": "Simon White", + "author_inst": "Helix" + }, + { + "author_name": "Andrew Dei Rossi", + "author_inst": "Helix" + }, + { + "author_name": "Dana Wyman", + "author_inst": "Helix" + }, + { + "author_name": "Pavitra Roychoudhury", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexander L. Greninger", + "author_inst": "University of Washington" + }, + { + "author_name": "Kathleen Hayashibara", + "author_inst": "Thermo Fisher Scientific" + }, + { + "author_name": "Eric Kil", + "author_inst": "Helix" + }, + { + "author_name": "Hang Dai", + "author_inst": "Helix" + }, + { + "author_name": "Tyler Cassens", + "author_inst": "Helix" + }, + { + "author_name": "Kevin Tsan", + "author_inst": "Helix" + }, + { + "author_name": "Jason Nguyen", + "author_inst": "Helix" + }, + { + "author_name": "Jimmy Ramirez", + "author_inst": "Helix" + }, + { + "author_name": "Scotty Carter", + "author_inst": "Helix" + }, + { + "author_name": "Elizabeth T. Cirulli", + "author_inst": "Helix" + }, + { + "author_name": "Kelly Schiabor Barrett", + "author_inst": "Helix" + }, + { + "author_name": "Nicole L Washington", + "author_inst": "Helix" + }, + { + "author_name": "Pedro Belda-Ferre", + "author_inst": "Helix" + }, + { + "author_name": "Sharoni Jacobs", + "author_inst": "Helix" + }, + { + "author_name": "Efren Sandoval", + "author_inst": "Helix" + }, + { + "author_name": "David Becker", + "author_inst": "Helix" + }, + { + "author_name": "James T Lu", + "author_inst": "Helix" + }, + { + "author_name": "Magnus Isaksson", + "author_inst": "Helix" + }, + { + "author_name": "William Lee", + "author_inst": "Helix" + }, + { + "author_name": "Shishi Luo", + "author_inst": "Helix" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.10.22272197", "rel_title": "Blood group O and post-COVID-19 syndrome", @@ -339162,89 +341655,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.10.22271805", - "rel_title": "SARS-CoV-2 seroconversion in response to infection and vaccination: A time series local study in Brazil", - "rel_date": "2022-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.10.22271805", - "rel_abs": "The investigation of antibodies raised against different SARS-CoV-2 antigens can help to determine the extent of previous SARS-CoV-2 infections in the population and track the humoral response to vaccination. Therefore, serological surveys can provide key information to better manage the pandemic and/or to implement the most effective vaccination program. Here we describe a time series anti-Nucleocapsid, anti-Spike IgG serological survey analysis in the city of Matinhos, PR, Brazil during the year of 2021. Seroconversion rates to the Nucleocapsid antigen was not influenced by gender or age. Comparison of the serological data with official COVID-19 cases in the city suggest that case sub notification is higher than 47%. Furthermore, by applying serological data, the corrected infection fatality rate was estimated to be lower than 2.4 % in contrast with the official estimative of 3.6 %. The rates of IgG reactive to Spike antigen resembled the curve of the fraction the population that had taken the second vaccine dose. Up to 82% of Spike seroconversion was detected in the end of 2021 confirming the effective of the COVID-19 vaccination program in the city. This SARS-CoV-2 serological study unraveled the SARS-CoV-2 infection rates and the response to vaccination in the city of Matinhos. It is likely that the numbers reported here may be similar in other cities in Brazil.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Luciano Huergo Sr.", - "author_inst": "Universidade Federal do Parana" - }, - { - "author_name": "Nigella M Paula", - "author_inst": "UFPR" - }, - { - "author_name": "Ana C.A. Goncalves", - "author_inst": "UFPR" - }, - { - "author_name": "Carlos H.S Kluge", - "author_inst": "UFPR" - }, - { - "author_name": "Paulo H.S.A Martins", - "author_inst": "UFPR" - }, - { - "author_name": "Haxley S.C Camargo", - "author_inst": "UFPR" - }, - { - "author_name": "Thamyres P Santana", - "author_inst": "UFPR" - }, - { - "author_name": "Lucas R.P. Farias", - "author_inst": "UFPR" - }, - { - "author_name": "Enio S Lima", - "author_inst": "UFPR" - }, - { - "author_name": "Juliane D. Aldrighi", - "author_inst": "UFPR" - }, - { - "author_name": "Guiomar T Jacotenski", - "author_inst": "UFPR" - }, - { - "author_name": "Leticia R Vargas", - "author_inst": "UFPR" - }, - { - "author_name": "Gisele Costa", - "author_inst": "UFPR" - }, - { - "author_name": "Karin V Weissheimer", - "author_inst": "UFPR" - }, - { - "author_name": "Mariana G Nazario", - "author_inst": "UFPR" - }, - { - "author_name": "Kadima N Teixeira", - "author_inst": "UFPR" - }, - { - "author_name": "Marcelo dos Santos Conzentino", - "author_inst": "UFPR" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.09.22271297", "rel_title": "Possible Role of P-selectin Adhesion in Long-COVID: A Comparative Analysis of a Long-COVID Case Versus an Asymptomatic Post-COVID Case", @@ -341171,6 +343581,33 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2022.03.10.483790", + "rel_title": "Evolutionary safety of death by mutagenesis", + "rel_date": "2022-03-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.10.483790", + "rel_abs": "Nucleoside analogs are a major class of antiviral drugs. Some act by increasing the viral mutation rate causing \"death by mutagenesis\" of the virus. Their mutagenic capacity, however, may lead to an evolutionary safety concern. We define evolutionary safety as a probabilistic assurance that the treatment will not generate an increased number of epidemiologically concerning mutated virus progeny. We develop a mathematical framework to estimate the total mutant load produced with and without mutagenic treatment. We predict rates of appearance of virus mutants as a function of the timing of treatment and the immune competence of patients, employing various assumptions about the vulnerability of the viral genome and its potential to generate undesired phenotypes. We focus on the case study of Molnupiravir, which is an FDA-approved treatment against COVID-19. We estimate that Molnupiravir is narrowly evolutionarily safe, subject to the current estimate of parameters. Evolutionary safety can be improved by restricting treatment to individuals with a low clearance rate and by designing treatments that lead to a greater increase in mutation rate. We report a simple rule to determine the fold-increase in mutation rate required to obtain evolutionary safety which is also applicable to other pathogen-treatment combinations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Gabriela Aleksandra Lobinska", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Yitzhak Tzachi Pilpel", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Martin Andreas Nowak", + "author_inst": "Harvard" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2022.03.10.483652", "rel_title": "Open modification searching of SARS-CoV-2-human protein interaction data reveals novel viral modification sites", @@ -341288,61 +343725,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.08.22272057", - "rel_title": "Physical, psychological and cognitive profile of post-COVID condition in healthcare workers, Quebec, Canada", - "rel_date": "2022-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.08.22272057", - "rel_abs": "ImportanceMost adults with COVID-19 do not require hospitalization, but the subsequent risk of post-COVID condition, including associated psychological and cognitive dysfunction, remains poorly understood among non-hospitalized versus hospitalized cases.\n\nObjectiveTo assess the prevalence and duration of post-COVID condition, including physical, psychological and cognitive symptoms.\n\nDesignCase series and case-control study between December 2020 and May 2021\n\nSettingHealthcare workers in Quebec, Canada\n\nParticipantsEligible cases were symptomatic healthcare workers with PCR-confirmed COVID-19 between July 2020 and May 2021. Among 17,717 contacted cases, 6061 (34%) participated. A random sample of symptomatic healthcare workers with negative PCR result between November 2020 and May 2021 served as controls. Among 11,498 contacted controls, 4390 (38%) participated.\n\nExposuresIn multivariable models, sociodemographic and clinical characteristics, as well as vaccine history, were evaluated as potential risk factors. Prevalence ratios compared self-reported cognitive dysfunctions (difficulty concentrating; difficulty organizing oneself; forgetfulness; loss of necessary items) among cases with post-COVID condition to controls, adjusting for psychological distress and fatigue.\n\nOutcomesPost-COVID condition was defined by symptoms persisting [≥]4 weeks or [≥]12 weeks after COVID-19 onset.\n\nResultsFour-week and 12-week post-COVID condition prevalences of 46% (2,746/5,943) and 40% (653/1,746), respectively, were observed among non-hospitalized cases and 76% (90/118) and 68% (27/37), respectively, among hospitalized cases. Hospitalization, female sex and age were associated with higher risk.\n\nA substantial proportion of non-hospitalized cases with 4-week post-COVID condition often or very often reported cognitive dysfunction, including concentration (33%) or organizing (23%) difficulties, forgetfulness (20%) and loss of necessary items (10%), with no decline at 12 weeks. All four aspects of cognitive dysfunction were 2.2 to 3.0 times more prevalent among cases with post-COVID condition than in controls, but also independently associated with psychological distress and fatigue.\n\nConclusions and relevancePost-COVID condition may be a frequent sequela of ambulatory COVID-19 in working-age adults, with important effects on cognition. With so many healthcare workers infected since the beginning of the COVID-19 pandemic, the ongoing implications for quality healthcare delivery could be profound should cognitive dysfunction and other severe post-COVID symptoms persist in a professionally-disabling way over the longer term.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSHow common and long-lasting are the physical, psychological and cognitive effects of post-COVID condition in healthcare workers, both hospitalized and non-hospitalized?\n\nFindingsThe prevalence of post-COVID condition was 46% at 4 weeks and 40% at 12 weeks among non-hospitalized cases and 76% and 68% among hospitalized cases. One third of non-hospitalized healthcare workers with post-COVID condition reported cognitive impairment, which was independently associated with persistent physical symptoms, but also psychological distress and fatigue.\n\nMeaningPersistent cognitive and other professionally-disabling sequelae of COVID-19 in essential workers could have critical implications for quality healthcare delivery during and after the pandemic.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Sara Carazo", - "author_inst": "Institut de sant\u00e9 publique du Qu\u00e9bec, Qu\u00e9bec, Canada" - }, - { - "author_name": "Danuta M Skowronski", - "author_inst": "BC Centre for Disease Control, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Robert Jr Laforce", - "author_inst": "CHU de Qu\u00e9bec - Universit\u00e9 Laval, Qu\u00e9bec, Canada" - }, - { - "author_name": "Denis Talbot", - "author_inst": "CHU de Qu\u00e9bec - Universit\u00e9 Laval, Qu\u00e9bec, Canada" - }, - { - "author_name": "Emilia L Falcone", - "author_inst": "University of Montreal, Montr\u00e9al, Canada" - }, - { - "author_name": "Denis Lalibert\u00e9", - "author_inst": "Laval University, Qu\u00e9bec, Canada" - }, - { - "author_name": "Geoffroy Denis", - "author_inst": "CIUSSS Centre Sud de Montr\u00e9al, Montr\u00e9al, Canada" - }, - { - "author_name": "Pierre Deshaies", - "author_inst": "CISSS de Chaudi\u00e8re Appalaches, L\u00e9vis, Qu\u00e9bec, Canada" - }, - { - "author_name": "Sandrine Hegg-Deloye", - "author_inst": "CHU de Q\u00e9bec - Universit\u00e9 Laval, Qu\u00e9bec, Canada" - }, - { - "author_name": "Gaston De Serres", - "author_inst": "Institut de sant\u00e9 publique du Qu\u00e9bec, Qu\u00e9bec, Canada" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.08.22272082", "rel_title": "Community Engagement to support COVID-19 Vaccine Uptake: A living systematic review protocol", @@ -343329,6 +345711,53 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2022.03.08.483429", + "rel_title": "Geneticin shows selective antiviral activity against SARS-CoV-2 by targeting programmed -1 ribosomal frameshifting", + "rel_date": "2022-03-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.08.483429", + "rel_abs": "SARS-CoV-2 is currently causing an unprecedented pandemic. While vaccines are massively deployed, we still lack effective large-scale antiviral therapies. In the quest for antivirals targeting conserved structures, we focused on molecules able to bind viral RNA secondary structures. Aminoglycosides are a class of antibiotics known to interact with the ribosomal RNA of both prokaryotes and eukaryotes and have previously been shown to exert antiviral activities by interacting with viral RNA. Here we show that the aminoglycoside geneticin is endowed with antiviral activity against all tested variants of SARS-CoV-2, in different cell lines and in a respiratory tissue model at non-toxic concentrations. The mechanism of action is an early inhibition of RNA replication and protein expression related to a decrease in the efficiency of the -1 programmed ribosomal frameshift (PRF) signal of SARS-CoV-2. Using in silico modelling, we have identified a potential binding site of geneticin in the pseudoknot of frameshift RNA motif. Moreover, we have selected, through virtual screening, additional RNA binding compounds, interacting with the same site with increased potency.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Carmine Varricchio", + "author_inst": "Cardiff School of Pharmacy and Pharmaceutical Sciences" + }, + { + "author_name": "Gregory Mathez", + "author_inst": "University Hospital of Vaud (CHUV)" + }, + { + "author_name": "Trestan Pillonel", + "author_inst": "University Hospital of Vaud (CHUV)" + }, + { + "author_name": "Claire Bertelli", + "author_inst": "University Hospital of Vaud (CHUV)" + }, + { + "author_name": "Laurent Kaiser", + "author_inst": "University of Geneva Hospitals" + }, + { + "author_name": "Caroline Tapparel", + "author_inst": "University of Geneva" + }, + { + "author_name": "Andrea Brancale", + "author_inst": "Cardiff School of Pharmacy and Pharmaceutical Sciences" + }, + { + "author_name": "Valeria Cagno", + "author_inst": "University Hospital of Vaud (CHUV)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.03.01.22271721", "rel_title": "The relative impact of vaccination momentum on COVID-19 rates of death in the USA in 2020/2021. The forgotten role of population wellness.", @@ -343502,85 +345931,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.06.22270594", - "rel_title": "Post COVID-19 Condition in South Africa: 3-month follow-up after hospitalisation with SARS-CoV-2", - "rel_date": "2022-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.06.22270594", - "rel_abs": "BackgroundPost COVID-19 Condition (PCC) as defined by WHO refers to a wide range of new, returning, or ongoing health problems experienced by COVID-19 survivors, and represents a rapidly emerging public health priority. We aimed to establish how this developing condition has impacted patients in South Africa and which population groups are at risk.\n\nMethodsIn this prospective cohort study, participants [≥]18 years who had been hospitalised with laboratory-confirmed SARS-CoV-2 infection during the second and third wave between December 2020 and August 2021 underwent telephonic follow-up assessment up at one-month and three-months after hospital discharge. Participants were assessed using a standardised questionnaire for the evaluation of symptoms, functional status, health-related quality of life and occupational status. Multivariable logistic regression models were used to determine factors associated with PCC.\n\nFindingsIn total, 1,873 of 2,413 (78%) enrolled hospitalised COVID-19 participants were followed up at three-months after hospital discharge. Participants had a median age of 52 years (IQR 41-62) and 960 (51.3%) were women. At three-months follow-up, 1,249 (66.7%) participants reported one or more persistent COVID-related symptom(s), compared to 1,978/2,413 (82.1%) at one-month post-hospital discharge. The most common symptoms reported were fatigue (50.3%), shortness of breath (23.4%), confusion or lack of concentration (17.5%), headaches (13.8%) and problems seeing/blurred vision (10.1%). On multivariable analysis, factors associated with new or persistent symptoms following acute COVID-19 were age [≥]65 years [adjusted odds ratio (aOR) 1.62; 95%confidence interval (CI) 1.00-2.61]; female sex (aOR 2.00; 95% CI 1.51-2.65); mixed ethnicity (aOR 2.15; 95% CI 1.26-3.66) compared to black ethnicity; requiring supplemental oxygen during admission (aOR 1.44; 95% CI 1.06-1.97); ICU admission (aOR 1.87; 95% CI 1.36-2.57); pre-existing obesity (aOR 1.44; 95% CI 1.09-1.91); and the presence of [≥]4 acute symptoms (aOR 1.94; 95% CI 1.19-3.15) compared to no symptoms at onset.\n\nInterpretationThe majority of COVID-19 survivors in this cohort of previously hospitalised participants reported persistent symptoms at three-months from hospital discharge, as well as a significant impact of PCC on their functional and occupational status. The large burden of PCC symptoms identified in this study emphasises the need for a national health strategy. This should include the development of clinical guidelines and training of health care workers, in identifying, assessing and caring for patients affected by PCC, establishment of multidisciplinary national health services, and provision of information and support to people who suffer from PCC.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Murray Dryden", - "author_inst": "National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Caroline Mudara", - "author_inst": "National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Caroline Vika", - "author_inst": "National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Lucille Blumberg", - "author_inst": "National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Natalie Mayet", - "author_inst": "National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa" - }, - { - "author_name": "Cheryl Cohen", - "author_inst": "School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South AfricaCentre for Respiratory Diseases and Meningitis, " - }, - { - "author_name": "Stefano Tempia", - "author_inst": "School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South AfricaCentre for Respiratory Diseases and Meningitis, " - }, - { - "author_name": "Arifa Parker", - "author_inst": "Divisions of General Medicine and Infectious Diseases, Faculty of Medicine and Health Sciences, Stellenbosch University and Tygerberg Hospital, Cape Town" - }, - { - "author_name": "Jeremy Nel", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of the Witwatersrand, Johannesburg" - }, - { - "author_name": "Rubeshan Perumal", - "author_inst": "Centre for Lung Infection and Immunity, Pulmonology, Division o ;South African Medical Research Council-CAPRISA HIV/TB Pathogenesis and Treatment Research Unit," - }, - { - "author_name": "Michelle Groome", - "author_inst": "National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa; School of Pathology, Faculty of He" - }, - { - "author_name": "Francesca Conradie", - "author_inst": "Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg" - }, - { - "author_name": "Norbert Ndjeka", - "author_inst": "Drug-Resistant TB, TB & HIV Directorate, National Department of Health, Pretoria, South Africa and University of KwaZulu-Natal, Durban" - }, - { - "author_name": "Louise Sigfrid", - "author_inst": "nternational Severe Actue Respiratory and emerging Infections Consortium (ISARIC) Global Support Centre, Nuffield Department of Medicine, University of Oxford, " - }, - { - "author_name": "Laura Merson", - "author_inst": "International Severe Actue Respiratory and emerging Infections Consortium (ISARIC), Pandemic Sciences Centre, University of Oxford, UK" - }, - { - "author_name": "Waasila Jassat", - "author_inst": "National Institute for Communicable Disease, Division of the National Health Laboratory Services, Johannesburg, South Africa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.03.02.22271808", "rel_title": "\"Pandemic of the unvaccinated\"? At midlife, white people are less vaccinated but still at less risk of Covid-19 mortality in Minnesota", @@ -345263,6 +347613,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.04.22271890", + "rel_title": "Protective antibodies and T cell responses to Omicron variant three months after the booster dose of BNT162b2 vaccine", + "rel_date": "2022-03-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.04.22271890", + "rel_abs": "The high number of mutations in the Omicron variant of SARS-CoV-2 cause its immune escape when compared to the earlier variants of concern (VOC). At least three vaccine doses are required for the induction of Omicron neutralizing antibodies and further reducing the risk for hospitalization. However, most of the studies have focused on the immediate response after the booster vaccination while the duration of immune response is less known. We here studied longitudinal serum samples from the vaccinated individuals up to three months after their third dose of the BNT162b2 vaccine for their capacity to produce protective antibodies and T cell responses to Wuhan and Omicron variants. After the second dose, the antibody levels to the unmutated spike protein were significantly decreased at three months, and only 4% of the individuals were able to inhibit Omicron spike interaction compared to 47%, 38%, and 14% of individuals inhibiting wild-type, delta, and beta variants spike protein. Nine months after the second vaccination, the antibody levels were similar to the levels before the first dose and none of the sera inhibited SARS-CoV-2 wild-type or any of the three VOCs. The booster dose remarkably increased antibody levels and their ability to inhibit all variants. Three months after the booster the antibody levels and the inhibition activity were trending lower but still up and not significantly different from their peak values at two weeks after the third dose. Although responsiveness towards mutated spike peptides was lost in less than 20 % of vaccinated individuals, the wild-type spike-specific CD4+ and CD8+ memory T cells were still present at three months after the booster vaccination in the majority of studied individuals. Our data show that two doses of the BNT62b2 vaccine are not sufficient to protect against the Omicron variant, however, the spike-specific antibodies and T cell responses are strongly elicited and well maintained three months after the third vaccination dose.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Paul Naaber", + "author_inst": "SYNLAB Eesti" + }, + { + "author_name": "Liina Tserel", + "author_inst": "University of Tartu" + }, + { + "author_name": "Kadri Kangro", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Epp Sepp", + "author_inst": "University of Tartu" + }, + { + "author_name": "Virge Jurjenson", + "author_inst": "SYNLAB Eesti" + }, + { + "author_name": "Jaanika Karner", + "author_inst": "University of Tartu" + }, + { + "author_name": "Liis Haljasmagi", + "author_inst": "University of Tartu" + }, + { + "author_name": "Uku Haljasorg", + "author_inst": "University of Tartu" + }, + { + "author_name": "Marilin Kuusk", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Joachim M Gerhold", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Anu Planken", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Mart Ustav", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Kai Kisand", + "author_inst": "University of Tartu" + }, + { + "author_name": "Part Peterson", + "author_inst": "University of Tartu" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.04.22271540", "rel_title": "The mutational steps of SARS-CoV-2 to become like Omicron within seven months: the story of immune escape in an immunocompromised patient.", @@ -345396,49 +347817,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.03.05.22271947", - "rel_title": "Efficacy and safety of intensified versus standard prophylactic anticoagulation therapy in patients with Covid-19: a systematic review and meta-analysis", - "rel_date": "2022-03-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.05.22271947", - "rel_abs": "BackgroundRandomised controlled trials (RCTs) have reported inconsistent effects from intensified anticoagulation on clinical outcomes in Covid-19. We performed an aggregate data meta-analysis from available trials to quantify effect on non-fatal and fatal outcomes and identify subgroups who may benefit.\n\nMethodsWe searched multiple databases for RCTs comparing intensified (intermediate or therapeutic dose) versus standard prophylactic dose anticoagulation in adults with laboratory-confirmed Covid-19 through 19 January 2022. The primary efficacy outcome was all-cause mortality at end of follow-up or discharge. We used random effects meta-analysis to estimate pooled risk ratios for mortality, thrombotic, and bleeding events, and performed subgroup analysis for clinical setting and dose of intensified anticoagulation.\n\nResultsEleven RCTs were included (n = 5873). Intensified anticoagulation was not associated with a reduction in mortality for up to 45 days compared with prophylactic anticoagulation: 17.5% (501/2861) died in the intensified anticoagulation group and 18.8% (513/2734) died in the prophylactic anticoagulation group, relative risk (RR) 0.93; 95%CI, 0.79 - 1.10. On subgroup analysis, there was a possible signal of mortality reduction for inpatients admitted to general wards, although with low precision and high heterogeneity (5 studies; RR 0.84; 95% CI, 0.49 - 1.44; I2 = 75%) and not significantly different to studies performed in the ICU (interaction P = 0.51). Risk of venous thromboembolism was reduced with intensified anticoagulation compared with prophylaxis (8 studies; RR 0.53, 95%CI 0.41 - 0.69; I2 = 0%). This effect was driven by therapeutic rather than intermediate dosing on subgroup analysis (interaction P =0.04). Major bleeding was increased with use of intensified anticoagulation (RR 1.73, 95% CI 1.17 - 2.56) with no interaction for dosing and clinical setting.\n\nConclusionIntensified anticoagulation has no effect on short term mortality among hospitalised adults with Covid-19 and is associated with increased risk of bleeding. The observed reduction in venous thromboembolism risk and trend towards reduced mortality in non-ICU hospitalised patients requires exploration in additional RCTs.\n\nSummaryIn this aggregate data meta-analysis, use of intensified anticoagulation had no effect on short term mortality among hospitalised adults with Covid-19 and was associated with increased risk of bleeding.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Nicola K Wills", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Nikhil Nair", - "author_inst": "Michael G DeGroote School of Medicine, McMaster University, Hamliton, Canada" - }, - { - "author_name": "Kayshap Patel", - "author_inst": "School of Medicine, University of Ottawa, Ontario, Canada" - }, - { - "author_name": "Omaike Sikder", - "author_inst": "Michael G DeGroote School of Medicine, McMaster University, Hamilton, Canada" - }, - { - "author_name": "Marguerite Adriaanse", - "author_inst": "University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "John Eikelboom", - "author_inst": "Michael G DeGroote School of Medicine, McMaster University, Hamilton, Canada" - }, - { - "author_name": "Sean Wasserman", - "author_inst": "University of Cape Town, Cape Town, South Africa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.07.481785", "rel_title": "SARS-CoV-2 Spike evolution influences GBP and IFITM sensitivity", @@ -346957,6 +349335,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2022.03.02.22271806", + "rel_title": "Covid-19 Exposure Assessment Tool (CEAT): Easy-to-use tool to quantify exposure based on airflow, group behavior, and infection prevalence in the community", + "rel_date": "2022-03-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271806", + "rel_abs": "The COVID-19 Exposure Assessment Tool (CEAT) allows users to compare respiratory relative risk to SARS-CoV-2 for various scenarios, providing understanding of how combinations of protective measures affect exposure, dose, and risk. CEAT incorporates mechanistic, stochastic and epidemiological factors including the: 1) emission rate of virus, 2) viral aerosol degradation and removal, 3) duration of activity/exposure, 4) inhalation rates, 5) ventilation rates (indoors/outdoors), 6) volume of indoor space, 7) filtration, 8) mask use and effectiveness, 9) distance between people, 10) group size, 11) current infection rates by variant, 12) prevalence of infection and immunity in the community, 13) vaccination rates of the community, and 14) implementation of COVID-19 testing procedures. Demonstration of CEAT, from published studies of COVID-19 transmission events, shows the model accurately predicts transmission. We also show how health and safety professionals at NASA Ames Research Center used CEAT to manage potential risks posed by SARS-CoV-2 exposures. Given its accuracy and flexibility, the wide use of CEAT will have a long lasting beneficial impact in managing both the current COVID-19 pandemic as well as a variety of other scenarios.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Brian Schimmoller", + "author_inst": "Signature Science LLC" + }, + { + "author_name": "Nidia S Trovao", + "author_inst": "Fogarty International Center, National Institutes of Health" + }, + { + "author_name": "Molly Isbell", + "author_inst": "Signature Science LLC" + }, + { + "author_name": "Chirag Goel", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Benjamin F Heck", + "author_inst": "Bastion Technologies, NASA Ames Research Center" + }, + { + "author_name": "Tenley C Archer", + "author_inst": "Biomea Fusion, Inc." + }, + { + "author_name": "Klint D Cardinal", + "author_inst": "Leidos, Inc., NASA Ames Research Center" + }, + { + "author_name": "Neil B Naik", + "author_inst": "Leidos, Inc., NASA Ames Research Center" + }, + { + "author_name": "Som Dutta", + "author_inst": "Mechanical & Aerospace Engineering, Utah State University" + }, + { + "author_name": "Ahleah Rohr Daniel", + "author_inst": "Space Biosciences Division, NASA Ames Research Center" + }, + { + "author_name": "Afshin Beheshti", + "author_inst": "KBR, NASA Ames Research Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.03.22271836", "rel_title": "The relationship between BMI and COVID-19: exploring misclassification and selection bias in a two-sample Mendelian randomisation study", @@ -347126,25 +349563,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.02.22271710", - "rel_title": "Daily tenofovir disoproxil fumarate/emtricitabine and hydroxychloroquine for pre-exposure prophylaxis of COVID-19: a double-blind placebo controlled randomized trial in healthcare workers", - "rel_date": "2022-03-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271710", - "rel_abs": "ObjectiveTo assess the effect of hydroxychloroquine (HCQ), Tenofovir disoproxil fumarate/Emtricitabine (TDF/FTC), and their combination as pre-exposure prophylaxis on the risk of symptomatic COVID-19.\n\nMethodsEPICOS is a double-blind, placebo-controlled randomized trial conducted in 51 hospitals in Spain, Bolivia, and Venezuela. Healthcare workers with negative SARS-CoV-2 IgM/IgG test were randomly assigned to: daily TDF/FTC plus HCQ for 12 weeks, TDF/FTC plus HCQ placebo, HCQ plus TDF/FTC placebo and TDF/FTC placebo plus HCQ placebo. The primary outcome was laboratory-confirmed, symptomatic COVID-19. We also studied any (symptomatic or asymptomatic) COVID-19 infection. We compared group-specific 14-week risks via differences and ratios with 95% confidence intervals (CI).\n\nResultsOf 1002 individuals screened, 926 (92.4%) were eligible; 64.2% recruited in Spain, 22.3% in Bolivia, and 13.6% in Venezuela. Median age was 38 years (range 18 - 68), 62.5% were female, 62.3% worked at inpatient care, and comorbidities were rare. Compared with the placebo group, 14-week risk ratios (95% CI) of symptomatic COVID-19 were 0.39 (0.00, 1.98) for TDF+HCQ, 0.34 (0.00, 2.06) for TDF, and 0.49 (0.00, 2.29) for HCQ. Corresponding risk ratios of any COVID-19 were 0.51 (0.21, 1.00) for TDF+HCQ, 0.81 (0.44, 1.49) for TDF, and 0.73 (0.41, 1.38) for HCQ. Adverse events were generally mild.\n\nConclusionA beneficial effect of TDF/FTC and HCQ, alone or in combination, as pre-exposure prophylaxis for COVID-19 cannot be ruled out but effect estimates are imprecise because the target sample size was not met. These findings support launching randomized trials of TDF/FTC for the early treatment of COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Julia Del Amo", - "author_inst": "Ministry of Health, Spain" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.02.22271673", "rel_title": "Predictive Model of Risk Factors of High Flow Nasal Cannula Using Machine Learning in COVID-19", @@ -348835,6 +351253,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.23.22271355", + "rel_title": "Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19", + "rel_date": "2022-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.23.22271355", + "rel_abs": "Estimating key aspects of transmission is crucial in infectious disease control. Serial intervals - the time between symptom onset in an infector and infectee - are fundamental, and help to define rates of transmission, estimates of reproductive numbers, and vaccination levels needed to prevent transmission. However, estimating the serial interval requires knowledge of individuals contacts and exposures (who infected whom), which is typically obtained through resource-intensive contact tracing efforts. We develop an alternate framework that uses virus sequences to inform who infected whom and thereby estimate serial intervals. The advantages are many-fold: virus sequences are often routinely collected to support epidemiological investigations and to monitor viral evolution. The genomic approach offers high resolution and cluster-specific estimates of the serial interval that are comparable with those obtained from contact tracing data. Our approach does not require contact tracing data, and can be used in large populations and over a range of time periods. We apply our techniques to SARS-CoV-2 sequence data from the first two waves of COVID-19 in Victoria, Australia. We find that serial interval estimates vary between clusters, supporting the need to monitor this key parameter and use updated estimates in onward applications. Compared to an early published serial interval estimate, using cluster-specific serial intervals can cause estimates of the effective reproduction number Rt to vary by a factor of up to 2-3. We also find that serial intervals estimated in settings such as schools and meat processing/packing plants tend to be shorter than those estimated in healthcare facilities.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jessica E Stockdale", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + }, + { + "author_name": "Kurnia Susvitasari", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + }, + { + "author_name": "Paul Tupper", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + }, + { + "author_name": "Benjamin Sobkowiak", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + }, + { + "author_name": "Nicola Mulberry", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + }, + { + "author_name": "Anders Gon\u00e7alves da Silva", + "author_inst": "Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for In" + }, + { + "author_name": "Anne E Watt", + "author_inst": "Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for In" + }, + { + "author_name": "Norelle Sherry", + "author_inst": "Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for In" + }, + { + "author_name": "Corinna Minko", + "author_inst": "Victorian Department of Health, Melbourne, Victoria, Australia" + }, + { + "author_name": "Benjamin P Howden", + "author_inst": "Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for In" + }, + { + "author_name": "Courtney R Lane", + "author_inst": "Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for In" + }, + { + "author_name": "Caroline Colijn", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.17.22270791", "rel_title": "Vaccine effectiveness and duration of protection against symptomatic and severe Covid-19 during the first year of vaccination in France", @@ -349016,65 +351497,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.03.02.22271552", - "rel_title": "A predictive model for hospitalization and survival to COVID-19 in a retrospective population-based study", - "rel_date": "2022-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271552", - "rel_abs": "The severe acute respiratory syndrome coronavirus (SARS-CoV-2) causing coronavirus disease 2019 (COVID-19) is highly transmissible and has been responsible for a pandemic associated with a high number of deaths. The clinical management of patients and the optimal use of resources are two important factors in reducing this mortality, especially in scenarios of high incidence. To this end, it is necessary to develop tools that allow early triage of patients with the minimal use of diagnostic tests and based on readily accessible data, such as electronic medical records. This work proposes the use of a machine learning model that allows the prediction of mortality and risk of hospitalization using simple demographic characteristics and comorbidities, using a COVID-19 dataset of 86867 patients. In addition, we developed a new method designed to deal with data imbalance problems. The model was able to predict with high accuracy (89-93%, ROC-AUC = 0.94) the patients final status (expired/discharged) and with medium accuracy the risk of hospitalization (71-73%, ROC-AUC = 0.75). These models were obtained by assembling and using easily obtainable clinical characteristics (2 demographic characteristics and 19 predictors of comorbidities). The most relevant features of these models were the following patient characteristics: age, sex, number of comorbidities, osteoarthritis, obesity, depression, and renal failure.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Alejandro Cisterna-Garcia", - "author_inst": "Departamento de Ingenieria de la Informacion y las Comunicaciones, Universidad de Murcia, Spain" - }, - { - "author_name": "Antonio Guillen-Teruel", - "author_inst": "Departamento de Ingenieria de la Informacion y las Comunicaciones, Universidad de Murcia, Spain" - }, - { - "author_name": "Marcos Caracena", - "author_inst": "Departamento de Ingenieria de la Informacion y las Comunicaciones, Universidad de Murcia, Spain" - }, - { - "author_name": "Enrique Perez", - "author_inst": "Departamento de Ingenieria de la Informacion y las Comunicaciones, Universidad de Murcia, Spain" - }, - { - "author_name": "Fernando Jimenez", - "author_inst": "Departamento de Ingenieria de la Informacion y las Comunicaciones, Universidad de Murcia, Spain" - }, - { - "author_name": "Francisco J. Francisco-Verdu", - "author_inst": "Departamento de Informatica, Servicio Murciano de Salud, Comunidad Autonoma de la Region de Murcia, Spain" - }, - { - "author_name": "Gabriel Reina", - "author_inst": "Servicio de Microbiologia. Clinica Universidad de Navarra, Pamplona, Spain" - }, - { - "author_name": "Enrique Gonzalez-Billalabeitia", - "author_inst": "Department of Medical Oncology. Hospital Universitario 12 de Octubre, Madrid, Spain" - }, - { - "author_name": "Jose T. Palma", - "author_inst": "Departamento de Ingenieria de la Informacion y las Comunicaciones, Universidad de Murcia, Spain" - }, - { - "author_name": "Alvaro Sanchez-Ferrer", - "author_inst": "Department of Biochemistry and Molecular Biology-A, Faculty of Biology, University of Murcia, Campus Espinardo, E-30100, Murcia, Spain" - }, - { - "author_name": "Juan A. Botia", - "author_inst": "Departamento de Ingenieria de la Informacion y las Comunicaciones, Universidad de Murcia, Spain" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.03.02.22271694", "rel_title": "Evidence of co-infection during Delta and Omicron variants of concern co-circulation, weeks 49-2021 to 02-2022, France", @@ -350697,6 +353119,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.02.22271385", + "rel_title": "Impact of Delta and Vaccination on SARS-CoV-2 transmission risk: Lessons for Emerging Breakthrough infections", + "rel_date": "2022-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271385", + "rel_abs": "With the continuous emergence of SARS-CoV-2 variants of concern and implementation of mass-scale interventions like vaccination, understanding factors affecting disease transmission has critical implications for control efforts. Here we used a simple adapted N95 mask sampling method to demonstrate the impact of circulating SARS-CoV-2 variants and vaccination on 92 COVID-19 patients to expel virus into the air translating to a transmission risk. Between July and September 2021, when the Delta was the dominant circulating strain in Mumbai, we noted a two-fold increase in the proportion of people expelling virus (95%), about an eighty-fold increase in median viral load and a three-fold increase in high emitter type (41%; people expelling >1000 viral copy numbers in 30 minutes) compared to initial strains of 2020. Eight percent of these patients continued to be high emitters even after eight days of symptom onset, suggesting a probable increased transmission risk for Delta strain even at this stage. There was no significant difference in expelling pattern between partial, full and un-vaccinated individuals suggesting similar transmission risk. We noted significantly more infections among vaccinated study patients and their household members than unvaccinated, probably due to increased duration from vaccination and/or increased risk behaviour upon vaccination due to lower perceived threat. This study provides biological evidence for possible continued transmission of the Delta strain even with vaccination, emphasizing the need to continue COVID-19 appropriate behaviour. The study also indicates that the mask method may be useful for screening future vaccine candidates, therapeutics or interventions for their ability to block transmission.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Kalpana Sriraman", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Ambreen Shaikh", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Smriti Vaswani", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Tejal Mestry", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Grishma Patel", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Shalini Sakthivel", + "author_inst": "The Foundation for Medical Research" + }, + { + "author_name": "Vikas Oswal", + "author_inst": "Vikas Nursing Home, Mumbai, India" + }, + { + "author_name": "Pratibha Kadam", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Kayzad Nilgiriwala", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Daksha Shah", + "author_inst": "Municipal Corporation of Greater Mumbai, Mumbai, India" + }, + { + "author_name": "Mangala Gomare", + "author_inst": "Municipal Corporation of Greater Mumbai,Mumbai, India" + }, + { + "author_name": "Nerges Mistry", + "author_inst": "The Foundation for Medical Research,, Mumbai, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.01.22271735", "rel_title": "Comparison of the reactogenicity and immunogenicity of a reduced and standard booster dose of the mRNA COVID-19 vaccine in healthy adults after two doses of inactivated vaccine.", @@ -350922,89 +353407,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.03.02.22271697", - "rel_title": "Recurrent SARS-CoV-2 Mutations in Immunodeficient Patients", - "rel_date": "2022-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271697", - "rel_abs": "Long-term SARS-CoV-2 infections in immunodeficient patients are an important source of variation for the virus but are understudied. Many case studies have been published which describe one or a small number of long-term infected individuals but no study has combined these sequences into a cohesive dataset. This work aims to rectify this and study the genomics of this patient group through a combination of literature searches as well as identifying new case series directly from the COG-UK dataset. The spike gene receptor binding domain (RBD) and N-terminal domains (NTD) were identified as mutation hotspots. Numerous mutations associated with variants of concern were observed to emerge recurrently. Additionally a mutation in the envelope gene, - T30I was determined to be the most recurrent frequently occurring mutation arising in persistent infections. A high proportion of recurrent mutations in immunodeficient individuals are associated with ACE2 affinity, immune escape, or viral packaging optimisation.\n\nThere is an apparent selective pressure for mutations which aid intra-host transmission or persistence which are often different to mutations which aid inter-host transmission, although the fact that multiple recurrent de novo mutations are considered defining for variants of concern strongly indicates that this potential source of novel variants should not be discounted.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Sam AJ Wilkinson", - "author_inst": "Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK, B15 2TT" - }, - { - "author_name": "Alex Richter", - "author_inst": "Institute of Immunology and Immunotherapy (III), College of Medical and Dental Sciences, University of Birmingham, UK, B15 2TT" - }, - { - "author_name": "Anna Casey", - "author_inst": "Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham, UK, B15 2TH." - }, - { - "author_name": "Husam Osman", - "author_inst": "Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham, UK, B15 2TH." - }, - { - "author_name": "Jeremy D Mirza", - "author_inst": "Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK, B15 2TT" - }, - { - "author_name": "Joanne Stockton", - "author_inst": "Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK, B15 2TT" - }, - { - "author_name": "Josh Quick", - "author_inst": "Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK, B15 2TT" - }, - { - "author_name": "Liz Ratcliffe", - "author_inst": "Queen Elizabeth Hospital, University Hospitals Birmingham, Birmingham, UK, B15 2TH." - }, - { - "author_name": "Natalie Sparks", - "author_inst": "Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK, B15 2TT" - }, - { - "author_name": "Nicola Cumley", - "author_inst": "Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK, B15 2TT" - }, - { - "author_name": "Radoslaw Poplawski", - "author_inst": "Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK, B15 2TT" - }, - { - "author_name": "Sam Nicholls", - "author_inst": "Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK, B15 2TT" - }, - { - "author_name": "Beatrix Kele", - "author_inst": "Virology Department, NHS East and South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, UK, EC1A 7BE." - }, - { - "author_name": "Kathryn Harris", - "author_inst": "Virology Department, NHS East and South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, UK, EC1A 7BE." - }, - { - "author_name": "- The COVID-19 Genomics UK (COG-UK) consortium", - "author_inst": "https://www.cogconsortium.uk - Full list of consortium names and affiliations are in the appendix" - }, - { - "author_name": "Thomas P Peacock", - "author_inst": "Department of Infectious Disease, Imperial College London, London, UK, W2 1PG" - }, - { - "author_name": "Nicholas J Loman", - "author_inst": "Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK, B15 2TT" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.01.22271582", "rel_title": "Duration of viable virus shedding in SARS-CoV-2 omicron variant infection", @@ -352595,6 +354997,33 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2022.02.27.482153", + "rel_title": "A strategy to optimize the peptide-based inhibitors against different mutants of the spike protein of SARS-CoV-2", + "rel_date": "2022-02-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.27.482153", + "rel_abs": "SARS-CoV-2 virus has caused high-priority health concerns at a global level. Vaccines have stalled the proliferation of viruses to some extent. Yet, the emergence of newer, potentially more infectious, and dangerous mutants such as delta and omicron are among the major challenges in finding a more permanent solution for this pandemic. The effectiveness of antivirals Molnupiravir and Paxlovid, authorized for emergency use by the FDA, are yet to be assessed at larger populations. Patients with a high risk of disease progression or hospitalization have received treatment with a combination of antibodies (antibody-cocktail). Most of the mutations leading to the new lineage of SARS-CoV-2 are found in the spike protein of this virus that plays a key role in facilitating host entry. The current study has investigated how to modify a promising peptide-based inhibitor of spike protein, LCB3, against common mutations in the target protein so that it retains its efficacy against the spike protein. LCB3 being a prototype for protein-based inhibitors is an ideal testing system to learn about protein-based inhibitors. Two common mutations N501Y and K417N are considered in this work. Using a structure-based approach that considers free energy decomposition of residues, distance, and the interactions between amino acids, we propose the substitutions of amino acid residues of LCB3 inhibitors. Our binding free energy calculations suggest a possible improvement in the binding affinity of existing inhibitor LCB3 to the mutant forms of the S-protein using simple substitutions at specific positions of the inhibitor. This approach, being general, can be used in different inhibitors and other mutations and help in fighting against SARS-CoV-2.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Prerna Priya", + "author_inst": "Purnea Mahila College" + }, + { + "author_name": "Abdul Basit", + "author_inst": "School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India" + }, + { + "author_name": "Pradipta Bandyopadhyay", + "author_inst": "School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.02.25.481974", "rel_title": "An immunoPET probe to SARS-CoV-2 reveals early infection of the male genital tract in rhesus macaques", @@ -352864,157 +355293,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.02.27.22271090", - "rel_title": "Comparison of Rapid Antigen Tests' Performance between Delta (B.1.61.7; AY.X) and Omicron (B.1.1.529; BA1) Variants of SARS-CoV-2: Secondary Analysis from a Serial Home Self-Testing Study", - "rel_date": "2022-02-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.27.22271090", - "rel_abs": "BackgroundThere is a need to understand the performance of rapid antigen tests (Ag-RDT) for detection of the Delta (B.1.61.7; AY.X) and Omicron (B.1.1.529; BA1) SARS-CoV-2 variants.\n\nMethodsParticipants without any symptoms were enrolled from October 18, 2021 to January 24, 2022 and performed Ag-RDT and RT-PCR tests every 48 hours for 15 days. This study represents a non-pre-specified analysis in which we sought to determine if sensitivity of Ag-RDT differed in participants with Delta compared to Omicron variant. Participants who were positive on RT-PCR on the first day of the testing period were excluded. Delta and Omicron variants were defined based on sequencing and date of first RT-PCR positive result (RT-PCR+). Comparison of Ag-RDT performance between the variants was based on sensitivity, defined as proportion of participants with Ag-RDT+ results in relation to their first RT-PCR+ result, for different duration of testing with rapid Ag-RDT. Subsample analysis was performed based on the result of participants second RT-PCR test within 48 hours of the first RT-PCR+ test.\n\nResultsFrom the 7,349 participants enrolled in the parent study, 5,506 met the eligibility criteria for this analysis. A total of 153 participants were RT-PCR+ (61 Delta, 92 Omicron); among this group, 36 (23.5%) tested Ag-RDT+ on the same day, and 84 (54.9%) tested Ag-RDT+ within 48 hours as first RT-PCR+. The differences in sensitivity between variants were not statistically significant (same-day: Delta 16.4% [95% CI: 8.2-28.1] vs Omicron 28.2% [95% CI: 19.4-38.6]; and 48-hours: Delta 45.9% [33.1-59.2] vs. Omicron 60.9% [50.1-70.9]). This trend continued among the 86 participants who had consecutive RT-PCR+ result (48-hour sensitivity: Delta 79.3% [60.3-92.1] vs. Omicron: 89.5% [78.5-96.0]). Conversely, the 38 participants who had an isolated RT-PCR+ remained consistently negative on Ag-RDT, regardless of the variant.\n\nConclusionsThe performance of Ag-RDT is not inferior among individuals infected with the SARS-CoV-2 Omicron variant as compared to the Delta variant. The improvement in sensitivity of Ag-RDT noted with serial testing is consistent between Delta and Omicron variant. Performance of Ag-RDT varies based on duration of RT-PCR+ results and more studies are needed to understand the clinical and public health significance of individuals who are RT-PCR+ for less than 48 hours.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Apurv Soni", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Carly Herbert", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Andreas Filippaios", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "John Broach", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Andres Colubri", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Nisha Fahey", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Kelsey Woods", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Janvi Nanavati", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Colton Wright", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Taylor Orwig", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Karen Gilliam", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Vik Kheterpal", - "author_inst": "Care Evolution, LLC" - }, - { - "author_name": "Thejas Suvarna", - "author_inst": "Care Evolution, LLC" - }, - { - "author_name": "Chris Nowak", - "author_inst": "Care Evolution, LLC" - }, - { - "author_name": "Summer Schrader", - "author_inst": "Care Evolution, LLC" - }, - { - "author_name": "Honghuang Lin", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Caitlin Pretz", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Didem Ayturk", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Elizabeth Orvek", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Julie Flahive", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Peter Lazar", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Qiming Shi", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Chad J Achenbach", - "author_inst": "Northwestern University" - }, - { - "author_name": "Robert L Murphy", - "author_inst": "Northwestern University" - }, - { - "author_name": "Matthew L Robinson", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Laura Gibson", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Pamela Stamegna", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Nathaniel Hafer", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Katherine Luzuriaga", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Bruce Barton", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Yukari C Manabe", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "David McManus", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "- RADx Clinical Studies Core Team", - "author_inst": "" - }, - { - "author_name": "- Test Us At Home Investigators", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.25.22271521", "rel_title": "Genomic surveillance of SARS-CoV-2 in a university community: insights into tracking variants, transmission, and spread of Gamma (P.1) variant", @@ -354553,6 +356831,65 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.02.24.481684", + "rel_title": "Dictionary learning for integrative, multimodal, and scalable single-cell analysis", + "rel_date": "2022-02-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.24.481684", + "rel_abs": "Mapping single-cell sequencing profiles to comprehensive reference datasets represents a powerful alternative to unsupervised analysis. Reference datasets, however, are predominantly constructed from single-cell RNA-seq data, and cannot be used to annotate datasets that do not measure gene expression. Here we introduce bridge integration, a method to harmonize singlecell datasets across modalities by leveraging a multi-omic dataset as a molecular bridge. Each cell in the multi-omic dataset comprises an element in a dictionary, which can be used to reconstruct unimodal datasets and transform them into a shared space. We demonstrate that our procedure can accurately harmonize transcriptomic data with independent single cell measurements of chromatin accessibility, histone modifications, DNA methylation, and protein levels. Moreover, we demonstrate how dictionary learning can be combined with sketching techniques to substantially improve computational scalability, and harmonize 8.6 million human immune cell profiles from sequencing and mass cytometry experiments. Our approach aims to broaden the utility of single-cell reference datasets and facilitate comparisons across diverse molecular modalities.\n\nAvailabilityInstallation instructions, documentations, and vignettes are available at http://www.satijalab.org/seurat", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yuhan Hao", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Tim Stuart", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Madeline Kowalski", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Saket Choudhary", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Paul Hoffman", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Austin Hartman", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Avi Srivastava", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Gesmira Molla", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Shaista Madad", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Carlos Fernandez-Granda", + "author_inst": "Center for Data Science, New York University" + }, + { + "author_name": "Rahul Satija", + "author_inst": "New York Genome Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2022.02.25.22271520", "rel_title": "Late-Ensemble of Convolutional Neural Networks with Test Time Augmentation for Chest XR COVID-19 Detection", @@ -354690,25 +357027,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.25.22271499", - "rel_title": "Reassessment of persistent symptoms, self-reported COVID-19 infection and SARS-CoV-2 serology in the SAPRIS-SERO cohort: identifying possible sub-syndromes of Long Covid.", - "rel_date": "2022-02-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.25.22271499", - "rel_abs": "BackgroundLong Covid remains a relatively new phenomenon with emerging understanding. Estimated UK prevalence of Long Covid with three or more symptoms lasting for 12 weeks or more was 2.2% at the end of 2021. The population-based French SAPRIS-SERO cohort has novel information about the pattern of symptoms of Long Covid that has been obscured by controversy around the original paper.\n\nMethodsSecondary analysis was used to describe and re-interpret the frequencies of persistent symptoms by IgG seropositivity and self-reported Long Covid in the published report of the SAPRIS-SERO survey. Participants in the cross-sectional analysis were 26 823 individuals from the French population-based CONSTANCES cohort, included between 2012 and 2019, who took part in the nested SAPRIS and SAPRIS-SERO surveys. Between May and November 2020, the Euroimmun enzyme-linked immunosorbent assay was used to detect anti-SARS-CoV-2 antibodies. Surveyed online between December 2020 and January 2021, participants self-reported previous COVID-19 infection and physical symptoms during the previous four weeks that were new since March 2020, and had persisted for at least eight weeks.\n\nResultsThere was similarity of prevalence over the majority of symptoms in those self-reporting COVID-19 infection, regardless of blood test result. Persistent symptoms significantly associated with self-reported COVID-19 infection and common in both groups include respiratory tract symptoms and a group of symptoms that might be related to chronic fatigue, malaise or postural issues. Seropositivity for IgG antibodies did not predict symptoms independently of self-reported Long Covid, except for anosmia.\n\nConclusionsThere may be three common sub-syndromes of Long Covid, one with persistent anosmia, another with other respiratory tract symptoms and a third, currently under researched, with symptoms relatable to chronic fatigue. Antibody tests are insufficient for case detection while Long Covid remains poorly understood.\n\nKey MessagesO_LIIgG seropositivity is insufficient to identify potential cases of Long Covid\nC_LIO_LIPersistent anosmia is very strongly associated with IgG seropositivity and may define a subsyndrome of Long Covid\nC_LIO_LIOther potential subsyndromes are those with persistent respiratory symptoms and those with persistent symptoms relatable to fatigue, malaise or postural issues\nC_LIO_LIThe Long Covid research effort should be rebalanced towards understanding the fatigue/tiredness subsyndrome.\nC_LI", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Nicola Spiers", - "author_inst": "University of Leicester" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.02.25.22271490", "rel_title": "Breakthrough SARS-CoV-2 Infection Outcomes in Vaccinated Patients with Chronic Liver Disease and Cirrhosis: A National COVID Cohort Collaborative Study", @@ -356359,6 +358677,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.02.24.22271468", + "rel_title": "Clinical and Virologic Factors associated with Outcomes of COVID-19 before and after Vaccination among Veterans: Retrospective Analysis from Six New England States", + "rel_date": "2022-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.24.22271468", + "rel_abs": "BackgroundA region-wide analysis of COVID-19 outcomes in New England has not been done. We aimed to characterize clinical, demographic, and vaccination status affecting COVID-19 clinical outcomes and describe viral epidemiology.\n\nMethodsClinical variables of Veterans with COVID-19 in Veterans Administration healthcare systems in six New England states from April 8, 2020, to September 2, 2021 were correlated with outcomes of 30-day mortality, non-psychiatric hospitalization, intensive care unit admission (ICU-care), and post-vaccination infection. We sequenced 754 whole viral genomes and 197 partial genomes.\n\nResultsOf 4,170 Veterans with COVID-19, 81% were White, 8% women, mean age was 60.1 {+/-}17.7 years, and 2,399 became fully vaccinated. Overall, 19% Veterans needed hospitalization, 2.8% required ICU-care, and 3.7% died. Veterans with post-vaccination COVID-19 were older, with higher rates of tobacco/drug use, CKD, and malignancy, and 0.38% died. Among the unvaccinated, ICU-care and mortality correlated with age, while hospitalization correlated with age, male sex, black race, drug use, chronic heart disease, COPD, CKD, and chronic liver disease. Age, CKD, and alcohol use correlated with hospitalization in vaccinated patients.\n\nMost New England Veterans (>97%) were infected with B.1 sub-lineages with the D614G mutation in 2020 and early 2021. B.1.617.2 lineage (71%) predominated after July 2021, including the post-vaccination infections.\n\nConclusionIn New England Veterans with mean age of 60 years, age and CKD significantly correlated with hospitalization regardless of vaccination-status. Age correlated with mortality and ICU-care among the unvaccinated. The Delta variant of SARS-CoV-2 (B.1.617.2) dominated post-vaccination infections.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Megan Lee", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Danielle Cosenino", + "author_inst": "VA Connecticut Healthcare System" + }, + { + "author_name": "Tassos C Kyriakides", + "author_inst": "VA Connecticut Healthcare System" + }, + { + "author_name": "Tricia Cavallaro", + "author_inst": "VA Connecticut Healthcare System" + }, + { + "author_name": "Gary Stack", + "author_inst": "VA Connecticut Healthcare System" + }, + { + "author_name": "Shaili Gupta", + "author_inst": "Yale School of Medicine" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.21.481324", "rel_title": "A single-dose of the deactivated rabies virus vectored COVID-19 vaccine, CORAVAX, is highly efficacious and alleviates lung inflammation in the hamster model.", @@ -356560,29 +358917,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.02.18.481096", - "rel_title": "Omicron and Alpha P680H block SARS-CoV2 spike protein from accessing cholinergic inflammatory pathway via \u03b19-nAChR mitigating the risk of MIS-C", - "rel_date": "2022-02-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.18.481096", - "rel_abs": "Sequence homology between neurotoxins and the site encompassing the furin cleavage site 680SPRRAR685 in the spike protein (S) of CoV2 suggested that this site could interact with nicotinic acetylcholine receptors (nAChRs). Molecular dynamics simulations confirm robust structural similarity between wild-type (WT) CoV2 and the binding motif of -conotoxin to 9 nAChR, which is known to modulate IL-1{beta} in immune cells. We show that the structural integrity of this binding motif is eliminated by Alpha P681H mutation, reemerged in Delta variant P681R, and disappeared again with Omicron N679H/P681H. Interactions between the toxin-mimic CoV2 motif and 9-nAChR are expected to trigger the release of pro-inflammatory cytokines an effect that is mollified by Alpha and Omicron. Clinical features of this interaction site are relevant because, contrary to most regions in the S protein, the furin binding site does not appear to trigger an immune response prior to cleavage, indicating that the cholinergic pathway should be activated in the respiratory tract and nasal mucosa where 9-nAChR co-localizes with the virus. The correlation of changes on this motif by the different variants closely matches the reported cases of Multisystem Inflammatory Syndrome in Children by the CDC, and predicts significant mitigation of MIS-C with the Omicron variant. Our findings strongly motivate further study of this cholinergic pathway as one source of the cytokine storm triggered by CoV2.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Carlos J. Camacho", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Ulises Santiago", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.02.21.481360", "rel_title": "Effect of an amyloidogenic SARS-COV-2 protein fragment on \u03b1-synuclein monomers and fibrils", @@ -357925,6 +360259,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.23.22271403", + "rel_title": "Quantifying antibody dynamics of severe and non-severe patients with COVID-19", + "rel_date": "2022-02-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.23.22271403", + "rel_abs": "COVID-19 pandemic is a major public health threat with unanswered questions regarding the role of the immune system in the severity level of the disease. In this paper, based on antibody kinetic data of patients with different disease severity, topological data analysis highlights clear differences in the shape of antibody dynamics between three groups of patients, which were non-severe, severe, and one intermediate case of severity. Subsequently, different mathematical models were developed to quantify the dynamics between the different severity groups. The best model was the one with the lowest media value of Akaike Information Criterion for all groups of patients. Although it has been reported high IgG level in severe patients, our findings suggest that IgG antibodies in severe patients may be less effective than non-severe patients due to early B cell production and early activation of the seroconversion process from IgM to IgG antibody.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Fernanda Ordonez-Jimenez", + "author_inst": "UNAM" + }, + { + "author_name": "Rodolfo Blanco-Rodriguez", + "author_inst": "UNAM" + }, + { + "author_name": "Alexis Erich S. Almocera", + "author_inst": "University of the Philippines Visayas" + }, + { + "author_name": "Gustavo Chinney-Herrera", + "author_inst": "UNAM" + }, + { + "author_name": "Esteban Abelardo Hernandez Vargas", + "author_inst": "UNAM" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.23.22271372", "rel_title": "Genomic surveillance of SARS-CoV-2 reveals emergence of Omicron BA.2 in Islamabad, Pakistan", @@ -358026,33 +360395,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2022.02.23.22271409", - "rel_title": "Olfactory loss is an early and reliable marker for COVID-19", - "rel_date": "2022-02-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.23.22271409", - "rel_abs": "Detection of early and reliable symptoms is important in relation to limiting the spread of an infectious disease. For COVID-19, the most prevalent symptom is either losing or experiencing reduced olfactory functions. Anecdotal evidence suggests that olfactory dysfunction is also one of the earlier symptoms of COVID-19 but objective measures supporting this notion are currently missing. To determine whether olfactory dysfunction is an early sign of COVID-19, we assessed available longitudinal data from a web-based interface enabling individuals to test their sense of smell by rating the intensity of selected household odors. Individuals continuously used the interface to assess their olfactory functions and at each login, in addition to odor ratings, recorded their symptoms and result from potential COVID-19 test. A total of 205 COVID-19 positive individuals and 156 pseudo-randomly matched control individuals lacking positive test provided longitudinal data which enabled us to assess olfactory functions in relation to their test results date. We found that odor intensity ratings started to decline in the COVID-19 group as early as 6 days prior to test result date. Symptoms such as sore throat, aches, and runny nose appear around the same point in time; however, with a lower predictability of a COVID-19 diagnose. Our results suggest that olfactory dysfunction is an early symptom but does not appear before other related COVID-19 symptoms. Olfactory dysfunction is, however, more predictive of an COVID-19 diagnose than other early symptoms.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Behzad Iravani", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Artin Arshamian", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Johan N Lundstrom", - "author_inst": "Karolinska Institutet" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "otolaryngology" - }, { "rel_doi": "10.1101/2022.02.23.22271381", "rel_title": "Long-term Durable Humoral Immune Response to Heterologous Antigenic Exposure Post six months by Natural SARS-CoV-2 Infection and Vaccination", @@ -359738,6 +362080,101 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.02.19.481107", + "rel_title": "Identification of a SARS-CoV-2 host metalloproteinase-dependent entry pathway differentially used by SARS-CoV-2 and variants of concern Alpha, Delta, and Omicron", + "rel_date": "2022-02-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.19.481107", + "rel_abs": "To infect cells, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) binds to angiotensin converting enzyme 2 (ACE2) via its spike glycoprotein (S), delivering its genome upon S-mediated membrane fusion. SARS-CoV-2 uses two distinct entry pathways: 1) a surface, serine protease-dependent or 2) an endosomal, cysteine protease-dependent pathway. In investigating serine protease-independent cell-cell fusion, we found that the matrix metalloproteinases (MMPs), MMP2/9, can activate SARS-CoV-2 S fusion activity, but not that of SARS-CoV-1. Importantly, metalloproteinase activation of SARS-CoV-2 S represents a third entry pathway in cells expressing high MMP levels. This route of entry required cleavage at the S1/S2 junction in viral producer cells and differential processing of variants of concern S dictated its usage. In addition, metalloproteinase inhibitors reduced replicative Alpha infection and abrogated syncytia formation. Finally, we found that the Omicron S exhibit reduced metalloproteinase-dependent fusion and viral entry. Taken together, we identified a MMP2/9-dependent mode of activation of SARS-CoV-2 S. As MMP2/9 are released during inflammation and severe COVID-19, they may play important roles in SARS-CoV-2 S-mediated cytopathic effects, tropism, and disease outcome.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Mehdi Benlarbi", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Genevi\u00e8ve Laroche", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Corby Fink", + "author_inst": "Western University" + }, + { + "author_name": "Kathy Fu", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Rory P Mulloy", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Alexandra Phan", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Ardeshir Ariana", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Corina M Stewart", + "author_inst": "University of Ottawa" + }, + { + "author_name": "J\u00e9r\u00e9mie Pr\u00e9vost", + "author_inst": "CRCHUM / Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Guillaume Beaudoin-Bussi\u00e8res", + "author_inst": "CRCHUM" + }, + { + "author_name": "Redaet Daniel", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Yuxia Bo", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Julien Yockell-Leli\u00e8vre", + "author_inst": "The Ottawa Hospital Research Institute" + }, + { + "author_name": "William L Stanford", + "author_inst": "The Ottawa Hospital Research Institute" + }, + { + "author_name": "Patrick M Gigu\u00e8re", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Samira Mubareka", + "author_inst": "Sunnybrook Research Institute and University of Toronto" + }, + { + "author_name": "Andr\u00e9s Finzi", + "author_inst": "Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Gregory A Dekaban", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Jimmy D Dikeakos", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Marceline C\u00f4t\u00e9", + "author_inst": "University of Ottawa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.02.19.481089", "rel_title": "Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection", @@ -359987,45 +362424,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.02.21.22271300", - "rel_title": "COVID infection rates, clinical outcomes, and racial/ethnic and gender disparities before and after Omicron emerged in the US", - "rel_date": "2022-02-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.21.22271300", - "rel_abs": "BackgroundSARS-CoV-2 infections and hospitalizations are rising in the US and other countries after the emergence of the Omicron variant. Currently, data on infection rates, severity and racial/ethnic and gender disparities from Omicron in the US is limited.\n\nMethodWe performed a retrospective cohort study of a large, geographically diverse database of patient electronic health records (EHRs) in the US. The study population comprised 881,473 patients who contracted SARS-CoV-2 infection for the first time between 9/1/2021-1/16/2022, including 147,964 patients infected when Omicron predominated (Omicron cohort), 633,581 when Delta predominated (Delta cohort) and another 99,928 infected when the Delta predominated but just before the Omicron variant was detected in the US (Delta-2 cohort). We examined monthly incidence rates of COVID-19 infections stratified by age groups, gender, race and ethnicity, compared severe clinical outcomes including emergency department (ED) visits, hospitalizations, intensive care unit (ICU) admissions, and mechanical ventilation use between propensity-score matched Omicron and Delta cohorts stratified by age groups (0-4, 5-17, 18-64 and [≥] 65 years), and examined racial/ethnic and gender differences in severe clinical outcomes.\n\nFindingsAmong 147,964 infected patients in the Omicron cohort (average age: 39.1 years), 56.7% were female, 2.4% Asian, 21.1% Black, 6.2% Hispanic, and 51.8% White. The monthly incidence rate of COVID infections (new cases per 1000 persons per day) was 0.5-0.7 when Delta predominated, and rapidly increased to 3.8-5.2 when Omicron predominated. In January 2022, the infection rate was highest in children under 5 years (11.0) among all age groups, higher in Black than in White patients (14.0 vs. 3.8), and higher in Hispanic than in non-Hispanic patients (8.9 vs. 3.1). After propensity-score matching for demographics, socio-economic determinants of health, comorbidities and medications, risks for severe clinical outcomes in the Omicron cohort were significantly lower than in the Delta cohort: ED visits: 10.2% vs. 14.6% (risk ratio or RR: 0.70 [0.68-0.71]); hospitalizations: 2.6% vs. 4.4% (RR: 0.58 [0.55-0.60]); ICU admissions: 0.47% vs. 1.00% (RR: 0.47 [0.43-0.51]); mechanical ventilation: 0.08% vs. 0.3% (RR: 0.25 [0.20-0.31]). Similar reduction in disease severity was observed for all age groups. There were significant racial/ethnic and gender disparities in severe clinical outcomes in the Omicron cohort, with Black, Hispanic patients having more ED visits and ICU admissions than White and non-Hispanic patients, respectively and women had fewer hospitalization and ICU admission than men.\n\nInterpretationThe incidence rate of COVID infection during the omicron predominant period (prevalence >92%) was 6-8 times higher than during the Delta predominant period that preceded it consistent with greater infectivity. The incidence rate was highest among those less than 5 years of age, and in Black and Hispanic patients. COVID infections occurring when the Omicron predominated were associated with significantly less frequent severe outcomes than in matched patients when the Delta variant predominated. There were significant racial, ethnic and gender disparities in severe clinical outcomes, with Black and Hispanic patients and men disproportionally impacted.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Rong Xu", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Lindsey Wang", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Nathan A berger", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "pamela B davis", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "David C Kaelber", - "author_inst": "MetroHealth, Cleveland" - }, - { - "author_name": "Nora D Volkow", - "author_inst": "NIDA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.21.22271249", "rel_title": "Bayesian Emulation and History Matching of JUNE", @@ -361812,6 +364210,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, + { + "rel_doi": "10.1101/2022.02.16.22270690", + "rel_title": "Narratives of the convalescent plasma donor in a Peruvian social security hospital: motivations, fears, expectations and experiences", + "rel_date": "2022-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.16.22270690", + "rel_abs": "ObjectivesTo know and explore from convalescent plasma donators voices the experience in the blood donation process at a Peruvian social security hospital.\n\nMethodsQualitative study with a phenomenological design. The investigation was carried out in 01 hospitals of the social security of Peru. Semi-structured interviews were carried out.\n\nResultsEleven donors of convalescent plasma were interviewed. The main motivations for donating were being able to contribute to national research and supporting patients affected by COVID-19. Fears focus on the possible risk of contagion within the hospital. Donors emphasised the attention and support of health personnel alongside the donation procedure. The main expectations and suggestions point towards greater dissemination of donation campaigns with special emphasis on safety. Likewise, an improvement in the time of the donation procedure (from enrolment to the extraction of convalescent plasma), and the implementation of friendly spaces to encourage future blood donation campaigns were highlighted.\n\nConclusionsThe experience of the convalescent plasma donors was positive. However, improvements must be made in terms of processes and infrastructure to ensure future successful blood donation campaigns.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Silvana M Matassini Eyzaguirre", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Christian Villanueva Yapa", + "author_inst": "Servicio de Medicina Transfusional, Hospital Nacional Egdardo Rebagliati, EsSalud, Lima, Per\u00fa" + }, + { + "author_name": "Ausberto Chunga Chunga", + "author_inst": "Servicio de Patolog\u00eda Cl\u00ednica, Hospital Nacional Egdardo Rebagliati Martins, EsSalud, Lima, Per\u00fa" + }, + { + "author_name": "Arturo Sagastegui Soto", + "author_inst": "Servicio de Medicina Transfusional, Hospital Nacional Egdardo Rebagliati, EsSalud, Lima, Per\u00fa" + }, + { + "author_name": "Ibeth Melania Neyra Vera", + "author_inst": "Servicio de Patolog\u00eda Cl\u00ednica, Hospital Nacional Egdardo Rebagliati Martins, EsSalud, Lima, Per\u00fa" + }, + { + "author_name": "Suly Soto-Ordo\u00f1ez", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Martina Guillermo Roman", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Martin Oyanguren Miranda", + "author_inst": "Servicio de Cuidados Intensivos, Hospital Nacional Egdardo Rebagliati Martins, EsSalud, Lima, Peru" + }, + { + "author_name": "Percy Soto-Becerra", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Yamilee Hurtado-Roca", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Jorge L Magui\u00f1a", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Roger Vladimir Araujo-Castillo", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2022.02.17.22271142", "rel_title": "Performance of three rapid antigen tests against the SARS-CoV-2 Omicron variant", @@ -362065,41 +364526,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.17.22271030", - "rel_title": "Clinical severity of Omicron sub-lineage BA.2 compared to BA.1 in South Africa", - "rel_date": "2022-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.17.22271030", - "rel_abs": "Early data indicated that infection with Omicron BA.1 sub-lineage was associated with a lower risk of hospitalisation and severe illness, compared to Delta infection. Recently, the BA.2 sub-lineage has increased in many areas globally. We aimed to assess the severity of BA.2 infections compared to BA.1 in South Africa. We performed data linkages for (i) national COVID-19 case data, (ii) SARS-CoV-2 laboratory test data, and (iii) COVID-19 hospitalisations data, nationally. For cases identified using TaqPath COVID-19 PCR, infections were designated as S-gene target failure (SGTF, proxy for BA.1) or S-gene positive (proxy for BA.2). Disease severity was assessed using multivariable logistic regression models comparing individuals with S-gene positive infection to SGTF-infected individuals diagnosed between 1 December 2021 to 20 January 2022. From week 49 (starting 5 December 2021) through week 4 (ending 29 January 2022), the proportion of S-gene positive infections increased from 3% (931/31,271) to 80% (2,425/3,031). The odds of being admitted to hospital did not differ between individuals with S-gene positive (BA.2 proxy) infection compared to SGTF (BA.1 proxy) infection (adjusted odds ratio (aOR) 0.96, 95% confidence interval (CI) 0.85-1.09). Among hospitalised individuals, after controlling for factors associated with severe disease, the odds of severe disease did not differ for individuals with S-gene positive infection compared to SGTF infection (aOR 0.91, 95%CI 0.68-1.22). These data suggest that while BA.2 may have a competitive advantage over BA.1 in some settings, the clinical profile of illness remains similar.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Nicole Wolter", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "WAASILA JASSAT", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "- DATCOV-Gen Author Group", - "author_inst": "" - }, - { - "author_name": "Anne von Gottberg", - "author_inst": "National Institute for Communicable Diseases" - }, - { - "author_name": "Cheryl Cohen", - "author_inst": "National Insitute for Communicable Diseases" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.18.22271199", "rel_title": "Characterizing SARS-CoV-2 transcription of subgenomic and genomic RNAs during early human infection using multiplexed ddPCR", @@ -363806,6 +366232,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.02.16.22271096", + "rel_title": "Analytical Sensitivity of the SalivaDirect\u2122 Assay on the Liberty16 for detecting SARS-CoV-2 B.1.1.529 Omicron", + "rel_date": "2022-02-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.16.22271096", + "rel_abs": "The newly emerged Omicron variant of SARS-CoV-2 has numerous mutations that are not found in other variants of concern (VOCs). Despite acquiring extended functions in adapting to the host-cell environment, the viral genetic variation exerts a potential negative impact on a molecular test, which in turn, compromises public health and safety. The Liberty16 has been clinically validated as a flexible and accessible device system for running the affordable SalivaDirect real time PCR detection assay for SARS-CoV-2 especially in low resource settings. Preliminary, based on in-silico sequence analysis, we found that Omicrons mutation at position 28,311 overlaps with the CDC 2019-nCoV_N1 probe binding region. In order to verify the performance of CDC 2019-nCoV-N1 primers-probe set in detecting the Omicron variant of SARS-CoV-2, plasmids containing Wuhan/WH01/2019 (wild-type) and B.1.1.529 (Omicron) sequences were serially diluted and subsequently directed for SalivaDirect RT-qPCR detection on Liberty16 using commercially procured reagents. Our findings provide analytical support for reports that the mutations in the Omicron variant have little or no impact on SalivaDirect assay in terms of amplification efficiency and detection sensitivity using either standard and the recently reported fast Liberty16 SalivaDirect thermal cycling protocols.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Yen Pei Tan", + "author_inst": "Ubiquitome Limited" + }, + { + "author_name": "Mila Al-Halbouni", + "author_inst": "Ubiquitome Limited" + }, + { + "author_name": "Ching-Huan Chen", + "author_inst": "Ubiquitome Limited" + }, + { + "author_name": "David B. Hirst", + "author_inst": "Ubiquitome Limited" + }, + { + "author_name": "Paul J. Pickering", + "author_inst": "Ubiquitome Limited" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.16.22271093", "rel_title": "A novel SEIR-e model for disease transmission and pathogen exposure", @@ -363951,41 +366412,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.02.15.22271016", - "rel_title": "Relative Virulence of SARS-CoV-2 Among Vaccinated and Unvaccinated Individuals Hospitalized with SARS-CoV-2", - "rel_date": "2022-02-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.15.22271016", - "rel_abs": "BackgroundThe rapid development of safe and effective vaccines against the SARS-CoV-2 virus has been a singular scientific achievement. Confounding due to health seeking behaviours and differential testing by vaccination status may bias analyses towards an apparent increase in infection severity following vaccination. We sought to determine whether risks of intensive care unit (ICU) admission and death were diminished significantly by vaccination, even in individuals for whom vaccination failed to prevent hospitalization.\n\nMethodsWe used data from Ontario, Canadas Case and Contact Management database, merged to a provincial vaccination dataset (COVaxON) to create a time-matched cohort of individuals who were hospitalized with SARS-CoV-2 infection. Each vaccinated individual was matched to up to five unvaccinated individuals based on test date of positive SARS-CoV-2 infection. Risk of ICU admission and death were evaluated using multivariable conditional logistic regression. Unmatched exploratory analyses were performed to identify sources of heterogeneity in vaccine effects.\n\nResultsIn 20,064 individuals (3,353 vaccinated and 16,711 unvaccinated) hospitalized with infection due to SARS-CoV-2 between January 1st, 2021 and January 5th, 2022, vaccination with 1, 2, or 3 doses significantly reduced the risk of ICU admission and death. An inverse dose-response relationship was observed between vaccine doses received and both outcomes (adjusted odds ratio (aOR) for ICU admission per additional dose: 0.66, 95% CI 0.62 to 0.71; aOR for death per additional dose: 0.78, 95% CI 0.72 to 0.84). The reduction in risk was greater for ICU admission than for death (P for heterogeneity <0.05), but no significant differences in risk were seen based on infecting variant of concern (VOC).\n\nInterpretationWe identified a decrease in the risk of ICU admission and death in vaccinated individuals compared to unvaccinated, time-matched controls, even when vaccines failed to prevent infection sufficiently severe to cause hospitalization. Even with diminished efficacy of vaccines against infection with novel VOCs, vaccines remain an important tool for reduction of ICU admission and mortality.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Alicia Grima", - "author_inst": "University of Toronto" - }, - { - "author_name": "Kiera Murison", - "author_inst": "University of Toronto" - }, - { - "author_name": "Alison Simmons", - "author_inst": "University of Toronto" - }, - { - "author_name": "Ashleigh Tuite", - "author_inst": "University of Toronto" - }, - { - "author_name": "David Fisman", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.16.22271068", "rel_title": "Reliability of citations of medRxiv preprints in articles published on COVID-19 in the world leading medical journals", @@ -365580,6 +368006,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.11.22270843", + "rel_title": "Evaluation of test-to-return after COVID-19 diagnosis in a Massachusetts public school district", + "rel_date": "2022-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270843", + "rel_abs": "The Centers for Disease Control allows rapid antigen testing (RAT) towards the end of a 5-day isolation for COVID-19 infection to determine eligibility to leave isolation. The impact of a test-to-return (TTR) program in schools is unknown. In January 2022 a Massachusetts school district initiated a TTR program utilizing a single school-administered RAT on days 5-9 after symptom onset or positive test, whichever was first. Of 636 students with COVID-19 infection, 408 (64.2%) participated in TTR; of these, 128 (31.4%) had a positive TTR rapid antigen test. Students who were symptomatic at any time during their infection were more likely to have a positive TTR than those who were never symptomatic (43.1% vs. 17.3%); positivity rates were lower when TTR was performed later during days 6-9. TTR may identify students who carry higher viral loads after recovery from COVID-19 infection thereby extending their isolation, while facilitating earlier return of those with negative results.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sandra B. Nelson", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Isaac Ravi Brenner", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Elizabeth Homan", + "author_inst": "Arlington Public Schools" + }, + { + "author_name": "Sarah Bott Lee", + "author_inst": "Arlington Public Schools" + }, + { + "author_name": "Christine Bongiorno", + "author_inst": "Town of Arlington, Massachusetts" + }, + { + "author_name": "Nira Pollock", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Andrea L Ciaranello", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.10.22270733", "rel_title": "Differential durability of humoral and T cell immunity after two and three BNT162b2 vaccinations in adults aged >80 years", @@ -365797,93 +368266,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.11.22270844", - "rel_title": "Source terms for benchmarking models of SARS-CoV-2 transmission via aerosols and droplets", - "rel_date": "2022-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270844", - "rel_abs": "There is ongoing and rapid advancement in approaches to modelling the fate of exhaled particles in different environments relevant to disease transmission. It is important that models are verified by comparison with each other using a common set of input parameters to ensure that model differences can be interpreted in terms of model physics rather than unspecified differences in model input parameters. In this paper, we define parameters necessary for such benchmarking of models of airborne particles exhaled by humans and transported in the environment during breathing and speaking.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Marc E.J. Stettler", - "author_inst": "Imperial College London" - }, - { - "author_name": "Robert T. Nishida", - "author_inst": "University of Alberta" - }, - { - "author_name": "Pedro M. de Oliveira", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Leo Mesquita", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Tyler Johnson", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Ed Galea", - "author_inst": "University of Greenwich" - }, - { - "author_name": "Angus Grandison", - "author_inst": "University of Greenwich" - }, - { - "author_name": "John Ewer", - "author_inst": "University of Greenwich" - }, - { - "author_name": "David Carruthers", - "author_inst": "CERC" - }, - { - "author_name": "Prashant Kumar", - "author_inst": "University of Surrey" - }, - { - "author_name": "Eldad Avital", - "author_inst": "Queen Mary University London" - }, - { - "author_name": "Asiri Obeysekara", - "author_inst": "Imperial College London" - }, - { - "author_name": "Denis Doorly", - "author_inst": "Imperial College London" - }, - { - "author_name": "Yannis Hardalupas", - "author_inst": "Imperial College London" - }, - { - "author_name": "David Green", - "author_inst": "Imperial College London" - }, - { - "author_name": "Simon Coldrick", - "author_inst": "Health and Safety Executive" - }, - { - "author_name": "Simon Parker", - "author_inst": "DSTL" - }, - { - "author_name": "Adam Boies", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.11.22270833", "rel_title": "SARS-CoV-2 IgG seroprevalence in blood donors located in three different federal states, Germany, July 2020 to June 2021-a follow-up", @@ -367858,6 +370240,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, + { + "rel_doi": "10.1101/2022.02.14.22270958", + "rel_title": "COVID-19 mortality and excess mortality among working-age Californians, by occupational sector: March 2020 through November 2021", + "rel_date": "2022-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.14.22270958", + "rel_abs": "BackgroundDuring the first year of the pandemic, essential workers faced higher rates of SARS-CoV-2 infection and COVID-19 mortality than non-essential workers. It is unknown whether disparities in pandemic-related mortality across occupational sectors have continued to occur, amidst SARS-CoV-2 variants and vaccine availability.\n\nMethodsWe obtained data on all deaths occurring in the state of California from 2016 through 2021. We restricted our analysis to California residents who were working age (18-65 years at time of death) and died of natural causes. Occupational sector was classified into 9 essential sectors; non-essential; or not in the labor market. We calculated the number of COVID-19 deaths in total and per capita that occurred in each occupational sector. Separately, using autoregressive integrated moving average models, we estimated total, per-capita, and relative excess natural-cause mortality by week between March 1, 2020, and November 30, 2021, stratifying by occupational sector. We additionally stratified analyses of occupational risk into regions with high versus low vaccine uptake, categorizing high-uptake regions as counties where at least 50% of the population completed a vaccination series by August 1, 2021.\n\nFindingsFrom March 2020 through November 2021, essential work was associated with higher COVID-19 and excess mortality compared with non-essential work, with the highest per-capita COVID-19 mortality in agriculture (131.8 per 100,000), transportation/logistics (107.1), manufacturing (103.3), and facilities (101.1). Essential workers continued to face higher COVID-19 and excess mortality during the period of widely available vaccines (March through November 2021). Between July and November 2021, emergency workers experienced higher per-capita COVID-19 mortality (113.7) than workers from any other sector. Essential workers faced the highest COVID-19 mortality in counties with low vaccination rates, a difference that was more pronounced during the period of the Delta surge in Summer 2021.\n\nInterpretationEssential workers have continued to bear the brunt of high COVID-19 and excess mortality throughout the pandemic, particularly in the agriculture, emergency, manufacturing, facilities, and transportation/logistics sectors. This high death toll has continued during periods of vaccine availability and the delta surge. In an ongoing pandemic without widespread vaccine coverage and anticipated threats of new variants, the US must actively adopt policies to more adequately protect essential workers.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yea-Hung Chen", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alicia R Riley", + "author_inst": "University of California, Santa Cruz" + }, + { + "author_name": "Kate A Duchowny", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Helene E Aschmann", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Ruijia Chen", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Mathew V Kiang", + "author_inst": "Stanford University" + }, + { + "author_name": "Alyssa Mooney", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Andrew C Stokes", + "author_inst": "Boston University" + }, + { + "author_name": "M Maria Glymour", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kirsten Bibbins-Domingo", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2022.02.11.22270859", "rel_title": "Clinical and economic benefits of lenzilumab plus standard of care compared with standard of care alone for the treatment of hospitalized patients with Coronavirus Disease 19 (COVID-19) from the perspective of National Health Service England", @@ -368047,25 +370484,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.13.22270900", - "rel_title": "Required COVID-19 Vaccination Certification to Attend Certain U.S. Professional Football Games in Fall 2021: A Natural Experiment", - "rel_date": "2022-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.13.22270900", - "rel_abs": "Four U.S. National Football League teams required vaccination certification against the SARS-CoV-2 virus of attendees at home games during the 2021 season. Using daily data on confirmed cases and vaccinations in counties surrounding these stadiums and stadiums that did not require certification, this study estimates the effects of the certification policy. Ordinary least squares regression was used to estimate the change in community spread of the virus after home games and away games relative to weeks that the teams did not play (bye weeks).\n\nCompared to counties in metropolitan areas near stadiums with no certification requirement, counties near stadiums that had a vaccination requirement had significantly less cases 14 days after home games. In the six weeks leading up to the beginning of the season, percent vaccinated increased in counties that were near stadiums requiring vaccination certification only if the prevalent preseason vaccination rate was relatively low. Required vaccination certification at venues for large gatherings appear to slow virus spread generally in nearby communities and increases vaccination percentages in areas with lower prevalent vaccination percentages.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Leon S. Robertson", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.02.13.22270901", "rel_title": "An observation and restoration model for the COVID-19 incidence curves", @@ -369780,6 +372198,45 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.02.10.22270744", + "rel_title": "Coronavirus Disease 2019 (COVID-19) Vaccine Boosting in Persons Already Protected by Natural or Vaccine-Induced Immunity", + "rel_date": "2022-02-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.10.22270744", + "rel_abs": "BackgroundThe purpose of this study was to evaluate whether boosting healthcare personnel, already reasonably protected by prior infection or vaccination, with a vaccine developed for an earlier variant of COVID-19 protects against the Omicron variant.\n\nMethodsEmployees of Cleveland Clinic who were previously infected with or vaccinated against COVID-19, and were working in Ohio the day the Omicron variant was declared a variant of concern, were included. The cumulative incidence of COVID-19 was examined over two months during an Omicron variant surge. Protection provided by boosting (analyzed as a time-dependent covariate) was evaluated using Cox proportional hazards regression. Analyses were adjusted for time since proximate overt immunologic challenge (POIC) as a time-dependent covariate.\n\nResultsAmong 39 766 employees, 8037 (20%) previously infected and the remaining previously vaccinated, COVID-19 occurred in 6230 (16%) during the study. Risk of COVID-19 increased with time since POIC. In multivariable analysis, boosting was independently associated with lower risk of COVID-19 among those with vaccine-induced immunity (HR, .43; 95% CI, .41-.46) as well as those with natural immunity (HR, .66; 95% CI, .58-.76). Among those with natural immunity, receiving 2 compared to 1 dose of vaccine was associated with higher risk of COVID-19 (HR, 1.54; 95% CI, 1.21-1.97).\n\nConclusionsAdministering a COVID-19 vaccine not designed for the Omicron variant, 6 months or more after prior infection or vaccination, protects against Omicron variant infection in both previously infected and previously vaccinated individuals. There is no evidence of an advantage to administering more than 1 dose of vaccine to previously infected persons.\n\nSummaryAmong 39 766 Cleveland Clinic employees already protected by prior infection or vaccination, vaccine boosting after 6 months was associated with significantly lower risk of COVID-19. After COVID-19 infection, there was no advantage to more than one dose of vaccine.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nabin K Shrestha", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Priyanka Shrestha", + "author_inst": "Stanford University" + }, + { + "author_name": "Patrick C Burke", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Amy S Nowacki", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Paul Terpeluk", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Steven M Gordon", + "author_inst": "Cleveland Clinic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.11.22270667", "rel_title": "Correlation between post-vaccination titres of combined IgG, IgA, and IgM anti-Spike antibodies and protection against breakthrough SARS-CoV-2 infection: a population-based longitudinal study (COVIDENCE UK)", @@ -369945,37 +372402,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2022.02.11.22270873", - "rel_title": "Evaluation of the specificity and accuracy of SARS-CoV-2 rapid antigen self-tests compared to RT-PCR from 1015 asymptomatic volunteers", - "rel_date": "2022-02-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270873", - "rel_abs": "ObjectiveEvaluation of the specificity and accuracy of four CE-approved SARS-CoV-2 antigen rapid self-tests (AG-ST) Anbio, Clungene, Hotgene and Mexacare.\n\nMethod1015 asymptomatic volunteers were screened for SARS-CoV-2 by means of an oropharyngeal swab taken by qualified personnel and subsequent RT-PCR testing. Each participant additionally performed nasal self-swabs for two of the four rapid antigen tests at the same day according to the manufacturers instructions. Study participants transmitted a photo and own interpretation of their test results to the study center. The results of the two self-tests provided by the participants were correlated with the results of the SARS-CoV-2 RT-PCR and independently assessed and evaluated by the study center.\n\nResultsNone of the volunteers tested positive upon RT-PCR, whereas 13 AG-ST showed a false positive test result (0.7 %). The highest false positivity rate was found for the Clungene test (2.1 % compared to 0.2 % for the other tests), while the highest test failure rate (invalid) was found for the Mexacare test (3.7%). The Anbio and Hotgene tests produced the fewest false positive results when evaluated by the participants and also showed the best agreement among themselves.\n\nConclusionSARS-CoV-2 Antigen rapid self-tests with higher false positive test rates, such as the Clungene test, or with high rates of invalid test results, such as the Mexacare test, are less suitable for screening purposes of asymptomatic study participants especially in low-prevalence settings. False positive or inadequate test results increase the burden on certified test laboratories due to verification PCR tests and cause a substantial economic loss due to unnecessary quarantine measurements and cause psychological stress in the affected study participants. In addition to earlier defined requirements for sensitivity for SARS-CoV-2 detection, a lower acceptance boundary for the false positivity rate of < 0.3% should be demanded.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Thomas Iftner", - "author_inst": "Universitaetsklinikum Tuebingen" - }, - { - "author_name": "Angelika Iftner", - "author_inst": "Universit\u00e4tsklinikum T\u00fcbingen: Universitatsklinikum Tubingen" - }, - { - "author_name": "Diana Pohle", - "author_inst": "Universit\u00e4tsklinikum T\u00fcbingen" - }, - { - "author_name": "Peter Martus", - "author_inst": "Universit\u00e4tsklinikum T\u00fcbingen: Universitatsklinikum Tubingen" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2022.02.11.22270698", "rel_title": "Clinico epidemiological profile of Omicron variant of SARS CoV2 in Rajasthan", @@ -371593,6 +374019,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.09.22270747", + "rel_title": "Immune responses after twofold SARS-CoV-2 immunisation in elderly residents and Health Care Workers in nursing homes and homes with assisted living support - Proposal for a correlate of protection", + "rel_date": "2022-02-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.09.22270747", + "rel_abs": "In the present study, we were interested in the decline over time of anti SARS-CoV-2 antibodies and SARS-CoV-2 specific T-cell responses after two doses of mRNA vaccines in total and by age group and comorbidity. The second goal was to suggest an immunological correlate for protection on an individual basis and to describe the probability of protection over time after second vaccination.\n\nWe analysed blood samples from 228 residents (median age 83.8 years) and from 273 Health Care Workers (HCW; median age 49.7 years) of five nursing homes and one home for the elderly with assisted living support. Participants had received two vaccinations. The blood samples were analysed for SARS-CoV-2 specific antibody and T-cell responses. We compared outcomes in the HCW and residents in the respective institutions. No breakthrough infections occurred during the study period. The initial immune responses in the younger participants were about 30 % higher than in the older ones. Over time, all parameters dropped continuously in all groups within the maximum observation period of 232 days. Comorbidities such as coronary heart disease or diabetes mellitus reduced the initial immune responses, regardless of age. In contrast to an almost linear decline in antibody levels, we observed that the interferon-gamma response remained at a constant level between about day 120 and 180, only to decline further thereafter.\n\nBased on our data, we propose on an individual level a correlate of protection: Persons who have a neutralizing capacity of 75 % (which would correspond to approx. 200 BAU/ml) and an interferon-gamma response above 200 mIU/ml should be considered to be protected resp. sufficiently immunized.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Julia Schiffner", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Nora Eisemann", + "author_inst": "Institute of Social Medicine and Epidemiology, University of Luebeck, Germany" + }, + { + "author_name": "Hannah Baltus", + "author_inst": "Institute of Social Medicine and Epidemiology, University of Luebeck, Germany" + }, + { + "author_name": "Sina Jensen", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Katharina Wunderlich", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Stefan Schuesseler", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Charlotte Eicker", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Bianca Teegen", + "author_inst": "Klinisch-Immunologisches Labor Stoecker, Luebeck, Germany" + }, + { + "author_name": "Doreen Boniakowsky", + "author_inst": "Vorwerker Diakonie gemeinnuetzige GmbH, Luebeck, Germany" + }, + { + "author_name": "Werner Solbach", + "author_inst": "Center for Infection and Inflammation Research, University of Luebeck, Luebeck, Germany, German Center for Infection Research (DZIF), Luebeck, Germany" + }, + { + "author_name": "Alexander Mischnik", + "author_inst": "Health Protection Authority, Luebeck, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.02.10.22270783", "rel_title": "Implementation and economic effects of local non-pharmaceutical interventions", @@ -371666,105 +374151,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.09.22270547", - "rel_title": "Cov2MS: an automated matrix-independent assay for mass spectrometric detection and measurement of SARS-CoV-2 nucleocapsid protein in infectious patients", - "rel_date": "2022-02-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.09.22270547", - "rel_abs": "INTRODUCTIONThe pandemic readiness toolbox needs to be extended, providing diagnostic tools that target different biomolecules, using orthogonal experimental setups and fit-for-purpose specification of detection. Here we build on a previous Cov-MS effort that used liquid chromatography-mass spectrometry (LC-MS) and describe a method that allows accurate, high throughput measurement of SARS-CoV-2 nucleocapsid (N) protein.\n\nMATERIALS and METHODSWe used Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA) technology to enrich and quantify proteotypic peptides of the N protein from trypsin-digested samples from COVID-19 patients.\n\nRESULTSThe Cov2MS assay was shown to be compatible with a variety of sample matrices including nasopharyngeal swabs, saliva and blood plasma and increased the sensitivity into the attomole range, up to a 1000-fold increase compared to direct detection in matrix. In addition, a strong positive correlation was observed between the SISCAPA antigen assay and qPCR detection beyond a quantification cycle (Cq) of 30-31, the level where no live virus can be cultured from patients. The automatable \"addition only\" sample preparation, digestion protocol, peptide enrichment and subsequent reduced dependency upon LC allow analysis of up to 500 samples per day per MS instrument. Importantly, peptide enrichment allowed detection of N protein in a pooled sample containing a single PCR positive sample mixed with 31 PCR negative samples, without loss in sensitivity. MS can easily be multiplexed and we also propose target peptides for Influenza A and B virus detection.\n\nCONCLUSIONSThe Cov2MS assay described is agnostic with respect to the sample matrix or pooling strategy used for increasing throughput and can be easily multiplexed. Additionally, the assay eliminates interferences due to protein-protein interactions including those caused by anti-virus antibodies. The assay can be adapted to test for many different pathogens and could provide a tool enabling longitudinal epidemiological monitoring of large numbers of pathogens within a population, applied as an early warning system.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Bart Van Puyvelde", - "author_inst": "ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University" - }, - { - "author_name": "Katleen Van Uytfanghe", - "author_inst": "Laboratory of Toxicology, Ghent University" - }, - { - "author_name": "Laurence Van Oudenhove", - "author_inst": "Waters Corporation" - }, - { - "author_name": "Ralf Gabriels", - "author_inst": "VIB-UGent Center for Medical Biotechnology" - }, - { - "author_name": "Tessa Van Royen", - "author_inst": "VIB-UGent Center for Medical Biotechnology, Department of Biochemistry and Microbiology" - }, - { - "author_name": "Arne Matthys", - "author_inst": "VIB-UGent Center for Medical Biotechnology, Department of Biochemistry and Microbiology" - }, - { - "author_name": "Morteza Razavi", - "author_inst": "SISCAPA Assay Technologies" - }, - { - "author_name": "Richard Yip", - "author_inst": "SISCAPA Assay Technologies" - }, - { - "author_name": "Terry Pearson", - "author_inst": "SISCAPA Assay Technologies" - }, - { - "author_name": "Marijn Van Hulle", - "author_inst": "Waters Corporation" - }, - { - "author_name": "Jan Claereboudt", - "author_inst": "Waters Corporation" - }, - { - "author_name": "Kevin Wyndham", - "author_inst": "Waters Corporation" - }, - { - "author_name": "Donald Jones", - "author_inst": "Leicester Cancer Research Centre, RKCSB, University of Leicester" - }, - { - "author_name": "Xavier Saelens", - "author_inst": "Ghent University and VIB" - }, - { - "author_name": "Geert Antoine Martens", - "author_inst": "AZ Delta General Hospital" - }, - { - "author_name": "Christophe Stove", - "author_inst": "Laboratory of Toxicology, Ghent University" - }, - { - "author_name": "Dieter Deforce", - "author_inst": "ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University" - }, - { - "author_name": "Lennart Martens", - "author_inst": "VIB-UGent Center for Medical Biotechnology" - }, - { - "author_name": "Hans P.C. Vissers", - "author_inst": "Waters Corporation" - }, - { - "author_name": "Norman Leigh Anderson", - "author_inst": "SISCAPA Assay Technologies, Inc." - }, - { - "author_name": "Maarten Dhaenens", - "author_inst": "ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.09.22270653", "rel_title": "COVID Testing in the Workplace: Return to Work Testing in an Occupational Cohort", @@ -373459,6 +375845,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.02.07.479477", + "rel_title": "The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature", + "rel_date": "2022-02-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.07.479477", + "rel_abs": "The NSP3 macrodomain of SARS CoV 2 (Mac1) removes ADP-ribosylation post-translational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the COVID-19 pandemic. Here, we determined neutron and X-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose-bound states. We characterize extensive solvation in the Mac1 active site, and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a re-evaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Galen J Correy", + "author_inst": "Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Daniel W Kneller", + "author_inst": "Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "Gwyndalyn Phillips", + "author_inst": "Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "Swati Pant", + "author_inst": "Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "Silvia Russi", + "author_inst": "Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA" + }, + { + "author_name": "Aina E Cohen", + "author_inst": "Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA" + }, + { + "author_name": "George Meigs", + "author_inst": "Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA" + }, + { + "author_name": "James M Holton", + "author_inst": "Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA" + }, + { + "author_name": "Stefan Gahbauer", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Michael C Thompson", + "author_inst": "Department of Chemistry and Chemical Biology, University of California Merced, CA 95343, USA" + }, + { + "author_name": "Alan Ashworth", + "author_inst": "Helen Diller Family Comprehensive Cancer, University of California San Francisco, CA 94158, USA" + }, + { + "author_name": "Leighton Coates", + "author_inst": "Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "Andrey Kovalevsky", + "author_inst": "Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "Flora Meilleur", + "author_inst": "Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "James S Fraser", + "author_inst": "Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.02.07.479471", "rel_title": "The mechanism of RNA capping by SARS-CoV-2", @@ -373600,33 +376061,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.02.07.479443", - "rel_title": "Olverembatinib inhibits SARS-CoV-2-Omicron variant-mediated cytokine release", - "rel_date": "2022-02-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.07.479443", - "rel_abs": "The Omicron variant has become dominant in the U.S. and around the world. This variant is found to be 2-fold more infectious than the Delta variant, posing a significant threat of severe cases and death. We and others have recently reported that the N-terminus domain (NTD) of the SARS-CoV-2 of various variants is responsible for inducing cytokine release in human PBMCs. Here, we demonstrate that the NTD of the Omicron variant remains highly effective at inducing cytokine release in human PBMCs. Furthermore, we show that Ponatinib and a novel compound, Olverembatinib, are potent Omicron NTD-mediated cytokine release inhibitors. Target profiling revealed that Olverembatinib blocks most of the previously identified kinases responsible for cytokine release. Together, we propose that Ponatinib and Olverembatinib may represent an attractive therapeutic option for treating moderate to severe COVID-19 cases.\n\nHIGHLIGHTSO_LIThe N-terminus domain (NTD) of the SARS-CoV-2 Omicron variant strongly induces multiple inflammatory molecules in PBMCs, unaffected by the mutations observed in the NTD.\nC_LIO_LIThe cytokine release mediated by the Omicron variant is comparable to the Delta variant.\nC_LIO_LIOlverembatinib, a clinical-stage multi-kinase inhibitor, potently inhibits Omicron NTD-mediated cytokine release.\nC_LIO_LIOlverembatinib could relieve severe symptoms associated with COVID-19 Omicron and Delta variants.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Marina Chan", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Eric Holland", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Taran Gujral", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.02.08.479634", "rel_title": "The oral drug nitazoxanide restricts SARS-CoV-2 infection and attenuates disease pathogenesis in Syrian hamsters", @@ -375537,6 +377971,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.02.07.22270555", + "rel_title": "Clinical outcomes in hospitalized vaccine-breakthrough COVID-19 cases compared with contemporary unvaccinated hospitalized adults", + "rel_date": "2022-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270555", + "rel_abs": "SummaryThe inactivated SARS-CoV-2 vaccine (CoronaVac(R)) has been the principal vaccine used in Chiles pre-booster immunization campaign. We compared major outcomes in 260 hospitalized vaccinated vs 507 unvaccinated adults with COVID-19 (mid-2021). The vaccinated group was much older, required less critical care, had lower hospital mortality (adjusted by age), and had shorter hospitalization than the unvaccinated. Benefits were most pronounced in those older than 59 years\n\nObjectiveTo compare major outcomes in fully vaccinated and unvaccinated adult persons hospitalized for COVID-19 in a general private hospital in Santiago, Chile during mid2021.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Marcelo J Wolff Sr.", + "author_inst": "Clinica Santa Maria; U. of Chile School of Medicine;" + }, + { + "author_name": "Margarita Gilabert", + "author_inst": "Clinica Santa Maria, Santiago, Chile" + }, + { + "author_name": "Rodrigo Hernandez", + "author_inst": "Clinica Santa maria, Santiago, Chile" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.07.22270613", "rel_title": "Time to reinfection and vaccine breakthrough SARS-CoV-2 infections: a retrospective cohort study", @@ -375726,61 +378187,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.07.22270593", - "rel_title": "Factors associated with higher levels of grief and support needs among people bereaved during the pandemic: Results from a national online survey", - "rel_date": "2022-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270593", - "rel_abs": "BackgroundThe COVID-19 pandemic has affected millions of peoples experiences of bereavement. We aimed to identify risk factors for grief and support needs.\n\nMethodsOnline survey of people bereaved in the UK (deaths 16 March 2020-2 January 2021), recruited via media, social media, national associations/organisations. Grief was assessed using the Adult Attitude to Grief (AAG) scale, which calculates an overall index of vulnerability (IOV) (range 0-36). Practical and emotional support needs were assessed in 13 domains.\n\nResults711 participants, mean age 49.5 (SD 12.9, range 18-90). 628 (88.6%) were female. Mean age of the deceased 72.2 (SD 16.1). 311 (43.8%) deaths were from confirmed/suspected COVID-19. Mean IOV was 20.41 (95% CI = 20.06 to 20.77). 28.2% exhibited severe vulnerability (IOV [≥] 24). In six support domains relating to psycho-emotional support, 50% to 60% of respondents reported high/fairly high levels of need. Grief and support needs increased strongly for close relationships with the deceased (versus more distant) and with reported social isolation and loneliness (P < 0.001), whereas they reduced with age of the deceased above 40 to 50. Other risk factors were place of death and reduced support from health professionals after death (P < 0.05).\n\nConclusionsHigh overall levels of vulnerability in grief and support needs were observed. Relationship with the deceased, age of the deceased, and social isolation and loneliness are potential indicators of those at risk of even higher vulnerability in grief and support needs. Healthcare professional support after death is associated with more positive bereavement outcomes.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Lucy E Selman", - "author_inst": "University of Bristol" - }, - { - "author_name": "Damian JJ Farnell", - "author_inst": "Cardiff University" - }, - { - "author_name": "Mirella Longo", - "author_inst": "Cardiff University" - }, - { - "author_name": "Silvia Goss", - "author_inst": "Cardiff University" - }, - { - "author_name": "Anna Torrens-Burton", - "author_inst": "Cardiff University" - }, - { - "author_name": "Kathy Seddon", - "author_inst": "Wales Cancer Research Centre" - }, - { - "author_name": "Catriona Mayland", - "author_inst": "University of Sheffield" - }, - { - "author_name": "Linda Machin", - "author_inst": "Keele University" - }, - { - "author_name": "Anthony Byrne", - "author_inst": "Cardiff University" - }, - { - "author_name": "Emily J Harrop", - "author_inst": "Cardiff University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.02.07.21268280", "rel_title": "Multicenter Validation of a Machine Learning Algorithm for Diagnosing Pediatric Patients with Multisystem Inflammatory Syndrome and Kawasaki Disease", @@ -377539,6 +379945,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.02.06.479332", + "rel_title": "A potent SARS-CoV-2 neutralizing antibody recognizing a conserved epitope with broad mutant variant and SARS-CoV activity.", + "rel_date": "2022-02-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.06.479332", + "rel_abs": "COVID-19 is the deadliest respiratory virus pandemic since 1918 and the latest of several coronavirus epidemics and pandemics in recent years. Despite the unprecedented response by both the government and private sectors to develop vaccines and therapies, the evolution of SARS-CoV-2 variants resistant to these interventions reveals a crucial need for therapeutics that maintain their efficacy against current and future mutant variants. Here we describe a SARS-CoV-2 neutralizing antibody, ABP-310, with potent activity against all variants tested including the Omicron variant. ABP-310 also displays potent neutralizing activity against SARS-CoV, highlighting the conserved nature of the ABP-310 epitope. By targeting a conserved epitope, we believe that ABP-310 has therapeutic promise not only against the current SARS-CoV-2 variants but would be expected to maintain efficacy against future variants and possibly even novel coronaviruses.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Adam J Pelzek", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Sanam Ebtehaj", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "James Lulo", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Lucy Zhang", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Olivia Balduf", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Lindsay Dolan", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Chaohua Zhang", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Shengqin Wan", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Gang An", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Awo Kankam", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Eugene Chan", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Shaun P Murphy", + "author_inst": "Abpro Corporation" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.02.06.479285", "rel_title": "Vaccine Protection Against the SARS-CoV-2 Omicron Variant in Macaques", @@ -377792,185 +380261,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2022.02.07.479349", - "rel_title": "Comprehensive Epitope Mapping of Broad Sarbecovirus Neutralizing Antibodies", - "rel_date": "2022-02-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.07.479349", - "rel_abs": "Omicron sub-lineage BA.2 has rapidly surged globally, accounting for over 60% of recent SARS-CoV-2 infections. Newly acquired RBD mutations and high transmission advantage over BA.1 urge the investigation of BA.2s immune evasion capability. Here, we show that BA.2 causes strong neutralization resistance, comparable to BA.1, in vaccinated individuals plasma. However, BA.2 displays more severe antibody evasion in BA.1 convalescents, and most prominently, in vaccinated SARS convalescents plasma, suggesting a substantial antigenicity difference between BA.2 and BA.1. To specify, we determined the escaping mutation profiles1,2 of 714 SARS-CoV-2 RBD neutralizing antibodies, including 241 broad sarbecovirus neutralizing antibodies isolated from SARS convalescents, and measured their neutralization efficacy against BA.1, BA.1.1, BA.2. Importantly, BA.2 specifically induces large-scale escape of BA.1/BA.1.1-effective broad sarbecovirus neutralizing antibodies via novel mutations T376A, D405N, and R408S. These sites were highly conserved across sarbecoviruses, suggesting that Omicron BA.2 arose from immune pressure selection instead of zoonotic spillover. Moreover, BA.2 reduces the efficacy of S309 (Sotrovimab)3,4 and broad sarbecovirus neutralizing antibodies targeting the similar epitope region, including BD55-5840. Structural comparisons of BD55-5840 in complexes with BA.1 and BA.2 spike suggest that BA.2 could hinder antibody binding through S371F-induced N343-glycan displacement. Intriguingly, the absence of G446S mutation in BA.2 enabled a proportion of 440-449 linear epitope targeting antibodies to retain neutralizing efficacy, including COV2-2130 (Cilgavimab)5. Together, we showed that BA.2 exhibits distinct antigenicity compared to BA.1 and provided a comprehensive profile of SARS-CoV-2 antibody escaping mutations. Our study offers critical insights into the humoral immune evading mechanism of current and future variants.", - "rel_num_authors": 41, - "rel_authors": [ - { - "author_name": "Yunlong Cao", - "author_inst": "Changping Laboratory, Beijing, P.R. China.;Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China.;Beijing Advanced Innovation" - }, - { - "author_name": "Ayijiang Yisimayi", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.;School of Life Sciences, Peking University, Beijing, 100871, P.R. China." - }, - { - "author_name": "Fanchong Jian", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.;College of Chemistry and Molecular Engineering, Peking University, Beijing, P.R" - }, - { - "author_name": "Tianhe Xiao", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.;Joint Graduate Program of Peking-Tsinghua-NIBS, Academy for Advanced Interdisci" - }, - { - "author_name": "Weiliang Song", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.;School of Life Sciences, Peking University, Beijing, 100871, P.R. China." - }, - { - "author_name": "Jing Wang", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.;School of Life Sciences, Peking University, Beijing, 100871, P.R. China." - }, - { - "author_name": "Shuo Du", - "author_inst": "School of Life Sciences, Peking University, Beijing, 100871, P.R. China." - }, - { - "author_name": "Zhiying Zhang", - "author_inst": "School of Life Sciences, Peking University, Beijing, 100871, P.R. China." - }, - { - "author_name": "Pulan Liu", - "author_inst": "School of Life Sciences, Peking University, Beijing, 100871, P.R. China." - }, - { - "author_name": "Xiaohua Hao", - "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China." - }, - { - "author_name": "Qianqian Li", - "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijin" - }, - { - "author_name": "Xiaosu Chen", - "author_inst": "Institute for Immunology, College of Life Sciences, Nankai University, Tianjin, P. R. China." - }, - { - "author_name": "Lei Wang", - "author_inst": "CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China" - }, - { - "author_name": "Peng Wang", - "author_inst": "Changping Laboratory, Beijing, P.R. China." - }, - { - "author_name": "Ran An", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." - }, - { - "author_name": "Yao Wang", - "author_inst": "Changping Laboratory, Beijing, P.R. China." - }, - { - "author_name": "Jing Wang", - "author_inst": "Changping Laboratory, Beijing, P.R. China." - }, - { - "author_name": "Peng Yang", - "author_inst": "CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China" - }, - { - "author_name": "Haiyan Sun", - "author_inst": "Changping Laboratory, Beijing, P.R. China." - }, - { - "author_name": "Lijuan Zhao", - "author_inst": "Changping Laboratory, Beijing, P.R. China.2Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China.;Beijing Advanced Innovation" - }, - { - "author_name": "Wen Zhang", - "author_inst": "Beijing Ditan Hospital, Capital Medical University" - }, - { - "author_name": "Dong Zhao", - "author_inst": "Beijing Ditan Hospital, Capital Medical University" - }, - { - "author_name": "Jiang Zheng", - "author_inst": "Changping Laboratory, Beijing, P.R. China." - }, - { - "author_name": "Lingling Yu", - "author_inst": "Changping Laboratory, Beijing, P.R. China." - }, - { - "author_name": "Can Li", - "author_inst": "Changping Laboratory, Beijing, P.R. China." - }, - { - "author_name": "Na Zhang", - "author_inst": "Changping Laboratory, Beijing, P.R. China." - }, - { - "author_name": "Rui Wang", - "author_inst": "Changping Laboratory, Beijing, P.R. China." - }, - { - "author_name": "Xiao Niu", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China." - }, - { - "author_name": "Sijie Yang", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China.Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing," - }, - { - "author_name": "Xuetao Song", - "author_inst": "Changping Laboratory, Beijing, P.R. China." - }, - { - "author_name": "Linlin Zheng", - "author_inst": "Changping Laboratory, Beijing, P.R. China." - }, - { - "author_name": "Zhiqiang Li", - "author_inst": "Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P.R. China;Peking-Tsinghua Center for Life Sciences, Peking University, Beij" - }, - { - "author_name": "Qingqing Gu", - "author_inst": "Changping Laboratory, Beijing, P.R. China." - }, - { - "author_name": "Fei Shao", - "author_inst": "Changping Laboratory, Beijing, P.R. China." - }, - { - "author_name": "Weijin Huang", - "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO" - }, - { - "author_name": "Youchun Wang", - "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO" - }, - { - "author_name": "Zhongyang Shen", - "author_inst": "Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University, Tianjin, P. R. China." - }, - { - "author_name": "Xiangxi Wang", - "author_inst": "CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China" - }, - { - "author_name": "Ronghua Jin", - "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing, P.R. China." - }, - { - "author_name": "Junyu Xiao", - "author_inst": "School of Life Sciences, Peking University, Beijing, 100871, P.R. China.;Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, P.R" - }, - { - "author_name": "Xiaoliang Sunney Xie", - "author_inst": "Changping Laboratory, Beijing, P.R. China.2Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, P.R. China.;Beijing Advanced Innovation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.02.05.479274", "rel_title": "EMoMiS: A Pipeline for Epitope-based Molecular Mimicry Search in Protein Structures with Applications to SARS-CoV-2", @@ -380117,6 +382407,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.04.22270433", + "rel_title": "The usefulness of D-dimer as a predictive marker for mortality in patients with COVID-19 hospitalized during the first wave in Italy.", + "rel_date": "2022-02-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.04.22270433", + "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) presents an urgent threat to global health. Identification of predictors of poor outcomes will assist medical staff in treatment and allocating limited healthcare resources.\n\nAimsThe primary aim was to study the value of D-dimer as a predictive marker for in-hospital mortality.\n\nMethodsThis was a cohort study. The study population consisted of hospitalized patients (age >18 years), who were diagnosed with COVID-19 based on real-time PCR at 9 hospitals during the first COVID-19 wave in Lombardy, Italy (Feb-May 2020). The primary endpoint was in-hospital mortality. Information was obtained from patient records. Statistical analyses were performed using a Fine-Gray competing risk survival model. Model discrimination was assessed using Harrells C-index and model calibration was assessed using a calibration plot.\n\nResultsOut of 1049 patients, 501 patients had evaluable data. Of these 501 patients, 96 died. The cumulative incidence of in-hospital mortality within 30 days was 20% (95CI: 16%-23%), and the majority of deaths occurred within the first 10 days. A prediction model containing D-dimer as the only predictor had a C-index of 0.66 (95%CI: 0.61-0.71). Overall calibration of the model was very poor. The addition of D-dimer to a model containing age, sex and co-morbidities as predictors did not lead to any meaningful improvement in either the C-index or the calibration plot.\n\nConclusionThe predictive value of D-dimer alone was moderate, and the addition of D-dimer to a simple model containing basic clinical characteristics did not lead to any improvement in model performance.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Shermarke Hassan", + "author_inst": "University of Milan" + }, + { + "author_name": "Barbara Ferrari", + "author_inst": "Policlinico di Milano: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Raffaella Rossio", + "author_inst": "Policlinico di Milano: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Vincenzo la Mura", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Andrea Artoni", + "author_inst": "Policlinico di Milano: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Roberta Gualtierotti", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Ida Martinelli", + "author_inst": "Policlinico di Milano: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Alessandro Nobili", + "author_inst": "Mario Negri Institute for Pharmacological Research Branch of Milan: Istituto di Ricerche Farmacologiche Mario Negri" + }, + { + "author_name": "Alessandra Bandera", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Andrea Gori", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Francesco Blasi", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Valter Monzani", + "author_inst": "Policlinico di Milano: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Giorgio Costantino", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Sergio Harari", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Frits Richard Rosendaal", + "author_inst": "Leiden Universitair Medisch Centrum: Leids Universitair Medisch Centrum" + }, + { + "author_name": "Flora Peyvandi", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "the COVID-19 Network working group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.05.22270499", "rel_title": "Comparative study of immunogenicity and safety of Gam-COVID-Vac and Sinopharm BBIBP-CorV vaccines in Belarus", @@ -380358,45 +382731,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.04.22270480", - "rel_title": "SARS-CoV-2 Omicron symptomatic infections in previously infected or vaccinated South African healthcare workers", - "rel_date": "2022-02-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.04.22270480", - "rel_abs": "We investigated Omicron infections among healthcare workers (HCW) presenting with symptoms of SARS-CoV-2 infection and evaluated the protective effect of vaccination or prior infection.\n\nBetween 24th November and 31st December 2021, HCW in Johannesburg, South Africa, were tested for SARS-CoV-2 infection by Nucleic Acid Amplification Test (NAAT). Blood samples collected either at the symptomatic visit or within 3-months prior, were tested for spike protein immunoglobulin G (IgG).\n\nOverall, 433 symptomatic HCW were included in the analysis, with 190 (43.9%) having an Omicron infection; 69 (16.7%) were unvaccinated and 270 (62.4%) received a single dose of Ad26.COV.2 vaccine. There was no difference in the odds of identifying Omicron between unvaccinated and Ad26.COV.2 vaccinated HCW (adjusted odds ratio [aOR] 0.81, 95% confidence interval [CI]: 0.46, 1.43). One-hundred and fifty-four (35.3%) HCW had at least one SARS-CoV-2 NAAT-confirmed prior infection; these had lower odds of Omicron infection compared with those without past infection (aOR 0.55, 95%CI: 0.36, 0.84). Anti-spike IgG concentration of 1549 binding antibody unit/mL was suggestive of significant reduction in the risk of symptomatic Omicron infection.\n\nWe found high reinfection and vaccine breakthrough infection rates with the Omicron variant among HCW. Prior infection and high anti-spike IgG concentration were protective against Omicron infection.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Marta Nunes", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Sthembile Sibanda", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Vicky Baillie", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Gaurav Kwatra", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Ricardo Aguas", - "author_inst": "University of Oxford" - }, - { - "author_name": "Shabir Madhi", - "author_inst": "University of the Witwatersrand" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.04.22270165", "rel_title": "Using multiple sampling strategies to estimate SARS-CoV-2 epidemiological parameters from genomic sequencing data", @@ -382203,6 +384537,53 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.02.03.22270401", + "rel_title": "RISK STRATIFICATION OF PATIENTS WITH COVID-19 DISEASE THROUGH THE USE OF CLINICAL SCORES IN AN EMERGENCY DEPARTMENT. A review of the literature", + "rel_date": "2022-02-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.03.22270401", + "rel_abs": "DISCLAIMER STATEMENTThe authors have withdrawn the manuscript because there are some errors in the Area Under the Curve values regarding to intensive care unit admission and mortality for some scores analyzed. The article must be revised in its conclusions in order to affirm that NEWS and NEWS2 are the best clinical scores to be used in Emergency to evaluate patients with Covid-19 disease.\n\nTherefore, the authors do not wish this work to be cited as reference for one project. If you have any questions, please contact the corresponding author.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Simone Zanella", + "author_inst": "APSS Trento" + }, + { + "author_name": "Francesco Zanella", + "author_inst": "APSS Trento" + }, + { + "author_name": "Alena Mancosu", + "author_inst": "University of Verona" + }, + { + "author_name": "Anna Brugnolli", + "author_inst": "Nursing School of Trento, University of Verona" + }, + { + "author_name": "Alessandro Carrara", + "author_inst": "APSS Trento" + }, + { + "author_name": "Anita Bevilacqua", + "author_inst": "Nursing School of Trento, University of Verona" + }, + { + "author_name": "Elisa Marinelli", + "author_inst": "Nursing School of Trento, University of Verona" + }, + { + "author_name": "Nicola Ricci", + "author_inst": "APSS Trento" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2022.02.03.22270417", "rel_title": "Fatality assessment and variant risk monitoring for COVID-19 using three new hospital occupancy related metrics", @@ -382344,49 +384725,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.03.22270389", - "rel_title": "Risk of severe COVID-19 from the Delta and Omicron variants in relation to vaccination status, sex, age and comorbidities: surveillance results from southern Sweden", - "rel_date": "2022-02-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.03.22270389", - "rel_abs": "The risk of severe COVID-19 disease requiring hospitalization with extensive oxygen supply was compared among infected cases during two calendar periods when Delta and Omicron, respectively, were the dominating virus variants in Scania county, Sweden. Adjustments were made for differences among cases in comorbidities, prior infection, vaccination status, age and sex. Markedly lower risks were observed from Omicron among the vaccinated in the present study. The risk of severe disease was also lower for unvaccinated during Omicron than during Delta, but remained high among older people and middle-aged males with comorbidities. Efforts to increase vaccination uptake across countries, populations and subgroups should thus remain a public health priority.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Fredrik Kahn", - "author_inst": "Lund University" - }, - { - "author_name": "Carl Bonander", - "author_inst": "University of Gothenburg" - }, - { - "author_name": "Mahnaz Moghaddassi", - "author_inst": "Lund University" - }, - { - "author_name": "Magnus Rasmussen", - "author_inst": "Lund University" - }, - { - "author_name": "Ulf Malmqvist", - "author_inst": "Skane University Hospital" - }, - { - "author_name": "Malin Inghammar", - "author_inst": "Lund University" - }, - { - "author_name": "Jonas Bjork", - "author_inst": "Lund University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.02.03.22270414", "rel_title": "Equitable COVID-19 vaccine prioritization: front-line workers or 65-74 year olds?", @@ -383945,6 +386283,201 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.02.03.22270391", + "rel_title": "Device-assessed sleep and physical activity in individuals recovering from a hospital admission for COVID-19: a prospective, multicentre study", + "rel_date": "2022-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.03.22270391", + "rel_abs": "ObjectivesTo describe physical behaviours following hospital admission for COVID-19 including associations with acute illness severity and ongoing symptoms.\n\nMethods1077 patients with COVID-19 discharged from hospital between March and November 2020 were recruited. Using a 14-day wear protocol, wrist-worn accelerometers were sent to participants after a five-month follow-up assessment. Acute illness severity was assessed by the WHO clinical progression scale, and the severity of ongoing symptoms was assessed using four previously reported data-driven clinical recovery clusters. Two existing control populations of office workers and type 2 diabetes were comparators.\n\nResultsValid accelerometer data from 253 women and 462 men were included. Women engaged in a mean{+/-}SD of 14.9{+/-}14.7 minutes/day of moderate-to-vigorous physical activity (MVPA), with 725.6{+/-}104.9 minutes/day spent inactive and 7.22{+/-}1.08 hours/day asleep. The values for men were 21.0{+/-}22.3 and 755.5{+/-}102.8 minutes/day and 6.94{+/-}1.14 hours/day, respectively. Over 60% of women and men did not have any days containing a 30-minute bout of MVPA. Variability in sleep timing was approximately 2 hours in men and women. More severe acute illness was associated with lower total activity and MVPA in recovery. The very severe recovery cluster was associated with fewer days/week containing continuous bouts of MVPA, longer sleep duration, and higher variability in sleep timing. Patients post-hospitalisation with COVID-19 had lower levels of physical activity, greater sleep variability, and lower sleep efficiency than a similarly aged cohort of office workers or those with type 2 diabetes.\n\nConclusionsPhysical activity and regulating sleep patterns are potential treatable traits for COVID-19 recovery programmes.", + "rel_num_authors": 45, + "rel_authors": [ + { + "author_name": "Tatiana Plekhanova", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Alex V Rowlands", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Rachael A Evans", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Charlotte L Edwardson", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Nicolette C Bishop", + "author_inst": "School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK" + }, + { + "author_name": "Charlotte E Bolton", + "author_inst": "University of Nottingham, Nottingham, UK" + }, + { + "author_name": "James D Chalmers", + "author_inst": "University of Dundee, Ninewells Hospital and Medical School, Dundee, UK" + }, + { + "author_name": "Melanie J Davies", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Enya Daynes", + "author_inst": "NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Annemarie B Docherty", + "author_inst": "Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Omer Elneima", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Neil J Greening", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Sharlene A Greenwood", + "author_inst": "King's College Hospital, Department of Physiotherapy and Renal Medicine, London, UK" + }, + { + "author_name": "Andrew P Hall", + "author_inst": "University Hospitals of Leicester NHS Trust, Leicester, UK" + }, + { + "author_name": "Victoria C Harris", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Ewen M Harrison", + "author_inst": "Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Joseph Henson", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Ling-Pei Ho", + "author_inst": "MRC Human Immunology Unit, University of Oxford, Oxford, UK" + }, + { + "author_name": "Alex Horsley", + "author_inst": "Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK" + }, + { + "author_name": "Linzy Houchen-Wolloff", + "author_inst": "Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Kamlesh Khunti", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Olivia C Leavy", + "author_inst": "Department of Health Sciences, University of Leicester, Leicester, UK" + }, + { + "author_name": "Nazir I Lone", + "author_inst": "Usher Institute, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Michael Marks", + "author_inst": "Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK" + }, + { + "author_name": "Ben Maylor", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Hamish J C McAuley", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Claire M Nolan", + "author_inst": "Harefield Respiratory Research Group, Royal Brompton and Harefield Clinical Group, Guys and St. Thomas NHS Foundation Trust, London, UK" + }, + { + "author_name": "Krisnah Poinasamy", + "author_inst": "Asthma UK and British Lung Foundation, London, UK" + }, + { + "author_name": "Jennifer K Quint", + "author_inst": "NHLI, Imperial College London, London, UK" + }, + { + "author_name": "Betty Raman", + "author_inst": "Radcliffe Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Matthew Richardson", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Jack A Sargeant", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Ruth M Saunders", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Marco Sereno", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Aarti Shikotra", + "author_inst": "NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Amisha Singapuri", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Michael Steiner", + "author_inst": "Department of Respiratory Sciences, University of Leicester, Leicester, UK" + }, + { + "author_name": "David J Stensel", + "author_inst": "NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Louise V Wain", + "author_inst": "Department of Health Sciences, University of Leicester, Leicester, UK" + }, + { + "author_name": "Julie Whitney", + "author_inst": "School of Life Course & Population Sciences, Kings College London, London, UK" + }, + { + "author_name": "Dan G Wootton", + "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Christopher E Brightling", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "William D-C Man", + "author_inst": "Royal Brompton and Harefield Clinical Group, Guys and St. Thomas NHS Foundation Trust, London, UK" + }, + { + "author_name": "Sally J Singh", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Tom Yates", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.03.22270396", "rel_title": "COVID-19 Vaccination is Associated with Decreasing Cases, Hospitalizations, and Deaths Across Age Groups and Variants over 9 months in Switzerland", @@ -384146,33 +386679,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.02.22270342", - "rel_title": "Occurrence of relative bradycardia and relative tachycardia in individuals diagnosed with COVID-19", - "rel_date": "2022-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.02.22270342", - "rel_abs": "BackgroundThe COVID-19 disease caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has become one of the worst global pandemics of the century causing tremendous human and economic suffering worldwide. While considered a respiratory disease, COVID-19 is known to cause cardiac complications. Wearable devices are well equipped to measure heart rate continuously and their popularity makes them valuable devices in the field of digital health. In this article, we use Fitbit devices to examine resting heart rate from individuals diagnosed with COVID-19 a\n\nMethodsThe Fitbit COVID-19 survey was conducted from May 2020 - June 2021. We collected resting heart rate data from 7,200 individuals (6,606 symptomatic, 594 asymptomatic) diagnosed with COVID-19 between March 2020 - December 2020, as well as from 463 individuals diagnosed with influenza between January 2020 - December 2020. Data from healthy individuals served as a control, in order to model the seasonal variation. We also computed heart rate variability and respiratory rate data for symptomatic COVID-19.\n\nFindingsResting Heart Rate is elevated during COVID-19 symptom onset, with average peak increases relative to the baseline of 1.8%{+/-}0.1% (3.4%{+/-}0.2%) for females (males), where the quoted numbers are mean and standard error of the mean. After the initial peak, the resting heart rate decreased and reached a minimum on average{approx} 13 days after symptom onset. The minimum value relative to the baseline is more negative for females (-1.75% {+/-} 0.1%) compared to males (0.08% {+/-} 0.2%). The resting heart rate then increased, reaching a second peak on average{approx} 28 days from symptom onset, before falling back to the baseline{approx} 112 days from symptom onset. All estimates vary with disease severity.\n\nInterpretationThe resting heart rate is modified for several months following a COVID-19 diagnosis. Interestingly, this effect is seen with seasonal influenza also, although the bradycardia minimum and the second tachycardia peak are often more pronounced in the case of symptomatic COVID-19. By computing resting heart rate daily, wearable devices can contribute to monitoring wellness during recovery from COVID-19, and seasonal influenza.\n\nFundingA.N., H.-W.S., and C.H. are supported by Fitbit Research, Google LLC.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, Google, and Google Scholar for research articles published in English up to Oct 31, 2021, using common search terms such as \"bradycardia and COVID-19\", \"cardiac complications and COVID-19\", etc. Articles were also retrieved by searching through citations of known literature. It is known that COVID-19 can cause cardiac complications such as bradycardia and arrhythmias. Using data from commercially available wearable devices, it has been shown previously that the resting heart is elevated during symptom onset, then decreases reaching a minimum, before rising again to attain a second peak, before finally returning to the baseline.\n\nAdded value of this studyWe present results from the largest (to our knowledge) dataset considered to-date, involving 7200 participants (6606 symptomatic and 594 asymptomatic) diagnosed with COVID-19. We also present results from 463 individuals diagnosed with influenza. Our large dataset allows us to perform more detailed examinations by age, disease severity, and sex. We also discuss the time evolution of heart rate variability and respiratory rate. The heart rate variability shows a similar time evolution as the resting heart rate but with opposite phase, while the respiratory rate decreases monotonously following the peak at symptom onset.\n\nImplications of all the available evidenceThe results presented in this work show that commercially available trackers and smart-watches can help in monitoring heart health in the weeks and months following a COVID-19 diagnosis. An estimate of the amplitude of the bradycardia dip may provide information valuable to critical care.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Aravind Natarajan", - "author_inst": "Google Inc" - }, - { - "author_name": "Hao-Wei Su", - "author_inst": "Google Inc." - }, - { - "author_name": "Conor Heneghan", - "author_inst": "Google Inc." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.02.03.22269612", "rel_title": "Biologic correlates of beneficial convalescent plasma therapy in a COVID-19 patient reveal disease resolution mechanisms", @@ -385783,6 +388289,33 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2022.02.01.478632", + "rel_title": "Design and development of potent h-ACE2 derived peptide mimetics in SARS-CoV-2 Omicron variant therapeutics", + "rel_date": "2022-02-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.01.478632", + "rel_abs": "The pandemic of COVID-19 has become the global health challenge due to the emergence of new variants. The Receptor binding domain (RBD) of spike protein that makes direct interaction with ACE-2 has shown unique mutated residues in most of the variants of concern (VOC). Recently WHO declared the Omicron (B.1.1.529) as VOC considering it as a highly mutated variant which includes a total of 60 mutations out of which 15 mutations occurred in RBD region of SARS-CoV-2. Inhibition of Protein-protein (Omicron RBD-h-ACE2) interaction was already proved to inhibit the viral infection. In this study, by using molecular dynamic simulations efforts are made to explore the atomistic details of Omicron RBD-h-ACE2 interaction. Based on MD simulations, h-ACE2 motif is found to be interacting with omicron RBD domain. Interaction analysis had provided key residues interacting with Omicron-RBD that helped to extract h-ACE2 peptide. Here, rational design of the peptides that have resemblance with h-ACE2 is done and the peptide library is subjected for inhibition studies against Omicron-RBD. The current study helped to identify the significant peptides that can inhibit Omicron-RBD. Altogether the performed studies will provide an opportunity to develop potential therapeutic peptidomimetics effective against Omicron variant of SARS-CoV-2.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Stanly M L Paul", + "author_inst": "University of Szeged" + }, + { + "author_name": "Swathi Nadendla", + "author_inst": "National Institute of Pharmaceutical Education and Research (NIPER) S.A.S. Nagar" + }, + { + "author_name": "Elizabeth M Sobhia", + "author_inst": "National Institute of Pharmaceutical Education and Research (NIPER) S.A.S. Nagar" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.02.01.478697", "rel_title": "Patterns of Volatility Across the Spike Protein Accurately Predict the Emergence of Mutations within SARS-CoV-2 Lineages", @@ -385936,45 +388469,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2022.02.02.478775", - "rel_title": "Intracellular flow cytometry complements RT-qPCR detection of circulating SARS-CoV-2 variants of concern", - "rel_date": "2022-02-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.02.478775", - "rel_abs": "Despite the efficacy of current vaccines against SARS-CoV-2, the spread of the virus is still not under control, as evidenced by the ongoing circulation of the highly contagious SARS-CoV-2 Omicron variant. Basic and antiviral research on SARS-CoV-2 relies on cellular assays of virus replication in vitro. In addition, accurate detection of virus-infected cells and released virus particles is needed to study virus replication and to profile new candidate antiviral drugs. Here, by flow cytometry, we detect SARS-CoV-2 infection at single cell level and distinguish infected Vero E6 cells from uninfected bystander cells. Furthermore, based on the viral nucleocapsid expression, subpopulations of infected cells that are in an early or late phase of viral replication can be differentiated. Importantly, this flow cytometric technique complements RT-qPCR detection and can be applied to all current SARS-CoV-2 variants of concern, including the highly mutated Omicron variant.\n\nMethod summaryThis study describes the characterization of SARS-CoV-2 infected cells using intracellular flow cytometric viral nucleocapsid staining that complements RT-qPCR quantification of viral RNA. The technique makes it possible to distinguish between infected cells in the early (low N) or late phase (high N) of viral replication. It can also be applied to the different variants of concern of SARS-CoV-2, including the Omicron variant.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Emiel Vanhulle", - "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy" - }, - { - "author_name": "Becky Provinciael", - "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy" - }, - { - "author_name": "Joren Stroobants", - "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy" - }, - { - "author_name": "Anita Camps", - "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy" - }, - { - "author_name": "Piet Maes", - "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Epidemiological Virology" - }, - { - "author_name": "Kurt Vermeire", - "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.02.02.22269880", "rel_title": "SARS-CoV-2 RT-qPCR testing of pooled saliva samples: a case study of 824 asymptomatic individuals and a questionnaire survey in Japan", @@ -387605,6 +390099,97 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.29.22270074", + "rel_title": "Partnering with Athletes to Assess Risk of COVID-Related Myocarditis", + "rel_date": "2022-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.29.22270074", + "rel_abs": "BackgroundMyocarditis in athletes is a feared complication of SARS-CoV-2, yet guidelines for screening with cardiac magnetic resonance imaging are lacking. Further, stakeholder involvement in the research is rare.\n\nHypothesisWe sought to determine the rates of cardiac magnetic resonance imaging evidence of SARS-CoV-2 related myocarditis in student athletes. We hypothesized that rates of myocarditis were lower than initially reported and that including athletes on the research team would enhance participant satisfaction and scientific integrity.\n\nMethodsAccordingly, when members of a hockey team were infected with SARS-CoV-2, we invited them and their team physicians to be part of the design of a study assessing the incidence of myocarditis. We performed cardiac magnetic resonance imaging on participating hockey players infected with SARS-CoV-2 and compared them to a healthy lacrosse cohort. Participants were given an optional survey to complete at the end of the study to assess their satisfaction with it.\n\nResultsFour hockey players and two team physicians joined the study team; eight hockey players and four lacrosse players participated in the study. Zero athletes met imaging criteria for myocarditis; delayed enhancement was observed in seven cases and three controls. Athletes supported sharing the findings with the participants. No athletes reported feeling uncomfortable participating, knowing other athletes participated on the research team.\n\nConclusionRates of SARS-CoV-2 myocarditis in young athletes appears to be lower than initially reported. Partnered research is important, especially in populations with more to lose, such as collegiate athletes; future studies should include stakeholders in the study design and execution.\n\nKey pointsCardiac MRI findings of myocarditis after COVID infection in young athletes is rare. Subjects of research studies appreciate involvement in the development of the study, and this also builds trust with the research team.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Bradley William Kay", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Attila Feher", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Samuel Reinhardt", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Jason Cuomo", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Stephanie Arlis-Mayor", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Matthew Lynch", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Kyle Johnson", + "author_inst": "Yale University" + }, + { + "author_name": "Phil Kemp", + "author_inst": "Yale University" + }, + { + "author_name": "Henry Wagner", + "author_inst": "Yale University" + }, + { + "author_name": "Tyler Welsh", + "author_inst": "Yale University" + }, + { + "author_name": "Jerome Lamy", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Dana Peters", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Hamid Mojibian", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Lawrence Young", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Rachel Lampert", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Robert McNamara", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Lauren Baldassarre", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Edward J Miller", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Erica S Spatz", + "author_inst": "Yale School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2022.02.01.22270170", "rel_title": "Detection of prevalent SARS-CoV-2 variant lineages in wastewater and clinical sequences from cities in Quebec, Canada", @@ -387838,77 +390423,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.01.31.22269194", - "rel_title": "An outbreak of SARS-CoV-2 in a public-facing office in England, 2021", - "rel_date": "2022-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.31.22269194", - "rel_abs": "Between August-September 2021, an outbreak of SARS-CoV-2, with an attack rate of 55% (22/40 workers), occurred in a public-facing office in England. To identify workplace and worker-related risk factors, a comprehensive investigation involving surface sampling, environmental assessment, molecular and serological testing, and worker questionnaires was performed in September - October 2021. The results affirm the utility of surface sampling to identify SARS-CoV-2 control deficiencies and the importance of evolving, site-specific risk assessments with layered COVID-19 mitigation strategies.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Barry Atkinson", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Karin van Veldhoven", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Ian Nicholls", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Matthew Coldwell", - "author_inst": "Health and Safety Executive" - }, - { - "author_name": "Adam Clarke", - "author_inst": "Health and Safety Executive" - }, - { - "author_name": "Gillian Frost", - "author_inst": "Health and Safety Executive" - }, - { - "author_name": "Christina J Atchison", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Amber I Raja", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Allan M Bennett", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Derek Morgan", - "author_inst": "Health and Safety Executive" - }, - { - "author_name": "Neil Pearce", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Tony Fletcher", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Elizabeth B Brickley", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Yiqun Chen", - "author_inst": "Health and Safety Executive" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.22.22269630", "rel_title": "Breakthrough SARS-CoV-2 infections in MS patients on disease modifying therapies", @@ -389267,6 +391781,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.01.30.22269980", + "rel_title": "Quantitative risk assessment of COVID-19 and serious illness among spectators at mass gathering events with vaccine-testing package implementation", + "rel_date": "2022-01-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.30.22269980", + "rel_abs": "While mass gathering events have resumed in conjunction with vaccine-testing (VT) packages, their effects on reducing COVID-19 risk remain unclear. Here, we used an environmental exposure model to analyze the effects of vaccinations and proof of negative test results on reducing infection risk and serious illness among spectators at mass gathering events. We then analyzed the difference in risk with and without VT and regular seat zoning. Risk of infection and serious illness were quantified using a model incorporating parameters such as vaccination coverage, vaccine prevention effectiveness, and sensitivity of polymerase chain reaction (PCR) or qualitative antigen tests. When vaccine prevention effectiveness was 50% (corresponding to 4 months for the delta variant and 1-2 months for the omicron variant after the second vaccine dose), the risk of infection and serious illness among vaccinated spectators were 0.32-0.40 and 0.13-0.16 times of those who tested negative, respectively. In contrast, the risks of infection and serious illness among vaccinated spectators without measures such as mask wearing were 4.0 and 1.6 times higher than those among unvaccinated spectators with such measures, respectively. The risk of infection with an 80% vaccination coverage and a vaccine prevention effectiveness of 20% (corresponding to 5-6 months for the delta variant or 3-4 months for the omicron variant after the second vaccine dose) was comparable to that of a 20% vaccine coverage and a vaccine prevention effectiveness of 80% (corresponding to 1-3 months for delta variant after the second vaccine dose). Regarding zoning, there was little difference in risk with a vaccination coverage of [≥]80%. Adherence to individual measures after vaccination and maintenance of high vaccine effectiveness among spectators at stadiums are important for reducing risk of infection and serious illness. Furthermore, seat zoning did not affect overall infection risk reduction.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Michio Murakami", + "author_inst": "Osaka University; National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Tsukasa Fujita", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Yuichi Iwasaki", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Masaki Onishi", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Wataru Naito", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Seiya Imoto", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Tetsuo Yasutaka", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.29.22270094", "rel_title": "Polygenic predisposition to venous thromboembolism is associated with increased COVID-19 positive testing rates", @@ -389608,53 +392165,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.27.22269840", - "rel_title": "Identification of thresholds on population density for understanding transmission of COVID-19", - "rel_date": "2022-01-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269840", - "rel_abs": "Pathways of transmission of coronavirus (COVID-19) disease in the human population are still emerging. However, empirical observations suggest that dense human settlements are the most adversely impacted, corroborating a broad consensus that human-to-human transmission is a key mechanism for the rapid spread of this disease. Here, using logistic regression techniques, estimates of threshold levels of population density were computed corresponding to the incidence in the human population. Regions with population densities greater than 3000 person per square mile in the United States have about 95% likelihood to get infected with COVID-19. Since case numbers of COVID-19 dynamically changed each day until November 30, 2020, ca. 4% of US counties were at 50% or higher risk of COVID-19 transmission. While threshold on population density is not the sole indicator for predictability of coronavirus in human population, yet it is one of the key variables on understanding and rethinking human settlement in urban landscapes.\n\nPlane language SummaryPopulation density is certainly one of the key factors influencing the transmission of infectious diseases like COVID-19. It is approximated that in continental United States, population density of 1192 per square mile and higher presents 50% probability of getting infected with COVID-19.\n\nKey PointsO_LIBased on data from the USA, the population density of 1192 persons per square mile represented a 50% or higher probability of risk of transmission of COVID-19.\nC_LIO_LIAbout 35 counties in the USA are at very high risk of transmission potential (95% or higher) for COVID-19.\nC_LIO_LIAnalysis shows the vulnerability of urban towns to respiratory infectious disease\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yusuf Jamal", - "author_inst": "University of Florida" - }, - { - "author_name": "Mayank Gangwar", - "author_inst": "University of Florida" - }, - { - "author_name": "Moiz Usmani", - "author_inst": "University of Florida" - }, - { - "author_name": "Alison Adams", - "author_inst": "University of Florida" - }, - { - "author_name": "Chang-Yu Wu", - "author_inst": "University of Florida" - }, - { - "author_name": "Thanh Huong Nguyen", - "author_inst": "University of Illinois, Urbana, IL" - }, - { - "author_name": "Rita Colwell", - "author_inst": "University of Maryland Institute of Advanced Computer Studies , University of Maryland, College Park, MD" - }, - { - "author_name": "Antarpreet Jutla", - "author_inst": "University of Florida" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.28.22270040", "rel_title": "Predicting clinical outcomes and hospitalization stay of hospitalized COVID-19 patients by using Deep Learning methods", @@ -391265,6 +393775,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.27.22269949", + "rel_title": "Tracking the progressive spread of the SARS-CoV-2 Omicron variant in Italy, December 2021 - January 2022", + "rel_date": "2022-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269949", + "rel_abs": "The SARS-CoV-2 variant of concern Omicron was first detected in Italy in November 2021. Data from three genomic surveys conducted in Italy between December 2021 and January 2022 suggest that Omicron became dominant in less than one month (prevalence on January 3: 78.6%-83.8%) with a doubling time of 2.7-3.1 days. The mean net reproduction number rose from about 1.15 in absence of Omicron to a peak of 1.83 for symptomatic cases and 1.33 for hospitalized cases, while it remained stable for critical cases.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Paola Stefanelli", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Filippo Trentini", + "author_inst": "Dondena Centre for Research on Social Dynamics and Public Policy, Bocconi University, Milan, Italy" + }, + { + "author_name": "Daniele Petrone", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Alessia Mammone", + "author_inst": "Ministero della Salute" + }, + { + "author_name": "Luigina Ambrosio", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Mattia Manica", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Giorgio Guzzetta", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Valeria D Andrea", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Valentina Marziano", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Agnese Zardini", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Carla Molina Grane", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA" + }, + { + "author_name": "Angela Di Martino", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Flavia Riccardo", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Antonino Bella", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Monica Sane Schepisi", + "author_inst": "Ministero della Salute" + }, + { + "author_name": "Francesco Maraglino", + "author_inst": "Ministero della Salute" + }, + { + "author_name": "Piero Poletti", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Anna Teresa Palamara", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Silvio Brusaferro", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Giovanni Rezza", + "author_inst": "Ministero della Salute" + }, + { + "author_name": "Patrizio Pezzotti", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Stefano Merler", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.28.22270022", "rel_title": "Continuing inequalities in COVID-19 mortality in England and Wales, and the changing importance of regional, over local, deprivation", @@ -391378,89 +393995,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.25.477724", - "rel_title": "Distinct genetic determinants and mechanisms of SARS-CoV-2 resistance to remdesivir", - "rel_date": "2022-01-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.25.477724", - "rel_abs": "The nucleoside analog remdesivir (RDV) is an FDA-approved antiviral for the treatment of SARS- CoV-2 infections, and as such it is critical to understand potential genetic determinants and barriers to RDV resistance. In this study, SARS-CoV-2 was subjected to 13 passages in cell culture with increasing concentrations of GS-441524, the parent nucleoside of RDV. At passage 13 the RDV resistance of the lineages ranged from 2.7-to 10.4-fold increase in EC50. Sequence analysis of the three lineage populations identified non-synonymous mutations in the nonstructural protein 12 RNA-dependent RNA polymerase (nsp12-RdRp): V166A, N198S, S759A, V792I and C799F/R. Two of the three lineages encoded the S759A substitution at the RdRp Ser759-Asp-Asp active motif. In one lineage, the V792I substitution emerged first then combined with S759A. Introduction of the S759A and V792I substitutions at homologous nsp12 positions in viable isogenic clones of the betacoronavirus murine hepatitis virus (MHV) demonstrated their transferability across CoVs, up to 38-fold RDV resistance in combination, and a significant replication defect associated with their introduction. Biochemical analysis of SARS-CoV-2 RdRp encoding S759A demonstrated a [~]10- fold decreased preference for RDV-triphosphate (RDV-TP) as a substrate, while nsp12-V792I diminished the UTP concentration needed to overcome the template-dependent inhibition associated with RDV. The in vitro selected substitutions here identified were rare or not detected in the >6 million publicly available nsp12-RdRp consensus sequences in the absence of RDV selection. The results define genetic and biochemical pathways to RDV resistance and emphasize the need for additional studies to define the potential for emergence of these or other RDV resistance mutations in various clinical settings.\n\nOne Sentence SummarySARS-CoV-2 develops in vitro resistance to remdesivir by distinct and complementary mutations and mechanisms in the viral polymerase", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Laura J. Stevens", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Andrea J. Pruijssers", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Hery W. Lee", - "author_inst": "University of Alberta" - }, - { - "author_name": "Calvin J. Gordon", - "author_inst": "University of Alberta" - }, - { - "author_name": "Egor P. Tchesnokov", - "author_inst": "University of Alberta" - }, - { - "author_name": "Jennifer Gribble", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Amelia S. George", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Tia M. Hughes", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Xiaotao Lu", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Jiani Li", - "author_inst": "Gilead Sciences, Inc." - }, - { - "author_name": "Jason K. Perry", - "author_inst": "Gilead Sciences, Inc." - }, - { - "author_name": "Danielle P. Porter", - "author_inst": "Gilead Sciences, Inc." - }, - { - "author_name": "Tomas Cihlar", - "author_inst": "Gilead Sciences, Inc." - }, - { - "author_name": "Timothy P. Sheahan", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Ralph S. Baric", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Matthias Gotte", - "author_inst": "University of Alberta" - }, - { - "author_name": "Mark R. Denison", - "author_inst": "Vanderbilt University Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.01.26.22269932", "rel_title": "Immunogenicity of COVID-19 mRNA Vaccines in Patients with Acute Myeloid Leukemia and Myelodysplastic Syndrome", @@ -393067,6 +395601,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2022.01.26.22269874", + "rel_title": "General practitioner wellbeing during the COVID-19 pandemic: a qualitative interview study", + "rel_date": "2022-01-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269874", + "rel_abs": "BackgroundWorkload pressures and poor job satisfaction have been reported by UK general practitioners (GPs) for some time. The COVID-19 pandemic presented new challenges, with growing international evidence of its negative impact on GPs mental health and wellbeing. While there has been wide commentary on this topic, UK research evidence is lacking. Developing greater understanding of these lived experiences and subgroup differences is important as doctor wellbeing may affect the sustainability of health care systems and quality of patient care.\n\nObjectivesTo explore the lived experience of UK GPs during COVID-19, and the pandemics impact on their psychological wellbeing.\n\nDesign and SettingIn-depth qualitative interviews, conducted remotely by telephone or video call, with NHS GPs.\n\nParticipantsGPs were sampled purposively across three career stages (early career, established and late career or retired GPs) with variation in other key demographics. A comprehensive recruitment strategy used multiple channels. Data were analysed thematically using Framework Analysis.\n\nResultsWe interviewed 40 GPs; most described generally negative sentiment and many displayed signs of psychological distress and burnout. Causes of stress and anxiety related to personal risk, workload, practice changes, public perceptions and leadership, teamworking and wider collaboration and personal challenges. GPs described facilitators of their wellbeing, including sources of support and plans to reduce clinical hours or change career path.\n\nConclusionsA range of factors detrimentally affected the wellbeing of GPs during the pandemic and we highlight the potential impact of this on workforce retention and quality of care. As the pandemic progresses and general practice faces continued challenges, urgent policy measures are now needed.\n\nStrengths and limitations of this studyO_LIWhile there is growing international evidence base demonstrating the impact of the COVID-19 pandemic on GPs wellbeing and much UK media coverage, this qualitative interview study provides much-needed research evidence of UK GPs lived experiences and wellbeing during COVID-19.\nC_LIO_LI40 GPs were sampled purposively to include GPs with different demographic and practice characteristics.\nC_LIO_LIWhile there are no easy solutions to the problems highlighted, this research provides increased contextualised understanding of how these experiences may impact future workforce retention and the sustainability of health systems longer-term.\nC_LIO_LISub-group differences by gender and age are reported; highlighting a potential need for further research and support targeted at specific groups.\nC_LIO_LIFindings are necessarily limited to the time of data collection (Spring/Summer 2021); further tensions in general practice have since arisen, particularly regarding negative and misleading media portrayal.\nC_LI", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Laura A Jefferson", + "author_inst": "University of York" + }, + { + "author_name": "Claire Heathcote", + "author_inst": "University of York" + }, + { + "author_name": "Karen Bloor", + "author_inst": "University of York" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2022.01.26.22269856", "rel_title": "Antibody and T cell responses to SARS-CoV-2 mRNA vaccines during maintenance therapy for immune-mediated inflammatory diseases", @@ -393348,109 +395909,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.27.22269904", - "rel_title": "Screening for SARS-CoV-2 in close contacts of individuals with confirmed infection: performance and operational considerations", - "rel_date": "2022-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269904", - "rel_abs": "BackgroundPoint-of-care and decentralized testing for SARS-CoV-2 is critical to inform public health responses. Performance evaluations in priority use cases such as contact tracing can highlight trade-offs in test selection and testing strategies.\n\nMethodsA prospective diagnostic accuracy study was conducted among close contacts of COVID-19 cases in Brazil. Two anterior nares swabs (ANS), a nasopharyngeal swab (NPS), and saliva were collected at all visits. Vaccination history and symptoms were assessed. Household contacts were followed longitudinally. Three rapid antigen tests and one molecular method were evaluated for usability and performance against reference RT-PCR on NPS.\n\nResultsFifty index cases and 214 contacts (64 household) were enrolled. Sixty-five contacts were RT-PCR positive during at least one visit. Vaccination did not influence viral load. Gamma variants were most prevalent; Delta emerged increasingly during implementation. Overall sensitivity of evaluated tests ranged from 33%-76%. Performance was higher among symptomatic cases and cases with Ct<34 and lower among oligo/asymptomatic cases. Assuming a 24-hour time-to-result for RT-PCR, the cumulative sensitivity of an ANS rapid antigen test was >70% and almost 90% after four days.\n\nConclusionsThe near immediate time-to-result for antigen tests significantly offsets lower analytical sensitivity in settings where RT-PCR results are delayed or unavailable.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Stephanie Zobrist", - "author_inst": "PATH" - }, - { - "author_name": "Michelle Oliveira-Silva", - "author_inst": "Centro de Pesquisa em Medicina Tropical (CEPEM)" - }, - { - "author_name": "Alexia Martines Vieira", - "author_inst": "Centro de Pesquisa em Medicina Tropical (CEPEM)" - }, - { - "author_name": "Pooja Bansil", - "author_inst": "PATH" - }, - { - "author_name": "Emily Gerth-Guyette", - "author_inst": "PATH" - }, - { - "author_name": "Brandon T Leader", - "author_inst": "PATH" - }, - { - "author_name": "Allison Golden", - "author_inst": "PATH" - }, - { - "author_name": "Hannah Slater", - "author_inst": "PATH" - }, - { - "author_name": "Catherine Duran de Lucena Cruz", - "author_inst": "Centro de Pesquisa em Medicina Tropical (CEPEM)" - }, - { - "author_name": "Eduardo Garbin", - "author_inst": "Centro de Pesquisa em Medicina Tropical (CEPEM)" - }, - { - "author_name": "Mariana Sagalovsky", - "author_inst": "PATH" - }, - { - "author_name": "Sampa Pal", - "author_inst": "PATH" - }, - { - "author_name": "Vin Gupta", - "author_inst": "Amazon.com" - }, - { - "author_name": "Leo Wolansky", - "author_inst": "The Rockefeller Foundation" - }, - { - "author_name": "Deusilene Souza Vieira Dall Acqua", - "author_inst": "Funda\u00e7\u00e3o Oswaldo Cruz (FIOCRUZ)" - }, - { - "author_name": "Felipe Gomes Naveca", - "author_inst": "Instituto Le\u00f4nidas e Maria Deane (ILMD), Funda\u00e7\u00e3o Oswaldo Cruz (FIOCRUZ)" - }, - { - "author_name": "Valdinete Alves do Nascimento", - "author_inst": "Instituto Le\u00f4nidas e Maria Deane (ILMD), Funda\u00e7\u00e3o Oswaldo Cruz (FIOCRUZ)" - }, - { - "author_name": "Juan Miguel Villalobos Salcedo", - "author_inst": "Funda\u00e7\u00e3o Oswaldo Cruz (FIOCRUZ)" - }, - { - "author_name": "Paul K Drain", - "author_inst": "University of Washington" - }, - { - "author_name": "Alexandre Dias Tavares Costa", - "author_inst": "Instituto Carlos Chagas - Fiocruz" - }, - { - "author_name": "Gonzalo J Domingo", - "author_inst": "PATH" - }, - { - "author_name": "Dhelio Pereira", - "author_inst": "Centro de Pesquisa em Medicina Tropical (CEPEM)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.27.22269976", "rel_title": "Evaluation of the CD4+ T cell response to SARS-CoV-2 infection and cross reactivity to beta variant in children of all ages", @@ -395229,6 +397687,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.18.22269420", + "rel_title": "Immune response to third SARS-CoV-2 vaccination in seronegative kidney transplant recipients: possible improvement by mycophenolate mofetil reduction", + "rel_date": "2022-01-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.18.22269420", + "rel_abs": "BackgroundModification of vaccination strategies is needed to improve the immune response to SARS-CoV-2 vaccination in kidney transplant recipients (KTRs).\n\nMethodsThis multicenter observational study aimed to determine antibody kinetics among 60 seropositive KTRs and analyzed the effects of the third vaccination against SARS-CoV-2 in 174 previously seronegative KTRs. We investigated whether mycophenolate mofetil (MMF) dose reduction by 25-50% prior the third vaccination influences vaccination success.\n\nResults18 of 60 (30%) seropositive KTRs became seronegative in the serological assay within six months. Loss of antibodies was predicted by low initial antibody levels ([≤]206.8 BAU/ml), older age, and impaired graft function. A third vaccination in previously seronegative KTRs induced seroconversion in 56 of 174 (32.1%) KTRs with median antibody levels 119 (76-353) BAU/ml and median neutralizing capacity titer of 1:10 (0- 1:40). Multivariate logistic regression revealed that initial antibody levels (OR 1.39, 95% CI 1.09-1.76), graft function (OR 0.05, 95% CI 0.01-0.39), time after transplantation (OR 1.04, 95% CI 1.02-1.07) and MMF trough levels (OR 0.43, 95% CI 0.21-0.88) correlated with seroconversion, p<0.05. After controlling for these confounders, the effect of MMF dose reduction was calculated using propensity score matching. KTRs in the MMF reduction group had significantly lower MMF serum concentrations prior to the third vaccination and were more likely to develop antibody levels [≥]35.2 BAU/ml than their matched KTRs (p=0.02).\n\nConclusionsTemporary reduction in MMF dose might be a promising approach to improve the immune response in KTRs.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Marta Kantauskaite", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Lias Mueller", + "author_inst": "University Hospital Duesseldorf" + }, + { + "author_name": "Jonas Hillebrandt", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Joshua Leon Lamberti", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Svenja Fischer", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Thilo Kolb", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Katrin Ivens", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Michael Koch", + "author_inst": "Nephrocare Mettmann" + }, + { + "author_name": "Marcel Andree", + "author_inst": "University Hospital Duesseldorf" + }, + { + "author_name": "Nadine Luebke", + "author_inst": "University Hospital Duesseldorf" + }, + { + "author_name": "Michael Schmitz", + "author_inst": "Klinikum Solingen" + }, + { + "author_name": "Tom Luedde", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Hans Martin Orth", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Torsten Feldt", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Heiner Schaal", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Ortwin Adams", + "author_inst": "University Hospital Duesseldorf" + }, + { + "author_name": "Claudia Schmidt", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Margarethe Kittel", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Eva Koenigshausen", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Lars Christian Rump", + "author_inst": "Heinrich-Heine University-Duesseldorf" + }, + { + "author_name": "Joerg Timm", + "author_inst": "University hospital Duesseldorf" + }, + { + "author_name": "Johannes Stegbauer", + "author_inst": "Heinrich-Heine-University Duesseldorf" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2022.01.20.21267627", "rel_title": "\"It affects every aspect of your life\": A qualitative study of the impact of delaying surgery during COVID-19", @@ -395438,41 +397999,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.26.22269877", - "rel_title": "The impacts of increased global vaccine sharing on the COVID-19 pandemic; a retrospective modelling study", - "rel_date": "2022-01-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269877", - "rel_abs": "BackgroundThe SARS-CoV-2 pandemic has generated considerable morbidity and mortality world-wide. While the protection offered by vaccines (and booster doses) offers a method of mitigating the worst effects, by the end of 2021 the distribution of vaccine was highly heterogeneous with some countries achieving over 90% coverage in adults by the end of 2021, while others have less than 2%. In part, this is due to the availability of sufficient vaccine, although vaccine hesitancy also plays a role.\n\nMethodsWe use an age-structured model of SARS-CoV-2 dynamics, matched to national data from 152 countries, to investigate the global impact of different vaccine sharing protocols during 2021. We assume a direct relationship between the emergence of variants with increased transmissibility and the cumulative amount of global infection, such that lower global prevalence leads to a lower reproductive number within each country. We compare five vaccine sharing scenarios, from the current situation, through sharing once a particular within-country threshold is reached (e.g. all over 40s have received 2 doses), to full sharing where all countries achieve equal age-dependent vaccine deployment.\n\nFindingsCompared to the observed distribution of vaccine uptake, we estimate full vaccine sharing would have generated a 1.5% (PI -0.1 - 4.5%) reduction in infections and a 11.3% (PI 0.6 - 23.2%) reduction in mortality globally by January 2022. The greatest benefit of vaccine sharing would have been experienced by low and middle income countries, who see an average 5.2% (PI 2.5% - 10.4%) infection reduction and 26.8% (PI 24.1% - 31.3%) mortality reduction. Many high income countries, that have had high vaccine uptake (most notably Canada, Chile, UK and USA), suffer increased infections and mortality under most of the sharing protocols investigated, assuming no other counter measures had been taken. However, if reductions in vaccine supply in these countries had been offset by prolonged use of non-pharmaceutical intervention measures, we predict far greater reductions in global infection and mortality of 64.5% (PI 62.6% - 65.4%) and 62.8% (PI 44.0% - 76.3%), respectively.\n\nInterpretationBy itself, our results suggest that although more equitable vaccine distribution would have had limited impact on overall infection numbers, vaccine sharing would have substantially reduced global mortality by providing earlier protection of the most vulnerable. If increased vaccine sharing from high income nations had been combined with slower easing of non pharmaceutical interventions to compensate for this, a large reduction in both infection and mortality globally would be expected, confounded by a lower risk of new variants arising.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sam Moore", - "author_inst": "University of Warwick" - }, - { - "author_name": "Edward M Hill", - "author_inst": "University of Warwick" - }, - { - "author_name": "Louise J Dyson", - "author_inst": "University of Warwick" - }, - { - "author_name": "Michael J Tildesley", - "author_inst": "University of Warwick" - }, - { - "author_name": "Matt J Keeling", - "author_inst": "University of Warwick" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.26.22269885", "rel_title": "SARS-CoV-2 anti-spike antibody levels following second dose of ChAdOx1 nCov-19 or BNT162b2 in residents of long-term care facilities in England (VIVALDI)", @@ -397471,6 +399997,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.23.22269669", + "rel_title": "Effects of 12 weeks of Multi-nutrient supplementation on the Immune and Musculoskeletal systems of Older Adults in Aged-Care (The Pomerium Study): Protocol for a Randomised Controlled Trial", + "rel_date": "2022-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.23.22269669", + "rel_abs": "IntroductionImmunosenescence leads to increased morbidity and mortality associated with viral infections and weaker vaccine responses. This has been well documented for seasonal influenza and the current pandemic with Sars-Cov2, which disproportionately impact older adults, particularly those in residential aged care facilities. Inadequate nutrient intake associated with impaired immunity, respiratory and muscle function are likely to augment the effects of immunosenescence. In this study, we test whether the effects of inadequate nutrition can be reversed by multi-nutrient supplementation, consequently enhancing vaccine responses, reducing the risk of viral infections, and improving respiratory and muscle function.\n\nMethods and analysisThe Pomerium Study is a 12-week, single-blinded, randomised, placebo-controlled trial testing the effects of two daily servings of an oral multi-nutrient supplement (330 kcal, 20g protein, 1.2g CaHMB, 449mg calcium, 520IU vitamin D3, and 25 vitamins and minerals) on the immune system and muscle and respiratory function of older adults in aged-care in Melbourne, Australia. 160 older adults ([≥]75 years old) will be recruited from aged-care facilities and randomised to treatment (multi-nutrient supplement) or control (usual care). Primary outcome is the change in T-cell subsets CD8+ and CD28null counts at 4 and 12 weeks post-intervention. Secondary outcomes measured at baseline and after 12 weeks post-intervention are multiple markers of immunosenescence, body composition (bioimpedance), handgrip strength (dynamometer), physical function (short physical performance battery), respiratory function (spirometry), and quality of life (EQ-5D-3L). Incidence and complications of COVID-19 and/or viral infections (i.e., hospitalisation, complications, or death) will be recorded throughout the trial.\n\nDiscussionIf the Pomerium Study demonstrates efficacy and safety of a multi-nutrient supplement on immune, muscle and respiratory function, it may be suitable as a strategy to reduce the adverse outcomes from seasonal influenza and viral infections such as COVID-19 in older adults in aged-care.\n\nFunding, Ethics, Registration and DisseminationThe study is funded by the Australian Medical Research Future Fund. It is approved by Melbourne Health Human Research Ethics Committee (Ref No. HREC/73985/MH-2021, ERM Ref No. RMH73985, Melbourne Health Site Ref No. 2021.115), and registered at ANZCTR (12621000420842). Results will be published in peer-reviewed journals and made available to aged-care stakeholders, including providers, residents, and government bodies.\n\nArticle Summary Strengths and LimitationsO_LIThis is the first study performing a comprehensive immune, respiratory and functional assessment in aged care residents after receiving a multi-nutrient solution that is commercially available.\nC_LIO_LIOur design and tested intervention assure that the results of the study will be rapidly translated into practice.\nC_LIO_LIThe main limitation is that any biological effect observed cannot be attributed to one component of the multi-nutrient supplement.\nC_LIO_LIAnother limitation is that the potential effect of group differences in energy intake on outcomes can only be monitored by assessing regular dietary intake and weight changes during the study period.\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Ahmed Al Saedi", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Ben Kirk", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Sandra Iuliano", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Jesse Zanker", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Sara Vogrin", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Lata Jayaram", + "author_inst": "Western Health" + }, + { + "author_name": "Shane Thomas", + "author_inst": "Australian Institute for Musculoskeletal Science (AIMSS)" + }, + { + "author_name": "Christine Golding", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Diana Navarro-Perez", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Petra Marusic", + "author_inst": "Australian Institute for Musculoskeletal Science (AIMSS)" + }, + { + "author_name": "Sean Leng", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Ralph Nanan", + "author_inst": "University of Sydney" + }, + { + "author_name": "Gustavo Duque", + "author_inst": "The University of Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "geriatric medicine" + }, { "rel_doi": "10.1101/2022.01.23.22269626", "rel_title": "Death review caused by Covid 19 in Bangladesh", @@ -397648,25 +400241,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.22.22269686", - "rel_title": "Border closure and travel restrictions to control the spread of COVID-19: an update to a Cochrane review", - "rel_date": "2022-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.22.22269686", - "rel_abs": "BackgroundCOVID-19 has proven to be more difficult to manage for many reasons including its high infectivity rate. One of the potential ways to limit its spread is by limiting free travel across borders, including via air travel. The objective of this systematic review is to identify, critically-appraise and summarize evidence on border closures and travel restrictions.\n\nMethodsThis review is based on the Cochrane review: \"International travel-related control measures to contain the COVID-19 pandemic\" and followed the same methodology. In brief, we searched for clinical and modelling studies in general health and COVID-19-specific bibliographic databases. The primary outcome categories were (i) cases avoided, (ii) cases detected, and (iii) a shift in epidemic development. Secondary outcomes were other infectious disease transmission outcomes, healthcare utilisation, resource requirements and adverse effects if identified in studies assessing at least one primary outcome.\n\nResultsWe included 43, mostly modelling, studies that met our inclusion criteria. Fourteen new studies were identified in the updated search, as well as updated companions (e.g., peer-reviewed publications that were previously only available as pre-prints). Most studies were of moderate to high quality. The added studies did not change the main conclusions of the Cochrane review nor the quality of the evidence (very low to low certainty). However, it did add to the evidence base for most outcomes.\n\nConclusionsWeak evidence supports the use of border closures to limit the spread of COVID-19 via air travel. Real-world studies are required to support these conclusions.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ahmed M Abou-Setta", - "author_inst": "University of Manitoba" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.24.22269530", "rel_title": "A qualitative study exploring the impact of the COVID-19 pandemic on People Who Inject Drugs (PWID) and drug service provision in the UK: PWID and service provider perspectives", @@ -399021,6 +401595,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.25.22269735", + "rel_title": "Acquired neutralizing breadth against SARS-CoV-2 variants including Omicron after three doses of mRNA COVID-19 vaccination and the vaccine efficacy", + "rel_date": "2022-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.25.22269735", + "rel_abs": "To investigate the induction of neutralizing antibodies against Omicron after two and three vaccine doses in recipients of different ages. Physicians at Kobe University Hospital who had received the second dose of the BNT162b2 mRNA vaccine. At 2 months after the second vaccinations, the positive rate of neutralizing antibody against Omicron was 28%, and the titer was significantly lower than those against other variants, 11.8-fold and 3.6-fold lower than those against D614G and Delta, respectively. Unlike Delta, that positive rates of neutralizing antibody against Omicron were low in all age groups, and there was no significant difference in titers among age groups. Seven months after the 2nd dose, the positive rate of neutralizing antibody against Omicron decreased to 6%, but after the booster,3rd vaccination, it increased to 100%, and the titer was much higher than those at 2 and 7 months post-vaccination, 32-fold and 39-fold respectively. The booster vaccination effect was also observed in the younger at 41-fold, middle-aged at 43-fold, and older at 27-fold groups compared to the 7-month titers. Surprisingly, higher-than-predicted titers of the neutralizing antibodies against Omicron were induced after the booster vaccination regardless of recipient age, while this effect was not observed after two doses, indicating the induction of antibodies against common epitopes by the booster vaccination. Three doses can be confidently recommended to suppress the pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Koichi Furukawa", + "author_inst": "Kobe Unibersity" + }, + { + "author_name": "Lidya Handayani Tjan", + "author_inst": "Kobe University" + }, + { + "author_name": "Yukiya Kurahashi", + "author_inst": "Kobe University" + }, + { + "author_name": "Silvia Sutandhio", + "author_inst": "Kobe University" + }, + { + "author_name": "Mitsuhiro Nishimura", + "author_inst": "Kobe University" + }, + { + "author_name": "Jun Arii", + "author_inst": "Kobe University" + }, + { + "author_name": "Yasuko Mori", + "author_inst": "Kobe University Graduate School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.24.22269781", "rel_title": "Effects of vaccination against COVID-19 on the emotional health of Peruvian older adults", @@ -399214,89 +401831,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.24.22269785", - "rel_title": "Clinical evaluation of the Diagnostic Analyzer for Selective Hybridization (DASH): a point-of-care PCR test for rapid detection of SARS-CoV-2 infection", - "rel_date": "2022-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.24.22269785", - "rel_abs": "BackgroundRapid and accurate testing for SARS-CoV-2 is an essential tool in the medical and public health response to the COVID-19 pandemic. An ideal test for COVID-19 would combine the sensitivity of laboratory-based PCR combined with the speed and ease of use of point-of-care (POC) or home-based rapid antigen testing.\n\nMethodsTo evaluate the performance of the Diagnostic Analyzer for Selective Hybridization (DASH) SARS-CoV-2 POC PCR (sample insertion to result time of 16 minutes), we conducted a cross-sectional study of adults with and without symptoms of COVID-19 at four clinical sites. We collected two bilateral anterior nasal swabs from each participant and information on COVID-19 symptoms, vaccination, and exposure. One swab was tested with the DASH SARS-CoV-2 POC PCR and the second in a central laboratory using Cepheid Xpert Xpress SARS-CoV-2 PCR. We assessed test concordance and calculated sensitivity, specificity, negative and positive predictive values using Xpert as the \"gold standard.\"\n\nResultsWe enrolled 315 and analyzed 313 participants with median age 42 years; 65% were female, 62% symptomatic, 75% had received [≥]2 doses of mRNA COVID-19 vaccine, and 16% currently COVID-19 positive. There were concordant results for 307 tests indicating an overall agreement for DASH of 0.98 [95% CI 0.96, 0.99] compared to Xpert. DASH performed at 0.96 [95% CI 0.86, 1.00] sensitivity and 0.98 [95% CI 0.96, 1.00] specificity, with a positive predictive value of 0.85 [95% CI 0.73, 0.96] and negative predictive value of 0.996 [95% CI 0.99, 1.00]. The six discordant tests between DASH and Xpert all had high Ct values (>30) on the respective positive assay. DASH and Xpert Ct values were highly correlated (R=0.89 [95% CI 0.81, 0.94]).\n\nConclusionsDASH POC SARS-CoV-2 PCR was accurate, easy to use, and provided fast results in real-life clinical settings with an overall performance similar to an EUA-approved laboratory-based PCR. Its compact design and ease of use are optimal for a variety of healthcare, and potentially community settings, including areas with lack of access to central laboratory-based PCR testing.\n\nSummaryDASH is an accurate, easy to use, and fast point-of-care test with applications for diagnosis and screening of SARS-CoV-2 infection.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Chad J Achenbach", - "author_inst": "Northwestern University" - }, - { - "author_name": "Matthew Caputo", - "author_inst": "Northwestern University" - }, - { - "author_name": "Claudia Hawkins", - "author_inst": "Northwestern University" - }, - { - "author_name": "Lauren C Balmert", - "author_inst": "Northwestern University" - }, - { - "author_name": "Chao Qi", - "author_inst": "Northwestern University" - }, - { - "author_name": "Joseph Odorisio", - "author_inst": "Northwestern University" - }, - { - "author_name": "Etienne Dembele", - "author_inst": "Northwestern University" - }, - { - "author_name": "Alema Jackson", - "author_inst": "Access Community Health Network" - }, - { - "author_name": "Hiba Abbas", - "author_inst": "Access Community Health Network" - }, - { - "author_name": "Jennifer K Frediani", - "author_inst": "Emory University" - }, - { - "author_name": "Joshua M Levy", - "author_inst": "Emory University" - }, - { - "author_name": "Paulina Alejandra Rebolledo", - "author_inst": "Rollis School of Public Health, Emory University" - }, - { - "author_name": "Russell R Kempker", - "author_inst": "Emory University" - }, - { - "author_name": "Annette M Esper", - "author_inst": "Emory University" - }, - { - "author_name": "Wilbur A Lam", - "author_inst": "Emory University" - }, - { - "author_name": "Greg S Martin", - "author_inst": "Emory University" - }, - { - "author_name": "Robert L Murphy", - "author_inst": "Northwestern University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.24.22269768", "rel_title": "Gasdermin-D activation by SARS-CoV-2 trigger NET and mediate COVID-19 immunopathology", @@ -400663,6 +403197,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.23.22269716", + "rel_title": "Evidence on the role of journal editors in the COVID19 infodemic: metascientific study analyzing COVID19 publication rates and patterns", + "rel_date": "2022-01-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.23.22269716", + "rel_abs": "ObjectiveInfodemic, a neologism characterizing an excess of fast-tracked low quality publications, has been employed to depict the scientific research response to the COVID19 crisis. The concept relies on the presumed exponential growth of research output. This study aimed to test the COVID19 infodemic claim by assessing publication rates and patterns of COVID19-related research and a control, a year prior.\n\nDesignA Reproduction Number of Publications (Rp) was conceived. It was conceptualized as a division of a week incidence of publications by the average of publications of the previous week. The publication growth rates of preprint and MEDLINE-indexed peer-reviewed literature on COVID19 were compared using the correspondent Influenza output, a year prior, as control. Rp for COVID19 and Influenza papers and preprints were generated and compared and then analyzed in light of the respective growth patterns of their papers and preprints.\n\nMain outcomesOutput growth rates and Reproduction Number of Publications (Rp).\n\nResultsCOVID19 peer-reviewed papers showed a fourteen fold increase compared to Influenza papers. COVID19 papers and preprints displayed an exponential growth curve until the 20th week. COVID19 papers displayed Rp=3.17{+/-}0.72, while the control group presented Rp=0.97{+/-}0.12. Their preprints exhibited Rp=2.18{+/-}0.54 and Rp=0.97{+/-}0.27 respectively, with no evidence of exponential growth in the control group, as its Rp remained approximately one.\n\nConclusionsCOVID19 publications displayed an epidemic pattern. As the growth patterns of COVID19 peer-reviewed articles and preprints were similar, and the majority of the COVID19 output came from indexed journals, not only authors but also editors appear to had played a significant part on the infodemic.\n\nReview protocolhttps://osf.io/q3zkw/?view_only=ff540dc4630b4c6e9a2639d732047324\n\nEthical aspectsNo ethical clarence was required as all analyzed data were publicly available.\n\nO_TEXTBOXSUMMARY BOX\n\n1. What is already known about this subject?\n\nMuch has been commented on 2020s excess of publications on COVID19. Independent studies found evidence of increased volume and speed of publication, decreased methodological quality, and qualitative variations in peer review of COVID19 papers, when compared to the scholarly output from before the pandemic. This phenomenon has been branded an infodemic, a neologism implying an epidemic of low-quality information on COVID19 when high quality scientific reports to inform health policies would have been needed the most.\n\n2. What are the new findings?\n\nNo study pushed the infodemic metaphor forward to analyze not only volume of publication but also publication rates comparing them to a control group as to clearly pinpoint an exponential phase of contagion in the infodemic (as it would take place in a real epidemic) through a mathematical analysis of the growth patterns and rates of those publications. In this paper, we were able to demonstrate that there has been an infodemic indeed and that the editor population was as susceptible to the infodemic bug as the author population because the exponential phase was shaped not only by authors but mainly by editors from PubMed-indexed journals.\n\n3.How might it impact clinical practice in the foreseeable future?\n\nThese results and conclusions are consequential to subsequent studies on rigor and depth of post publication peer review and on editorial practices within the life and health sciences research community.\n\nC_TEXTBOX", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Gabriel Grisi", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Joao de Deus Barreto Segundo", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Camila Veronica Freire", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Denise Matias", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Mariana Cruz", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Larrie Rabelo Laporte", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Daniel Medina", + "author_inst": "Universidade Federal do Reconcavo da Bahia" + }, + { + "author_name": "Thiago Masashi Taniguchi", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Leticia Requiao", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Bruno Goes", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Luis Claudio Lemos Correia", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.01.24.22269734", "rel_title": "SARS-CoV-2 viremia precedes an IL6 response in severe COVID-19 patients: results of a longitudinal prospective cohort", @@ -400908,73 +403501,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.20.22269539", - "rel_title": "Comparison between mid-nasal swabs and buccal swabs for SARS-CoV-2 detection in mild COVID-19 patients", - "rel_date": "2022-01-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.20.22269539", - "rel_abs": "BackgroundThe use of rapid antigen diagnostics tests (Ag-RDT) has gained widespread acceptance as an alternative method for diagnosis of COVID-19 outside of health care settings. Various authors have reported that saliva is a reliable specimen, alternative to nasopharyngeal and mid-nasal swabs, to detect SARS-CoV-2 infections by RT-PCR. We assessed the performance of buccal swabs containing saliva for SARS-CoV-2 detection by Ag-RDT, using mid-nasal specimens as a reference in the northern area of Barcelona (Catalonia, Spain)\n\nMethodsIn the context of routine clinical diagnosis of mild COVID-19 patients, we enrolled 300 adults in a study to directly compare mid-nasal swabs and saliva specimens for SARS-CoV-2 detection by Ag-RDT.. When mid-nasal and buccal Ag-RDTs showed discordant results, a third mid-nasal swab was collected and analysed by RT-PCR.\n\nResultsPaired samples were successfully obtained in 300 suspected cases of SARS-CoV-2 infection. Of the 300 paired samples, Ag-RDT with the mid-nasal swab detected 139 (46.3%) positive COVID-19 cases. In comparison, buccal swabs showed a sensitivity and specificity of 31.7% (44/139) and 98.8% (159/161), respectively. 65 discordant results with positive mid-nasal swabs and negative buccal swabs were tested by RT-qPCR. All samples tested by Rt-PCR resulted positive, with a mean cycle threshold (Ct) of 28.3 (SD 7.3).\n\nConclusionOur findings show that mid-nasal swabs have better performance than buccal swabs for detecting SARS-CoV-2 with Ag-RDT tests. Of note, the sensitivity of buccal samples was affected in samples with high viral loads (Ct<33), suggesting that buccal swabs might not be sensitive enough to detect individuals at risk of transmission. Taken together, the existing literature and the results provided in our analysis we advise against the use of buccal specimens for SARS-CoV-2 diagnostics with Ag-RDT.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Ignacio Blanco MD, PhD", - "author_inst": "Gerencia Territorial Metropolitana Nord, Institut Catala de la Salut, Barcelona, Spain." - }, - { - "author_name": "Concepcion Violan MD, PhD", - "author_inst": "Unitat de Suport a la Recerca Metropolitana Nord, Fundacio Institut Universitari per a la recerca a lAtencio Primaria Jordi Gol i Gurina (IDIAP J Gol)." - }, - { - "author_name": "Clara Suner PhD", - "author_inst": "Fight Aids and Infectious Disease Foundation" - }, - { - "author_name": "Julio Garcia-Prieto MD", - "author_inst": "Direccio dAtencio Primaria Metropolitana Nord, Institut Catala de la Salut." - }, - { - "author_name": "Maria Jose Argerich MSc", - "author_inst": "Direccio dAtencio Primaria Metropolitana Nord, Institut Catala de la Salut." - }, - { - "author_name": "Meritxell Rodriguez-Illana BSc", - "author_inst": "Direccio dAtencio Primaria Metropolitana Nord, Institut Catala de la Salut." - }, - { - "author_name": "Nemesio Moreno MD", - "author_inst": "Direccio dAtencio Primaria Metropolitana Nord, Institut Catala de la Salut." - }, - { - "author_name": "Pere-Joan Cardona MD, PhD", - "author_inst": "Servei de Microbiologia, LCMN, Hospital Universitari Germans Trias i Pujol , Badalona, Catalonia, Spain" - }, - { - "author_name": "Ana Blanco PhD", - "author_inst": "Servei de Microbiologia, LCMN, Hospital Universitari Germans Trias i Pujol , Badalona, Catalonia, Spain" - }, - { - "author_name": "Pere Toran-Montserrat MD", - "author_inst": "Unitat de Suport a la Recerca Metropolitana Nord, Fundacio Institut Universitari per a la recerca a lAtencio Primaria Jordi Gol i Gurina (IDIAP J Gol)." - }, - { - "author_name": "Bonaventura Clotet MD, PhD", - "author_inst": "Servicio de Enfermedades Infecciosas del Hospital Germans Trias i Pujol" - }, - { - "author_name": "Jose Maria Bonet MD", - "author_inst": "Direccio dAtencio Primaria Metropolitana Nord, Institut Catala de la Salut." - }, - { - "author_name": "Nuria Prat MD", - "author_inst": "Direccio dAtencio Primaria Metropolitana Nord, Institut Catala de la Salut." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.21.22269605", "rel_title": "Severe outcomes in residents of Long Term Care Facilities following infection with SARS-CoV-2 Omicron variant (VIVALDI study)", @@ -402777,6 +405303,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.01.17.475291", + "rel_title": "Comprehensive Evaluation of ACE2-Fc Combination with Neutralization Antibody on Broad Protection against SARS-CoV-2 and Its Variants", + "rel_date": "2022-01-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.17.475291", + "rel_abs": "Emerging SARS-CoV-2 variants are threatening the efficacy of antibody therapies. Combination treatments including ACE2-Fc have been developed to overcome the evasion of neutralizing antibodies (NAbs) in individual cases. Here we conducted a comprehensive evaluation of this strategy by combining ACE2-Fc with NAbs of diverse epitopes on the RBD. NAb+ACE2-Fc combinations efficiently neutralized HIV-based pseudovirus carrying the spike protein of the Delta or Omicron variants, achieving a balance between efficacy and breadth. In an antibody escape assay using replication-competent VSV-SARS-CoV-2-S, all the combinations had no escape after fifteen passages. By comparison, all the NAbs without combo with ACE2-Fc had escaped within six passages. Further, the VSV-S variants escaped from NAbs were neutralized by ACE2-Fc, revealing the mechanism of NAb+ACE2-Fc combinations survived after fifteen passages. We finally examined ACE2-Fc neutralization against pseudovirus variants that were resistant to the therapeutic antibodies currently in clinic. Our results suggest ACE2-Fc is a universal combination partner to combat SARS-CoV-2 variants including Delta and Omicron.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Haoneng Tang", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Yong Ke", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Hang Ma", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Lei Han", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China; Jecho Institu" + }, + { + "author_name": "Lei Wang", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Huifang Zong", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Yunsheng Yuan", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Zhenyu Wang", + "author_inst": "Jecho Biopharmaceuticals Co., Ltd. Tianjin 300467, China" + }, + { + "author_name": "Yang He", + "author_inst": "Jecho Biopharmaceuticals Co., Ltd. Tianjin 300467, China" + }, + { + "author_name": "Yunsong Chang", + "author_inst": "Jecho Biopharmaceuticals Co., Ltd. Tianjin 300467, China" + }, + { + "author_name": "Shusheng Wang", + "author_inst": "Jecho Laboratories, Inc. Frederick, MD 21704, USA" + }, + { + "author_name": "Junjun Liu", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Yali Yue", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Wenbo Xu", + "author_inst": "National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, China" + }, + { + "author_name": "Xiaoju Zhang", + "author_inst": "Zhengzhou University Peoples Hospital; Henan Provincial Peoples Hospital, Department of Respiratory and Critical Care Medicine, Zhengzhou 450003, Henan, China" + }, + { + "author_name": "Ziqi Wang", + "author_inst": "Zhengzhou University Peoples Hospital; Henan Provincial Peoples Hospital, Department of Respiratory and Critical Care Medicine, Zhengzhou 450003, Henan, China" + }, + { + "author_name": "Li Yang", + "author_inst": "Zhengzhou University Peoples Hospital; Henan Provincial Peoples Hospital, Department of Respiratory and Critical Care Medicine, Zhengzhou 450003, Henan, China" + }, + { + "author_name": "Hua Chen", + "author_inst": "Jecho Laboratories, Inc. Frederick, MD 21704, USA" + }, + { + "author_name": "Yanlin Bian", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Baohong Zhang", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Yunji Liao", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Haiyang Yin", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Yi Chen", + "author_inst": "Zhengzhou University Peoples Hospital; Henan Provincial Peoples Hospital, Clinical Research Service Center, Zhengzhou 450003, Henan, China" + }, + { + "author_name": "En Zhang", + "author_inst": "School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Municipal Veterinary Key Laboratory, Shanghai 200240, China" + }, + { + "author_name": "Xiaoxiao Zhang", + "author_inst": "School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Municipal Veterinary Key Laboratory, Shanghai 200240, China" + }, + { + "author_name": "Hua Jiang", + "author_inst": "Jecho Biopharmaceuticals Co., Ltd. Tianjin 300467, China; Jecho Laboratories, Inc. Frederick, MD 21704, USA" + }, + { + "author_name": "Yueqing Xie", + "author_inst": "Jecho Laboratories, Inc. Frederick, MD 21704, USA" + }, + { + "author_name": "John Gilly", + "author_inst": "Jecho Biopharmaceuticals Co., Ltd. Tianjin 300467, China; Jecho Laboratories, Inc. Frederick, MD 21704, USA" + }, + { + "author_name": "Mingyuan Wu", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Tao Sun", + "author_inst": "School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Municipal Veterinary Key Laboratory, Shanghai 200240, China" + }, + { + "author_name": "Jianwei Zhu", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China; Jecho Biophar" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2022.01.20.477105", "rel_title": "In Silico Analysis Of The Effects Of Omicron Spike Amino Acid Changes On The Interactions With Human ACE2 Receptor And Structurally Characterized Complexes With Human Antibodies", @@ -402934,85 +405599,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.01.20.477115", - "rel_title": "ESCPE-1 Mediates Retrograde Endosomal Sorting of the SARS-CoV-2 Host Factor Neuropilin-1", - "rel_date": "2022-01-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.20.477115", - "rel_abs": "Endosomal sorting maintains cellular homeostasis by recycling transmembrane proteins and associated proteins and lipids (termed cargoes) from the endosomal network to multiple subcellular destinations, including retrograde traffic to the trans-Golgi network (TGN). Viral and bacterial pathogens subvert retrograde trafficking machinery to facilitate infectivity. Here, we develop a proteomic screen to identify novel retrograde cargo proteins of the Endosomal SNX-BAR Sorting Complex Promoting Exit-1 (ESCPE-1). Using this methodology, we identify Neuropilin-1 (NRP1), a recently characterised host factor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, as a cargo directly bound and trafficked by ESCPE-1. ESCPE-1 mediates retrograde trafficking of engineered nanoparticles functionalised with the NRP1-interacting peptide of the SARS-CoV-2 Spike protein. ESCPE-1 sorting of NRP1 may therefore play a role in the intracellular membrane trafficking of NRP1-interacting viruses such as SARS-CoV-2.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Boris Simonetti", - "author_inst": "School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K." - }, - { - "author_name": "James L Daly", - "author_inst": "School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K." - }, - { - "author_name": "Lorena Simon-Gracia", - "author_inst": "Laboratory of Precision and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia." - }, - { - "author_name": "Katja Klein", - "author_inst": "School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K." - }, - { - "author_name": "Saroja Weeratunga", - "author_inst": "Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, 4072, Australia." - }, - { - "author_name": "Carlos Anton-Plagaro", - "author_inst": "School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K." - }, - { - "author_name": "Allan Tobi", - "author_inst": "Laboratory of Precision and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia." - }, - { - "author_name": "Lorna Hodgson", - "author_inst": "School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K." - }, - { - "author_name": "Philip Lewis", - "author_inst": "Proteomics Facility, School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K." - }, - { - "author_name": "Kate J Heesom", - "author_inst": "Proteomics Facility, School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K." - }, - { - "author_name": "Deborah K Shoemark", - "author_inst": "School of Biochemistry and BrisSynBio Centre, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K." - }, - { - "author_name": "Andrew D Davidson", - "author_inst": "School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K." - }, - { - "author_name": "Brett M Collins", - "author_inst": "Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, 4072, Australia." - }, - { - "author_name": "Tambet Teesalu", - "author_inst": "Laboratory of Precision and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia." - }, - { - "author_name": "Yohei Yamauchi", - "author_inst": "School of Cellular and Molecular Medicine, Faculty of Life Sciences, Biomedical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K." - }, - { - "author_name": "Peter J Cullen", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2022.01.20.476458", "rel_title": "First detection of SARS-CoV-2 infection in Canadian wildlife identified in free-ranging white-tailed deer (Odocoileus virginianus) from southern Quebec, Canada", @@ -404531,6 +407117,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2022.01.20.22269321", + "rel_title": "Extreme \u03b3' fibrinogen levels in COVID-19 patients", + "rel_date": "2022-01-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.20.22269321", + "rel_abs": "BackgroundCOVID-19 progression can be accompanied by a \"cytokine storm\" that leads to secondary sequelae such as thrombosis and acute respiratory distress syndrome. Several inflammatory cytokines have been associated with COVID-19 progression, but have far too much daily intra-individual variability to be useful in tracking the course of the disease. In contrast, we have shown that the inflammatory biomarker {gamma} fibrinogen ({gamma} Fbg) has a 6-fold lower coefficient of variability compared to other inflammatory markers such as hs-CRP. Objectives: The aims of the study were to measure {gamma} Fbg in serial blood samples from COVID-19 patients at a tertiary care medical center in order to investigate its association with clinical measures of disease progression.\n\nMethodsCOVID-19 patients at a tertiary care medical center were retrospectively enrolled between 3/16/2020 and 8/1/2020. {gamma} Fbg was measured using a commercial ELISA. Results: Our results showed that nine out of the seventeen patients with COVID-19 had extremely high levels of {gamma} Fbg. {gamma} Fbg levels were significantly associated with the need for ECMO and with mortality.\n\nConclusionsWe found that COVID-19 patients can develop extraordinarily high levels of {gamma} Fbg. The previous highest {gamma} Fbg level that we are aware of was 80.3 mg/dL found in a study of 10,601 participants in the ARIC study. These results have several important clinical implications. {gamma} Fbg contains a high affinity binding site for thrombin that binds to anion-binding exosite II on thrombin and protects it from inactivation by heparin. High levels of {gamma} Fbg therefore provide a reservoir of heparin-resistant clot-bound thrombin when the {gamma} Fbg is clotted. These findings have potential implications regarding prophylactic anticoagulation of COVID-19 patients and suggest that heparin prophylaxis may be less effective than using other anticoagulants, particularly direct thrombin inhibitors.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "David Henry Farrell", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Matthew Hudkins", + "author_inst": "OHSU" + }, + { + "author_name": "Heather Hamilton", + "author_inst": "OHSU" + }, + { + "author_name": "Samantha J Underwood", + "author_inst": "OHSU" + }, + { + "author_name": "Elizabeth N Dewey", + "author_inst": "OHSU" + }, + { + "author_name": "Diana E Kazmierczak", + "author_inst": "OHSU" + }, + { + "author_name": "Steven C Kazmierczak", + "author_inst": "OHSU" + }, + { + "author_name": "William B Messer", + "author_inst": "OHSU" + }, + { + "author_name": "Akram Khan", + "author_inst": "OHSU" + }, + { + "author_name": "Martin A Schreiber", + "author_inst": "OHSU" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.20.22269618", "rel_title": "Molecular diagnosis of SARS-CoV-2: a validation of saliva samples", @@ -404720,49 +407361,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.20.22269491", - "rel_title": "Antigenic determinants of SARS-CoV-2-specific CD4+ T cell lines reveals M protein-driven dysregulation of interferon signaling", - "rel_date": "2022-01-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.20.22269491", - "rel_abs": "We generated CD4+ T cell lines (TCLs) reactive to either SARSCoV-2 spike (S) or membrane (M) proteins from unexposed naive T cells from six healthy donor volunteers to understand in fine detail whether the S and M structural proteins have intrinsic differences in driving antigen-specific CD4+ T cell responses. Having shown that each of the TCLs were antigen-specific and antigen-reactive, single cell mRNA analyses demonstrated that SARS-CoV-2 S and M proteins drive strikingly distinct molecular signatures. Whereas the S-specific responses are virtually indistinguishable from those responses induced by other viral antigens (e.g. CMV), the M protein-specific CD4+ TCLs have a transcriptomic signature that indicate a marked suppression of interferon signaling, characterized by a downregulation of the genes encoding ISG15, IFITM1, IFI6, MX1, STAT1, OAS1, IFI35, IFIT3 and IRF7 (a molecular signature which is not dissimilar to that found in severe COVID-19). Our study suggests a potential link between the antigen specificity of the SARS-CoV-2-reactive CD4+ T cells and the development of specific sets of adaptive immune responses. Moreover, the balance between T cells of significantly different specificities may be the key to understand how CD4+ T cell dysregulation can determine the clinical outcomes of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Pedro H Gazzinelli-Guimaraes", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Gayatri Sanku", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Allergy & Immunology" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute For Allergy & Immunology" - }, - { - "author_name": "Paul Schaughency", - "author_inst": "NIH" - }, - { - "author_name": "Justin Lack", - "author_inst": "NIH" - }, - { - "author_name": "Thomas Nutman", - "author_inst": "NIAID" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.20.22269586", "rel_title": "BNT162b2 vaccine boosts neutralizing antibodies to ancestral SARS-CoV-2 & Omicron variant in adults who previously received two doses of inactivated vaccine", @@ -406509,6 +409107,69 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.01.17.476644", + "rel_title": "Nirmatrelvir, an orally active Mpro inhibitor, is a potent inhibitor of SARS-CoV-2 Variants of Concern", + "rel_date": "2022-01-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.17.476644", + "rel_abs": "New variants of SARS-CoV-2 with potential for enhanced transmission, replication, and immune evasion capabilities continue to emerge causing reduced vaccine efficacy and/or treatment failure. As of January 2021, the WHO has defined five variants of concern (VOC): B.1.1.7 (Alpha, ), B.1.351 (Beta, {beta}), P.1 (Gamma, {gamma}), B.1.617.2 (Delta, {delta}), and B.1.1.529 (Omicron, o). To provide a therapeutic option for the treatment of COVID-19 and variants, Nirmatrelvir, the antiviral component of PAXLOVID, an oral outpatient treatment recently authorized for conditional or emergency use treatment of COVID-19, was developed to inhibit SARS-CoV-2 replication. Nirmatrelvir (PF-07321332) is a specific inhibitor of coronavirus main protease (Mpro, also referred to as 3CLpro), with potent antiviral activity against several human coronaviruses, including SARS-CoV-2, SARS-CoV, and MERS (Owen et al, Science 2021. doi: 10.1126/science.abl4784). Here, we evaluated PF-07321332 against the five SARS-CoV-2 VOC (, {beta}, {gamma}, {delta},, o) and two Variants of Interest or VOI, C.37 ({lambda}) and B.1.621 (), using qRT-PCR in VeroE6 cells lacking the P-glycoprotein (Pgp) multidrug transporter gene (VeroE6 P-gp knockout cells). Nirmatrelvir potently inhibited USA-WA1/2020 strain, and , {beta}, {gamma}, {lambda}, {delta}, , and o variants in VeroE6 P-gp knockout cells with mean EC50 values 38.0 nM, 41.0 nM, 127.2 nM, 24.9 nM, 21.2 nM, 15.9 nM, 25.7 nM and 16.2 nM, respectively. Sequence analysis of the Mpro encoded by the variants showed ~100% identity of active site amino acid sequences, reflecting the essential role of Mpro during viral replication leading to ability of Nirmatrelvir to exhibit potent activity across all the variants.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Devendra K. Rai", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + }, + { + "author_name": "Irina Yurgelonis", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + }, + { + "author_name": "Patricia McMonagle", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + }, + { + "author_name": "Hussin A. Rothan", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA." + }, + { + "author_name": "Li Hao", + "author_inst": "Pfizer Worldwide Researhc, Development & Medical, Pearl River, NY 10965, USA." + }, + { + "author_name": "Alexey Gribenko", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA." + }, + { + "author_name": "Elizabeth Titova", + "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA" + }, + { + "author_name": "Barry Kreiswirth", + "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA" + }, + { + "author_name": "Kris M. White", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA, and Global Health Emerging Pathogens Institute, Icahn School of Med" + }, + { + "author_name": "Yuao Zhu", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + }, + { + "author_name": "Annaliesa S. Anderson", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + }, + { + "author_name": "Rhonda D. Cardin", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.01.17.22269283", "rel_title": "ELF5 is a respiratory epithelial cell-specific risk gene for severe COVID-19", @@ -406722,57 +409383,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.17.476677", - "rel_title": "Prediction and validation of host cleavage targets of SARS-CoV-2 3C like protease", - "rel_date": "2022-01-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.17.476677", - "rel_abs": "How SARS-CoV-2 causes the observed range of clinical manifestations and disease severity remains poorly understood. SARS-CoV-2 encodes for two proteases (3CLPro and PLPro), vital for viral production, but also promiscuous with respect to host protein targets, likely contributing to the range of disease. Pharmacological inhibition of the 3C-like3 protease has revealed remarkable reduction in hospitalization and death in phase 2/3 clinical studies. However, the mechanisms responsible for the pathology mediated by those proteases are still unclear. In this study, we develop a bioinformatic algorithm, leveraging experimental data from SARS-CoV, to predict host cleavage targets of the SARS-CoV-2 3C-like protease, or 3CLPro. We capture targets of the 3CL protease described previously for SARS-CoV, and we identify hundreds of new putative targets. We experimentally validate a number of these predicted targets, including the giant sarcomeric protein Obscurin, and show that expression of 3CL protease alone recapitulates the sarcomeric disorganization seen by SARS-CoV-2 infection of hiPSC-derived cardiomyocytes. Our data provide a resource to identify putative host cleavage targets of 3CL protease that contribute to mechanisms and heterogeneity of disease in COVID-19 and future coronavirus outbreaks.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Nora Yucel", - "author_inst": "UNIVERSITY OF PENNSYLVANIA" - }, - { - "author_name": "Silvia Marchiano", - "author_inst": "University of Washington" - }, - { - "author_name": "Evan Tchelepi", - "author_inst": "NetQuest" - }, - { - "author_name": "Quentin McAfee", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Nehaar Nimmagadda", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Andy Ren", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Sam Shi", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Charles E Murry", - "author_inst": "University of Washington" - }, - { - "author_name": "Zoltan Arany", - "author_inst": "UNIVERSITY OF PENNSYLVANIA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.01.17.476685", "rel_title": "Nirmatrelvir, Molnupiravir, and Remdesivir maintain potent in vitro activity against the SARS-CoV-2 Omicron variant", @@ -408426,6 +411036,81 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2022.01.14.22269074", + "rel_title": "Evaluation of an emergency safe supply drug and managed alcohol program in COVID-19 isolation hotel shelters for people experiencing homelessness", + "rel_date": "2022-01-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.14.22269074", + "rel_abs": "BackgroundDuring a COVID-19 outbreak in the congregate shelter system in Halifax, Nova Scotia, Canada, a multidisciplinary health care team provided an emergency \"safe supply\" of pharmaceutical-grade medications and beverage-grade alcohol to facilitate isolation in COVID-19 hotel shelters for residents who are dependent on these substances. We aimed to evaluate (a) substances and dosages provided, and (b) effectiveness and safety of the program.\n\nMethodsWe retrospectively reviewed medical records of all COVID-19 isolation hotel shelter residents during May 2021. We extracted data on medication and alcohol dosages provided each day. The primary outcome was residents prematurely leaving isolation against public health orders. Adverse events included (a) overdose; (b) intoxication; and (c) diversion, selling, or sharing of medications or alcohol.\n\nResultsOver 25 days, 77 isolation hotel residents were assessed (mean age 42 {+/-} 14 years; 24% women). Sixty-two (81%) residents were provided medications, alcohol, or cigarettes. Seventeen residents (22%) received opioid agonist treatment medications (methadone, buprenorphine, or slow-release oral morphine) and 27 (35%) received hydromorphone tablets. Thirty-one (40%) residents received stimulant tablets with methylphenidate (27; 35%), dextroamphetamine (8; 10%), or lisdexamfetamine (2; 3%). Six residents (8%) received benzodiazepines. Forty-two (55%) residents received alcohol, including 41 (53%) with strong beer, three (3%) with wine, and one (1%) with hard liquor. Over 14 days in isolation, mean daily dosages increased of hydromorphone (45 {+/-} 32 to 57 {+/-} 42mg), methylphenidate (51 {+/-} 28 to 77 {+/-} 37mg), dextroamphetamine (33 {+/-} 16 to 46 {+/-} 13mg), and alcohol (12.3 {+/-} 7.6 to 13.0 {+/-} 6.9 standard drinks). Six residents (8%) left isolation prematurely, but four of those residents returned. Over 1,059 person-days in isolation, there were zero overdoses. Documented concerns regarding intoxication occurred six times (0.005 events/person-day) and medication diversion or sharing three times (0.003 events/person-day).\n\nConclusionsAn emergency safe supply and managed alcohol program, paired with housing, was associated with low rates of adverse events and high rates of successful completion of the 14-day isolation period in COVID-19 isolation hotel shelters. This supports the effectiveness and safety of emergency safe supply prescribing and managed alcohol in this setting.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Thomas D Brothers", + "author_inst": "Dalhousie University; University College London" + }, + { + "author_name": "Malcolm Leaman", + "author_inst": "North End Community Health Centre" + }, + { + "author_name": "Matthew Bonn", + "author_inst": "Canadian Association of People who Use Drugs (CAPUD)" + }, + { + "author_name": "Dan Lewer", + "author_inst": "University College London" + }, + { + "author_name": "Jacqueline Atkinson", + "author_inst": "Mobile Outreach Street Health (MOSH), North End Community Health Centre" + }, + { + "author_name": "John Fraser", + "author_inst": "North End Community Health Centre" + }, + { + "author_name": "Amy Gillis", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Michael Gniewek", + "author_inst": "Dalhousie University; Direction 180" + }, + { + "author_name": "Leisha Hawker", + "author_inst": "North End Community Health Centre; Dalhousie University" + }, + { + "author_name": "Heather Hayman", + "author_inst": "Mobile Outreach Street Health (MOSH), North End Community Health Centre" + }, + { + "author_name": "Peter Jorna", + "author_inst": "Nova Pharmacy" + }, + { + "author_name": "David Martell", + "author_inst": "Dalhousie University; Direction 180" + }, + { + "author_name": "Tiffany O'Donnell", + "author_inst": "Mobile Outreach Street Health (MOSH), North End Community Health Centre; Dalhousie University" + }, + { + "author_name": "Helen Rivers-Bowerman", + "author_inst": "Mobile Outreach Street Health (MOSH), North End Community Health Centre" + }, + { + "author_name": "Leah Genge", + "author_inst": "Mobile Outreach Street Health (MOSH), North End Community Health Centre; Dalhousie University; Direction 180" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "addiction medicine" + }, { "rel_doi": "10.1101/2022.01.16.22269377", "rel_title": "The Impact of State Paid Sick Leave Policies on Longitudinal Weekday Workplace Mobility During the COVID-19 Pandemic", @@ -408559,61 +411244,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.16.22269388", - "rel_title": "Sero-Prevalence of Covid-19 among workers in Malaysia", - "rel_date": "2022-01-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.16.22269388", - "rel_abs": "From the beginning of the pandemic in Feb 2020, Malaysia has been through 4 waves of outbreak, the magnitude of each wave is several orders larger than the preceding one. By the end of the fourth wave in October 2021, Malaysia has among the highest death toll in Asia, cumulative incidence of confirmed cases has reached 7.0% (>30% in Klang Valley). However it remains uncertain what is the true proportion of the population infected.\n\nWe conducted a sero-survey on 1078 workers from 17 worksites in Klang Valley and Perak between July and September 2021. We tested them for SARS-CoV-2-specific antibodies using Ecotest, a lateral flow immunoassay (LFIA). The ability of antibody testing to detect prior infection depends on the assay and sero-reversion. We therefore adjusted the prevalence estimates to correct for potential misclassification bias due to the use of LFIA and sero-reversion using test sensitivity and specificity results estimated from an independent validation study.\n\nThe mean age of the workers was 32 years, 89% were male and migrant workers comprised 81% of all subjects, 59% the subjects were from Klang valley. 33% of workers had prior RT-PCR confirmed Covid-19 infections. We estimated 82.2 percent of workers had been infected by Covid-19 by July-September 2021. Prevalence was 99.9% among migrant workers and 12.1% among local workers. Klang Valley, the most industrialized region in Malaysia where most migrant workers are found, had 100% prevalence, giving an infection-to-case ratio (ICF) of [~]3.\n\nOur sero-prevalence results show that the incidence of Covid19 is extremely high among migrant workers in Malaysia, consistent with findings from other countries such as Kuwait and Singapore which also hosted large number of migrant workers.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Noorliza Mohamad Noordin", - "author_inst": "National Public Health Laboratory" - }, - { - "author_name": "Aziyati Omar", - "author_inst": "National Public Health Laboratory" - }, - { - "author_name": "Ishmah Hana Isharudin", - "author_inst": "National Public Health Laboratory" - }, - { - "author_name": "Raisah Idris", - "author_inst": "National Public Health Laboratory" - }, - { - "author_name": "Yukie Chem", - "author_inst": "National Public Health Laboratory" - }, - { - "author_name": "Intan Surianne Mat Sahat", - "author_inst": "National Public Health Laboratory" - }, - { - "author_name": "Selvanesan Sengol", - "author_inst": "National Public Health Laboratory" - }, - { - "author_name": "Zirwatul Adilah Aziz", - "author_inst": "National Public Health Laboratory" - }, - { - "author_name": "Zhuo zhi Lim", - "author_inst": "Healthy Malaysia Society" - }, - { - "author_name": "Teck Onn Lim", - "author_inst": "Healthy Malaysia Society" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.13.22269234", "rel_title": "Increased airborne transmission of COVID-19 with new variants. Implications for health policies.", @@ -410108,6 +412738,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.11.22269069", + "rel_title": "Hydroxychloroquine/Chloroquine in COVID-19 With Focus on Hospitalized Patients - A Systematic Review", + "rel_date": "2022-01-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.11.22269069", + "rel_abs": "BackgroundIn the beginning of the COVID-19 pandemic, many hospitalized patients received empiric hydroxychloroquine/chloroquine (HC/CQ). Although some retrospective-observational trials suggested potential benefit, all subsequent randomized clinical trials (RCTs) failed to show benefit and use generally ceased. Herein, we summarize key studies that clinicians advising patients on HC/CQs efficacy:safety calculus in hospitalized COVID-19 patients would want to know about in a practical one-stop-shopping source.\n\nMethodsPubmed and Google were searched on November 4, 2021. Search words included: COVID-19, hydroxychloroquine, chloroquine, in vitro, animal studies, clinical trials, and meta-analyses. Studies were assessed for import and included if considered impactful for benefit:risk assessment.\n\nResultsThese searches led to inclusion of 12 in vitro and animal reports; 12 retrospective-observational trials, 19 interventional clinical trials (17 RCTs, 1 single-arm, 1 controlled but unblinded), and 51 meta-analyses in hospitalized patients.\n\nInconsistent efficacy was seen in vitro and in animal studies for coronaviruses and nil in SARS-CoV-2 animal models specifically. Most retrospective-observational studies in hospitalized COVID-19 patients found no efficacy; QT prolongation and increased adverse events and mortality were reported in some. All RCTs and almost all meta-analyses provided robust data showing no benefit in overall populations and subgroups, yet concerning safety issues in many.\n\nConclusionsHC/CQ have inconsistent anti-coronavirus efficacy in vitro and in animal models, and no convincing efficacy yet substantial safety issues in the overwhelming majority of retrospective-observational trials, RCTs, and meta-analyses in hospitalized COVID-19 patients. HC/CQ should not be prescribed for hospitalized COVID-19 patients outside of clinical trials.\n\nKey Summary PointsPreclinical hydroxychloroquine/chloroquine in vitro studies found inconsistent activity against coronaviruses including SARS-CoV-2.\n\nPreclinical hydroxychloroquine/chloroquine animals studies found inconsistent efficacy for coronaviruses in general and none for SARS-CoV-2.\n\nThe overhwelming majority of RCTs and retrospective-observational trials found no benefit for hydroxychloroquine/chloroquine in hospitalized COVID-19 patients, and many found concerning safety signals.\n\nThe majority of RCTs and retrospective-observational trials found no benefit for hydroxychloroquine/chloroquine in COVID-19 outpatients or for pre- or post-exposure prophylaxis, and some found concerning safety signals.\n\nThe overwhelming majority of meta-analyses found no benefit for hydroxychloroquine/chloroquine in COVID-19 inpatients, outpatients, or for prophylaxis, and many found concerning safety signals.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Daniel Freilich", + "author_inst": "Bassett Medical Center" + }, + { + "author_name": "Jennifer Victory", + "author_inst": "Bassett Research Institute" + }, + { + "author_name": "Anne Gadomski", + "author_inst": "Bassett Research Institute" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.13.476204", "rel_title": "Covariance predicts conserved protein residue interactions important to the emergence and continued evolution of SARS-CoV-2 as a human pathogen", @@ -410185,45 +412842,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.13.22269102", - "rel_title": "Effects of medical school on mental health and sleep habits", - "rel_date": "2022-01-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.13.22269102", - "rel_abs": "BACKGROUND and OBJECTIVESThis study aims to define changes in anxiety and depression among medical students while evaluating the association of sleep habits and other risk factors, including exercise habits and a diagnosis of chronic disease. The effect of the COVID-19 pandemic was also evaluated.\n\nDESIGNA cohort of first- and second-year medical students was evaluated longitudinally using survey methods to quantify changes from pre-medical school and summer break to each semester in medical school throughout years one and two.\n\nMETHODSData was analyzed using Generalized Linear Mixed Models (GLMMs) on the numeric responses of General Anxiety Disorder-7 (GAD-7), Patient Health Questionnaire-9 (PHQ-9), and Pittsburg Sleep Quality Index. Additional assessments evaluated exercise habits, chronic disease, and impact of COVID-19 Pandemic.\n\nRESULTSDepression, anxiety, and sleep habits displayed a cyclical change that was associated with the academic cycle. The COVID-19 pandemic was never significant. Medical students who had a chronic disease diagnosis had increased severity. Exercise did not play a role.\n\nCONCLUSIONThe main driver for depression, anxiety, and poor sleep quality was the academic cycle, while the COVID-19 pandemic did not have an impact on mental health.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Blake McKinley", - "author_inst": "Department of Primary Care, Rocky Vista University College of Osteopathic Medicine, Ivins, Utah, 84738" - }, - { - "author_name": "Bryan Daines", - "author_inst": "Department of Primary Care, Rocky Vista University College of Osteopathic Medicine, Ivins, Utah, 84738" - }, - { - "author_name": "Mitchell Allen", - "author_inst": "Department of Primary Care, Rocky Vista University College of Osteopathic Medicine, Ivins, Utah, 84738" - }, - { - "author_name": "Kayd Pulsipher", - "author_inst": "Department of Primary Care, Rocky Vista University College of Osteopathic Medicine, Ivins, Utah, 84738" - }, - { - "author_name": "Isain Zapata", - "author_inst": "Department of Biomedical Sciences, Rocky Vista University College of Osteopathic Medicine Parker, CO 80134" - }, - { - "author_name": "Benjamin Wilde", - "author_inst": "Department of Primary Care, Rocky Vista University College of Osteopathic Medicine, Ivins, Utah, 84738" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2022.01.13.22269022", "rel_title": "A national survey of early treatment seeking behavior among those with incident SARS-CoV-2 infection", @@ -412250,6 +414868,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.12.22269048", + "rel_title": "A unique dexamethasone-dependent gene expression profile in the lungs of COVID-19 patients", + "rel_date": "2022-01-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.12.22269048", + "rel_abs": "Local immunopathogenesis of COVID-19 acute respiratory distress syndrome (CARDS) and the effects of systemic dexamethasone (DXM) treatment on pulmonary immunity in COVID-19 remain insufficiently understood. To provide further insight into insight into immune regulatory mechanisms in the lungs of CARDS (with and without DXM treatment) and critically ill non-COVID-19 patients (without DXM treatment), transcriptomic RNA-seq analysis of bronchoalveolar lavage fluid (BALF) was performed in these patients. Functional analysis was performed using gene ontology and a blood transcription module, and gene expression of select pro-inflammatory cytokines, interferon-stimulated genes (ISGs) and auto-IFN antibodies were assessed. We found 550 and 2173 differentially expressed genes in patients with non-DXM-CARDS and DXM-CARDS, respectively. DXM-CARDS was characterized by upregulation of genes related to pulmonary innate and adaptive immunity, notably B-cell and complement pathway activation, antigen presentation, phagocytosis and FC-gamma receptor signalling. Pro-inflammatory genes were not differentially expressed in CARDS vs. non-COVID-19, nor did they differ according to DXM. Most ISGs were specifically upregulated in CARDS, particularly in non-DXM-CARDS. Auto-IFN autoantibodies were detectable in BALF of some CARDS patients. In conclusion, DXM treatment was not associated with regulation of pro-inflammatory pathways in CARDS but with regulation of other specific local innate and adaptive immune responses.\n\nsummaryThis study identifies differentially expressed genes in bronchoalveolar fluid of COVID-19 acute respiratory distress patients with a distinct RNA expression profile of those treated with dexamethasone. These results challenge the concept of a COVID-19 specific cytokine storm.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ulrik Fahnoe", + "author_inst": "Copenhagen University Hospital - Amager and Hvidovre; Copenhagen University" + }, + { + "author_name": "Andreas Ronit", + "author_inst": "Copenhagen University Hospital - Amager and Hvidovre" + }, + { + "author_name": "Ronan M.G. Berg", + "author_inst": "Copenhagen University Hospital - Rigshospitalet; Copenhagen University" + }, + { + "author_name": "Sofie E.G. Joergensen", + "author_inst": "Aarhus University Hospital; Aarhus University" + }, + { + "author_name": "Trine H. Mogensen", + "author_inst": "Aarhus University Hospital; Aarhus University" + }, + { + "author_name": "Alexander P. Underwood", + "author_inst": "Copenhagen University Hospital - Amager and Hvidovre" + }, + { + "author_name": "Troels K.H. Scheel", + "author_inst": "The Rockefeller University; University of Copenahagen" + }, + { + "author_name": "Jens Bukh", + "author_inst": "Copenhagen University Hospital - Amager and Hvidovre; Copenhagen University" + }, + { + "author_name": "Ronni R. Plovsing", + "author_inst": "Copenhagen University Hospital - Amager and Hvidovre; Copenhagen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.01.13.22269236", "rel_title": "Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples", @@ -412411,65 +415080,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.01.13.22269078", - "rel_title": "COVID-19 infection and vaccination rates in healthcare workers in British Columbia, Canada: A Longitudinal Urban versus Rural Analysis of the Impact of the Vaccine Mandate", - "rel_date": "2022-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.13.22269078", - "rel_abs": "PurposeHealthcare workers (HCWs) play a critical role in responding to the COVID-19 pandemic. Early in the pandemic, urban centres were hit hardest globally; rural areas gradually became more impacted. We compared COVID-19 infection and vaccine uptake in HCWs living in urban versus rural locations within, and between, two health authorities in British Columbia (BC), Canada. We also analyzed the impact of a vaccine mandate for HCWs.\n\nMethodsWe tracked laboratory-confirmed SARS-CoV-2 infections, positivity rates, and vaccine uptake in 29,021 HCWs in Interior Health (IH) and 24,634 HCWs in Vancouver Coastal Health (VCH), by occupation, age, and home location, comparing to the general population in that region. We then evaluated the impact of infection rates as well as the mandate on vaccination uptake.\n\nResultsBy October 27, 2021, the date that unvaccinated HCWs were prohibited from providing healthcare, only 1.6% in VCH yet 6.5% in IH remained unvaccinated. Rural workers in both areas had significantly higher unvaccinated rates compared with urban dwellers. Over 1,800 workers, comprising 6.4% of rural HCWs and 3.3% of urban HCWs, remained unvaccinated and set to be terminated from their employment. While the mandate prompted a significant increase in second doses, the impact on the unvaccinated was less clear.\n\nConclusionsAs rural areas often suffer from under-staffing, loss of HCWs could have serious impacts on healthcare provision as well as on the livelihoods of unvaccinated HCWs. Greater efforts are needed to understand how to better address the drivers of rural-related vaccine hesitancy as the pandemic continues.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Annalee Yassi", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Stephen Barker", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Karen Lockhart", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Deanne Taylor", - "author_inst": "Interior Health" - }, - { - "author_name": "Devin Harris", - "author_inst": "Interior Health" - }, - { - "author_name": "Harsh Hundal", - "author_inst": "Interior Health" - }, - { - "author_name": "Jennifer M. Grant", - "author_inst": "Vancouver Coastal Health" - }, - { - "author_name": "Arnold Ikedichi Okpani", - "author_inst": "University of British Columbia, Canada" - }, - { - "author_name": "Sue Pollock", - "author_inst": "Interior Health" - }, - { - "author_name": "Stacy Sprague", - "author_inst": "Vancouver Coastal Health" - }, - { - "author_name": "Chad Kim Sing", - "author_inst": "Vancouver Coastal Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2022.01.12.475688", "rel_title": "matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2", @@ -414296,6 +416906,137 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.11.475947", + "rel_title": "SARS-CoV-2 drives NLRP3 inflammasome activation in human microglia through spike-ACE2 receptor interaction", + "rel_date": "2022-01-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.11.475947", + "rel_abs": "Coronavirus disease-2019 (COVID-19) is primarily a respiratory disease, however, an increasing number of reports indicate that SARS-CoV-2 infection can also cause severe neurological manifestations, including precipitating cases of probable Parkinsons disease. As microglial NLRP3 inflammasome activation is a major driver of neurodegeneration, here we interrogated whether SARS-CoV-2 can promote microglial NLRP3 inflammasome activation utilising a model of human monocyte-derived microglia. We identified that SARS-CoV-2 isolates can bind and enter microglia, triggering inflammasome activation in the absence of viral replication. Mechanistically, microglial NLRP3 could be both primed and activated with SARS-CoV-2 spike glycoprotein in a NF-{kappa}B and ACE2-dependent manner. Notably, virus- and spike protein-mediated inflammasome activation in microglia was significantly enhanced in the presence of -synuclein fibrils, which was entirely ablated by NLRP3-inhibition. These results support a possible mechanism of microglia activation by SARS-CoV-2, which could explain the increased vulnerability to developing neurological symptoms akin to Parkinsons disease in certain COVID-19 infected individuals, and a potential therapeutic avenue for intervention.\n\nSIGNIFICANCE STATEMENTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) principally affects the lungs, however there is evidence that the virus can also reach the brain and lead to chronic neurological symptoms. In this study, we examined the interaction SARS-CoV-2 with brain immune cells, by using an ex-vivo model of human monocyte-derived microglia. We identified robust activation of the innate immune sensor complex, NLRP3 inflammasome, in cells exposed to SARS-CoV-2. This was dependent on spike protein-ACE2 receptor interaction and was potentiated in the presence of -synuclein. We therefore identify a possible mechanism for SARS-CoV-2 and increased vulnerability to developing neurological dysfunction. These findings support a potential therapeutic avenue for treatment of SARS-CoV-2 driven neurological manifestations, through use of NLRP3 inflammasome or ACE2 inhibitors.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Eduardo A Albornoz", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Alberto A Amarilla", + "author_inst": "School of Chemistry and molecular Biosciences, University of Queensland" + }, + { + "author_name": "Naphak Modhiran", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Sandra Parker", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Xaria X Li", + "author_inst": "School of biomedical sciences, University of Queensland" + }, + { + "author_name": "Danushka K Wijesundara", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Adriana Pliego Zamora", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Christopher LD McMillan", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Benjamin Liang", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Nias Y.G Peng", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Julian D.J Sng", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Fatema Tuj Saima", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Devina Paramitha", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Rhys Parry", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Michael S Avumegah", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Ariel Isaacs", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Martin Lo", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Zaray Miranda-Chacon", + "author_inst": "Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile" + }, + { + "author_name": "Daniella Bradshaw", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Constanza Salinas-Rebolledo", + "author_inst": "Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile" + }, + { + "author_name": "Niwanthi W Rajapakse", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Trent Munro", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Alejandro Rojas-Fernandez", + "author_inst": "Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile" + }, + { + "author_name": "Paul R Young", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Katryn J Stacey", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Alexander A Khromykh", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Keith J Chappell", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Daniel Watterson", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Trent M Woodruff", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2022.01.11.475327", "rel_title": "Systemic infection of SARS-CoV-2 in free ranging Leopard (Panthera pardus fusca) in India", @@ -414453,61 +417194,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2022.01.11.475889", - "rel_title": "Favipiravir, umifenovir and camostat mesylate: a comparative study against SARS-CoV-2", - "rel_date": "2022-01-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.11.475889", - "rel_abs": "Since the first cases the coronavirus disease caused by SARS-CoV-2 (COVID-19) reported in December 2019, worldwide continuous efforts have been placed both for the prevention and treatment of this infectious disease. As new variants of the virus emerge, the need for an effective antiviral treatment continues. The concept of preventing SARS-CoV-2 on both pre-entry and post-entry stages has not been much studied. Therefore, we compared the antiviral activities of three antiviral drugs which have been currently used in the clinic. In silico docking analyses and in vitro viral infection in Vero E6 cells were performed to delineate their antiviral effectivity when used alone or in combination. Both in silico and in vitro results suggest that the combinatorial treatment by favipiravir and umifenovir or camostat mesylate has more antiviral activity against SARS-CoV-2 rather than single drug treatment. These results suggest that inhibiting both viral entry and viral replication at the same time is much more effective for the antiviral treatment of SARS-CoV-2.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Mehmet Altay Unal", - "author_inst": "Ankara University Stem Cell" - }, - { - "author_name": "Omur Besbinar", - "author_inst": "Ankara University Stem Cell Institute" - }, - { - "author_name": "Hasan Nazir", - "author_inst": "Department of Chemistry, Faculty of Science, Ankara University" - }, - { - "author_name": "Gokce Yagmur Summak", - "author_inst": "Stem Cell Institute, Ankara University" - }, - { - "author_name": "Fatma Bayrakdar", - "author_inst": "Republic of Turkey Ministry of Health" - }, - { - "author_name": "Lucia Gemma Delogu", - "author_inst": "Department of Biomedical Sciences, University of Padua, Padua, Italy" - }, - { - "author_name": "Tambay Taskin", - "author_inst": "Atabay Pharmaceutical Company," - }, - { - "author_name": "Sibel Aysil Ozkan", - "author_inst": "Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University" - }, - { - "author_name": "Kamil Can Akcali", - "author_inst": "Department of Biophysics, Faculty of Medicine, Ankara University" - }, - { - "author_name": "Acelya Yilmazer", - "author_inst": "Stem Cell Institute, Ankara University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2022.01.11.22268981", "rel_title": "Rapid and Accurate Identification of SARS-CoV-2 Omicron Variants Using Droplet Digital PCR (RT-ddPCR)", @@ -416034,6 +418720,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.07.22268883", + "rel_title": "Safety and immunogenicity of the BBIBP-CorV vaccine in adolescents aged 12-17 years in Thai population, prospective cohort study.", + "rel_date": "2022-01-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.07.22268883", + "rel_abs": "IntroductionCOVID-19 pandemic affects all populations worldwide, including adolescents. Adolescents can develop a severe form of COVID-19, especially with comorbidity underlying. The prior studies of the mRNA COVID-19 vaccine showed excellent effectiveness in adolescents. Therefore, this study aimed to evaluate the safety and effectiveness of the BBIBP-CorV vaccine with the immunobridging approach in Thai adolescents.\n\nMethodsThis single-center, prospective cohort study compared the immunogenicity after 2 doses of the BBIBO-CorV vaccine with 21 days interval of participants aged 12-17 years with 18-30 years at Chulabhorn Hospital, Chulabhorn Royal Academy, Bangkok, Thailand. The key eligible criteria were healthy or had stable pre-existing comorbidity participants, aged 12-17 years. The primary endpoint was the anti-receptor binding domain antibody concentration at 4 weeks after dose 2 of the vaccine. In addition, safety profiles were solicited adverse events within 7 days after each dose of vaccine and any adverse events through 1 month after dose 2 of the vaccine.\n\nResultsFour weeks after the second vaccination, the GMC of anti-RBD antibody in the adolescent cohort was 102.9 BAU/mL (95%CI; 91.0-116.4) and 36.9 BAU/mL (95%CI; 30.9-44.0) in the adult cohort. The GMR of the adolescent cohort was 2.79 (95%CI; 2.25-3.46, p-value; <0.0001) compared with the adult cohort which met non-inferiority criteria. The reactogenicity was slightly less reported in the adolescent cohort compared with the adult cohort. No serious adverse events were reported in both cohorts.\n\nConclusionVaccination with the BBIBP-CorV vaccine in the adolescent participants was safe and effective.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Kriangkrai Tawinprai", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Taweegrit Siripongboonsitti", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Thachanun Porntharukchareon", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Preeda Vanichsetakul", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Saraiorn Thonginnetra", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Krongkwan Niemsorn", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Pathariya Promsena", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Manunya Tandhansakul", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Naruporn Kasemlawan", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Natthanan Ruangkijpaisal", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Narin Banomyong", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Nanthida Phattraprayoon", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Teerapat Ungtrakul", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Kasiruck Wittayasak", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Nawarat Thonwirak", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Kamonwan Soonklang", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Gaidganok Sornsamdang", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Nithi Mahanonda", + "author_inst": "Chulabhorn Royal Academy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.08.22268953", "rel_title": "Anti-PEG antibodies boosted in humans by SARS-CoV-2 lipid nanoparticle mRNA vaccine", @@ -416247,41 +419020,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical ethics" }, - { - "rel_doi": "10.1101/2022.01.08.22268611", - "rel_title": "SARS-CoV-2-positive patients display considerable differences in proteome diversity in urine, nasopharyngeal, gargle solution and bronchoalveolar lavage fluid samples", - "rel_date": "2022-01-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.08.22268611", - "rel_abs": "BackgroundProteome profile changes post-severe acute respiratory syndrome coronavirus 2 (post-SARS-CoV-2) infection in different body sites of humans remains an active scientific investigation whose solutions stand a chance of providing more information on what constitutes SARS-CoV-2 pathogenesis. While proteomics has been used to understand SARS-CoV-2 pathogenesis, there are limited data about the status of proteome profile in different human body sites infected by the sarscov2 virus. To bridge the gap, our study aims to profile the proteins secreted in urine, bronchoalveolar lavage fluid (BALF), gargle solution, and nasopharyngeal samples and assess the proteome differences in these body samples collected from SARS-CoV-2-positive patients.\n\nMaterials and methodsWe downloaded publicly available proteomic data from (https://www.ebi.ac.uk/pride/). The data we downloaded had the following identifiers: i) PXD019423, n=3 from Charles Tanford Protein Center in Germany. ii) PXD018970, n=15 from Beijing Proteome Research Centre, China. iii)PXD022085, n=5 from Huazhong University of Science and Technology, China, and iv) PXD022889, n=18 from Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA. MaxQuant was used for the peptide spectral matching using humans, and SARS-CoV-2 was downloaded from the UniProt database (access date 13th October 2021).\n\nResultsThe individuals infected with SARS-CoV-2 viruses displayed a different proteome diversity from the different body sites we investigated. Overall, we identified 1809 proteins across the four different sample types we compared. Urine and BALF samples had significantly more abundant SARS-CoV-2 proteins than the other body sites we compared. Urine samples had 257(33.7%) unique proteins, followed by nasopharyngeal with 250(32.8%) unique proteins. Garage solution and BALF had 38(5%) and 73(9.6%) unique proteins.\n\nConclusionsUrine, gargle solution, nasopharyngeal, and bronchoalveolar lavage fluid samples have different protein diversity in individuals infected with SARS-CoV-2. Moreover, our data demonstrated that a given body site is characterized by a unique set of proteins in SARS-CoV-2 seropositive individuals.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Javan Okendo", - "author_inst": "Systems and Chemical Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health " - }, - { - "author_name": "Clarisse Musanabaganwa", - "author_inst": "Rwanda Biomedical Centre, Kigali, Rwanda" - }, - { - "author_name": "Peter Mwangi", - "author_inst": "Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa" - }, - { - "author_name": "Martin Nyaga", - "author_inst": "Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa" - }, - { - "author_name": "Harris Onywera", - "author_inst": "Division of Medical Microbiology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cap" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.08.22268954", "rel_title": "Direct Comparison of SARS Co-V-2 Nasal RT- PCR and Rapid Antigen Test (BinaxNOWTM) at a Community Testing Site During an Omicron Surge", @@ -417791,6 +420529,117 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.07.475248", + "rel_title": "Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2", + "rel_date": "2022-01-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.07.475248", + "rel_abs": "SARS-CoV-2 lineages are continuously evolving. As of December 2021, the AY.4.2 Delta sub-lineage represented 20 % of sequenced strains in UK and has been detected in dozens of countries. It has since then been supplanted by the Omicron variant. AY.4.2 displays three additional mutations (T95I, Y145H and A222V) in the N-terminal domain (NTD) of the spike when compared to the original Delta variant (B.1.617.2) and remains poorly characterized. Here, we analyzed the fusogenicity of the AY.4.2 spike and the sensitivity of an authentic AY.4.2 isolate to neutralizing antibodies. The AY.4.2 spike exhibited similar fusogenicity and binding to ACE2 than Delta. The sensitivity of infectious AY.4.2 to a panel of monoclonal neutralizing antibodies was similar to Delta, except for the anti-RBD Imdevimab, which showed incomplete neutralization. Sensitivity of AY.4.2 to sera from individuals having received two or three doses of Pfizer or two doses of AstraZeneca vaccines was reduced by 1.7 to 2.1 fold, when compared to Delta. Our results suggest that mutations in the NTD remotely impair the efficacy of anti-RBD antibodies. The temporary spread of AY.4.2 was not associated with major changes in spike function but rather to a partially reduced neutralization sensitivity.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Nell Saunders", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Delphine Planas", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "William Henry Bolland", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Christophe Rodriguez", + "author_inst": "AP-HP" + }, + { + "author_name": "Slim Fourati", + "author_inst": "AP-HP" + }, + { + "author_name": "Julian Buchrieser", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Cyril Planchais", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Matthieu Prot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Isabelle Staropoli", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Florence Guivel-Benhassine", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Francoise Porrot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "David Veyer", + "author_inst": "AP-HP" + }, + { + "author_name": "Helene Pere", + "author_inst": "AP-HP" + }, + { + "author_name": "Nicolas Robillard", + "author_inst": "AP-HP" + }, + { + "author_name": "Madelina Saliba", + "author_inst": "AP-HP" + }, + { + "author_name": "Artem Baidaliuk", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Aymeric Seve", + "author_inst": "CHR Orleans" + }, + { + "author_name": "Laurent Hocqueloux", + "author_inst": "CHR Orleans" + }, + { + "author_name": "Thierry Prazuck", + "author_inst": "CHR Orleans" + }, + { + "author_name": "Hugo Mouquet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Etienne Simon-Loriere", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Timothee Bruel", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Jean-Michel Pawlotsky", + "author_inst": "AP-HP" + }, + { + "author_name": "Olivier Schwartz", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.01.10.475620", "rel_title": "Strong SARS-CoV-2 N-specific CD8+ T immunity induced by engineered extracellular vesicles associates with protection from lethal infection in mice.", @@ -417920,157 +420769,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.08.22268865", - "rel_title": "A method for variant agnostic detection of SARS-CoV-2, rapid monitoring of circulating variants, detection of mutations of biological significance, and early detection of emergent variants such as Omicron", - "rel_date": "2022-01-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.08.22268865", - "rel_abs": "The rapid emergence of new SARS-CoV-2 variants raises a number of public health questions including the capability of diagnostic tests to detect new strains, the efficacy of vaccines, and how to map the geographical distribution of variants to better understand patterns of transmission and possible load on healthcare resources. Next-Generation Sequencing (NGS) is the primary method for detecting and tracing the emergence of new variants, but it is expensive, and it can take weeks before sequence data is available in public repositories. Here, we describe a Polymerase Chain Reaction (PCR)-based genotyping approach that is significantly less expensive, accelerates reporting on SARS-CoV-2 variants, and can be implemented in any testing lab performing PCR.\n\nSpecific Single Nucleotide Polymorphisms (SNPs) and indels are identified that have high positive percent agreement (PPA) and negative percent agreement (NPA) compared to NGS for the major genotypes that circulated in 2021. Using a 48-marker panel, testing on 1,128 retrospective samples yielded a PPA and NPA in the 96.3 to 100% and 99.2 to 100% range, respectively, for the top 10 most prevalent lineages. The effect on PPA and NPA of reducing the number of panel markers was also explored.\n\nIn addition, with the emergence of Omicron, we also developed an Omicron genotyping panel that distinguishes the Delta and Omicron variants using four (4) highly specific SNPs. Data from testing demonstrates the capability to use the panel to rapidly track the growing prevalence of the Omicron variant in the United States in December 2021.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Eric Lai", - "author_inst": "Personalized Science" - }, - { - "author_name": "David Becker", - "author_inst": "Helix OpCo" - }, - { - "author_name": "Pius Brzoska", - "author_inst": "Thermo Fisher Scientific" - }, - { - "author_name": "Tyler Cassens", - "author_inst": "Helix OpCo" - }, - { - "author_name": "Jeremy Davis-Turak", - "author_inst": "ROSALIND" - }, - { - "author_name": "Evan Diamond", - "author_inst": "Thermo Fisher Scientific" - }, - { - "author_name": "Manohar Furtado", - "author_inst": "Thermo Fisher Scientific" - }, - { - "author_name": "Manoj Gandhi", - "author_inst": "Thermo Fisher Scientific" - }, - { - "author_name": "Dale Gort", - "author_inst": "ShoreFront Strategies" - }, - { - "author_name": "Alexander L Greninger", - "author_inst": "The University of Washington; Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Pooneh Hajian", - "author_inst": "The University of Washington" - }, - { - "author_name": "Kathleen Hayashibara", - "author_inst": "Thermo Fisher Scientific" - }, - { - "author_name": "Emily B Kennedy", - "author_inst": "OOMVELT" - }, - { - "author_name": "Marc Laurent", - "author_inst": "Helix OpCo" - }, - { - "author_name": "William Lee", - "author_inst": "Helix OpCo" - }, - { - "author_name": "Nicole A Leonetti", - "author_inst": "Helix OpCo" - }, - { - "author_name": "Jean Lozach", - "author_inst": "ROSALIND" - }, - { - "author_name": "James Lu", - "author_inst": "Helix OpCo" - }, - { - "author_name": "Jason M Nguyen", - "author_inst": "Helix OpCo" - }, - { - "author_name": "K M Clair O'Donovan", - "author_inst": "Biocomx" - }, - { - "author_name": "Troy Peck", - "author_inst": "Helix OpCo" - }, - { - "author_name": "Gail E Radcliffe", - "author_inst": "Radcliffe Consulting" - }, - { - "author_name": "Jimmy M Ramirez", - "author_inst": "Helix OpCo" - }, - { - "author_name": "Pavitra Roychoudhury", - "author_inst": "The University of Washington; Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Efren Sandoval", - "author_inst": "Helix OpCo" - }, - { - "author_name": "Brian Walsh", - "author_inst": "Innova Group" - }, - { - "author_name": "Marianne Weinell", - "author_inst": "Biocomx" - }, - { - "author_name": "Cassandra Wesselman", - "author_inst": "ROSALIND" - }, - { - "author_name": "Timothy Wesselman", - "author_inst": "ROSALIND" - }, - { - "author_name": "Simon White", - "author_inst": "Helix OpCo" - }, - { - "author_name": "Stephen Williams", - "author_inst": "Thermo Fisher Scientific" - }, - { - "author_name": "David Wong", - "author_inst": "Helix OpCo" - }, - { - "author_name": "Yufei Yu", - "author_inst": "Biocomx" - }, - { - "author_name": "Richard S Creager", - "author_inst": "NaviDx" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.05.475172", "rel_title": "High seroprevalence of SARS-CoV-2 in white-tailed deer (Odocoileus virginianus) at one of three captive cervid facilities in Texas", @@ -419785,6 +422483,33 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2022.01.06.475246", + "rel_title": "Climate Surveys of Biomedical PhD Students and Training Faculty Members in the Time of Covid", + "rel_date": "2022-01-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.06.475246", + "rel_abs": "In July 2020, four months into the disruption of normal life caused by the Covid-19 pandemic, we assessed the institutional climate within the School of Medicine. Voluntary surveys were completed by 135 graduate students in 11 PhD-granting programs and by 83 members of the graduate training faculty. Several themes emerged. PhD students work hard, but the number of hours spent on research-related activities has declined during the pandemic. The students are worried about the pandemics impact on their research productivity, consequent delays in their graduation, and diminished future job prospects. Many late stage PhD students feel they do not have adequate time or resources to plan for their future careers. Symptoms of anxiety and/or depression are prevalent in 51% of the students, based on answers to standardized questions. Most students report they have strong mentoring relationships with their faculty advisors and like their programs, but they identify to a lesser extent with the medical school as a whole. Faculty think highly of their graduate students and are also worried about the pandemics impact upon productivity and the welfare of students. Students are interested in access to an Ombuds office, which is currently being organized by the medical school. Moving forward, the school needs to address issues of bias, faculty diversity, support for mentor training, professional development, and the imposter syndrome. We must also work to create a climate in which many more graduate students feel that they are valued members of the academic medicine community.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Deepti Ramadoss", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Meghan Campbell McCord", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Johm P Horn", + "author_inst": "University of Pittsburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2022.01.05.21268323", "rel_title": "Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey", @@ -420046,125 +422771,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.05.22268782", - "rel_title": "Protection afforded by prior infection against SARS-CoV-2 reinfection with the Omicron variant", - "rel_date": "2022-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.22268782", - "rel_abs": "BACKGROUNDNatural SARS-CoV-2 infection elicits strong protection against reinfection with the Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2) variants. However, the Omicron (B.1.1.529) variant harbors multiple mutations that can mediate immune evasion. We estimated effectiveness of prior infection in preventing reinfection (PES) with Omicron and other SARS-CoV-2 variants in Qatar.\n\nMETHODSPES was estimated using the test-negative, case-control study design, employing a methodology that was recently investigated and validated for derivation of robust estimates for PES. Cases (PCR-positive persons with a variant infection) and controls (PCR-negative persons) were exact-matched by sex, 10-year age group, nationality, and calendar time of PCR test, to control for known differences in the risk of exposure to SARS-CoV-2 infection in Qatar.\n\nRESULTSPES against symptomatic reinfection was estimated at 90.2% (95% CI: 60.2-97.6) for Alpha, 84.8% (95% CI: 74.5-91.0) for Beta, 92.0% (95% CI: 87.9-94.7) for Delta, and 56.0% (95% CI: 50.6-60.9) for Omicron. Only 1 Alpha, 2 Beta, 0 Delta, and 2 Omicron reinfections progressed to severe COVID-19. None progressed to critical or fatal COVID-19. PES against hospitalization or death due to reinfection was estimated at 69.4% (95% CI: -143.6-96.2) for Alpha, 88.0% (95% CI: 50.7-97.1) for Beta, 100% (95% CI: 43.3-99.8) for Delta, and 87.8% (95% CI: 47.5-97.1) for Omicron.\n\nCONCLUSIONSProtection afforded by prior infection in preventing symptomatic reinfection with Alpha, Beta, or Delta is robust, at about 90%. While such protection against reinfection with Omicron is lower, it is still considerable at nearly 60%. Prior-infection protection against hospitalization or death at reinfection appears robust, regardless of variant.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Heba Altarawneh", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Hiam Chemaitelly", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Patrick Tang", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Mohammad Rubayet Hasan", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Suelen Qassim", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Houssein H. Ayoub", - "author_inst": "Qatar University" - }, - { - "author_name": "Sawsan AlMukdad", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "HADI M. YASSINE", - "author_inst": "Qatar University" - }, - { - "author_name": "Fatiha Benslimane", - "author_inst": "Qatar University" - }, - { - "author_name": "Hebah A. Al Khatib", - "author_inst": "Qatar University" - }, - { - "author_name": "Peter Coyle", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Zaina Al Kanaani", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Einas Al Kuwari", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Andrew Jeremijenko", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Anvar Hassan Kaleeckal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Ali Nizar Latif", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Riyazuddin Mohammad Shaik", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hanan F. Abdul Rahim", - "author_inst": "Qatar University" - }, - { - "author_name": "Gheyath Nasrallah", - "author_inst": "Qatar University" - }, - { - "author_name": "Mohamed Ghaith Al Kuwari", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Adeel A Butt", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hamad Eid Al Romaihi", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Mohamed H. Al-Thani", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Abdullatif Al Khal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Roberto Bertollini", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Laith J Abu-Raddad", - "author_inst": "Weill Cornell Medicine-Qatar" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.05.22268820", "rel_title": "Vaccinating children against COVID-19: commentary and mathematical modelling", @@ -421602,6 +424208,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.03.22268704", + "rel_title": "Immune responses to inactivated and vector-based vaccines in individuals previously infected with SARS-CoV-2", + "rel_date": "2022-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.03.22268704", + "rel_abs": "Immunity wanes in individuals previously infected with SARS-CoV-2, and vaccinating those individuals may help reduce reinfection. Herein, reactogenicity and immunogenicity following vaccination with inactivated (CoronaVac) and vector-based (ChAdOx1-S, AZD1222) vaccines were examined in previously infected individuals. Immune response was also compared between short and long intervals between first date of detection and vaccination. Adverse events were mild but were higher with AZD1222 than with CoronaVac. Baseline IgG-specific antibodies and neutralizing activity were significantly higher with shorter than longer intervals. With a single-dose vaccine, IgG and IgA-specific binding antibodies, neutralizing activity, and total interferon-gamma response peaked at 14 days. Immune response was significantly higher in recovered individuals than in infection-naive individuals. Antibody response was greater with longer than shorter intervals. AZD1222 induced higher antibody and T cell responses than those of CoronaVac. Thus, to achieve immunity, individuals with prior SARS-CoV-2 exposure may require only a single dose of AZD1222 or two doses of CoronaVac to achieve the immune response. These findings supported vaccine strategies in previously infected individuals.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Nungruthai Suntronwong", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Ritthideach Yorsaeng", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Chompoonut Auphimai", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Thanunrat Thongmee", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Preeyaporn Vichaiwattana", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Sitthichai Kanokudom", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Suvichada Assawakosri", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Pornjarim Nilyanimit", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Donchida Srimuan", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Thaksaporn Thatsanatorn", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Natthinee Sudhinaraset", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Nasamon Wanlapakorn", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Yong Poovorawan", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.01.03.22268681", "rel_title": "Reported Cases of Multisystem Inflammatory Syndrome in Children Aged 12 to 20 Years in the United States Who Received COVID-19 Vaccine, December 2020 through August 2021", @@ -421775,105 +424448,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.05.475037", - "rel_title": "An elite broadly neutralizing antibody protects SARS-CoV-2 Omicron variant challenge", - "rel_date": "2022-01-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.05.475037", - "rel_abs": "The strikingly high transmissibility and antibody evasion of SARS-CoV-2 Omicron variant have posted great challenges on the efficacy of current vaccines and antibody immunotherapy.Here, we screened 34 BNT162b2-vaccinees and cloned a public broadly neutralizing antibody (bNAb) ZCB11 from an elite vaccinee. ZCB11 neutralized all authentic SARS-CoV-2 variants of concern (VOCs), including Omicron and OmicronR346K with potent IC50 concentrations of 36.8 and 11.7 ng/mL, respectively. Functional analysis demonstrated that ZCB11 targeted viral receptor-binding domain (RBD) and competed strongly with ZB8, a known RBD-specific class II NAb. Pseudovirus-based mapping of 57 naturally occurred single mutations or deletions revealed that only S371L resulted in 11-fold neutralization resistance, but this phenotype was not observed in the Omicron variant. Furthermore,prophylactic ZCB11 administration protected lung infection against both the circulating pandemic Delta and Omicron variants in golden Syrian hamsters. These results demonstrated that vaccine-induced ZCB11 is a promising bNAb for immunotherapy against pandemic SARS-CoV-2 VOCs.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Biao Zhou", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Runhong Zhou", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Jasper Fuk-Woo Chan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Mengxiao Luo", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Qiaoli Peng", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Shuofeng Yuan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Bobo Wing-Yee Mok", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Bohao Chen", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Pui Wang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Vincent Kwok-Man Poon", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Hin Chu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Chris Chung-Sing Chan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Jessica Oi-Ling Tsang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Chris Chun-Yiu Chan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Ka-Kit Au", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Hiu-On Man", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Lu Lu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Kelvin Kai-Wang To", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Honglin Chen", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Kwok-Yung Yuen", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Zhiwei Chen", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.01.04.474974", "rel_title": "Sequence assignment validation in cryo-EM models with checkMySequence", @@ -423360,6 +425934,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.01.05.22268637", + "rel_title": "Personal Resilience, Social Support, and Organizational Support Impact Burnout among Nurses During COVID-19", + "rel_date": "2022-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.22268637", + "rel_abs": "BackgroundNurses have been under heavy workloads since the outbreak of COVID-19 and are at a high risk of infection, leading to a high level of psychosocial risk. This can adversely affect nurses both psychologically and physically. Burnout is caused by prolonged stress during work. In the nursing profession, burnout is common, potentially affecting the well-being of nurses and their productivity. The identification of factors that may contribute to maintaining mental health and reducing burnout among frontline nurses during a pandemic is essential.\n\nPurposeThe purpose of this study was to explore how personal resilience, social support, and organizational support impact burnout among frontline staff nurses.\n\nMethodsThis study involved 129 registered nurses from a COVID-19 designated hospital using four standardized scales.\n\nResultsThe mean age of the respondents was 29.46 years (standard deviation = 4.89). The mean number of years respondents worked in this organization was 5.60 years and the nursing profession was 4.16 years. Most of the respondents were female and held a bachelors degree in nursing. Multiple regression analysis was performed to predict burnout. Burnout was statistically significantly predicted by the multiple regression model (R2 = .420, F (3, 125) = 10.941, p < .0001; adjusted R2 = .406). Personal resilience, social support, and organizational support added statistically significantly to the prediction of burnout (p < .05).\n\nConclusionFindings from multiple regression analysis showed that nurses with low resilience and those who perceived inadequate social and organizational support had a higher risk of reporting more burnout. As a result of a bivariate analysis, there was no significant correlation between nurse variables and burnout level, except for age, which was negatively correlated with burnout level. Accordingly, young nurses tend to experience burnout, and nurse directors and managers must address this problem.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Hanan Daghash", + "author_inst": "Al-Ghad International Colleges for Health Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "nursing" + }, { "rel_doi": "10.1101/2022.01.05.22268646", "rel_title": "SARS-CoV-2 Genetic diversity and lineage dynamics of in Egypt", @@ -423589,25 +426182,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.05.22268786", - "rel_title": "Narrowing gap in regional and age-specific excess mortality in the first year and a half of COVID-19 in Hungary", - "rel_date": "2022-01-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.22268786", - "rel_abs": "In the first year and a half of the pandemic, the excess mortality in Hungary was 28,400, which was 1,700 lower than the official statistics on COVID-19 deaths. This discrepancy can be partly explained by protective measures instated during the COVID-19 pandemic that decreased the intensity of the seasonal flu outbreak, which caused on average 3,000 deaths per year. Compared to the second wave of the COVID-19 pandemic, the third wave showed a reduction in the differences in excess mortality between age groups and regions. The excess mortality rate for people aged 75+ fell significantly in the third wave, partly due to the vaccination schedule and the absence of a normal flu season. For people aged 40-77, the excess mortality rate rose slightly in the third wave. Between regions, excess mortality was highest in Northern Hungary and Western Transdanubia, and much lower in Central Hungary, where the capital is located. The excess mortality rate for men was almost twice as high as that for women in almost all age groups.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Csaba G. Toth", - "author_inst": "Centre for Economic and Regional Studies" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.04.22268750", "rel_title": "Cell-mediated and humoral immune response to SARS-CoV-2 vaccination and booster dose in immunosuppressed patients", @@ -425482,6 +428056,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.02.22268629", + "rel_title": "Cognitive predictors of vaccine hesitancy and COVID-19 mitigation behaviors in a population representative sample", + "rel_date": "2022-01-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.02.22268629", + "rel_abs": "With the continued threat of COVID-19, predictors of vaccination hesitancy and mitigation behaviors are critical to identify. Prior studies have found that cognitive factors are associated with some COVID-19 mitigation behaviors, but few studies employ representative samples and to our knowledge no prior studies have examined cognitive predictors of vaccine hesitancy. The purpose of the present study, conducted among a large national sample of Canadian adults, was to examine associations between cognitive variables (executive function, delay discounting, and temporal orientation) and COVID-19 mitigation behaviors (vaccination, mask wearing, social distancing, and hand hygiene). Findings revealed that individuals with few executive function deficits, limited delay discounting and who adopted a generally future-orientation mindset were more likely to be double-vaccinated and to report performing COVID-19 mitigation behaviors with high consistency. The most reliable findings were for delay discounting and future orientation, with executive function deficits predicting mask wearing and hand hygiene behaviors but not distancing and vaccination. These findings identify candidate mediators and moderators for health communication messages targeting COVID-19 mitigation behaviors and vaccine hesitancy.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anna Hudson", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Peter A Hall", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Sara Hitchman", + "author_inst": "University of Zurich" + }, + { + "author_name": "Gang Meng", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Geoffrey T Fong", + "author_inst": "University of Waterloo" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.30.21268571", "rel_title": "Estimation the state of the Covid-19 epidemic curve in Mayotte", @@ -425707,45 +428316,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.02.22268641", - "rel_title": "Integrin/TGF-Beta1 inhibitor GLPG-0187 blocks SARS-CoV-2 Delta and Omicron pseudovirus infection of airway epithelial cells which could attenuate disease severity", - "rel_date": "2022-01-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.02.22268641", - "rel_abs": "As COVID-19 continues to pose major risk for vulnerable populations including the elderly, immunocompromised, patients with cancer, and those with contraindications to vaccination, novel treatment strategies are urgently needed. SARS-CoV-2 infects target cells via RGD-binding integrins either independently or as a co-receptor with surface receptor angiotensin-converting enzyme 2 (ACE2). We used pan-integrin inhibitor GLPG-0187 to demonstrate blockade of SARS-CoV-2 pseudovirus infection of target cells. Omicron pseudovirus infected normal human small airway epithelial (HSAE) cells significantly less than D614G or Delta variant pseudovirus, and GLPG-0187 effectively blocked SARS-CoV-2 pseudovirus infection in a dose-dependent manner across multiple viral variants. GLPG-0187 inhibited Omicron and Delta pseudovirus infection of HSAE cells more significantly than other variants. Pre-treatment of HSAE cells with MEK inhibitor (MEKi) VS-6766 enhanced inhibition of pseudovirus infection by GLPG-0187. Because integrins activate TGF-{beta} signaling, we compared plasma levels of active and total TGF-{beta} in COVID-19+ patients. Plasma TGF-{beta}1 levels correlated with age, race, and number of medications upon presentation with COVID-19, but not with sex. Total plasma TGF-{beta}1 levels correlated with activated TGF-{beta}1 levels. In our preclinical studies, Omicron infects lower airway lung cells less efficiently than other COVID-19 variants. Moreover, inhibition of integrin signaling prevents SARS-CoV-2 Delta and Omicron pseudovirus infectivity, and may mitigate COVID-19 severity through decreased TGF-{beta}1 activation. This therapeutic strategy may be further explored through clinical testing in vulnerable and unvaccinated populations.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kelsey E. Huntington", - "author_inst": "Brown University" - }, - { - "author_name": "Lindsey Carlsen", - "author_inst": "Brown University" - }, - { - "author_name": "Eui-Young So", - "author_inst": "Brown University" - }, - { - "author_name": "Matthias Piesche", - "author_inst": "Universidad Catolica del Maule" - }, - { - "author_name": "Olin Liang", - "author_inst": "Brown University" - }, - { - "author_name": "Wafik El-Deiry", - "author_inst": "Brown University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.02.22268634", "rel_title": "Vaccines Elicit Highly Cross-Reactive Cellular Immunity to the SARS-CoV-2 Omicron Variant", @@ -427360,6 +429930,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2021.12.29.21268529", + "rel_title": "Humoral immune responses against SARS-CoV-2 variants including omicron in solid organ transplant recipients after three doses of a COVID-19 mRNA vaccine", + "rel_date": "2022-01-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.29.21268529", + "rel_abs": "BackgroundSolid organ transplant recipients (SOTR), who typically receive post-transplant immunosuppression, show increased COVID-19-related mortality. It is unclear whether an additional dose of COVID-19 vaccines in SOTR can overcome the reduced immune responsiveness against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants.\n\nMethodsWe performed a prospective cohort study of 53 SOTR receiving SARS-CoV-2 vaccination into a prospective cohort study performing detailed immunoprofiling of humoral immune responses against SARS-CoV-2 and its variants.\n\nResultsPrior to the additional vaccine dose, 60.3% of SOTR showed no measurable neutralization and only 18.9% demonstrated neutralizing activity of >90% following two vaccine doses. More intensive immunosuppression, antimetabolites in particular, negatively impacted antiviral immunity. While absolute IgG levels were lower in SOTR than controls, antibody titers against microbial recall antigens were in fact higher. In contrast, SOTR showed reduced vaccine-induced IgG/IgA antibody titers against SARS-CoV-2 and its delta variants. Vaccinated SOTR showed a markedly fewer linear B cell epitopes, indicating reduced B cell diversity. Importantly, a third vaccine dose led to an increase in anti-SARS-CoV-2 antibody titers and neutralizing activity across alpha, beta and delta variants. However, we observed a significant decrease in anti-spike antibody titers with the omicron variant.\n\nConclusionsOnly a small subgroup of SOTR generated functionally relevant antibodies after completing the initial vaccine series based on dysfunctional priming of immune responses against novel antigens. An additional dose of the vaccine results in dramatically improved antibody responses against all SARS-CoV-2 variants except omicron.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Kapil K. Saharia", + "author_inst": "Institute of Human Virology, University of Maryland School of Medicine" + }, + { + "author_name": "Jennifer S. Husson", + "author_inst": "Institute of Human Virology, University of Maryland School of Medicine" + }, + { + "author_name": "Silke V. Niederhaus", + "author_inst": "Department of Surgery, University of Maryland School of Medicine" + }, + { + "author_name": "Thierry Iraguha", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Stephanie V. Avila", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Youngchae J. Yoo", + "author_inst": "Institute of Human Virology, University of Maryland School of Medicine" + }, + { + "author_name": "Nancy M. Hardy", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Xiaoxuan Fan", + "author_inst": "University of Maryland Greenebaum Comprehensive Cancer Center" + }, + { + "author_name": "Destiny Omili", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Alice Crane", + "author_inst": "Department of Surgery, University of Maryland School of Medicine" + }, + { + "author_name": "Amber Carrier", + "author_inst": "Department of Surgery, University of Maryland School of Medicine" + }, + { + "author_name": "Wen Y. Xie", + "author_inst": "Department of Surgery, University of Florida College of Medicine" + }, + { + "author_name": "Erica Vander Mause", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Kim Hankey", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Sheri Bauman", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Patricia Lesho", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Heather D. Mannuel", + "author_inst": "University of Maryland Greenebaum Comprehensive Cancer Center" + }, + { + "author_name": "Ashish Ahuja", + "author_inst": "Department of Medicine, University of Maryland Medical Center" + }, + { + "author_name": "Minu Mathew", + "author_inst": "Divison of Infectious Diseases, University of Maryland School of Medicine" + }, + { + "author_name": "James Avruch", + "author_inst": "Department of Surgery, University of Maryland School of Medicine" + }, + { + "author_name": "John Baddley", + "author_inst": "Institute of Human Virology, University of Maryland School of Medicine" + }, + { + "author_name": "Olga Goloubeva", + "author_inst": "Department of Epidemiology and Public Health, University of Maryland Greenebaum Comprehensive Cancer Center" + }, + { + "author_name": "Kirti Shetty", + "author_inst": "Division of Hepatology/Liver Transplantation, University of Maryland School of Medicine," + }, + { + "author_name": "Saurabh Dahiya", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Aaron P. Rapoport", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Tim Luetkens", + "author_inst": "Department of Microbiology and Immunology, University of Maryland" + }, + { + "author_name": "Djordje Atanackovic", + "author_inst": "University of Maryland Greenebaum Comprehensive Cancer Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "transplantation" + }, { "rel_doi": "10.1101/2021.12.30.21268565", "rel_title": "Effectiveness of COVID-19 vaccines against Omicron or Delta infection", @@ -427505,181 +430198,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.30.21267519", - "rel_title": "Antibody binding and ACE2 binding inhibition is significantly reduced for the Omicron variant compared to all other variants of concern", - "rel_date": "2022-01-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.30.21267519", - "rel_abs": "The rapid emergence of the Omicron variant and its large number of mutations has led to its classification as a variant of concern (VOC) by the WHO(1). Initial studies on the neutralizing response towards this variant within convalescent and vaccinated individuals have identified substantial reductions(2-8). However many of these sample sets used in these studies were either small, uniform in nature, or were compared only to wild-type (WT) or, at most, a few other VOC. Here, we assessed IgG binding, (Angiotensin-Converting Enzyme 2) ACE2 binding inhibition, and antibody binding dynamics for the omicron variant compared to all other VOC and variants of interest (VOI)(9), in a large cohort of infected, vaccinated, and infected and then vaccinated individuals. While omicron was capable of binding to ACE2 efficiently, antibodies elicited by infection or immunization showed reduced IgG binding and ACE2 binding inhibition compared to WT and all VOC. Among vaccinated samples, antibody binding responses towards omicron were only improved following administration of a third dose. Overall, our results identify that omicron can still bind ACE2 while pre-existing antibodies can bind omicron. The extent of the mutations appear to inhibit the development of a neutralizing response, and as a result, omicron remains capable of evading immune control.", - "rel_num_authors": 40, - "rel_authors": [ - { - "author_name": "Daniel Junker", - "author_inst": "NMI" - }, - { - "author_name": "Matthias Becker", - "author_inst": "NMI" - }, - { - "author_name": "Teresa Wagner", - "author_inst": "NMI" - }, - { - "author_name": "Philipp D Kaiser", - "author_inst": "NMI" - }, - { - "author_name": "Sandra Maier", - "author_inst": "NMI" - }, - { - "author_name": "Tanja M Grimm", - "author_inst": "NMI" - }, - { - "author_name": "Johanna Griesbaum", - "author_inst": "NMI" - }, - { - "author_name": "Patrick Marsall", - "author_inst": "NMI" - }, - { - "author_name": "Jens Gruber", - "author_inst": "NMI" - }, - { - "author_name": "Bjoern Traenkle", - "author_inst": "NMI" - }, - { - "author_name": "Constanze Heinzel", - "author_inst": "Institute for Tropical Medicine, University of Tuebingen" - }, - { - "author_name": "Yudi T Pinilla", - "author_inst": "Institute for Tropical Medicine, University of Tuebingen" - }, - { - "author_name": "Jana Held", - "author_inst": "Institute for Tropical Medicine, University of Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Rolf Fendel", - "author_inst": "Eberhard Karls Universitat Tubingen" - }, - { - "author_name": "Andrea Kreidenweiss", - "author_inst": "University of Tuebingen" - }, - { - "author_name": "Annika Nelde", - "author_inst": "University of Tuebingen" - }, - { - "author_name": "Yacine Maringer", - "author_inst": "University of Tuebingen" - }, - { - "author_name": "Sarah Schroeder", - "author_inst": "University Hospital Tuebingen" - }, - { - "author_name": "Juliane S Walz", - "author_inst": "University of Tuebingen" - }, - { - "author_name": "Karina Althaus", - "author_inst": "University Hospital Tuebingen" - }, - { - "author_name": "Guenalp Uzun", - "author_inst": "University Hospital Tuebingen" - }, - { - "author_name": "Marco Mikus", - "author_inst": "University Hospital Tuebingen" - }, - { - "author_name": "Tamam Bakchoul", - "author_inst": "University Hospital Tuebingen" - }, - { - "author_name": "Katja Schenke-Layland", - "author_inst": "NMI" - }, - { - "author_name": "Stefanie Bunk", - "author_inst": "University Hospital Tuebingen" - }, - { - "author_name": "Helene Haeberle", - "author_inst": "University Hospital Tuebingen" - }, - { - "author_name": "Michael Bitzer", - "author_inst": "University Hospital Tuebingen" - }, - { - "author_name": "Siri Goepel", - "author_inst": "University Hospital Tuebingen" - }, - { - "author_name": "Hanna Renk", - "author_inst": "University Children's Hospital Tuebingen" - }, - { - "author_name": "Jonathan Remppis", - "author_inst": "University Children's Hospital Tuebingen" - }, - { - "author_name": "Corinna Engel", - "author_inst": "University Children's Hospital Tuebingen" - }, - { - "author_name": "Axel R Franz", - "author_inst": "University Children's Hospital Tuebingen" - }, - { - "author_name": "Manuela Harries", - "author_inst": "Helmholtz Zentrum for Infektionsforschung" - }, - { - "author_name": "Barbora Kessel", - "author_inst": "Helmholtz Zentrum for Infektionsforschung" - }, - { - "author_name": "Monika Strengert", - "author_inst": "Helmholtz Center for Infection Research" - }, - { - "author_name": "Gerard Krause", - "author_inst": "Helmholtz Center for Infection Research" - }, - { - "author_name": "Anne Zeck", - "author_inst": "NMI" - }, - { - "author_name": "Ulrich Rothbauer", - "author_inst": "NMI" - }, - { - "author_name": "Alex Dulovic", - "author_inst": "NMI" - }, - { - "author_name": "Nicole Schneiderhan-Marra", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.30.21268532", "rel_title": "Waning of SARS-CoV-2 Antibody levels response to inactivated cellular vaccine over 6 months among healthcare workers", @@ -429594,6 +432112,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.24.474110", + "rel_title": "Reduced infectivity but increased immune escape of the new SARS-CoV-2 variant of concern Omicron", + "rel_date": "2021-12-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.24.474110", + "rel_abs": "A new detected SARS-CoV-2 variant Omicron (B.1.1.529) had reported from more than 80 countries. In the past few weeks, a new wave of infection driven by Omicron is in progress. Omicron Spike (S) protein pseudotyped virus was used to determine the effect of S mutations on its capacity of infectivity and immune evasion. Our results showed the lower entry efficiency and less cleavage ability of Omicron than D614G variant. Pseudotype-based neutralizing assay was performed to analyze neutralizing antibodies elicited by previously infection or the RBD-based protein subunit vaccine ZF2001 against the Omicron variant. Sera sampled at around one month after symptom onset from 12 convalescents who were previously infected by SARS-CoV-2 original strain shows a more than 20-fold decrease of neutralizing activity against Omicron variant, when compared to D614G variant. Among 12 individuals vaccinated by RBD subunit vaccine, 58.3% (7/12) sera sampled at 15-60 days after 3rd-dose vaccination did not neutralize Omicron. Geometric mean titers (GMTs, 50% inhibitory dose [ID50]) of these sera against Omicron were 9.4-fold lower than against D614G. These results suggested a higher risk of Omicron breakthrough infections and reduced efficiency of the protective immunity elicited by existing vaccines. There are important implications about the modification and optimization of the current epidemic prevention and control including vaccine strategies and therapeutic antibodies against Omicron variant.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jie Hu", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Pai Peng", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Kang Wu", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Quan-xin Long", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Juan Chen", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Kai Wang", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Ni Tang", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Ailong Huang", + "author_inst": "Chongqing Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.30.21268537", "rel_title": "The rich-to-poor vaccine donation game: When will self-interested countries donate their surplus vaccines during pandemics?", @@ -429715,109 +432280,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.29.474402", - "rel_title": "Structural and functional characterizations of altered infectivity and immune evasion of SARS-CoV-2 Omicron variant", - "rel_date": "2021-12-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.29.474402", - "rel_abs": "The SARS-CoV-2 Omicron with increased fitness is spreading rapidly worldwide. Analysis of cryo-EM structures of the Spike (S) from Omicron reveals amino acid substitutions forging new interactions that stably maintain an \"active\" conformation for receptor recognition. The relatively more compact domain organization confers improved stability and enhances attachment but compromises the efficiency of viral fusion step. Alterations in local conformation, charge and hydrophobic microenvironments underpin the modulation of the epitopes such that they are not recognized by most NTD- and RBD-antibodies, facilitating viral immune escape. Apart from already existing mutations, we have identified three new immune escape sites: 1) Q493R, 2) G446S and 3) S371L/S373P/S375F that confers greater resistance to five of the six classes of RBD-antibodies. Structure of the Omicron S bound with human ACE2, together with analysis of sequence conservation in ACE2 binding region of 25 sarbecovirus members as well as heatmaps of the immunogenic sites and their corresponding mutational frequencies sheds light on conserved and structurally restrained regions that can be used for the development of broad-spectrum vaccines and therapeutics.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Zhen Cui", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Pan Liu", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Nan Wang", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Lei Wang", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Kaiyue Fan", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Qianhui Zhu", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Kang Wang", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Ruihong Chen", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Rui Feng", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Zijing Jia", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Minnan Yang", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Boling Zhu", - "author_inst": "the Center for Biological Imaging (CBI), Institute of Biophysics, Chinese Academy of Science" - }, - { - "author_name": "Wangjun Fu", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Tianming Chu", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Leilei Feng", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Yide Wang", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Xinran Pei", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Peng Yang", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Xiaoliang Sunney Xie", - "author_inst": "School of life Science, Peking University" - }, - { - "author_name": "Lei Cao", - "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Yunlong Richard Cao", - "author_inst": "Peking University" - }, - { - "author_name": "Xiangxi Wang", - "author_inst": "CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Bi" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.12.30.474535", "rel_title": "Broad neutralization of SARS-CoV-2 variants by an inhalable bispecific single-domain antibody", @@ -431588,6 +434050,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2021.12.27.21268459", + "rel_title": "Immunogenicity of heterologous BNT162b2 booster in fully vaccinated individuals with CoronaVac against SARS-CoV-2 variants Delta and Omicron: the Dominican Republic Experience", + "rel_date": "2021-12-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.27.21268459", + "rel_abs": "The recent emergence of the SARS-CoV-2 Omicron variant is raising concerns because of its increased transmissibility and by its numerous spike mutations with potential to evade neutralizing antibodies elicited by COVID-19 vaccines. The Dominican Republic was among the first countries in recommending the administration of a third dose COVID-19 vaccine to address potential waning immunity and reduced effectiveness against variants. Here, we evaluated the effects of a heterologous BNT162b2 mRNA vaccine booster on the humoral immunity of participants that had received a two-dose regimen of CoronaVac, an inactivated vaccine used globally. We found that heterologous CoronaVac prime followed by BNT162b2 booster regimen induces elevated virus-specific antibody levels and potent neutralization activity against the ancestral virus and Delta variant, resembling the titers obtained after two doses of mRNA vaccines. While neutralization of Omicron was undetectable in participants that had received a two-dose regimen of CoronaVac vaccine, BNT162b2 booster resulted in a 1.4-fold increase in neutralization activity against Omicron, compared to two-dose mRNA vaccine. Despite this increase, neutralizing antibody titers were reduced by 6.3-fold and 2.7-fold for Omicron compared to ancestral and Delta variant, respectively. Surprisingly, previous SARS-CoV-2 infection did not affect the neutralizing titers for Omicron in participants that received the heterologous regimen. Our findings have immediate implications for multiples countries that previously used a two-dose regimen of CoronaVac and reinforce the notion that the Omicron variant is associated with immune escape from vaccines or infection-induced immunity, highlighting the global need for vaccine boosters to combat the impact of emerging variants.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Eddy Perez-Then", + "author_inst": "Ministry of Health, Santo Domingo, Dominican Republic." + }, + { + "author_name": "Carolina Lucas", + "author_inst": "Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA." + }, + { + "author_name": "Valter Silva Monteiro", + "author_inst": "Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA." + }, + { + "author_name": "Marija Miric", + "author_inst": "Two Oceans in Health, Santo Domingo, Dominican Republic." + }, + { + "author_name": "Vivian Brache", + "author_inst": "Departamento de Investigaciones Biomedicas, Clinica Evangelina Rodriguez, PROFAMILIA. Santo Domingo, Dominican Republic." + }, + { + "author_name": "Leila Cochon", + "author_inst": "Departamento de Investigaciones Biomedicas, Clinica Evangelina Rodriguez, PROFAMILIA. Santo Domingo, Dominican Republic." + }, + { + "author_name": "Chantal B.F. Vogels", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA." + }, + { + "author_name": "Elena De la Cruz", + "author_inst": "Departamento de Investigaciones Biomedicas, Clinica Evangelina Rodriguez, PROFAMILIA. Santo Domingo, Dominican Republic." + }, + { + "author_name": "Aidelis Jorge", + "author_inst": "Departamento de Investigaciones Biomedicas, Clinica Evangelina Rodriguez, PROFAMILIA. Santo Domingo, Dominican Republic." + }, + { + "author_name": "Margarita De los Santos", + "author_inst": "Departamento de Investigaciones Biomedicas, Clinica Evangelina Rodriguez, PROFAMILIA. Santo Domingo, Dominican Republic." + }, + { + "author_name": "Patricia Leon", + "author_inst": "Laboratorio de Referencia, Dominican Republic." + }, + { + "author_name": "Mallery I. Breban", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA." + }, + { + "author_name": "Kendall Billig", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA." + }, + { + "author_name": "Inci Yildirim", + "author_inst": "Department of Pediatric, Section of Infectious Diseases and Global Health; Yale University School of Medicine, New Haven, CT, USA." + }, + { + "author_name": "Claire Pearson", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, USA" + }, + { + "author_name": "Randy Downing", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, USA" + }, + { + "author_name": "Emily Gagnon", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, USA" + }, + { + "author_name": "Anthony Muyombwe", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, USA" + }, + { + "author_name": "Jafar Razeq", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, USA" + }, + { + "author_name": "Melissa Campbell", + "author_inst": "Department of Pediatric, Section of Infectious Diseases and Global Health; Yale University School of Medicine, New Haven, CT, USA." + }, + { + "author_name": "Albert Ko", + "author_inst": "Yale University School of Public Health" + }, + { + "author_name": "Saad B. Omer", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA." + }, + { + "author_name": "Nathan D Grubaugh", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Sten H. Vermund", + "author_inst": "Yale School of Public Health, New Haven, CT, USA." + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Yale University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.27.21268416", "rel_title": "Divergent SARS CoV-2 Omicron-specific T- and B-cell responses in COVID-19 vaccine recipients", @@ -431825,101 +434402,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.12.27.21268348", - "rel_title": "COVID-19 in children in NSW, Australia, during the 2021 Delta outbreak: Severity and Disease spectrum", - "rel_date": "2021-12-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.27.21268348", - "rel_abs": "Objective(s)To describe the severity and clinical spectrum of SARS-CoV-2 infection in Australian children during the 2021 Delta outbreak.\n\nDesign, Setting & ParticipantsA prospective cohort study of children <16 years with a positive SARS-CoV-2 nucleic acid test cared for by the Sydney Childrens Hospital Network (SCHN) virtual and inpatient medical teams between 1 June - 31 October 2021.\n\nMain outcome measuresDemographic and clinical data from all admitted patients and a random sample of outpatients managed under the SCHN virtual care team were analysed to identify risk factors for admission to hospital.\n\nResultsThere were 17,474 SARS-CoV-2 infections in children <16 years in NSW during the study period, of whom 11,985 (68.6%) received care coordinated by SCHN. Twenty one percent of children infected with SARS-CoV-2 were asymptomatic. For every 100 SARS-CoV-2 infections in children <16 years, 1.26 (95% CI 1.06 to 1.46) required hospital admission for medical care; while 2.46 (95% CI 2.18 to 2.73) required admission for social reasons only. Risk factors for hospitalisation for medical care included age <6 months, a history of prematurity, age 12 to <16 years, and a history of medical comorbidities (aOR 7.23 [95% CI 2.92 to 19.4]). Of 17,474 infections, 15 children (median age 12.8years) required ICU admission; and 294 children required hospital admission due to social or welfare reasons.\n\nConclusionThe majority of children with SARS-CoV-2 infection (Delta variant) had asymptomatic or mild disease. Hospitalisation was uncommon and occurred most frequently in young infants and adolescents with comorbidities. More children were hospitalised for social reasons than for medical care.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Phoebe Williams", - "author_inst": "Faculty of Medicine and Health, University of Sydney" - }, - { - "author_name": "Archana Koirala", - "author_inst": "National Centre for Immunisation Research and Surveillance" - }, - { - "author_name": "Gemma Saravanos", - "author_inst": "Faculty of Medicine and Health, University of Sydney" - }, - { - "author_name": "Laura Lopez", - "author_inst": "National Centre for Immunisation Research and Surveillance" - }, - { - "author_name": "Catherine Glover", - "author_inst": "National Centre for Immunisation Research and Surveillance" - }, - { - "author_name": "Ketaki Sharma", - "author_inst": "National Centre for Immunisation Research and Surveillance" - }, - { - "author_name": "Tracey Williams", - "author_inst": "Sydney Children's Hospitals Network" - }, - { - "author_name": "Emma Carey", - "author_inst": "National Centre for Immunisation Research and Surveillance" - }, - { - "author_name": "Nadine Shaw", - "author_inst": "Sydney Children's Hospitals Network" - }, - { - "author_name": "Emma Dickins", - "author_inst": "Sydney Children's Hospitals Network" - }, - { - "author_name": "Neela Sitaram", - "author_inst": "Sydney Children's Hospitals Network" - }, - { - "author_name": "Joanne Ging", - "author_inst": "Sydney Children's Hospitals Network" - }, - { - "author_name": "Paula Bray", - "author_inst": "Sydney Children's Hospitals Network" - }, - { - "author_name": "Nigel Crawford", - "author_inst": "Royal Children's Hospital, Melbourne and Murdoch Children's Research Institute" - }, - { - "author_name": "Brendan McMullan", - "author_inst": "Sydney Children's Hospitals Network" - }, - { - "author_name": "Kristine Macartney", - "author_inst": "National Centre for Immunisation Research and Surveillance" - }, - { - "author_name": "Nicholas Wood", - "author_inst": "National Centre for Immunisation Research and Surveillance" - }, - { - "author_name": "Beth Fulton", - "author_inst": "Sydney Children's Hospitals Network" - }, - { - "author_name": "Christine Lau", - "author_inst": "Sydney Children's Hospitals Network" - }, - { - "author_name": "Philip N Britton", - "author_inst": "University of Sydney" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.24.21268174", "rel_title": "Emergence in Southern France of a new SARS-CoV-2 variant of probably Cameroonian origin harbouring both substitutions N501Y and E484K in the spike protein", @@ -433714,6 +436196,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.27.474218", + "rel_title": "Vaccine-breakthrough infection by the SARS-CoV-2 Omicron variant elicits broadly cross-reactive immune responses", + "rel_date": "2021-12-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.27.474218", + "rel_abs": "Highly transmissible SARS-CoV-2 Omicron variant has posted a new crisis for COVID-19 pandemic control. Within a month, Omicron is dominating over Delta variant in several countries probably due to immune evasion. It remains unclear whether vaccine-induced memory responses can be recalled by Omicron infection. Here, we investigated host immune responses in the first vaccine-breakthrough case of Omicron infection in Hong Kong. We found that the breakthrough infection rapidly recruited potent cross-reactive broad neutralizing antibodies (bNAbs) against current VOCs, including Alpha, Beta, Gamma, Delta and Omicron, from unmeasurable IC50 values to mean 1:2929 at around 9-12 days, which were higher than the mean peak IC50 values of BioNTech-vaccinees. Cross-reactive spike- and nucleocapsid-specific CD4 and CD8 T cell responses were detected. Similar results were also obtained in the second vaccine-breakthrough case of Omicron infection. Our preliminary findings may have timely implications to booster vaccine optimization and preventive strategies of pandemic control.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Runhong Zhou", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Kelvin Kai-Wang To", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Qiaoli Peng", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Jacky Man-Chun Chan", + "author_inst": "Princess Margaret Hospital" + }, + { + "author_name": "Haode Huang", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Dawei Yang", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Bosco Hoi-Shiu Lam", + "author_inst": "Princess Margaret Hospital" + }, + { + "author_name": "Vivien Wai-Man Chuang", + "author_inst": "Quality & Safety Division, Hospital Authority" + }, + { + "author_name": "Jian-Piao Cai", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Na Liu", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Ka-Kit Au", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Owen Tak-Yin Tsang", + "author_inst": "Princess Margaret Hospital" + }, + { + "author_name": "Kwok-Yung Yuen", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Zhiwei Chen", + "author_inst": "The University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.26.472655", "rel_title": "Evaluation of maternal-infant dyad inflammatory cytokines in pregnancies affected by maternal SARS-CoV-2 infection in early and late gestation.", @@ -433923,33 +436476,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.28.474338", - "rel_title": "Improved binding affinity of the Omicron's spike protein with hACE2 receptor is the key factor behind its increased virulence", - "rel_date": "2021-12-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.28.474338", - "rel_abs": "The new variant of SARS-CoV-2, Omicron, has been quickly spreading in many countries worldwide. Compared to the original virus, Omicron is characterized by several mutations in its genomic region, including spike proteins receptor-binding domain (RBD). We have computationally investigated the interaction between RBD of both wild-type and omicron variants with hACE2 receptor using molecular dynamics and MM-GBSA based binding free energy calculations. The mode of the interaction between Omicrons RBD to the human ACE2 (hACE2) receptor is similar to the original SARS-CoV-2 RBD except for a few key differences. The binding free energy difference shows that the spike protein of Omicron has increased binding affinity for the hACE-2 receptor. The mutated residues in the RBD showed strong interactions with a few amino acid residues of the hACE2. More specifically, strong electrostatic interactions (salt bridges) and hydrogen bonding were observed between R493 and R498 residues of the Omicron RBD with D30/E35 and D38 residues of the hACE2, respectively. Other mutated amino acids in the Omicron RBD, e.g. S496 and H505, also exhibited hydrogen bonding with the hACE2 receptor. The pi-stacking interaction was also observed between tyrosine residues (RBD-Tyr501: hACE2-Tyr41) in the complex, which contributes majorly to binding free energies suggesting this as one of the key interactions stabilizing the complex formation. The structural insights of RBD:hACE2 complex, their binding mode information and residue wise contributions to binding free energy provide insight on the increased transmissibility of Omicron and pave the way to design and optimize novel antiviral agents.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rajender Kumar", - "author_inst": "KTH Royal Institute of Technology" - }, - { - "author_name": "Murugan Natarajan Arul", - "author_inst": "KTH" - }, - { - "author_name": "Vaibhav Srivastava", - "author_inst": "KTH" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.12.26.474085", "rel_title": "SARS-CoV-2 Omicron-B.1.1.529 Variant leads to less severe disease than Pango B and Delta variants strains in a mouse model of severe COVID-19", @@ -435900,6 +438426,85 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.12.26.473325", + "rel_title": "Comparative analysis of single cell lung atlas of bat, cat, tiger and pangolin", + "rel_date": "2021-12-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.26.473325", + "rel_abs": "Horseshoe bats (Rhinolophus sinicus) might help maintain coronaviruses severely affecting human health, such as SARS-CoV and SARS-CoV-2. It has long been suggested that bats may be more tolerant of viral infection than other mammals due to their unique immune system, but the exact mechanism remains to be fully explored. During the COVID-19 pandemic, multiple animal species were diseased by SARS-CoV-2 infection, especially in the respiratory system. Herein, single-cell transcriptomic data of the lungs of a horseshoe bat, a cat, a tiger, and a pangolin were generated. The receptor distribution of twenty-eight respiratory viruses belonging to fourteen viral families were characterized for the four species. Comparison on the immune-related transcripts further revealed limited cytokine activations in bats, which might explain the reason why bats experienced only mild diseases or even no symptoms upon virus infection. Our findings might increase our understanding of the immune background of horseshoe bats and their insensitivity to virus infections.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Xiran Wang", + "author_inst": "National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong L" + }, + { + "author_name": "Zhihua Ou", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China." + }, + { + "author_name": "Peiwen Ding", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Chengcheng Sun", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; School of Basic Medicine, Qing" + }, + { + "author_name": "Daxi Wang", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China." + }, + { + "author_name": "Jiacheng Zhu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Wendi Wu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; School of Basic Medicine, Qing" + }, + { + "author_name": "Yanan Wei", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; School of Basic Medicine, Qing" + }, + { + "author_name": "Xiangning Ding", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Lihua Luo", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Meiling Li", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Wensheng Zhang", + "author_inst": "School of Basic Medical Sciences, Binzhou Medical University, No. 346, Guanhai Road, Laishan District, Yantai City, Shandong, China" + }, + { + "author_name": "Xin Jin", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Jian Sun", + "author_inst": "National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong L" + }, + { + "author_name": "Huan Liu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Dongsheng Chen", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.21.21268143", "rel_title": "Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission", @@ -436505,37 +439110,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.24.21268382", - "rel_title": "Early estimates of SARS-CoV-2 Omicron variant severity based on a matched cohort study, Ontario, Canada", - "rel_date": "2021-12-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.24.21268382", - "rel_abs": "While it is now evident that Omicron is rapidly replacing Delta, largely due to immune escape, it is less clear how the severity of Omicron compares to Delta. In Ontario, we sought to examine hospitalization and death associated with Omicron, as compared to cases infected with Delta. We conducted a matched cohort study, considering time to hospitalization or death as the outcome. Cases were matched on gender, age, vaccination status, health region and onset date. We identified 29,594 Omicron cases that met eligibility criteria, of which 11,622 could be matched with at least one Delta case (N=14,181). There were 59 (0.51%) hospitalizations and 3 (0.03%) deaths among matched Omicron cases, compared to 221 (1.6%) hospitalizations and 17 (0.12%) deaths among matched Delta cases. The risk of hospitalization or death was 65% lower (hazard ratio, HR=0.35, 95%CI: 0.26, 0.46) among Omicron cases compared to Delta cases, while risk of intensive care unit admission or death was 83% lower (HR=0.17, 95%CI: 0.08, 0.37). While severity is likely to be reduced, the absolute number of hospitalizations and impact on the healthcare system may nevertheless be significant due to the increased transmissibility of Omicron.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ana Cecilia Ulloa", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Sarah A Buchan", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Nick Daneman", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Kevin Antoine Brown", - "author_inst": "Public Health Ontario" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.22.21268217", "rel_title": "Humoral Immunogenicity of Three COVID-19 mRNA Vaccine Doses in Patients with Inflammatory Bowel Disease", @@ -438234,6 +440808,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.23.21267374", + "rel_title": "Immunogenicity and Safety Following a Homologous Booster Dose of a SARS-CoV-2 recombinant spike protein vaccine (NVX-CoV2373): A Phase 2 Randomized Placebo-Controlled Trial", + "rel_date": "2021-12-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21267374", + "rel_abs": "BackgroundEmerging SARS-CoV-2 variants and evidence of waning vaccine efficacy present significant obstacles toward controlling the COVID-19 pandemic. Booster doses of SARS-CoV-2 vaccines may address these concerns by both amplifying and broadening the immune responses seen with initial vaccination regimens.\n\nMethodsIn a phase 2 study, a single booster dose of a SARS-CoV-2 recombinant spike protein vaccine with Matrix-M adjuvant (NVX-CoV2373) was administered to healthy adult participants 18 to 84 years of age approximately 6 months following their primary two-dose vaccination series. Safety and immunogenicity parameters were assessed, including assays for IgG, MN50, and hACE2 receptor binding inhibition against the ancestral SARS-CoV-2 strain and select variants (B.1.351 [Beta], B.1.1.7 [Alpha], B.1.617.2 [Delta], and B.1.1.529 [Omicron]). This trial is registered with ClinicalTrials.gov, NCT04368988.\n\nFindingsAn incremental increase in the incidence of solicited local and systemic reactogenicity events was observed with subsequent vaccinations. Following the booster, incidence rates of local and systemic reactions were 82.5% (13.4% [≥] Grade 3) and 76.5% (15.3% [≥] Grade 3), respectively, compared to 70.0% (5.2% [≥] Grade 3) and 52.8% (5.6% [≥] Grade 3), respectively, following the primary vaccination series. Events were primarily mild or moderate in severity and transient in nature, with a median duration of 1.0 to 2.5 days. Immune responses seen 14 days following the primary vaccination series were compared with those observed 28 days following the booster (Day 35 and Day 217, respectively). For the ancestral SARS-CoV-2 strain, serum IgG geometric mean titers (GMTs) increased [~]4.7-fold from 43,905 ELISA units (EU) at day 35 to 204,367 EU at Day 217. Neutralization (MN50) assay GMTs showed a similar increase of [~]4.1-fold from 1,470 at day 35 to 6,023 at Day 217. A functional hACE2 receptor binding inhibition assay analyzing activity against ancestral and variant strains of SARS-CoV-2 at Day 189 vs Day 217 found 54.4-fold (Ancestral), 21.9-fold (Alpha), 24.5-fold (Beta), 24.4-fold (Delta), and 20.1-fold (Omicron) increases in titers. An anti-rS IgG activity assay comparing the same time points across the same SARS-CoV-2 strains found titers improved 61.2-fold, 85.9-fold, 65.0-fold, 92.5-fold, and 73.5-fold, respectively.\n\nInterpretationAdministration of a booster dose of NVX-CoV2373 approximately 6 months following the primary vaccination series resulted in an incremental increase in reactogenicity along with enhanced immune responses. For both the prototype strain and all variants evaluated, immune responses following the booster were notably higher than those associated with high levels of efficacy in phase 3 studies of the vaccine.\n\nFundingNovavax(R) and the Coalition for Epidemic Preparedness Innovations (CEPI(R)).", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Raburn Mallory", + "author_inst": "Novavax" + }, + { + "author_name": "Neil Formica", + "author_inst": "Novavax" + }, + { + "author_name": "Susan Pfeiffer", + "author_inst": "Novavax" + }, + { + "author_name": "Bethanie Wilkinson", + "author_inst": "Novavax" + }, + { + "author_name": "Alex Marcheschi", + "author_inst": "Novavax" + }, + { + "author_name": "Gary Albert", + "author_inst": "Novavax" + }, + { + "author_name": "Heather McFall", + "author_inst": "Novavax" + }, + { + "author_name": "Michelle Robinson", + "author_inst": "Novavax" + }, + { + "author_name": "Joyce Plested", + "author_inst": "Novavax" + }, + { + "author_name": "MingZhu Zhu", + "author_inst": "Novavax" + }, + { + "author_name": "Shane Cloney-Clark", + "author_inst": "Novavax" + }, + { + "author_name": "Bin Zhou", + "author_inst": "Novavax" + }, + { + "author_name": "Gordon Chau", + "author_inst": "Novavax" + }, + { + "author_name": "Andreana Robertson", + "author_inst": "Novavax" + }, + { + "author_name": "Sonia Maciejewski", + "author_inst": "Novavax" + }, + { + "author_name": "Gale Smith", + "author_inst": "Novavax" + }, + { + "author_name": "Nita Patel", + "author_inst": "Novavax" + }, + { + "author_name": "Gregory M Glenn", + "author_inst": "Novavax" + }, + { + "author_name": "Filip Dubovsky", + "author_inst": "Novavax" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.23.21268332", "rel_title": "Extending upon: What effect might border screening have on preventing importation of COVID-19 compared with other infections? - Considering the additional effect of post-arrival isolation", @@ -438319,61 +440984,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.24.21268367", - "rel_title": "Genomic surveillance reveals the emergence of SARS-CoV-2 Lineage A from Islamabad Pakistan", - "rel_date": "2021-12-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.24.21268367", - "rel_abs": "The lineage A of SARS-CoV-2 has been around the world since the start of the pandemic. In Pakistan the last case of lineage A was reported in April, 2021 since then no case has been reported. In November, 2021 during routine genomic surveillance at National Institute of Health we have found 07 cases of lineage A from Islamabad, Pakistan. The study reports two novel deletions in the spike glycoprotein. One 09 amino acid deletion (68-76 a.a) is found in the S1 subunit while another 10 amino acid deletion (679-688 a.a) observed at the junction of S1/S2 referred as furin cleavage site. The removal of furin cleavage site may result in impaired virus replication thus decreasing its pathogenesis. The actual impact of these two deletions on the virus replication and disease dynamics needs to be studied in detail. Moreover, the enhanced genomic surveillance will be required to track the spread of this lineage in other parts of the country.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Massab Umair", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Aamer Ikram", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Zaira Rehman", - "author_inst": "National Institute of Health (Pakistan)" - }, - { - "author_name": "Syed Adnan Haider", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Nazish Badar", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Muhammad Ammar", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Qasim Ali", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Abdul Ahad", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Rana Suleman", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Muhammad Salman", - "author_inst": "National Institute of Health" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.25.21268301", "rel_title": "Serial interval and basic reproduction number of SARS-CoV-2 Omicron variant in South Korea", @@ -439984,6 +442594,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.22.21268265", + "rel_title": "Infrared spectroscopy enables rapid, robust, portable COVID-19 saliva screening based on pathophysiological response to SARS-CoV-2", + "rel_date": "2021-12-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268265", + "rel_abs": "Fourier-transform infrared (FTIR) spectroscopy provides a (bio)chemical snapshot of the sample, and was recently proposed for COVID-19 saliva screening in proof-of-concept cohort studies. As a step towards translation of this technology, we conducted controlled validation experiments in multiple biological systems. SARS-CoV-2 or UV-inactivated SARS-CoV-2 were used to infect Vero E6 cells in vitro, and K18-hACE2 mice in vivo. Potentially infectious culture supernatant or mouse oral lavage samples were treated with ethanol or Trizol to 75% (v/v) for attenuated total reflectance (ATR)-FTIR spectroscopy, or RT-PCR, respectively. The control condition, UV-inactivated SARS-CoV-2 elicited strong biochemical changes in culture supernatant/oral lavage despite lack of replication determined by RT-PCR or cell culture infectious dose 50%. Crucially, we show that active SARS-CoV-2 infection induced additional FTIR signals over the UV-inactivated SARS-CoV-2 infection, which correspond to innate immune response, aggregated proteins, and RNA. For human patient cohort prediction, we achieved high sensitivity of 93.48% on leave-on-out cross validation (n=104 participants) for predicting COVID-19 positivity using a partial least squares discriminant analysis model, in agreement with recent studies. However, COVID-19 patients negative on follow-up (RT-PCR on day of saliva sampling) were poorly predicted in this model. Importantly, COVID-19 vaccination did not lead to mis-classification of COVID-19 negatives. Meta-analysis revealed SARS-CoV-2 induced increase in Amide II band in all arms of this study and recent studies, indicative of altered {beta}-sheet structures in secreted proteins. In conclusion, ATR-FTIR is a robust, simple, portable method for COVID-19 saliva screening based on detection of pathophysiological responses to SARS-CoV-2.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Seth Kazmer", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Gunter Hartel", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Harley Robinson", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Renee S Richards", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Kexin Yan", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Sebastiaan J. Van Hal", + "author_inst": "NSW Health Pathology: New South Wales Health Pathology" + }, + { + "author_name": "Raymond Chan", + "author_inst": "NSW Health Pathology: New South Wales Health Pathology" + }, + { + "author_name": "Andrew Hind", + "author_inst": "Agilent Technologies Australia" + }, + { + "author_name": "David Bradley", + "author_inst": "Agilent Technologies Australia" + }, + { + "author_name": "Fabian Zieschang", + "author_inst": "Agilent Technologies Australia" + }, + { + "author_name": "Daniel J Rawle", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Thuy T Le", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "David W Reid", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Andreas Suhrbier", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Michelle M Hill", + "author_inst": "QIMR Berghofer Medical Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.23.21267893", "rel_title": "Echinacea as a Potential Force against Coronavirus Infections? A Mini-Review of Randomized Controlled Trials in Adults and Children", @@ -440137,85 +442822,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.23.21268293", - "rel_title": "Neutralising antibody activity against SARS-CoV-2 variants, including Omicron, in an elderly cohort vaccinated with BNT162b2", - "rel_date": "2021-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268293", - "rel_abs": "SARS-CoV-2 variants threaten the effectiveness of tools we have developed to mitigate against serious COVID-19. This is especially true in clinically vulnerable sections of society including the elderly. Using sera from BNT162b2 (Pfizer-BioNTech) vaccinated individuals aged between 70 and 89 (vaccinated with two doses 3-weeks apart) we examined the neutralising antibody (nAb) response to wildtype SARS-CoV-2. Between 3 and 20-weeks post 2nd dose, nAb titres dropped 4.9-fold to a median titre of 21.3 (ND80) with 21.6% of individuals having no detectable nAbs at the later time point. Experiments examining the neutralisation of twenty-one different SARS-CoV-2 variant spike proteins confirmed a significant potential for antigenic escape, especially for the Omicron (BA.1), Beta (B.1.351), Delta (B.1.617.2), Theta (P.3), C.1.2 and B.1.638 variants. Interestingly, however, the recently-emerged sub-lineage AY.4.2 was more efficiently neutralised than parental Delta pseudotypes. Combining pseudotype neutralisation with specific receptor binding domain (RBD) ELISAs we confirmed that changes to position 484 in the spike RBD were predominantly responsible for SARS-CoV-2 nAb escape, although the effect of spike mutations is both combinatorial and additive. Lastly, using sera from the same individuals boosted with a 3rd dose of BNT162b2 we showed that high overall levels of neutralising antibody titre can provide significant levels of cross-protection against Omicron. These data provide evidence that SARS-CoV-2 neutralising antibodies wane over time and that antigenically variable SARS-CoV-2 variants are circulating, highlighting the importance of ongoing surveillance and booster programmes. Furthermore, they provide important data to inform risk assessment of new SARS-CoV-2 variants, such as Omicron, as they emerge.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Joseph Newman", - "author_inst": "The Pirbright Institute" - }, - { - "author_name": "Nazia Thakur", - "author_inst": "The Pirbright Institute" - }, - { - "author_name": "Thomas P Peacock", - "author_inst": "Imperial College - London" - }, - { - "author_name": "Dagmara Bialy", - "author_inst": "The Pirbright Institute" - }, - { - "author_name": "Ahmed ME Elreafey", - "author_inst": "The Pirbright Institute" - }, - { - "author_name": "Carlijn Bogaardt", - "author_inst": "University of Surrey" - }, - { - "author_name": "Daniel L Horton", - "author_inst": "University of Surrey" - }, - { - "author_name": "Sammy Ho", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Thivya Kankeyan", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Christine Carr", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Katja Hoschler", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Wendy S Barclay", - "author_inst": "Imperial College - London" - }, - { - "author_name": "Gayatri Amirthalingam", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Kevin Brown", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Bryan Charleston", - "author_inst": "The Pirbright Institute" - }, - { - "author_name": "Dalan Bailey", - "author_inst": "The Pirbright Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.23.21268284", "rel_title": "Sharp Increases in Drug Overdose Deaths Among High-School-Age Adolescents During the US COVID-19 Epidemic and Illicit Fentanyl Crisis", @@ -441981,6 +444587,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.22.21268021", + "rel_title": "Omicron outbreak at a private gathering in the Faroe Islands, infecting 21 of 33 triple-vaccinated healthcare workers", + "rel_date": "2021-12-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268021", + "rel_abs": "There are concerns that the SARS-CoV-2 Omicron variant evades immune responses due to unusually high numbers of mutations on the spike protein. Here we report a super-spreading event of Omicron infections amongst triple-vaccinated healthcare workers, infecting 21 of 33 attending a private gathering in the Faroe Islands.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Gunnhild Helmsdal", + "author_inst": "General Practitioner Service, Vestmanna, Faroe Islands" + }, + { + "author_name": "Olga Kristina Hansen", + "author_inst": "Office of the Chief Medical Officer, Torshavn, Faroe Islands" + }, + { + "author_name": "Lars Fodgaard Moller", + "author_inst": "Office of the Chief Medical Officer, Torshavn, Faroe Islands" + }, + { + "author_name": "Debes Hammershaimb Christiansen", + "author_inst": "Faroese Food and Veterinary Authority, Torshavn, Faroe Islands" + }, + { + "author_name": "Maria Skaalum Petersen", + "author_inst": "The Faroese Hospital System, Torshavn, Faroe Islands" + }, + { + "author_name": "Marnar Fridheim Kristiansen", + "author_inst": "University of the Faroe Islands, Torshavn, Faroe Islands" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.22.21268274", "rel_title": "SARS-CoV-2 Antigen Tests Predict Infectivity Based on Viral Culture: Comparison of Antigen, PCR Viral Load, and Viral Culture Testing on a Large Sample Cohort", @@ -442154,37 +444799,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.23.21267953", - "rel_title": "Covid Vaccines for Children with Developmental Disabilities: Parent Survey of Willingness and Concerns", - "rel_date": "2021-12-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21267953", - "rel_abs": "ObjectiveWhile 1-in-6 US children has a developmental disability (DD), and such children are disproportionately affected by COVID-19, little is known about their vaccination status. We surveyed US parents of children with DDs to ascertain willingness and concerns regarding COVID-19 vaccines.\n\nMethodsAn online survey was distributed to national, statewide, and regional DD networks from June-September 2021. (Vaccines were authorized for adolescents in May 2021.) We report associations between vaccine willingness and concerns and: race/ethnicity, child age, in-person schooling, routine/flu vaccinations, and DD diagnoses. Willingness was categorized as Got /Will Get ASAP (high), Wait and See/Only if Required, or Definitely Not.\n\nResults393 parents (51.2% white) responded. Willingness differed by age (p<.001). High willingness was reported for 75.3%, 48.9%, and 38.1% of children aged 12-17, 6-11 and 0-5 years-old, respectively. Willingness differed by Autism diagnosis (p<.001) and routine and flu vaccination status (p<.01). Predominant concerns included side effects (89%) and children with disabilities not being in trials (79%). Less common concerns were: COVID not serious enough in children to warrant vaccine (22%) and misinformation (e.g., microchips, 5G, DNA changes) (24%). Concerns about vaccine safety differed by age (p<.05) and were highest for young children. In age-stratified adjusted models, Autism was positively associated with high willingness for 6-11year-olds (OR= 2.66, 95% CI= 1.12-6.35).\n\nConclusionParents of children with DD are more willing for them to receive COVID-19 vaccines, compared to the general population. While few factors predicted willingness to vaccinate, addressing safety and developmental concerns regarding young children is warranted.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Karen Bonuck", - "author_inst": "Einstein College of Medicine-Montefiore Medical Center" - }, - { - "author_name": "Suzannah Iadarola", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Qi Gao", - "author_inst": "Einstein College of Medicine-Montefiore Medical Center" - }, - { - "author_name": "Joanne Siegel", - "author_inst": "Einstein College of Medicine-Montefiore Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.12.21.21268119", "rel_title": "Deafferentation of Olfactory Bulb in Subjects Dying with COVID-19", @@ -444055,6 +446669,237 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.17.473248", + "rel_title": "SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion", + "rel_date": "2021-12-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.17.473248", + "rel_abs": "The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.", + "rel_num_authors": 54, + "rel_authors": [ + { + "author_name": "Bo Meng", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Isabella Ferreira", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Adam Abdullahi", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Niluka Goonawardane", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Akatsuki Saito", + "author_inst": "University of Miyazaki" + }, + { + "author_name": "Izumi Kimura", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Daichi Yamasoba", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Steven A Kemp", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Guido Papa", + "author_inst": "LMB Cambridge" + }, + { + "author_name": "Saman Fatihi", + "author_inst": "CSIR Institute of Genomics and Integrative Biology, Delhi, India" + }, + { + "author_name": "Surabhi Rathore", + "author_inst": "CSIR Institute of Genomics and Integrative Biology, Delhi, India" + }, + { + "author_name": "Pehuen Perera Gerba", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Terumasa Ikeda", + "author_inst": "Kumamoto Univ" + }, + { + "author_name": "Mako Toyoda", + "author_inst": "Kumamoto University, Kumamoto" + }, + { + "author_name": "Toong Seng Tan", + "author_inst": "Kuramochi Clinic Interpark" + }, + { + "author_name": "Jin Kuramochi", + "author_inst": "Kuramochi Clinic Interpark" + }, + { + "author_name": "Shigeki Mitsunaga", + "author_inst": "National Institute of Genetics, Mishima, Shizuoka" + }, + { + "author_name": "Takamasa Ueno", + "author_inst": "Kumamoto University, Kumamoto" + }, + { + "author_name": "Oscar Charles", + "author_inst": "University College London" + }, + { + "author_name": "Dami Collier", + "author_inst": "University of Cambridge" + }, + { + "author_name": "- CITIID-NIHR BioResource COVID-19 Collaboration", + "author_inst": "-" + }, + { + "author_name": "- The Genotype to Phenotype Japan (G2P-Japan) Consortium", + "author_inst": "-" + }, + { + "author_name": "- Ecuador-COVID19 Consortium", + "author_inst": "-" + }, + { + "author_name": "John Bradley", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Jinwook Choi", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Kenneth Smith", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Elo Madissoon", + "author_inst": "Wellcome Sanger Institute" + }, + { + "author_name": "Kerstin Meyer", + "author_inst": "Wellcome Sanger Institute" + }, + { + "author_name": "Petra Mlcochova", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Rainer Doffinger", + "author_inst": "Cambridge University Hospitals NHS Trust" + }, + { + "author_name": "Sarah A Teichmann", + "author_inst": "Cambridge University" + }, + { + "author_name": "Leo James", + "author_inst": "MRC LMB" + }, + { + "author_name": "Joo Hyeon Lee", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Teresa Brevini", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Matteo Pizzuto", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Myra Hosmillo", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Donna Mallery", + "author_inst": "MRC LMB Cambridge" + }, + { + "author_name": "Samantha Zepeda", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexandra Walls", + "author_inst": "University of Washington" + }, + { + "author_name": "Anshu Joshi", + "author_inst": "University of Washington" + }, + { + "author_name": "John Bowen", + "author_inst": "University of Washington" + }, + { + "author_name": "John Briggs", + "author_inst": "University of Heidelberg" + }, + { + "author_name": "Alex Sigal", + "author_inst": "Africa Health Research Institute, Durban, South Africa" + }, + { + "author_name": "Laurelle Jackson", + "author_inst": "Africa Health Research Institute, Durban, South Africa" + }, + { + "author_name": "Sandile Cele", + "author_inst": "Africa Health Research Institute, Durban, South Africa" + }, + { + "author_name": "Anna De Marco", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Fotios Sampaziotis", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Davide Corti", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + }, + { + "author_name": "Nicholas Matheson", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ian Goodfellow", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Lipi Thukral", + "author_inst": "CSIR Institute of Genomics and Integrative Biology, Delhi, India" + }, + { + "author_name": "Kei Sato", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Ravindra K Gupta", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.17.473140", "rel_title": "Human genetic variants associated with COVID-19 severity are enriched in immune and epithelium regulatory networks", @@ -444220,105 +447065,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.12.20.473401", - "rel_title": "Arsenal of Nanobodies for Broad-Spectrum Countermeasures against Current and Future SARS-CoV-2 Variants of Concerns", - "rel_date": "2021-12-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.20.473401", - "rel_abs": "Nanobodies offer several potential advantages over mAbs for the control of SARS-CoV-2. Their ability to access cryptic epitopes conserved across SARS-CoV-2 variants of concern (VoCs) and feasibility to engineer modular, multimeric designs, make these antibody fragments ideal candidates for developing broad-spectrum therapeutics against current and continually emerging SARS-CoV-2 VoCs. Here we describe a diverse collection of 37 anti-SARS-CoV-2 spike glycoprotein nanobodies extensively characterized as both monovalent and IgG Fc-fused bivalent modalities. The panel of nanobodies were shown to have high intrinsic affinity; high thermal, thermodynamic and aerosolization stability; broad subunit/domain specificity and cross-reactivity across many VoCs; wide-ranging epitopic and mechanistic diversity; high and broad in vitro neutralization potencies; and high neutralization efficacies in hamster models of SARS-CoV-2 infection, reducing viral burden by up to six orders of magnitude to below detectable levels. In vivo protection was demonstrated with anti-RBD and previously unreported anti-NTD and anti-S2 nanobodies. This collection of nanobodies provides a therapeutic toolbox from which various cocktails or multi-paratopic formats could be built to tackle current and future SARS-CoV-2 variants and SARS-related viruses. Furthermore, the high aerosol-ability of nanobodies provides the option for effective needle-free delivery through inhalation.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Martin A Rossotti", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Henk van Faassen", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Anh Tran", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Joey Sheff", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Jagdeep A Sandhu", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Diana Duque", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Melissa Hewitt", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Sophie Wen", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Rubee Bavananthasivam", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Saina Beitari", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Kevin Matte", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Genevieve Laroche", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Patrick M Giguere", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Christian Gervais", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Matthew Stuible", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Julie Guimond", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Sylvie Perret", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Greg Hussack", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Marc-Andre Langlois", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Yves Durocher", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Jamshid Tanha", - "author_inst": "National Research Council Canada" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2021.12.19.473391", "rel_title": "SARS-CoV-2 spike conformation determines plasma neutralizing activity", @@ -446300,6 +449046,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.20.21268134", + "rel_title": "Activity of convalescent and vaccine serum against a B.1.1.529 variant SARS-CoV-2 isolate", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.20.21268134", + "rel_abs": "The B.1.1.529 (Omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified in November of 2021 in South Africa and Botswana as well as in a sample of a traveler from South Africa in Hong Kong.1,2 Since then, B.1.1.529 has been detected in many countries globally. This variant seems to be more infectious than B.1.617.2 (Delta), has already caused super spreader events3 and has outcompeted Delta within weeks in several countries and metropolitan areas. B.1.1.529 hosts an unprecedented number of mutations in its spike gene and early reports have provided evidence for extensive immune escape and reduced vaccine effectiveness.2,4-6 Here, we investigated the neutralizing and binding activity of sera from convalescent, mRNA double vaccinated, mRNA boosted as well as convalescent double vaccinated and convalescent boosted individuals against wild type, B.1.351 and B.1.1.529 SARS-CoV-2 isolates. Neutralizing activity of sera from convalescent and double vaccinated participants was undetectable to very low against B.1.1.529 while neutralizing activity of sera from individuals who had been exposed to spike three or four times was maintained, albeit at strongly reduced levels. Binding to the B.1.1.529 receptor binding domain (RBD) and N-terminal domain (NTD) was reduced in convalescent not vaccinated but was mostly retained in vaccinated individuals.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Juan Manuel Carreno", + "author_inst": "ISMMS" + }, + { + "author_name": "Hala Alshammary", + "author_inst": "ISMMS" + }, + { + "author_name": "Johnstone Tcheou", + "author_inst": "ISMMS" + }, + { + "author_name": "Gagandeep Singh", + "author_inst": "ISMMS" + }, + { + "author_name": "Ariel Raskin", + "author_inst": "ISMMS" + }, + { + "author_name": "Hisaaki Kawabata", + "author_inst": "ISMMS" + }, + { + "author_name": "Levy Sominsky", + "author_inst": "ISMMS" + }, + { + "author_name": "Jordan Clark", + "author_inst": "ISMMS" + }, + { + "author_name": "Daniel C. Adelsberg", + "author_inst": "ISMMS" + }, + { + "author_name": "Dominika Bielak", + "author_inst": "ISMMS" + }, + { + "author_name": "Ana Silvia Gonzalez-Reiche", + "author_inst": "ISMMS" + }, + { + "author_name": "PSP/PARIS Study Group", + "author_inst": "ISMMS" + }, + { + "author_name": "Komal Srivastava", + "author_inst": "ISMMS" + }, + { + "author_name": "Emilia M Sordillo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Goran Bajic", + "author_inst": "ISMMS" + }, + { + "author_name": "Harm van Bakel", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Viviana Simon", + "author_inst": "Icahn School of Medicine" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.20.21268124", "rel_title": "SARS-CoV-2 vaccine effectiveness and breakthrough infections in maintenance dialysis patients", @@ -446465,81 +449298,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.12.16.21267766", - "rel_title": "High-Quality and Easy-to-Regenerate Personal Filter", - "rel_date": "2021-12-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.16.21267766", - "rel_abs": "Proper respiratory tract protection is the key factor to limiting the rate of COVID-19 spread and providing a safe environment for health care workers. Traditional N95 (FFP2) respirators are not easy to regenerate and thus create certain financial and ecological burdens; moreover, their quality may vary significantly. A solution that would overcome these disadvantages is desirable. In this study a commercially available knit polyester fleece fabric was selected as the filter material, and a total of 25 filters of different areas and thicknesses were prepared. Then, the size-resolved filtration efficiency (40-400 nm) and pressure drop were evaluated at a volumetric flow rate of 95 L/min. We showed the excellent synergistic effect of expanding the filtration area and increasing the number of filtering layers on the filtration efficiency; a filter cartridge with 8 layers of knit polyester fabric with a surface area of 900 cm2 and sized 25 x 14 x 8 cm achieved filtration efficiencies of 98 % at 95 L/min and 99.5 % at 30 L/min. The assembled filter kit consists of a filter cartridge (14 Pa) carried in a small backpack connected to a half mask with a total pressure drop of 84 Pa at 95 L/min. In addition, it is reusable, and the filter material can be regenerated at least ten times by simple methods, such as boiling. We have demonstrated a novel approach for creating high-quality and easy-to-breathe-through respiratory protective equipment that reduces operating costs and is a green solution because it is easy to regenerate.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Max Fraenkl", - "author_inst": "Center of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice" - }, - { - "author_name": "Milos Krbal", - "author_inst": "Center of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice" - }, - { - "author_name": "Jakub Houdek", - "author_inst": "Center of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice" - }, - { - "author_name": "Zuzana Olmrova Zmrhalova", - "author_inst": "Center of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice" - }, - { - "author_name": "Borivoj Prokes", - "author_inst": "Center of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice" - }, - { - "author_name": "Petr Hejda", - "author_inst": "Center of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice" - }, - { - "author_name": "Stanislav Slang", - "author_inst": "Center of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice" - }, - { - "author_name": "Jan Prikryl", - "author_inst": "Center of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice" - }, - { - "author_name": "Jakub Ondracek", - "author_inst": "Institute of Chemical Process Fundamentals, v.v.i., Academy of Sciences of the Czech Republic" - }, - { - "author_name": "Otakar Makes", - "author_inst": "Institute of Chemical Process Fundamentals, v.v.i., Academy of Sciences of the Czech Republic" - }, - { - "author_name": "Juraj Kostyk", - "author_inst": "Institute of Chemical Process Fundamentals, v.v.i., Academy of Sciences of the Czech Republic" - }, - { - "author_name": "Petr Nasadil", - "author_inst": "Textile Testing Institute, Brno" - }, - { - "author_name": "Pavel Malcik", - "author_inst": "Textile Testing Institute, Brno" - }, - { - "author_name": "Vladimir Zdimal", - "author_inst": "Institute of Chemical Process Fundamentals, v.v.i., Academy of Sciences of the Czech Republic" - }, - { - "author_name": "Miroslav Vlcek", - "author_inst": "Center of Materials and Nanotechnologies, Faculty of Chemical Technology, University of Pardubice" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.12.19.21268052", "rel_title": "Time Between Viral Loads for People with HIV during the COVID-19 Pandemic", @@ -448114,6 +450872,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.21.21267983", + "rel_title": "GB0139, an inhaled small molecule inhibitor of galectin-3, in COVID-19 pneumonitis: a randomised, controlled, open-label, phase 2a experimental medicine trial of the safety, pharmacokinetics, and potential therapeutic value", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.21.21267983", + "rel_abs": "RationaleHigh galectin-3 levels predict poor outcomes in patients with COVID-19. Galectin-3 activates monocytes and macrophages which are directly implicated in COVID-19 immunopathology and the cytokine storm. GB0139 is a potent thiodigalactoside galectin-3 inhibitor and may reduce the severe effects of the disease. We report safety and pharmacokinetics and pharmacodynamics of the inhaled galectin-3 inhibitor, GB0139, and assess clinical outcomes and key systemic inflammatory biomarkers in hospitalised patients with COVID-19 (ClinicalTrials.gov/EudraCT identifier: NCT04473053/2020-002230-32).\n\nMethodsAdults with COVID-19 requiring oxygen, and with pneumonitis on x-ray, were randomised to receive standard of care (SOC; including dexamethasone; n=21) or SOC plus 10 mg GB0139 twice daily for 48 hours, then once daily for [≤]14 days (n=20).\n\nResultsPatients aged 27-87 years were enrolled from July 2020; the final patient completed the 90-day follow-up in April 2021. GB0139+SOC was well tolerated with no treatment-related serious adverse events reported. Incidences of adverse events were similar between treatment arms (40 with GB0139+SOC vs 35 with SOC). Plasma GB0139 was measurable in all patients after inhaled exposure, with moderate interpatient variability, and demonstrated target engagement with decreased circulating galectin (overall treatment effect post-hoc over days 2-7: p=0{middle dot}0099 vs SOC). Rate of decline in fraction of inspired oxygen (%) requirement was significantly greater in the GB0139+SOC arm with a posterior mean difference of -1{middle dot}51 (95% highest posterior density: -2{middle dot}90, -0{middle dot}189) versus SOC. Plasma levels of biomarkers associated with inflammation, coagulopathy, major organ function and fibrosis showed a downward trend versus SOC.\n\nConclusionsGB0139+SOC was well tolerated and achieved clinically relevant plasma concentrations and target engagement. This, and the reduction in markers associated with inflammatory, coagulation, fibrosis, and reduction in inspired oxygen (%) over SOC alone, indicates the therapeutic potential for inhaled GB0139 in hospitalised patients with COVID-19.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Erin Gaughan", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Tariq Sethi", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Tom Quinn", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Nikhil Hirani", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Andrew Mills", + "author_inst": "Exploristics" + }, + { + "author_name": "Annya M. Bruce", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Alison MacKinnon", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Vassilios Aslanis", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Feng Li", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Richard O'Connor", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Richard A. Parker", + "author_inst": "Edinburgh Clinical Trials Unit, Usher Institute, University of Edinburgh" + }, + { + "author_name": "John Norrie", + "author_inst": "Edinburgh Clinical Trials Unit, Usher Institute, University of Edinburgh" + }, + { + "author_name": "James Dear", + "author_inst": "Centre for Cardiovascular Science, University of Edinburgh" + }, + { + "author_name": "Ahsan R. Akram", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Oliver Koch", + "author_inst": "Infectious Diseases Department, NHS Lothian" + }, + { + "author_name": "Jie Wang-Jairaj", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Robert J. Slack", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Lise Gravelle", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Bertil Lindmark", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Kevin Dhaliwal", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.12.19.21268028", "rel_title": "Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa", @@ -448591,69 +451444,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.16.472391", - "rel_title": "Reduced sera neutralization to Omicron SARS-CoV-2 by bothinactivated and protein subunit vaccines and the convalescents", - "rel_date": "2021-12-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.16.472391", - "rel_abs": "Omicron variant continues to spread all over the world. There are lots of scientific questions remaining to be answered for such a devastating variant. There are a dozen of vaccines already in clinical use. The very urgent scientific question would be whether or not these vaccines can protect Omicron variant. Here, we tested the sera from both convalescents and vaccine recipients receiving either inactivated or protein subunits vaccines (CoronaVac from Sinovac, or BBIBP-CoV from Sinopharm, or ZF2001 from Zhifei longcom) for the binding antibody titers (ELISA) and neutralization antibodies titers (pseudovirus neutralization assay). We showed that Omicron do have severe immune escape in convalescents, with 15 of 16 were negative in neutralization. By contrast, in vaccinees who received three jabs of inactivated or protein subunit vaccine, the neutralizing activity was much better preserved. Especially in the ZF2001 group with an extended period of the second and third jab (4-6 months) remains 100% positive in Omicron neutralization, with only 3.1-folds reduction in neutralizing antibody (NAb) titer. In this case, we proposed that, the multi-boost strategy with an extended interval between the second and third jab for immune maturation would be beneficial for NAb against devastating variants such as Omicron.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Xin Zhao", - "author_inst": "Institute of Microbiology, Chinese Academy of Sciences, Beijing, China" - }, - { - "author_name": "Dedong Li", - "author_inst": "Institute of Microbiology, Chinese Academy of Sciences, Beijing, China" - }, - { - "author_name": "Wenjing Ruan", - "author_inst": "Institute of Microbiology, Chinese Academy of Sciences, Beijing, China" - }, - { - "author_name": "Rong Zhang", - "author_inst": "Institute of Microbiology, Chinese Academy of Sciences, Beijing, China" - }, - { - "author_name": "Anqi Zheng", - "author_inst": "Institute of Microbiology, Chinese Academy of Sciences, Beijing, China" - }, - { - "author_name": "Shitong Qiao", - "author_inst": "Institute of Microbiology, Chinese Academy of Sciences, Beijing, China" - }, - { - "author_name": "Xinlei Zheng", - "author_inst": "Institute of Microbiology, Chinese Academy of Sciences, Beijing, China" - }, - { - "author_name": "Yingze Zhao", - "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" - }, - { - "author_name": "Zhihai Chen", - "author_inst": "Beijing Ditan Hospital" - }, - { - "author_name": "Lianpan Dai", - "author_inst": "Institute of Microbiology" - }, - { - "author_name": "Pengcheng Han", - "author_inst": "College of Life Science and Technology, Southeast University, Nanjing, China." - }, - { - "author_name": "George Fu Gao", - "author_inst": "Institute of Microbiology Chinese Academy of Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.12.16.473025", "rel_title": "In vitro and computational analysis of the putative furin cleavage site (RRARS) in the divergent spike protein of the rodent coronavirus AcCoV-JC34 (sub-genus luchacovirus)", @@ -450268,6 +453058,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.18.21267819", + "rel_title": "Knowledge, Attitude and Practices towards COVID 19 pandemic among homeless street young adults in Lusaka, Zambia: A Mixed Methods Approach", + "rel_date": "2021-12-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.18.21267819", + "rel_abs": "ObjectiveTo determine the knowledge, attitude and practices towards COVID-19 among homeless street young adults in Lusaka district, Zambia.\n\nMethodsA total of 89 young street adults aged between 16-35 years were sampled. A concurrent mixed methods approach was used, Structured questionnaires and focused group discussion, to achieve the objectives. STATA 13 was used to produce Descriptive statistics while thematic analysis was used to analyze the qualitative data.\n\nResultsMajority of the survey participants were male 67(78%), 55(62%) were single while 53(59%) had attained a Primary School Education. The majority of the participants received the COVID-19 information through the radio (61%). Only 44 (49%)% had adequate knowledge on Covid-19 of whom 70 (78.6%) had a positive attitude towards COVID-19. However, the 65(73%) had a low risk perception of contracting the disease. Further, 66 (74.2%) had a positive attitude towards the effectiveness of precautionary behaviors and measures. The finding also revealed that only 3(3.3%) had good practice towards the Covid-19 preventative measures overall with (SD:0).\n\nConclusionKnowledge and attitudes towards COVID-19 were quite high among homeless street adults. However, their good practices were alarmingly low. Specific strategies for them being a vulnerable group are required.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kahilu Samuyachi", + "author_inst": "Keeping Girls in School Project-Ministry of Education, Lusaka, Zambia" + }, + { + "author_name": "Mowa Zambwe", + "author_inst": "Workers Compensation Fund Control Board" + }, + { + "author_name": "Mutale Sampa", + "author_inst": "University of Zambia" + }, + { + "author_name": "Peter J. Chipimo", + "author_inst": "Zambia National Public Health Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.18.21268026", "rel_title": "Measurement of the extent of Anxiety and Depression that has occurred in college students due to the COVID 19 pandemic: An Survey based cross-sectional study.", @@ -450349,53 +453170,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.17.21267997", - "rel_title": "Perceptions and Attitudes Towards COVID-19 Vaccination Amongst Pregnant and Postpartum Individuals", - "rel_date": "2021-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267997", - "rel_abs": "IntroductionThis study aims to characterize attitudes towards COVID-19 vaccination and to evaluate factors associated with vaccine uptake amongst pregnant individuals.\n\nMethodsAn anonymous survey was distributed to a convenience sample of pregnant individuals receiving prenatal care at two large urban academic hospitals in a single healthcare network in Massachusetts. Individual demographic variables were included in the survey along with questions assessing attitudes towards COVID-19 and vaccination in pregnancy.\n\nResultsOf 477 respondents, 233 (49.3%) had received or were scheduled to receive a COVID-19 vaccine. Age, White race, non-Hispanic/LatinX ethnicity, working from home, and typical receipt of the influenza vaccine were associated with COVID-19 vaccination. 276 respondents (58.4%) reported that their provider recommended the COVID-19 vaccine in pregnancy; these participants were more likely to have received a vaccine (OR 5.82, 95% confidence interval [CI] 3.68-9.26). Vaccinated individuals were less likely to be worried about the effects of the vaccine on themselves (OR 0.18, 95% CI 0.12-0.27) or their developing babies (OR 0.17, 95% CI 0.11-0.26). Unvaccinated individuals were less likely to report that it is easy to schedule a COVID-19 vaccine (OR 0.56, 95% CI 0.34-0.93), to travel to receive a vaccine (OR 0.19, 95% CI 0.10-0.36), and to miss work to receive a vaccine (OR 0.30, 95% CI 0.18-0.48).\n\nConclusionsStrategies are needed to improve patient education regarding vaccine side effects and safety in pregnancy and to change policy to make it feasible for pregnant patients to schedule and miss work without loss of pay to get vaccinated.\n\nKey PointsO_LIThere were racial and ethnic disparities in COVID-19 vaccination.\nC_LIO_LIUnvaccinated respondents were more likely to be concerned about vaccine effects for themselves or their growing babies.\nC_LIO_LIUnvaccinated respondents cited work and scheduling-related barriers to vaccination, indicating areas for advocacy\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Molly R. Siegel", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Mario I. Lumbreras-Marquez", - "author_inst": "Brigham and Womens Hospital" - }, - { - "author_name": "Kaitlyn James", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Brandon R. McBay", - "author_inst": "Harvard TH Chan School of Public Health" - }, - { - "author_name": "Kathryn J. Gray", - "author_inst": "Brigham and Womens Hospital" - }, - { - "author_name": "Juliana Schantz-Dunn", - "author_inst": "Brigham and Womens Hospital" - }, - { - "author_name": "Khady Diouf", - "author_inst": "Brigham and Womens Hospital" - }, - { - "author_name": "Ilona T Goldfarb", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.12.17.21267998", "rel_title": "Provider Confidence in Counseling Preconception, Pregnant, and Postpartum Patients Regarding COVID-19 Vaccination", @@ -452210,6 +454984,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.12.17.21267968", + "rel_title": "Patients' and carers' experiences of, and engagement with remote home monitoring services for COVID-19 patients: a rapid mixed-methods study", + "rel_date": "2021-12-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267968", + "rel_abs": "IntroductionRemote home monitoring models were implemented during the COVID-19 pandemic to shorten hospital length of stay, reduce unnecessary hospital admission, readmission and infection, and appropriately escalate care. Within these models, patients are asked to take and record readings and escalate care if advised. There is limited evidence on how patients and carers experience these services. This study aimed to evaluate patient experiences of, and engagement with, remote home monitoring models for COVID-19.\n\nMethodsA rapid mixed-methods study in England. We conducted a cross-sectional survey and interviews with patients and carers. Interview findings were summarised using rapid assessment procedures sheets and grouping data into themes (using thematic analysis). Survey data were analysed using descriptive statistics.\n\nResultsWe received 1069 surveys (18% response rate) and conducted interviews with patients (n=59) and carers (n=3). Care relied on support from staff members, and family/friends. Patients and carers reported positive experiences and felt that the service and human contact reassured them and was easy to engage with. Yet, some patients and carers identified problems with engagement. Engagement was influenced by: patient factors such as health and knowledge, support from family/friends and staff, availability and ease-of-use of informational and material resources (e.g. equipment), and service factors.\n\nConclusionRemote home monitoring models place responsibility on patients to self-manage symptoms in partnership with staff; yet many patients required support and preferred human contact (especially for identifying problems). Caring burden and experiences of those living alone, and barriers to engagement should be considered when designing and implementing remote home monitoring services.\n\nPatient or public contributionFor this evaluation, members of the study team met with service user and public members of the BRACE PPI group and Health and Care Panel and patient representatives from RSET in a series of workshops. These workshops informed study design, data collection tools, data interpretation and to discuss study dissemination for Phase 2. For example, patient facing documents, such as the consent form, topic guides, patient survey and patient information sheet were reviewed by this group. Additionally, PPI members helped to pilot patient surveys and interview guides with the research team. We also asked some members of the public to pilot the patient survey. Members of the PPI group were given the opportunity to comment on the manuscript. One PPI member commented on the manuscript and the manuscript was amended accordingly.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Holly Walton", + "author_inst": "University College London" + }, + { + "author_name": "Cecilia Vindrola-Padros", + "author_inst": "University College London" + }, + { + "author_name": "Nadia Crellin", + "author_inst": "Nuffield Trust" + }, + { + "author_name": "Manbinder S Sidhu", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Lauren Herlitz", + "author_inst": "University College London" + }, + { + "author_name": "Ian Litchfield", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Jo Ellins", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Pei Li Ng", + "author_inst": "University College London" + }, + { + "author_name": "Efthalia Massou", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Sonila M Tomini", + "author_inst": "University College London" + }, + { + "author_name": "Naomi J Fulop", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.12.16.21267932", "rel_title": "A Single Dose of COVID-19 mRNA Vaccine Induces Airway Immunity in COVID-19 Convalescent Patients", @@ -452435,89 +455268,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.12.15.472874", - "rel_title": "Distinguishing COVID-19 infection and vaccination history by T cell reactivity", - "rel_date": "2021-12-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.15.472874", - "rel_abs": "SARS-CoV-2 infection and COVID-19 vaccines elicit memory T cell responses. Here, we report the development of two new pools of Experimentally-defined T cell epitopes derived from the non-spike Remainder of the SARS-CoV-2 proteome (CD4RE and CD8RE). The combination of T cell responses to these new pools and Spike (S) were used to discriminate four groups of subjects with different SARS-CoV-2 infection and COVID-19 vaccine status: non-infected, non-vaccinated (I-V-); infected and non-vaccinated (I+V-); infected and then vaccinated (I+V+); and non-infected and vaccinated (I-V+). The overall classification accuracy based on 30 subjects/group was 89.2% in the original cohort and 88.5% in a validation cohort of 96 subjects. The T cell classification scheme was applicable to different mRNA vaccines, and different lengths of time post-infection/post-vaccination. T cell responses from breakthrough infections (infected vaccinees, V+I+) were also effectively segregated from the responses of vaccinated subjects using the same classification tool system. When all five groups where combined, for a total of 239 different subjects, the classification scheme performance was 86.6%. We anticipate that a T cell-based immunodiagnostic scheme able to classify subjects based on their vaccination and natural infection history will be an important tool for longitudinal monitoring of vaccination and aid in establishing SARS-CoV-2 correlates of protection.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Esther Dawen Yu", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Eric Wang", - "author_inst": "La Jolla Institue for Immunology" - }, - { - "author_name": "Emily Garrigan", - "author_inst": "La Jolla Institue for Immunology" - }, - { - "author_name": "Benjamin Goodwin", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Aaron Sutherland", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "James Chang", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Rosa Isela Galvez", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Jose Mateus", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Stephen A Rawlings", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Davey M Smith", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "April Frazier", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Jennifer M Dan", - "author_inst": "La jolla Institute for Immunology" - }, - { - "author_name": "Shane Crotty", - "author_inst": "La Jolla Institute For Immunology (LJI)" - }, - { - "author_name": "Alba Grifoni", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Ricardo da Silva Antunes", - "author_inst": "La Jolla Institute for Immunology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.12.15.472828", "rel_title": "An infectious SARS-CoV-2 B.1.1.529 Omicron virus escapes neutralization by several therapeutic monoclonal antibodies", @@ -453888,6 +456638,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2021.12.16.21267902", + "rel_title": "Waning of mRNA-1273 vaccine effectiveness against SARS-CoV-2 infection in Qatar", + "rel_date": "2021-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.16.21267902", + "rel_abs": "BACKGROUNDIn early 2021, Qatar launched a mass immunization campaign with Modernas mRNA-1273 COVID-19 vaccine. We assessed persistence of real-world mRNA-1273 effectiveness against SARS-CoV-2 infection and against COVID-19 hospitalization and death.\n\nMETHODSEffectiveness was estimated using test-negative, case-control study design, between January 1 and December 5, 2021. Effectiveness was estimated against documented infection (a PCR-positive swab, regardless symptoms), and against any severe (acute-care hospitalization), critical (ICU hospitalization), or fatal COVID-19.\n\nRESULTSBy December 5, 2021, 2,962 breakthrough infections had been recorded among those who received two mRNA-1273 doses. Of these infections, 19 progressed to severe COVID-19 and 4 to critical, but none to fatal disease. mRNA-1273 effectiveness against infection was negligible for the first two weeks after the first dose, increased to 65.5% (95% CI: 62.7-68.0%) 14 or more days after the first dose, and reached its peak at about 90% in the first three months after the second dose. Effectiveness declined gradually starting from the fourth month after the second dose and was below 50% by the 7th month after the second dose. Effectiveness against severe, critical, or fatal COVID-19 reached its peak at essentially 100% right after the second dose, and there was no evidence for declining effectiveness over time. Effectiveness against symptomatic versus asymptomatic infection demonstrated the same pattern of waning, but effectiveness against symptomatic infection was consistently higher than that against asymptomatic infection and waned more slowly.\n\nCONCLUSIONSmRNA-1273-induced protection against infection appears to wane month by month after the second dose. Meanwhile, protection against hospitalization and death appears robust with no evidence for waning for several months after the second dose.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Houssein H. Ayoub", + "author_inst": "Qatar University" + }, + { + "author_name": "HADI M. YASSINE", + "author_inst": "Qatar University" + }, + { + "author_name": "Fatiha Benslimane", + "author_inst": "Qatar University" + }, + { + "author_name": "Heba A. Al Khatib", + "author_inst": "Qatar University" + }, + { + "author_name": "Patrick Tang", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Mohammad Rubayet Hasan", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Peter Coyle", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Zaina Al Kanaani", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Einas Al Kuwari", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hanan F. Abdul Rahim", + "author_inst": "Qatar University" + }, + { + "author_name": "Gheyath Nasrallah", + "author_inst": "Qatar University" + }, + { + "author_name": "Mohamed Ghaith Al Kuwari", + "author_inst": "Primary Health Care Corporation" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hamad Eid Al Romaihi", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Mohamed H. Al-Thani", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Abdullatif Al Khal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.16.21267703", "rel_title": "Evaluation of SARS-CoV-2 Antibody Point of Care Devices in the Laboratory and Clinical Setting", @@ -454029,149 +456886,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.12.15.21267794", - "rel_title": "Changing of therapeutic trends between the 1st and 2nd wave did not reduce COVID-19 related mortality of renal transplant recipients: a national registry study.", - "rel_date": "2021-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.15.21267794", - "rel_abs": "SARS-CoV-2 pandemic evolved in two consecutive waves over 2020 (for France: 1st wave from March 1 to July 31; and 2nd wave from August 1 to December 31). Improvements in the management of COVID-19 led to a reduction of mortality rates in hospitalized patients during the second wave. Whether this progress also benefited to kidney transplant recipients (KTR), a population particularly vulnerable to severe COVID-19, remained unclear.\n\nIn France, 957 KTR were hospitalized for COVID-19 in 2020 and their data were prospectively collected in the French SOT COVID registry. The presentation, management, and outcomes of the 359 KTR diagnosed during the 1st wave were compared to those of the 598 of the 2nd wave. Baseline comorbidities were largely similar between KTR of the 2 waves. Maintenance immunosuppression was reduced in most patients but withdrawal of antimetabolite (73.7% vs 58.4%, p<0.001) or CNI (32.1% vs 16.6%, p<0.001) was less frequent during the 2nd wave. Hydroxychloroquine and azithromycin that were commonly used during the 1st wave (21.7% and 30.9%, respectively) were almost abandoned during the 2nd. In contrast, the use of high dose corticosteroids doubled (19.5% vs. 41.6%, p<0.001). Despite these changing trends in COVID-19 management, 60-day mortality was not statistically different between the 2 waves (25.3% vs. 23.9%; Log Rank, p=0.48).\n\nWe conclude that changing of therapeutic trends during 2020 did not reduce COVID-19 related mortality in KTR. Our data indirectly support the importance of vaccination and monoclonal neutralizing anti-SARS-CoV-2 antibodies to protect KTR from severe COVID-19.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Bastien Berger", - "author_inst": "Department of Transplantation, Nephrology and Clinical Immunology, Edouard Herriot Hospital, Hospices civils de Lyon, Lyon, France." - }, - { - "author_name": "Marc Hazzan", - "author_inst": "Department of Nephrology and Transplantation, University of Lille, Lille, France." - }, - { - "author_name": "Nassim Kamar", - "author_inst": "Department of Nephrology and Transplantation, University of Toulouse, Toulouse, France." - }, - { - "author_name": "Helene Francois", - "author_inst": "Nephrology and Renal Transplantation Department, AP-HP (Assistance Publique-Hopitaux de Paris), Hopital Tenon, Paris, France." - }, - { - "author_name": "Marie Matignon", - "author_inst": "AP-HP, Institut Francilien de Recherche en Nephrologie et Transplantation, Groupe Hospitalier Henri-Mondor/Albert-Chenevier, Virus-Immunite-Cancer, IMRB (Instit" - }, - { - "author_name": "Clarisse Greze", - "author_inst": "Department of Nephrology and Transplantation, Hopital Bichat, Paris, France" - }, - { - "author_name": "Philippe Gatault", - "author_inst": "Department of Nephrology and Transplantation, University of Tours, Tours, France." - }, - { - "author_name": "Luc Frimat", - "author_inst": "Department of Nephrology, University of Lorraine, CHRU-Nancy, Vandoeuvre, France; INSERM CIC-EC CIE6, Nancy, France." - }, - { - "author_name": "Pierre-Francois Westeel", - "author_inst": "Department of Nephrology and Transplantation, University of Amiens, Amiens, France." - }, - { - "author_name": "Valentin Goutaudier", - "author_inst": "Department of Nephrology and Transplantation, University of Montpellier, Montpellier, France." - }, - { - "author_name": "Renaud Snanoudj", - "author_inst": "Nephrology and Renal Transplantation Department, Hopital Foch, Paris, France." - }, - { - "author_name": "Charlotte Colosio", - "author_inst": "Department of Nephrology and Transplantation, University of Reims, Reims, France." - }, - { - "author_name": "Antoine Sicard", - "author_inst": "Service de Nephrologie-Dialyse-Transplantation, Hopital Pasteur 2, CHU de Nice, Unite de Recherche Clinique Cote d'Azur (UR2CA), Universite Cote d'Azur, Nice, F" - }, - { - "author_name": "Dominique Bertrand", - "author_inst": "Department of Nephrology and Transplantation, University of Rouen, Rouen, France." - }, - { - "author_name": "Christiane Mousson", - "author_inst": "Department of Nephrology and Transplantation, University of Dijon, Dijon, France." - }, - { - "author_name": "Jamal Bamoulid", - "author_inst": "Department of Nephrology, University of Besancon, Besancon, France." - }, - { - "author_name": "Antoine Thierry", - "author_inst": "Department of Nephrology and Transplantation, University of Poitiers, Poitiers, France." - }, - { - "author_name": "Dany Anglicheau", - "author_inst": "Service de Nephrologie et Transplantation Adultes, Hopital Universitaire Necker - APHP Centre - Universite de Paris INEM INSERM U 1151 - CNRS UMR 8253, Paris, F" - }, - { - "author_name": "Lionel Couzi", - "author_inst": "Service de Nephrologie-Transplantation-Dialyse-Apherese, Hopital Pellegrin, CHU de Bordeaux Pellegrin, Unite Mixte de Recherche \"ImmunoConcEpT\" 5164 - Universit" - }, - { - "author_name": "Jonathan Maurice Chemouny", - "author_inst": "University of Rennes, CHU Rennes, Inserm, EHESP, Irset (Institut de Recherche en Sante, Environnement et Travail) - UMR_S 1085, CIC-P 1414, Rennes, France." - }, - { - "author_name": "Agnes Duveau", - "author_inst": "Department of Nephrology and Transplantation, University of Angers, Angers, France." - }, - { - "author_name": "Valerie Moal", - "author_inst": "Centre de Nephrologie et Transplantation Renale, Aix Marseille Universite, Hopitaux Universitaires de Marseille, Hopital Conception, Marseille, France." - }, - { - "author_name": "Yannick Le Meur", - "author_inst": "Department of Nephrology, CHU de Brest, UMR1227, Lymphocytes B et Autoimmunite, Universite de Brest, Inserm, Labex IGO, Brest, France." - }, - { - "author_name": "Gilles Blancho", - "author_inst": "Department of Nephrology and Transplantation, Centre Hospitalier Universitaire de Nantes, Nantes, France." - }, - { - "author_name": "Jerome Tourret", - "author_inst": "Nephrology and Renal Transplantation Department, AP-HP (Assistance Publique-Hopitaux de Paris), Hopital de la Pities Salpetriere, Paris, France." - }, - { - "author_name": "Paolo Malvezzi", - "author_inst": "Department of Nephrology, University of Grenoble, Grenoble, France" - }, - { - "author_name": "Christophe Mariat", - "author_inst": "Department of Nephrology and Transplantation, University of St Etienne, St Etienne, France." - }, - { - "author_name": "Jean-Philippe Rerolle", - "author_inst": "Department of Nephrology and Transplantation, University of Limoges, Limoges, France." - }, - { - "author_name": "Nicolas Bouvier", - "author_inst": "Department of Nephrology and Transplantation, University of Caen, Caen, France." - }, - { - "author_name": "- the French SOT COVID Registry", - "author_inst": "" - }, - { - "author_name": "Sophie Caillard", - "author_inst": "Department of Nephrology and Transplantation, Strasbourg University Hospital, Strasbourg, France. INSERM, IRM UMR-S 1109, University of Strasbourg, Strasbourg, " - }, - { - "author_name": "Olivier Thaunat", - "author_inst": "Department of Transplantation, Nephrology and Clinical Immunology, Hopital Edouard Herriot, Hospices Civils de Lyon, Universite Claude Bernard Lyon 1, Lyon, Fra" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "transplantation" - }, { "rel_doi": "10.1101/2021.12.14.472554", "rel_title": "Relationship between monomer packing and receptor binding domain pocket status in the spike trimer of SARS-CoV-2 variants", @@ -456021,6 +458735,217 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.13.21267368", + "rel_title": "Acute COVID-19 severity and 16-month mental morbidity trajectories in patient populations of six nations", + "rel_date": "2021-12-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267368", + "rel_abs": "BACKGROUNDThe aim of this multinational study was to assess the development of adverse mental health symptoms among individuals diagnosed with COVID-19 in the general population by acute infection severity up to 16 months after diagnosis.\n\nMETHODSParticipants consisted of 247 249 individuals from seven cohorts across six countries (Denmark, Estonia, Iceland, Norway, Scotland, and Sweden) recruited from April 2020 through August 2021. We used multivariable Poisson regression to contrast symptom-prevalence of depression, anxiety, COVID-19 related distress, and poor sleep quality among individuals with and without a diagnosis of COVID-19 at entry to respective cohorts by time (0-16 months) from diagnosis. We also applied generalised estimating equations (GEE) analysis to test differences in repeated measures of mental health symptoms before and after COVID-19 diagnosis among individuals ever diagnosed with COVID-19 over time.\n\nFINDINGSA total of 9979 individuals (4%) were diagnosed with COVID-19 during the study period and presented overall with a higher symptom burden of depression (prevalence ratio [PR] 1{middle dot}18, 95% confidence interval [95% CI] 1{middle dot}03-1{middle dot}36) and poorer sleep quality (1{middle dot}13, 1{middle dot}03-1{middle dot}24) but not with higher levels of symptoms of anxiety or COVID-19 related distress compared with individuals without a COVID-19 diagnosis. While the prevalence of depression and COVID-19 related distress attenuated with time, the trajectories varied significantly by COVID-19 acute infection severity. Individuals diagnosed with COVID-19 but never bedridden due to their illness were consistently at lower risks of depression and anxiety (PR 0{middle dot}83, 95% CI 0{middle dot}75-0{middle dot}91 and 0{middle dot}77, 0{middle dot}63-0{middle dot}94, respectively), while patients bedridden for more than 7 days were persistently at higher risks of symptoms of depression and anxiety (PR 1{middle dot}61, 95% CI 1{middle dot}27-2{middle dot}05 and 1{middle dot}43, 1{middle dot}26-1{middle dot}63, respectively) throughout the 16-month study period.\n\nCONCLUSIONAcute infection severity is a key determinant of long-term mental morbidity among COVID-19 patients.", + "rel_num_authors": 49, + "rel_authors": [ + { + "author_name": "Ingibjorg Magnusdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Aniko Lovik", + "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Anna Bara Unnarsdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Daniel L. McCartney", + "author_inst": "Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK" + }, + { + "author_name": "Helga Ask", + "author_inst": "Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway" + }, + { + "author_name": "Kadri Koiv", + "author_inst": "Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia" + }, + { + "author_name": "Lea Arregui Nordahl Christoffersen", + "author_inst": "Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Sverre Urnes Johnson", + "author_inst": "Department of Psychology, University of Oslo, Oslo, Norway" + }, + { + "author_name": "Andrew M McIntosh", + "author_inst": "Division of Psychiatry, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Anna K. Kahler", + "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Archie Campbell", + "author_inst": "Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK" + }, + { + "author_name": "Arna Hauksdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Chloe Fawns-Ritchie", + "author_inst": "Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK" + }, + { + "author_name": "Christian Erikstrup", + "author_inst": "Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark" + }, + { + "author_name": "Dorte Helenius", + "author_inst": "Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Drew Altschul", + "author_inst": "Department of Psychology, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Edda Bjork Thordardottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Elias Eythorsson", + "author_inst": "Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Emma M. Frans", + "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Gunnar Tomasson", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Harpa Lind Jonsdottir", + "author_inst": "Faculty of Psychology, University of Iceland School of Health Sciences, Reykjavik, Iceland" + }, + { + "author_name": "Harpa Runarsdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Henrik Hjalgrim", + "author_inst": "Danish Cancer Society Research Center, Copenhagen, Denmark" + }, + { + "author_name": "Hronn Hardardottir", + "author_inst": "Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Juan Gonzalez-Hijon", + "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Karina Banasik", + "author_inst": "Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark" + }, + { + "author_name": "Khoa Manh Dinh", + "author_inst": "Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark" + }, + { + "author_name": "Li Lu", + "author_inst": "Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway" + }, + { + "author_name": "Lili Milani", + "author_inst": "Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia" + }, + { + "author_name": "Lill Trogstad", + "author_inst": "Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway" + }, + { + "author_name": "Maria Didriksen", + "author_inst": "Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Omid V. Ebrahimi", + "author_inst": "Department of Psychology, University of Oslo, Oslo, Norway" + }, + { + "author_name": "Patrick F. Sullivan", + "author_inst": "Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA" + }, + { + "author_name": "Per Minor Magnus", + "author_inst": "Centre of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway" + }, + { + "author_name": "Qing Shen", + "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Ragnar Nesvag", + "author_inst": "Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway." + }, + { + "author_name": "Reedik Magi", + "author_inst": "Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia" + }, + { + "author_name": "Runolfur Palsson", + "author_inst": "Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Sisse Rye Ostrowski", + "author_inst": "Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Thomas Werge", + "author_inst": "Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Asle Hoffart", + "author_inst": "Department of Psychology, University of Oslo, Oslo, Norway" + }, + { + "author_name": "David J. Porteous", + "author_inst": "Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK" + }, + { + "author_name": "Fang Fang", + "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Johanna Jakobsdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Kelli Lehto", + "author_inst": "Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia" + }, + { + "author_name": "Ole A. Andreassen", + "author_inst": "NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway" + }, + { + "author_name": "Ole B.V. Pedersen", + "author_inst": "Department of Clinical Immunology, Zealand University Hospital, Denmark" + }, + { + "author_name": "Thor Aspelund", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Unnur Anna Valdimarsdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.14.21267418", "rel_title": "COVID-19 vaccination and Guillain-Barre syndrome: analyses using the National Immunoglobulin Database", @@ -456278,53 +459203,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.14.21267783", - "rel_title": "Dynamics of anti-Spike IgG antibody level after full BNT162b2 COVID-19 vaccination in health care workers", - "rel_date": "2021-12-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267783", - "rel_abs": "IntroductionThe administration of a third vaccine is ongoing in many countries, but the evaluation of vaccine-induced immunity is still insufficient. This study evaluated anti-spike IgG levels in 373 health care workers six months after the BNT162b2 vaccination.\n\nMethodsDynamics of anti-spike IgG levels six months after the 2nd vaccination were assessed in 49 participants (Analysis-1). A cross-sectional assessment of anti-spike IgG level was performed in 373 participants (Analysis-2). Participants positive for anti-nucleocapsid IgG or IgM and receiving immunosuppressants were excluded from Analysis-2.\n\nResultsIn Analysis 1, the median anti-spike IgG level was lower in the older age group and decreased consistently after the second vaccination regardless of age. In Analysis-2, the anti-spike IgG level was significantly negatively associated with age (r = -0.35, p < 0.01). This correlation remained statistically significant (r = -0.28, p < 0.01) even after adjusting for sex, BMI, smoking habits, alcohol drinking habits, allergies, and the presence of fever or other adverse reactions at the time of the vaccination. Alcohol drinking habit was also associated with the anti-spike IgG level; daily alcohol drinkers had significantly lower anti-spike IgG levels than never alcohol drinkers. Sex, smoking habit, allergy, and fever and other side effects after the vaccination were not associated with anti-spike IgG levels six months after the 2nd vaccination.\n\nConclusionsSix months after the vaccination, the anti-spike IgG level was substantially low among older persons and daily alcohol drinkers.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Hiroaki Ikezaki", - "author_inst": "Kyushu University Hospital" - }, - { - "author_name": "Ryoko Nakashima", - "author_inst": "Kyushu University Hospital" - }, - { - "author_name": "Kahori Miyoshi", - "author_inst": "Haradoi Hospital" - }, - { - "author_name": "Yuichi Hara", - "author_inst": "Haradoi Hospital" - }, - { - "author_name": "Jun Hayashi", - "author_inst": "Haradoi Hospital" - }, - { - "author_name": "Hiroshi Hara", - "author_inst": "Haradoi Hospital" - }, - { - "author_name": "Hideyuki Nomura", - "author_inst": "Haradoi Hospital" - }, - { - "author_name": "Nobuyuki Shimono", - "author_inst": "Kyushu University Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.15.21267847", "rel_title": "COVID-19 vaccination, from first dose to booster: New insights into the frequency of most common systemic adverse events and possible booster nocebo effects based on a systematic review", @@ -458123,6 +461001,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.10.21267574", + "rel_title": "Safety and immunogenicity of a heterologous booster of protein subunit vaccine MVC-COV1901 after two doses of adenoviral vector vaccine AZD1222", + "rel_date": "2021-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.10.21267574", + "rel_abs": "We report the interim safety and immunogenicity results in participants administrated with a booster dose of protein subunit vaccine MVC-COV1901 at 12 or 24 weeks after two doses of AZD1222 (ChAdOx1 nCoV-19). In subjects fully vaccinated with two doses of AZD1222, waning antibody immunity was apparent within six months of the second dose of AZD1222. At one month after the MVC-COV1901 booster dose, anti-SARS-CoV-2 spike IgG antibody titers and neutralizing antibody titers were 14- and 8.6-fold increased, respectively, when compared to the titer levels on the day of the booster dose. We also observed 5.2- and 5.6-fold increases in neutralizing titer levels against wildtype and Omicron variant pseudovirus after the booster dose, respectively. These interim results support the use of MVC-COV1901 as a heterologous booster for individuals vaccinated with AZD1222.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Shu-Hsing Cheng", + "author_inst": "Taoyuan General Hospital" + }, + { + "author_name": "Yi-Chun Lin", + "author_inst": "Taoyuan General Hospital" + }, + { + "author_name": "Cheng-Pin Chen", + "author_inst": "Taoyuan General Hospital" + }, + { + "author_name": "Chien-Yu Cheng", + "author_inst": "Taoyuan General Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.10.21267582", "rel_title": "Echinacea purpurea for the Long-term Prevention of Viral Respiratory Tract Infections during COVID-19 Pandemic: A Randomized, Open, Controlled, Exploratory Clinical Study", @@ -458536,41 +461445,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.13.21267727", - "rel_title": "Adult life-course trajectories of psychological distress and economic outcomes in midlife during the COVID-19 pandemic", - "rel_date": "2021-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267727", - "rel_abs": "This study used two British birth cohorts to examine whether pre-pandemic trajectories of psychological distress were associated with a greater risk of changes in financial and employment situation during the pandemic, as well as increased need for government support and use of other methods to mitigate their economic situation. We identified 5 differential life-course trajectories of psychological distress from adolescence to midlife and explored their relation to changes in financial and employment circumstances at different stages during the pandemic from May 2020 to March 2021, applying multinomial logistic regression and controlling for numerous early life covariates. In addition, we ran modified Poisson models with robust standard errors to identify whether different trajectories were more likely to have been supported by the benefit system, payment holidays, borrowing and other methods of mitigating the economic shock. We found that despite the UK governments economic response package economic inequalities for pre-pandemic psychological distress trajectories with differential onset, severity and chronicity across the life-course were exacerbated by the COVID-19 economic shock. Furthermore, the subsequent cut in government support, alongside increases in the cost of living may widen economic inequalities for differential pre-pandemic psychological distress trajectories, which in turn may also worsen mental health. This work highlights, different pre-pandemic trajectories of psychological distress were more vulnerable to economic shock.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Vanessa Moulton", - "author_inst": "UCL" - }, - { - "author_name": "Alice Sullivan", - "author_inst": "UCL" - }, - { - "author_name": "Alissa Goodman", - "author_inst": "UCL" - }, - { - "author_name": "Sam Parsons", - "author_inst": "UCL" - }, - { - "author_name": "George Ploubidis", - "author_inst": "UCL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.12.13.21267077", "rel_title": "Change in Finances, Peer Access, and Mental Health Among Trans and Non-binary People in Canada During COVID-19", @@ -460225,6 +463099,141 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.11.472236", + "rel_title": "Isolation and comparative analysis of antibodies that broadly neutralize sarbecoviruses", + "rel_date": "2021-12-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.11.472236", + "rel_abs": "The devastation caused by SARS-CoV-2 has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo. Comparative studies with other receptor-binding domain (RBD)-directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses and thus its promise as an agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well conserved among sarbecoviruses, but also uncovered a new antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well for the development of a pan-sarbecovirus vaccine.\n\nOne sentence summaryA monoclonal antibody that neutralizes or binds all sarbecoviruses tested and represents a reproducible antibody class.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Lihong Liu", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Sho Iketani", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Yicheng Guo", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Ryan Casner", + "author_inst": "Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA" + }, + { + "author_name": "Eswar Reddem", + "author_inst": "Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA" + }, + { + "author_name": "Manoj S. Nair", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Jian Yu", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Jasper Chan", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Maple Wang", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Gabriele Cerutti", + "author_inst": "Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA" + }, + { + "author_name": "Zhiteng Li", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Candace Castagna", + "author_inst": "Institute of Comparative Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA" + }, + { + "author_name": "Laura Corredor", + "author_inst": "Institute of Comparative Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA" + }, + { + "author_name": "Hin Chu", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Shuofeng Yuan", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Vincent Poon", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Chris Chan", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Zhiwei Chen", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Yang Luo", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Marcus Cunningham", + "author_inst": "Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA" + }, + { + "author_name": "Alejandro Chavez", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA" + }, + { + "author_name": "Michael Yin", + "author_inst": "Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA" + }, + { + "author_name": "David Perlin", + "author_inst": "Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA" + }, + { + "author_name": "Moriya Tsuji", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Kwok-Yung Yuen", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Peter Kwong", + "author_inst": "Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA" + }, + { + "author_name": "Zizhang Sheng", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Yaoxing Huang", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Lawrence Shapiro", + "author_inst": "Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA" + }, + { + "author_name": "David D. Ho", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.13.21267761", "rel_title": "SARS-CoV-2 Omicron variant escapes neutralization by vaccinated and convalescent sera and therapeutic monoclonal antibodies", @@ -460350,61 +463359,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.12.10.471928", - "rel_title": "Language Models for the Prediction of SARS-CoV-2 Inhibitors", - "rel_date": "2021-12-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.10.471928", - "rel_abs": "The COVID-19 pandemic highlights the need for computational tools to automate and accelerate drug design for novel protein targets. We leverage deep learning language models to generate and score drug candidates based on predicted protein binding affinity. We pre-trained a deep learning language model (BERT) on [~]9.6 billion molecules and achieved peak performance of 603 petaflops in mixed precision. Our work reduces pre-training time from days to hours, compared to previous efforts with this architecture, while also increasing the dataset size by nearly an order of magnitude. For scoring, we fine-tuned the language model using an assembled set of thousands of protein targets with binding affinity data and searched for inhibitors of specific protein targets, SARS-CoV-2 Mpro and PLpro. We utilized a genetic algorithm approach for finding optimal candidates using the generation and scoring capabilities of the language model. Our generalizable models accelerate the identification of inhibitors for emerging therapeutic targets.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Andrew E Blanchard", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "John Gounley", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Debsindhu Bhowmik", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Mayanka Chandra Shekar", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Isaac Lyngaas", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Shang Gao", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Junqi Yin", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Aristeidis Tsaris", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Feiyi Wang", - "author_inst": "Oak Ridge National Laboratory" - }, - { - "author_name": "Jens Glaser", - "author_inst": "Oak Ridge National Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.12.12.472253", "rel_title": "Scanning the RBD-ACE2 molecular interactions in Omicron variant", @@ -461839,6 +464793,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.12.472286", + "rel_title": "The Omicron variant is highly resistant against antibody-mediated neutralization - implications for control of the COVID-19 pandemic", + "rel_date": "2021-12-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.12.472286", + "rel_abs": "The rapid spread of the SARS-CoV-2 Omicron variant suggests that the virus might become globally dominant. Further, the high number of mutations in the viral spike-protein raised concerns that the virus might evade antibodies induced by infection or vaccination. Here, we report that the Omicron spike was resistant against most therapeutic antibodies but remained susceptible to inhibition by Sotrovimab. Similarly, the Omicron spike evaded neutralization by antibodies from convalescent or BNT162b2-vaccinated individuals with 10- to 44-fold higher efficiency than the spike of the Delta variant. Neutralization of the Omicron spike by antibodies induced upon heterologous ChAdOx1/BNT162b2-vaccination or vaccination with three doses of BNT162b2 was more efficient, but the Omicron spike still evaded neutralization more efficiently than the Delta spike. These findings indicate that most therapeutic antibodies will be ineffective against the Omicron variant and that double immunization with BNT162b2 might not adequately protect against severe disease induced by this variant.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Markus Hoffmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Nadine Kr\u00fcger", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Sebastian Schulz", + "author_inst": "Friedrich-Alexander-Universit\u00e4 Erlangen-N\u00fcrnberg" + }, + { + "author_name": "Anne Cossmann", + "author_inst": "Medizinische Hochschule Hannover" + }, + { + "author_name": "Cheila Rocha", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fc Primatenforschung" + }, + { + "author_name": "Amy Kempf", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Inga Nehlmeier", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Luise Graichen", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Anna-Sophie Moldenhauer", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Martin Sebastian Winkler", + "author_inst": "Universit\u00e4tsmedizin G\u00f6ttingen" + }, + { + "author_name": "Martin Lier", + "author_inst": "Universit\u00e4tsmedizin G\u00f6ttingen" + }, + { + "author_name": "Alexandra Dopfer-Jablonka", + "author_inst": "Medizinische Hochschule Hannover" + }, + { + "author_name": "Hans-Martin J\u00e4ck", + "author_inst": "Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg" + }, + { + "author_name": "Georg Behrens", + "author_inst": "Medizinische Hochschule Hannover" + }, + { + "author_name": "Stefan P\u00f6hlmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut f\u00fcr Primatenforschung" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.09.471735", "rel_title": "The T cell receptor repertoire reflects the dynamics of the immune response to vaccination", @@ -461976,25 +465005,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.12.09.21267556", - "rel_title": "Predicted Symptomatic Effectiveness of Pfizer-BioNTech BNT162b2 Vaccine Against Omicron Variant of SARS-CoV-2", - "rel_date": "2021-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267556", - "rel_abs": "This paper presents predictions of the symptomatic effectiveness of the Pfizer-BioNTech BNT162b2 (Comirnaty) vaccine against Omicron B.1.1.529, the latest SARS-CoV-2 variant of concern. They were obtained assuming fold decreases in Omicron neutralisation by vaccine-induced antibodies versus neutralisation of the virus Wild Type. A 25-fold decrease was assumed based on Omicron pseudovirus neutralisation study by Pfizer and BioNTech; a 94-fold, based on live-Omicron neutralisation study in South Africa; and 40, 80 and 120 folds, hypothesised based on genetic information. The effectiveness of two vaccine doses was predicted as 66% (42, 86), 48% (25, 72) and 42% (20, 66) for up to five months starting 2-4 weeks after the second dose, for the 25, 80 and 120 folds, respectively. The effectiveness of booster vaccination was predicted under a highly conservative assumption that the third dose would increase neutralisation by only 3.3 folds compared to the second dose. The predictions of effectiveness for up to five months, starting 2-4 weeks after the third dose, were 81% (59, 95), 67% (43, 87) and 61% (37, 82) for the 25, 80 and 120 folds, respectively. Despite the large fold decreases considered, the vaccine could still provide substantial protection, particularly after a booster and against severe disease. The paper is accompanied by free software which can be used to predict the symptomatic effectiveness of Comirnaty against Omicron under different neutralisation folds, including those obtained experimentally.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Oleg Volkov", - "author_inst": "Xitific LTD" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.08.21267455", "rel_title": "Analytical evaluation of thirty-two SARS-CoV-2 lateral flow antigen tests demonstrates sensitivity remains with the SARS-CoV-2 Gamma lineage.", @@ -464085,6 +467095,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.10.21267338", + "rel_title": "Mental health indicators in Sweden over a 12-month period during the COVID-19 pandemic", + "rel_date": "2021-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.10.21267338", + "rel_abs": "BackgroundThe ongoing COVID-19 pandemic has had an unprecedented impact on the lives of people globally and is expected to have profound effects on mental health. Yet, self-reported large-scale online surveys on mental health are still relatively uncommon. Here we aim to describe the mental health burden experienced in Sweden using baseline data of the Omtanke2020 Study.\n\nMethodSelf-reported baseline data collected over a 12-month period (June 9, 2020-June 8, 2021) from the longitudinal online survey of the Omtanke2020 Study including 27,950 adults in Sweden. Participants were volunteers or actively recruited through existing cohorts and after providing informed consent responded to monthly online questionnaires on socio-demographics, mental and physical health, COVID-19 infection, and impact. Poisson regression was fitted to assess the relative risk of high mental health burden (depression, anxiety, and COVID-19 specific PTSD).\n\nResultThe overall proportion of persons with high level of symptoms was 15.6%, 9.5% and 24.5% for depression, anxiety, and COVID-19 specific PTSD, respectively. Overall, 43.4% of the participants had significant, clinically relevant symptoms for at least one mental health outcome and 7.3% had significant symptoms for all three outcomes. We also observed differences in the prevalence of these symptoms across strata of sex, age, recruitment type, COVID-19 status, region, and seasonality.\n\nConclusionWhile the proportion of persons with high mental health burden remains higher than in pre-pandemic publications, our estimates are lower than previously reported levels of depression, anxiety, and PTSD during the pandemic in Sweden and elsewhere.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Anik\u00f3 Lovik", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Juan Gonz\u00e1lez-Hij\u00f3n", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Anna K. K\u00e4hler", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Unnur A. Valdimarsd\u00f3ttir", + "author_inst": "University of Iceland, Karolinska Institutet" + }, + { + "author_name": "Emma M. Frans", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Nancy L. Pedersen", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Per Hall", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Kamila Czene", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Patrick F. Sullivan", + "author_inst": "University of North Carolina, Karolinska Institutet" + }, + { + "author_name": "Fang Fang", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.12.09.21267349", "rel_title": "Down-regulation of SARS-CoV-2 neutralizing antibodies in vaccinated smokers", @@ -464334,49 +467399,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2021.12.08.21267433", - "rel_title": "A Phenome Wide Association Study of Severe COVID-19 Genetic Risk Variants", - "rel_date": "2021-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267433", - "rel_abs": "BackgroundGenetic loci associated with risk of severe COVID-19 infection have been identified and individuals with complicated COVID-19 infections often have multiple comorbidities.\n\nObjectiveIdentify known and unidentified comorbidities associated with genetic loci linked to risk of severe COVID-19 infection.\n\nMethodsA Phenome Wide Association Study (PheWAS) was conducted in 247,448 unrelated, white individuals from the UK Biobank to test the association of 1,402 unique phenotypes with ten genome-wide significant severe-COVID risk single nucleotide polymorphisms (SNP) identified from prior studies. A validation PheWAS was conducted in 2,247 white individuals from the CATHGEN.\n\nResultsFour of the ten tested genetic loci showed significant phenotypic associations in UK Biobank after FDR adjustment. Vascular dementia significantly associated with rs7271165 near TMEM65 on 8q24.13 in individuals with the C risk allele (OR 5.66 [95% CI 2.21-11.85], q=0.049). We identified 40 novel phenotype associations with rs657152 on 9q34.2 coinciding with the ABO gene with individuals with the A COVID risk allele having higher odds of heart failure (OR 1.09 [95% CI 1.03-1.14], q=0.004), diabetes mellitus (OR 1.05 [95% CI 1.02-1.07], q=0.004) and hypercholesterolemia (OR 1.04 [95% CI 1.02-1.06], q=6.3x10-5). Eight phenotypes associated with rs1819040 near KANSL1 on 17q21.31 in individuals with the A risk allele including atrial fibrillation and flutter (OR 1.07 [95% CI 1.04-1.10], q=0.0084) and pulmonary fibrosis (OR 0.80 [95% CI 0.71-0.89], q=0.035). Ten novel phenotypic associations were identified in association with rs74956615 on 19p13.2 near the TYK2 gene including individuals with the A COVID risk allele having lower odds of psoriatic arthropathy (OR 0.31 [95% CI 0.20-0.47], q=4.5x10-5), rheumatoid arthritis (OR 0.83 [95% CI 0.64-0.83], p=1.4x10-6) and thyrotoxicosis with or without goiter (OR 0.77 [95% CI 0.68-0.87], p-6.9x10-5). Two associations for rs1819040 (KANSL1) and seven associations for rs74956615 (TYK2) validated in CATHGEN.\n\nConclusionsUsing a broad PheWAS approach in a large discovery and validation cohort, we have identified novel phenotypic associations with risk alleles for severe COVID-19 infection. Interestingly, the ABO locus was associated with comorbidities that are also risk factors for severe COVID-19 infection, suggesting that this locus has pleiotropic effects and provides a potential mechanism for this association. The 19p13 locus was associated with lower risk of autoimmune disease, these findings may have broad implications for the importance of multiple comorbidities across both infectious and non-infectious diseases and may provide insight in the molecular function of the genes near these genetic risk loci.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jessica A. Regan", - "author_inst": "Duke University" - }, - { - "author_name": "Jawan Abdulrahim", - "author_inst": "Duke University" - }, - { - "author_name": "Nathan Bihlmeyer", - "author_inst": "Duke University" - }, - { - "author_name": "Carol Haynes", - "author_inst": "Duke University" - }, - { - "author_name": "Lydia Coulter Kwee", - "author_inst": "Duke University" - }, - { - "author_name": "Manesh Patel", - "author_inst": "Duke University" - }, - { - "author_name": "Svati H. Shah", - "author_inst": "Duke University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.12.08.21267482", "rel_title": "NIH Funding of COVID-19 Research in 2020: a Cross Sectional Study", @@ -465891,6 +468913,89 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.07.471590", + "rel_title": "A novel bacterial protease inhibitor adjuvant in RBD-based COVID-19 vaccine formulations increases neutralizing antibodies, specific germinal center B cells and confers protection against SARS-CoV-2 infection.", + "rel_date": "2021-12-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.07.471590", + "rel_abs": "In this work we evaluated recombinant receptor binding domain (RBD) based vaccine formulation prototypes with potential for further clinical development. We assessed different formulations containing RBD plus Alum, AddaS03, AddaVax or the combination of Alum and U-Omp19: a novel Brucella spp. protease inhibitor vaccine adjuvant. Results show that the vaccine formulation composed of U-Omp19 and Alum as adjuvants have a better performance: it significantly increased mucosal and systemic neutralizing antibodies in comparison to antigen plus Alum, AddaVax or AddaS03. Antibodies induced with the formulation containing U-Omp19 not only increased their neutralization capacity against the wild-type virus but also cross neutralized alpha, lambda and gamma variants with similar potency. Also, addition of U-Omp19 to vaccine formulation increased the frequency of RBD-specific geminal center B cells and plasmablasts. Additionally, U-Omp19+Alum formulation induced RBD-specific Th1 and CD8+ T cell responses in spleens and lungs. Finally, this vaccine formulation conferred protection against an intranasal SARS-CoV-2 challenge of K18-hACE2 mice.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Lorena M Coria", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Lucas M Saposnik", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Celeste Pueblas Castro", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Eliana F Castro", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Laura A Bruno", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "William B Stone", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Paula S Perez", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y SIDA (INBIRS, Universidad de Buenos Aires - CONICET)" + }, + { + "author_name": "M. Laura Darriba", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Lucia B Chemes", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Julieta Alcain", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Ignacio Mazzitelli", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y SIDA (INBIRS, Universidad de Buenos Aires - CONICET)" + }, + { + "author_name": "Augusto Varese", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y SIDA (INBIRS, Universidad de Buenos Aires - CONICET)" + }, + { + "author_name": "Melisa Salvatori", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y SIDA (INBIRS, Universidad de Buenos Aires - CONICET)" + }, + { + "author_name": "Albert J Auguste", + "author_inst": "Virginia Polytechnic Institute and State University" + }, + { + "author_name": "Diego E Alvarez", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Karina A Pasquevich", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Juliana Cassataro", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.08.471814", "rel_title": "Nanotrap Particles Improve Nanopore Sequencing of SARS-CoV-2 and Other Respiratory Viruses", @@ -466148,141 +469253,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, - { - "rel_doi": "10.1101/2021.12.08.21267502", - "rel_title": "Measurement of SARS-CoV-2 antigens in plasma of pediatric patients with acute COVID-19 or MIS-C using an ultrasensitive and quantitative immunoassay", - "rel_date": "2021-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.08.21267502", - "rel_abs": "BackgroundDetection of SARS-CoV-2 antigens in blood has high sensitivity in adults with acute COVID-19, but sensitivity in pediatric patients is unclear. Recent data suggest that persistent SARS-CoV-2 spike antigenemia may contribute to multisystem inflammatory syndrome in children (MIS-C). We quantified SARS-CoV-2 nucleocapsid (N) and spike (S) antigens in blood of pediatric patients with either acute COVID-19 or MIS-C using ultrasensitive immunoassays (Meso Scale Discovery).\n\nMethodsPlasma was collected from inpatients (<21 years) enrolled across 15 hospitals in 15 US states. Acute COVID-19 patients (n=36) had a range of disease severity and positive nasopharyngeal SARS-CoV-2 RT-PCR within 24 hours of blood collection. Patients with MIS-C (n=53) met CDC criteria and tested positive for SARS-CoV-2 (RT-PCR or serology). Controls were patients pre-COVID-19 (n=67) or within 24h of negative RT-PCR (n=43).\n\nResultsSpecificities of N and S assays were 95-97% and 100%, respectively. In acute COVID-19 patients, N/S plasma assays had 89%/64% sensitivity, respectively; sensitivity in patients with concurrent nasopharyngeal swab cycle threshold (Ct) [≤] 35 were 93%/63%. Antigen concentrations ranged from 1.28-3,844 pg/mL (N) and 1.65-1,071 pg/mL (S) and correlated with disease severity. In MIS-C, antigens were detected in 3/53 (5.7%) samples (3 N-positive: 1.7, 1.9, 121.1 pg/mL; 1 S-positive: 2.3 pg/mL); the patient with highest N had positive nasopharyngeal RT-PCR (Ct 22.3) concurrent with blood draw.\n\nConclusionsUltrasensitive blood SARS-CoV-2 antigen measurement has high diagnostic yield in children with acute COVID-19. Antigens were undetectable in most MIS-C patients, suggesting that persistent antigenemia is not a common contributor to MIS-C pathogenesis.\n\nKey pointsIn a U.S. pediatric cohort tested with ultrasensitive immunoassays, SARS-CoV-2 nucleocapsid antigens were detectable in most patients with acute COVID-19, and spike antigens were commonly detectable. Both antigens were undetectable in almost all MIS-C patients.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "George B Sigal", - "author_inst": "Meso Scale Diagnostics" - }, - { - "author_name": "Tanya Novak", - "author_inst": "Boston Children's Hospital and Harvard Medical School" - }, - { - "author_name": "Anu Mathew", - "author_inst": "Meso Scale Diagnostics" - }, - { - "author_name": "Janet Chou", - "author_inst": "Boston Children's Hospital and Harvard Medical School" - }, - { - "author_name": "Yubo Zhang", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Navaratnam Manjula", - "author_inst": "Meso Scale Diagnostics" - }, - { - "author_name": "Predeepthi Bathala", - "author_inst": "Meso Scale Diagnostics" - }, - { - "author_name": "Jessica Joe", - "author_inst": "Meso Scale Diagnostics" - }, - { - "author_name": "Nikhil Padmanabhan", - "author_inst": "Meso Scale Diagnostics" - }, - { - "author_name": "Daniel Romero", - "author_inst": "Meso Scale Diagnostics" - }, - { - "author_name": "Gabriella Allegri-Machado", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Jill Joerger", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Laura L Loftis", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Stephanie P Schwartz", - "author_inst": "University of North Carolina at Chapel Hill Children's Hospital" - }, - { - "author_name": "Tracie C Walker", - "author_inst": "University of North Carolina at Chapel Hill Children's Hospital" - }, - { - "author_name": "Julie C Fitzgerald", - "author_inst": "The University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Keiko M Tarquinio", - "author_inst": "Emory University School of Medicine, Children's Healthcare of Atlanta" - }, - { - "author_name": "Matt S Zinter", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jennifer E Schuster", - "author_inst": "Childrens Mercy Kansas City" - }, - { - "author_name": "Natasha B Halasa", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Melissa L Cullimore", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Aline B Maddux", - "author_inst": "University of Colorado School of Medicine and Children's Hospital Colorado" - }, - { - "author_name": "Mary A Staat", - "author_inst": "Cincinnati Children's Hospital Medical Center" - }, - { - "author_name": "Katherine Irby", - "author_inst": "Arkansas Children's Hospital" - }, - { - "author_name": "Heidi R Flori", - "author_inst": "Mott Childrens Hospital and University of Michigan" - }, - { - "author_name": "Bria M Coates", - "author_inst": "Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Childrens Hospital of Chicago" - }, - { - "author_name": "Hillary Crandall", - "author_inst": "University of Utah" - }, - { - "author_name": "Shira J Gertz", - "author_inst": "Saint Barnabas Medical Center" - }, - { - "author_name": "Adrienne G Randolph", - "author_inst": "Boston Childrens Hospital and Harvard Medical School" - }, - { - "author_name": "Nira R Pollock", - "author_inst": "Boston Children's Hospital and Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.08.21267478", "rel_title": "Single cell gene expression profiling of nasal ciliated cells reveals distinctive biological processes related to epigenetic mechanisms in patients with severe COVID-19", @@ -467441,6 +470411,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.06.471215", + "rel_title": "The influence of new SARS-CoV-2 variant Omicron (B.1.1.529) on vaccine efficacy, its correlation to Delta Variants: a computational approach", + "rel_date": "2021-12-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.06.471215", + "rel_abs": "The newly discovered COVID variant B.1.1.529 in Botswana has more than 30 mutations in spike and many other in non-spike proteins, far more than any other SARS-CoV-2 variant accepted as a variant of concern by the WHO and officially named Omicron, and has sparked concern among scientists and the general public. Our findings provide insights into structural modification caused by the mutations in the Omicrons receptor-binding domain and look into the effects on interaction with the hosts neutralising antibodies CR3022, B38, CB6, P2B-2F6, and REGN, as well as ACE2R using an in silico approach. We have employed secondary structure prediction, structural superimposition, protein disorderness, molecular docking, and MD simulation to investigate host-pathogen interactions, immune evasion, and transmissibility caused by mutations in the RBD region of the spike protein of the Omicron variant and compared it to the Delta variants (AY.1, AY.2, & AY.3) and wild type. Computational analysis revealed that the Omicron variant has a higher binding affinity for the human ACE2 receptor than the wild and Delta (AY.1 and AY.2 strains), but lower than the Delta AY.3 strain. MD simulation and docking analysis suggest that the omicron and Delta AY.3 were found to have relatively unstable and compact RBD structures and hampered interactions with antibodies more than wild and Delta (AY.1 and AY.2), which may lead to relatively more pathogenicity and antibody escape. In addition, we observed lower binding affinity of Omicron for human monoclonal antibodies (CR3022, B38, CB6, and P2B2F6) when compared to wild and Delta (AY.1 & AY.2). However, the binding affinity of Omicron RBD variants for CR3022, B38, and P2B2F6 antibodies is lower as compared to Delta AY.3, which might promote immune evasion and reinfection and needs further experimental investigation.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Prashant Ranjan", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Neha", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Chandra Devi", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Kaviyapriya Arulmozhi Devar", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Parimal Das", + "author_inst": "Banaras Hindu University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.07.21267442", "rel_title": "Dynamic analysis and evaluation of asymptomatic infection in the spread of COVID-19", @@ -467570,53 +470575,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.06.21267388", - "rel_title": "Deviations in Predicted COVID-19 cases in the US during early months of 2021 relate to rise in B.1.526 and its family of variants", - "rel_date": "2021-12-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.06.21267388", - "rel_abs": "ObjectiveTo investigate the abrogation of COVID-19 case declines from predicted rates in the US in relationship to viral variants and mutations.\n\nDesignEpidemiological prediction and time series study of COVID-19 in the US by State.\n\nSettingCommunity testing and sequencing of COVID-19 in the US.\n\nParticipantsTime series US COVID-19 case data from the Johns Hopkins University CSSE database. Time series US Variant and Mutation data from the GISAID database.\n\nMain outcome measuresPrimary outcomes were statistical modeling of US state deviations from epidemiological predictions, percentage of COVID-19 variants, percentage of COVID-19 mutations, and reported SARS-CoV-2 infections.\n\nResultsDeviations in epidemiological predictions of COVID-19 case declines in the North Eastern US in March 2021 were highly positively related to percentage of B.1.526 (Iota) lineage (p < 10e - 7) and B.1.526.2 (p < 10 - 8) and the T95I mutation (p < 10e - 9). They were related inversely to B.1.427 and B.1.429 (Epsilon) and there was a trend for association with B.1.1.7 (Alpha) lineage.\n\nConclusionDeviations from accurate predictive models are useful for investigating potential immune escape of COVID-19 variants at the population level. The B.1.526 and B.1.526.2 lineages likely have a high potential for immune escape and should be designated as variants of concern. The T95I mutation which is present in the B.1.526, B.1.526.2, and B.1.617.2 (Delta) lineages in the US warrants further investigation as a mutation of concern.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Pawan Nandakishore", - "author_inst": "Colaberry Inc." - }, - { - "author_name": "Meng Lui", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Rishab Prakash", - "author_inst": "Data Informatics Center for Epidemiology, PathCheck Foundation" - }, - { - "author_name": "Surya Gourneni", - "author_inst": "Academics for the Future of Science Inc." - }, - { - "author_name": "Rohan Sukumaran", - "author_inst": "Data Informatics Center for Epidemiology, PathCheck Foundation" - }, - { - "author_name": "Jonathan M. Berman", - "author_inst": "New York Institute of Technology" - }, - { - "author_name": "Swaminathan A. Iyer", - "author_inst": "University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Christin A. Glorioso", - "author_inst": "University of California, San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.07.21267416", "rel_title": "Mortality trends and lengths of stay among hospitalized COVID-19 patients in Ontario and Quebec (Canada): a population-based cohort study of the first three epidemic waves", @@ -469483,6 +472441,33 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.12.05.471290", + "rel_title": "Constructing a multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and co-infecting microbes", + "rel_date": "2021-12-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.05.471290", + "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has caused millions of deaths worldwide. Many efforts have focused on unraveling the mechanism of the viral infection to develop effective strategies for treatment and prevention. Previous studies have provided some clarity on the protein-protein interaction linkages occurring during the life cycle of viral infection; however, we lack a complete understanding of the full interactome, comprising human miRNAs and protein-coding genes and co-infecting microbes. To comprehensively determine this, we developed a statistical modeling method using latent Dirichlet allocation (called MLCrosstalk, for multiple-layer crosstalk) to fuse many types of data to construct the full interactome of SARS-CoV-2. Specifically, MLCrosstalk is able to integrate samples with multiple layers of information (e.g., miRNA and microbes), enforce a consistent topic distribution on all data types, and infer individual-level linkages (i.e., differing between patients). We also implement a secondary refinement with network propagation to allow our microbe-gene linkages to address larger network structures (e.g., pathways). Using MLCrosstalk, we generated a list of genes and microbes linked to SARS-CoV-2. Interestingly, we found that two of the identified microbes, Rothia mucilaginosa and Prevotella melaninogenica, show distinct patterns representing synergistic and antagonistic relationships with the virus, respectively. We also identified several SARS-COV-2-associated pathways, including the VEGFA-VEGFR2 and immune response pathways, which may provide potential targets for drug design.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Shaoke Lou", + "author_inst": "Yale University" + }, + { + "author_name": "Tianxiao Li", + "author_inst": "Yale University" + }, + { + "author_name": "Mark Gerstein", + "author_inst": "Yale university" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.05.471277", "rel_title": "A zebrafish model of COVID-19-associated cytokine storm syndrome reveals differential proinflammatory activities of Spike proteins of SARS-CoV-2 variants of concern.", @@ -469868,53 +472853,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.05.471310", - "rel_title": "A sarbecovirus found in Russian bats uses human ACE2", - "rel_date": "2021-12-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.05.471310", - "rel_abs": "Spillover of sarbecoviruses from animals to humans has resulted in outbreaks of severe acute respiratory syndrome SARS-CoVs and the ongoing COVID-19 pandemic. Efforts to identify the origins of SARS-CoV-1 and -2 has resulted in the discovery of numerous animal sarbecoviruses - the majority of which are only distantly related to known human pathogens and do not infect human cells. The receptor binding domain (RBD) on sarbecoviruses engages receptor molecules on the host cell and mediates cell invasion. Here, we tested the receptor tropism and serological cross reactivity for RBDs from two sarbecoviruses found in Russian horseshoe bats. While these two viruses are in a viral lineage distinct from SARS-CoV-1 and -2, one virus, Khosta-2, was capable of using human ACE2 to facilitate cell entry. Viral pseudotypes with a recombinant, SARS-CoV-2 spike encoding for the Khosta 2 RBD were resistant to both SARS-CoV-2 monoclonal antibodies and serum from individuals vaccinated for SARS-CoV-2. Our findings further demonstrate that sarbecoviruses circulating in wildlife outside of Asia also pose a threat to global health and ongoing vaccine campaigns against SARS-CoV-2\n\nONE SENTENCE SUMMARYEuropean bat coronaviruses that are only distantly related to SARS-CoV-2 but use the same cell entry route, escape the immune response against SARS-CoV-2 vaccines, driving the need for broader vaccines.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Stephanie N. Seifert", - "author_inst": "Washington State University" - }, - { - "author_name": "Shuangyi Bai", - "author_inst": "Washington State University" - }, - { - "author_name": "Stephen Fawcett", - "author_inst": "Washington State University" - }, - { - "author_name": "Elizabeth B. Norton", - "author_inst": "Tulane University" - }, - { - "author_name": "Kevin J. Zwezdaryk", - "author_inst": "Tulane University" - }, - { - "author_name": "James Robinson", - "author_inst": "Tulane" - }, - { - "author_name": "Bronwyn Gunn", - "author_inst": "Washington State University" - }, - { - "author_name": "Michael C Letko", - "author_inst": "NIH/NIAID" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.12.04.471236", "rel_title": "An antibody-escape calculator for mutations to the SARS-CoV-2 receptor-binding domain", @@ -471181,6 +474119,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.06.21267289", + "rel_title": "Testing the Validity of the Modified Vaccine Attitude Question Battery across 22 Languages with a Large-scale International Survey Dataset", + "rel_date": "2021-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.06.21267289", + "rel_abs": "In this study, we tested the validity of the modified version of the Vaccine Attitude Question Battery (VAQB) across 22 different languages. Validity test was conducted with a large-scale international survey dataset, COVIDiSTRESSII Global Survey, collected from 20,601 participants from 62 countries. We employed exploratory and confirmatory factor analysis, measurement invariance test, and measurement alignment for internal validity test. Moreover, we examined correlation between the VAQB score, vaccination intent, compliance with preventive measures, and trust in public health-related agents. The results reported that the modified VAQB, which included five items, showed good validity across 22 languages with measurement alignment. Furthermore, the VAQB score showed negative association with vaccination intent, compliance, and trust as expected. The findings from this study provide additional evidence supporting the validity of the modified VAQB in 22 languages for future large-scale international research on COVID-19 and vaccination.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Hyemin Han", + "author_inst": "University of Alabama" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.06.21267101", "rel_title": "SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia", @@ -471586,45 +474543,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.12.06.21267084", - "rel_title": "Predicted CTL responses from pressured epitopes in SARS-CoV-2 correlate with COVID-19 severity", - "rel_date": "2021-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.06.21267084", - "rel_abs": "Heterogeneity in susceptibility among individuals to COVID-19 has been evident through the pandemic worldwide. Protective cytotoxic T lymphocyte (CTL) responses generated against pathogens in certain individuals are known to impose selection pressure on the pathogen, thus driving emergence of new variants. In this study, we focus on the role played by host genetic heterogeneity in terms of HLA-genotypes in determining differential COVID-19 severity in patients and dictating mechanisms of immune evasion adopted by SARS-CoV-2 due to the imposed immune pressure at global and cohort levels. We use bioinformatic tools for CTL epitope prediction to identify epitopes under immune pressure. Using HLA-genotype data of COVID-19 patients from a local cohort, we observe that asymptomatic individuals recognize a larger number of pressured epitopes which could facilitate emergence of mutations at these epitopic regions to overcome the protectivity they offer to the host. Based on the severity of COVID-19, we also identify HLA-alleles and epitopes that offer higher protectivity against severe disease in infected individuals. Finally, we shortlist a set of pressured and protective epitopes that represent regions in the viral proteome that are under higher immune pressure across SARS-CoV-2 variants due to the protectivity they offer. Identification of such epitopes could potentially aid in prediction of indigenous variants of SARS-CoV-2 and other pathogens, defined by the distribution of HLA-genotypes among members of a population.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Vishal N Rao", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Ushashi Banerjee", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Narmada Sambaturu", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Sneha Chunchanur", - "author_inst": "Bangalore Medical College and Research Institute" - }, - { - "author_name": "Ambica R", - "author_inst": "Bangalore Medical College and Research Institute" - }, - { - "author_name": "Nagasuma Chandra", - "author_inst": "Indian Institute of Science" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.06.21267356", "rel_title": "A prospective diagnostic evaluation of accuracy of self-taken and healthcare worker-taken swabs for rapid COVID-19 testing", @@ -473283,6 +476201,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.12.03.21267281", + "rel_title": "Safety and immunogenicity of the third booster dose with inactivated, viral vector, and mRNA COVID-19 vaccines in fully immunized healthy adults with inactivated vaccine", + "rel_date": "2021-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.03.21267281", + "rel_abs": "The coronavirus disease-2019 (COVID-19) pandemic has become a severe healthcare problem worldwide since the first outbreak in late December 2019. Currently, the COVID-19 vaccine has been used in many countries, but it is still unable to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection despite patients receiving full vaccination doses. Therefore, we aimed to appraise the booster effect of the different platforms of vaccines, including inactivated vaccine (BBIBP), viral vector vaccine (AZD122), and mRNA vaccine (BNT162b2) in healthy adults who received the full dose of inactivated vaccine (CoronaVac). The booster dose was safe with no serious adverse events. Moreover, the immunogenicity indicated that the booster dose with viral vector and mRNA vaccine achieved a significant proportion of Ig anti-receptor binding domain (RBD), IgG anti-RBD, and IgA anti-S1 booster response. In contrast, inactivated vaccine achieved a lower booster response than others. Consequently, the neutralization activity of vaccinated serum had a high inhibition of over 90% against SARS-CoV-2 wild-type and their variants (B.1.1.7-alpha, B.1.351-beta, and B.1.617.2-delta). In addition, IgG anti-nucleocapsid was observed only among the group that received the BBIBP booster. Our study found a significant increase in levels of interferon gamma-secreting T-cell response after the additional viral vector or mRNA booster vaccination. This study showed that administration with either viral vector (AZD1222) or mRNA (BNT162b2) boosters in individuals with a history of two doses of inactivated vaccine (CoronaVac) obtained great immunogenicity with acceptable adverse events.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Sitthichai Kanokudom", + "author_inst": "Center of Excellence in Clinical Virology, Department of Biochemistry, Osteoarthritis and Musculoskeleton Research Unit, Faculty of Medicine, Chulalongkorn Univ" + }, + { + "author_name": "Suvichada Assawakosri", + "author_inst": "Center of Excellence in Clinical Virology, Department of Biochemistry, Osteoarthritis and Musculoskeleton Research Unit, Faculty of Medicine, Chulalongkorn Univ" + }, + { + "author_name": "Nungruthai Suntronwong", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Chompoonut Auphimai", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Pornjarim Nilyanimit", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Preeyaporn Vichaiwattana", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Thanunrat Thongmee", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Ritthideach Yorsaeng", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Donchida Srimuan", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Thaksaporn Thatsanatorn", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Sirapa Klinfueng", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Natthinee Sudhinaraset", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Nasamon Wanlapakorn", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Sittisak Honsawek", + "author_inst": "Department of Biochemistry, Osteoarthritis and Musculoskeleton Research Unit, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospita" + }, + { + "author_name": "Yong Poovorawan", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Thailand and FRS(T), the Royal Society of Thailand" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.12.04.21267294", "rel_title": "Characteristics of Patients Referred to a Cardiovascular Disease Clinic for Post-Acute Sequelae of SARS-CoV-2 Infection", @@ -473384,33 +476377,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.12.02.21267210", - "rel_title": "Post-traumatic Stress Risk among COVID-19 Survivors in Colombia", - "rel_date": "2021-12-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.02.21267210", - "rel_abs": "The studys objective was to establish the prevalence and variables associated with post-traumatic stress disorder risk (PTSD-R) in a sample of COVID-19 survivors in Santa Marta, Colombia. A cross-sectional study was designed with a non-probabilistic sample of adult COVID-19 survivors. Participants were demographically characterized and completed scales for depression risk, insomnia risk, and PTSD-R. Three hundred and thirty COVID-19 survivors between 18 and 89 years participated; 61.52% were women. The frequency of depression risk was 49.70%; insomnia risk, 60.61%; and PTSD-R, 13.33%. Depression risk (OR = 41.43, 95% CI 5.54 - 311.63), insomnia risk (OR = 5.25, 95% CI 1.77 - 18.71), low income (OR = 3.46, 95% CI 1.38 - 8.67) and being married or free union (OR = 2.65, 95% CI 1.13 - 6.22) were associated with PTSD-R. In conclusion, two out of every fifteen COVID-19 survivors are in PTSD-R. Depression and insomnia risk are strongly associated with PTSD-R in COVID-19 survivors.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Adalberto Campo-Arias", - "author_inst": "Universidad del Magdalena" - }, - { - "author_name": "John Carlos Pedrozo-Pupo", - "author_inst": "Universidad del Magdalena" - }, - { - "author_name": "Edwin Herazo", - "author_inst": "Human behavioral Research Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.12.02.21267190", "rel_title": "Healthcare worker risk of COVID-19: A 20-month analysis of protective measures from vaccination and beyond", @@ -475005,6 +477971,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.12.03.21266538", + "rel_title": "Introduction and community transmission of SARS-CoV-2 lineage A.2.5 in Florida with novel spike INDELS", + "rel_date": "2021-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.03.21266538", + "rel_abs": "SARS-CoV-2 (SC2) variants of concern (VOC) continue to emerge and spread globally, threatening the use of monoclonal antibody therapies and vaccine effectiveness. Several mutations in the SC2 spike glycoprotein have been associated with reduction in antibody neutralization. Genomic surveillance of SC2 variants has been imperative to inform the public health response regarding the use of clinical therapies in specific jurisdictions based on the proportion of particular variants (e.g., Gamma (P.1)) in a region. Florida Department of Health Bureau of Public Health Laboratories (BPHL) performs tiled-amplicon whole genome sequencing for baseline and targeted surveillance of SC2 isolates in Florida from clinical specimens collected from county health departments and hospitals throughout the state. Here, we describe the introduction of SC2 lineage A.2.5 in Florida, which contains S:L452R (a substitution of therapeutic concern) and two novel Spike INDELS, the deletion of 141-143 and ins215AGY, with unknown implications on immune response. The A.2.5 lineage was first detected in Florida among an outbreak at a healthcare facility in January 2021, and subsequent A.2.5 isolates were detected across all geographical regions throughout the state. A time-scaled maximum clade credibility phylogeny determined there were at least eight separate introductions of A.2.5 in the state. The time of introduction of a monophyletic Florida clade was established to be December 2020. The Spike INDELS were determined to reside in the N-terminal domain, a region associated with antibody neutralization. As community transmission of SARS-CoV-2 in Florida continues, genomic surveillance of circulating variants in Florida and the detection of emerging variants are critical for informing public health response to COVID-19.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sarah E Schmedes", + "author_inst": "Bureau of Public Health Laboratories, Florida Department of Health" + }, + { + "author_name": "Taj Azarian", + "author_inst": "Burnett School of Biomedical Sciences, University of Central Florida" + }, + { + "author_name": "Eleonora Cella", + "author_inst": "Burnett School of Biomedical Sciences, University of Central Florida" + }, + { + "author_name": "Jessy Motes", + "author_inst": "Bureau of Public Health Laboratories, Florida Department of Health" + }, + { + "author_name": "Omer Tekin", + "author_inst": "Bureau of Public Health Laboratories, Florida Department of Health" + }, + { + "author_name": "James Weiss", + "author_inst": "Bureau of Public Health Laboratories, Florida Department of Health" + }, + { + "author_name": "Nancimae Miller", + "author_inst": "Pathology Consultants of South Broward, Memorial Healthcare System" + }, + { + "author_name": "Jason Blanton", + "author_inst": "Bureau of Public Health Laboratories, Florida Department of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.03.21267155", "rel_title": "High viral loads: what drives fatal cases of COVID-19 in vaccinees? an autopsy study", @@ -475198,45 +478211,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.12.01.470353", - "rel_title": "Possible Interference in Protein - Protein interaction as a new approach in microinhibition of respiratory pathogens on nasal- oral epithelium: An early on-screen study with reference toSARS-Cov-2-ACE2 binding interference", - "rel_date": "2021-12-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.01.470353", - "rel_abs": "Upper and lower respiratory pathogens - both microbes and viruses -are responsible for very high morbidity, man-hour loss, residual long term clinical conditions and even mortality. In india only, high incidence of annual respiratory infections - both UT and LT - demands prophylactic intervention in addition to all therapeutic interventions available.The issue of respiratory infections is more pronounced now in the backdrop of nearly uncontrolled high incidences of SARS-Cov-2 affection resulting in death and damage of human lives to the extent of hundreds of millions spreading over entire world, with incidence variations from country to country. After the initial unanswered phase of spread of SARS-Cov-2 virus with attendant unseen mortalities, quickest invention of a series of unusual vaccines have stemmed the lethal progress to a very significant extent, although vaccinating each and every human subject - nearly 8 to 9 bn in supremely divided world -economically-- is an unthinkable proposition where economic disparity dictates vaccine availability and implementation.Moreover, being of highly unstable nucleic acid composition, the original virus, by now has a thick set of variants around the globe with variable clinical outcome. Given this complex background of scanty availability and inefficient implementation, there always is a need of a preventive approach which can possibly micro-fix the pathogens, including SARS-2 on nasal epithelium so as to interfere with viral [or any pathogen] entry through specified receptor gate[s] or any other ways. The present formulation is under study -- as a candidate of interference on nasal / oral mucosa for all respiratory pathogens. This brief report describes dry on-screen studies of protein - protein interaction as well as its possible interference by an amino acid Lysine. Phospholipid bilayerresponses in presence of added loads of the same essential amino acid -Lysine - showed unusual and unexplained behavior both in structural integrity as well in spatial orientation.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Debatosh Datta", - "author_inst": "APOLLO HOSPITAL KOLKATA" - }, - { - "author_name": "Suyash Pant", - "author_inst": "National Institute of Pharmaceutical Education and Research, Kolkata" - }, - { - "author_name": "Devendra Kumar Dhaked", - "author_inst": "National Institute of Pharmaceutical Education and Research, Kolkata" - }, - { - "author_name": "Somasundaram Arumugam", - "author_inst": "National Institute of Pharmaceutical Education and Research, Kolkata" - }, - { - "author_name": "Ravichandiran Velayutham", - "author_inst": "National Institute of Pharmaceutical Education and Research, Kolkata" - }, - { - "author_name": "Pallab Datta", - "author_inst": "National Institute of Pharmaceutical Education and Research, Kolkata" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.12.01.470810", "rel_title": "Development of Web Application for the Comparison of Segment Variability with Sequence Evolution and Immunogenic Properties for Highly Variable Proteins: An Application to Viruses.", @@ -476803,6 +479777,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.02.21267185", + "rel_title": "Tajima D test accurately forecasts Omicron / COVID-19 outbreak", + "rel_date": "2021-12-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.02.21267185", + "rel_abs": "On 26 November 2021, the World Health Organization designated the SARS-CoV-2 variant B.1.1.529, Omicron, a variant of concern. However, the phylogenetic and evolutionary dynamics of this variant remain unclear. An analysis of the 131 Omicron variant sequences from November 9 to November 28, 2021 reveals that variants have diverged into at least 6 major subgroups. 86.3% of the cases have an insertion at amino acid 214 (INS214EPE) of the spike protein. Neutrality analysis of DH (-2.814, p<0.001) and Zengs E (0.0583, p=1.0) tests suggested that directional selection was the major driving force of Omicron variant evolution. The synonymous (Dsyn) and nonsynonymous (Dnonsyn) polymorphisms of the Omicron variant spike gene were estimated with Tajimas D statistic to eliminate homogenous effects. Both D ratio (Dnonsyn/Dsyn, 1.57) and {Delta}D (Dsyn-Dnonsyn, 0.63) indicate that purifying selection operates at present. The low nucleotide diversity (0.00008) and Tajima D value (-2.709, p<0.001) also confirms that Omicron variants had already spread in human population for more than the 6 weeks than has been reported. These results, along with our previous analysis of Delta and Lambda variants, also supports the validity of the Tajimas D test score, with a threshold value as -2.50, as an accurate predictor of new COVID-19 outbreaks.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ting-Yu Yeh", + "author_inst": "Institute of Marine and Environmental Technology" + }, + { + "author_name": "Gregory P. Contreras", + "author_inst": "Auxergen Inc." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.30.21267071", "rel_title": "Increased risk of psychiatric sequelae of COVID-19 is highest early in the clinical course", @@ -476928,77 +479925,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.11.30.21267085", - "rel_title": "TREATMENT COSTS FOR COVID-19 PATIENTS IN A TERTIARY HOSPITAL FROM SERBIA", - "rel_date": "2021-12-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.30.21267085", - "rel_abs": "IntroductionAim of our study was to identify total costs of COVID-19 inpatients treatment in an upper-middle income country from Southeast Europe.\n\nMethodsThis retrospective, observational cost of illness study was performed from National Health Insurance Fund perspective and included a cohort of 118 males and 78 females admitted to COVID-19 ward units of a tertiary center, during the first wave of epidemics.\n\nResultsThe median of total costs in the non-survivors subgroup (n=43) was 3279.16 Euro (4023.34, 355.20, 9909.61) which is higher than in the survivors (n=153) subgroup 747.10 Euro (1088.21, 46.71, 3265.91). The odds ratio of Charlson Comorbidity Index total score and every 100-Euros increase of patients total hospital treatment costs for fatal outcome were 1.804 (95% confidence interval 1.408-2.311, p<0.001) and 1.050 (1.029-1.072, p<0.001), respectively.\n\nConclusionsDirect medical treatment costs for COVID-19 inpatients represent significant economic burden. The link between increased costs and unfavorable final outcome should be further explored.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Predrag S. Sazdanovic", - "author_inst": "Ministry of Health of the Republic of Serbia, Belgrade, Serbia; University of Kragujevac, Faculty of Medical Sciences, Department of Anatomy, Kragujevac, Serbia" - }, - { - "author_name": "Slobodan Milisavljevic", - "author_inst": "University Clinical Centre Kragujevac, Directorate & Pandemic Preparedness Managerial Board, Kragujevac, Serbia; University Clinical Centre Kragujevac, Faculty " - }, - { - "author_name": "Dragan R. Milovanovic", - "author_inst": "University Clinical Centre Kragujevac, Department of Clinical Pharmacology, Kragujevac, Serbia; University of Kragujevac, Faculty of Medical Sciences, Departmen" - }, - { - "author_name": "Slobodan M. Jankovic", - "author_inst": "University Clinical Centre Kragujevac, Department of Clinical Pharmacology, Kragujevac, Serbia; University of Kragujevac, Faculty of Medical Sciences, Departmen" - }, - { - "author_name": "Dejan Baskic", - "author_inst": "Public Health Institute, Kragujevac, Serbia; University of Kragujevac, Faculty of Medical Sciences, Centre for Molecular Medicine and Stem Cell Research, Kraguj" - }, - { - "author_name": "Dragana Ignjatovic Ristic", - "author_inst": "University Clinical Centre Kragujevac, Clinic for Psychiatry, Kragujevac, Serbia; University of Kragujevac, Faculty of Medical Sciences, Department of Psychiatr" - }, - { - "author_name": "Dejana Ruzic Zecevic", - "author_inst": "University Clinical Centre Kragujevac, Department of Clinical Pharmacology, Kragujevac, Serbia; University of Kragujevac, Faculty of Medical Sciences, Departmen" - }, - { - "author_name": "Aleksandra Tomic Lucic", - "author_inst": "University Clinical Centre Kragujevac, Clinic for Internal Medicine, Kragujevac, Serbia; University of Kragujevac, Faculty of Medical Sciences, Department of In" - }, - { - "author_name": "Natasa Djordjevic", - "author_inst": "University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacology and Toxicology, Kragujevac, Serbia" - }, - { - "author_name": "Danijela Jovanovic", - "author_inst": "University Clinical Centre Kragujevac, Department of Anesthesiology and Reanimatology, Kragujevac, Serbia; University Clinical Centre Kragujevac, Faculty of Med" - }, - { - "author_name": "Andjelka Stojkovic", - "author_inst": "University Clinical Centre Kragujevac, Clinic of Pediatrics, Kragujevac; Serbia; University of Kragujevac, Faculty of Medical Sciences, Department of Pediatrics" - }, - { - "author_name": "Tatjana Lazarevic", - "author_inst": "University Clinical Centre Kragujevac, Emergency Department, Kragujevac; Serbia; University of Kragujevac, Faculty of Medical Sciences, Department of Internal M" - }, - { - "author_name": "Milica Begovic Cvetkovic", - "author_inst": "University Clinical Centre Kragujevac, Clinic for Internal Medicine, Kragujevac, Serbia" - }, - { - "author_name": "Marina J. Kostic", - "author_inst": "University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacology and Toxicology, Kragujevac, Serbia" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2021.12.01.21267100", "rel_title": "The impact of the COVID-19 pandemic on hospital services for patients with cardiac diseases: a scoping review", @@ -478521,6 +481447,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2021.11.29.21267041", + "rel_title": "COVID-19 Variant Detection with a High-Fidelity CRISPR-Cas12 Enzyme", + "rel_date": "2021-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.29.21267041", + "rel_abs": "Laboratory tests for the accurate and rapid identification of SARS-CoV-2 variants can potentially guide the treatment of COVID-19 patients and inform infection control and public health surveillance efforts. Here we present the development and validation of a rapid COVID-19 variant DETECTR(R) assay incorporating loop-mediated isothermal amplification (LAMP) followed by CRISPR-Cas12 based identification of single nucleotide polymorphism (SNP) mutations in the SARS-CoV-2 spike (S) gene. This assay targets the L452R, E484K/Q/A, and N501Y mutations that are associated with nearly all circulating viral lineages and identifies the two circulating variants of concern, Delta and Omicron. In a comparison of three different Cas12 enzymes, only the newly identified enzyme CasDx1 was able to accurately identify all targeted SNP mutations. An analysis pipeline for CRISPR-based SNP identification from 139 clinical samples yielded an overall SNP concordance of 98% and agreement with SARS-CoV-2 lineage classification of 138/139 compared to viral whole-genome sequencing. We also showed that detection of the single E484A mutation was necessary and sufficient to accurately identify Omicron from other major circulating variants in patient samples. These findings demonstrate the utility of CRISPR-based DETECTR(R) as a faster and simpler diagnostic than sequencing for SARS-CoV-2 variant identification in clinical and public health laboratories.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Clare L Fasching", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Venice Servellita", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Bridget McKay", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Vaishnavi Nagesh", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "James P Broughton", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Noah Brazer", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Baolin Wang", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Alicia Sotomayor-Gonzalez", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Kevin Reyes", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Jessica Streithorst", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Rachel N Deraney", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Emma Stanfield", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Carley G Hendriks", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Steve Miller", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Jesus Ching", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Janice S Chen", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Charles Y Chiu", + "author_inst": "University of California San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.29.21267042", "rel_title": "Favipiravir for the Treatment of Coronavirus Disease 2019; a propensity score-matched cohort study", @@ -478754,53 +481763,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.30.21267048", - "rel_title": "Risk of Hospitalization, severe disease, and mortality due to COVID-19 and PIMS-TS in children with SARS-CoV-2 infection in Germany", - "rel_date": "2021-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.30.21267048", - "rel_abs": "BackgroundAlthough children and adolescents have a lower burden of SARS-CoV-2-associated disease as compared to adults, assessing absolute risk among children remains difficult due to a high rate of undetected cases. However, without more accurate case numbers, reliable risk analyses are impossible.\n\nMethodsWe combine data from three sources -- a national seroprevalence study (the SARS-CoV-2 KIDS study), the German statutory notification system and a nationwide registry on children and adolescents hospitalized with either SARS-CoV-2 or Pediatric Inflammatory Multisystem Syndrome (PIMS-TS) -- in order to provide reliable estimates on childrens hospitalization, intensive care admission and death due to COVID-19 and PIMS-TS.\n\nResultsWhile the overall hospitalization rate associated with SARS-CoV-2 infection was 35.9 per 10,000 children, ICU admission rate was 1.7 per 10,000 and case fatality was 0.09 per 10,000. Children without comorbidities were found to be significantly less likely to suffer from a severe or fatal disease course. The lowest risk was observed in children aged 5-11 without comorbidities. In this group, the ICU admission rate was 0.2 per 10,000 and case fatality could not be calculated, due to an absence of cases. The overall PIMS-TS rate was 1 per 4,000 SARS-CoV-2 infections, the majority being children without comorbidities.\n\nConclusionOverall, the SARS-CoV-2-associated burden of a severe disease course or death in children and adolescents is low. This seems particularly the case for 5-11-year-old children without comorbidities. By contrast, PIMS-TS plays a major role in overall disease burden among all pediatric age groups.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Anna-Lisa Sorg", - "author_inst": "Institute of Social Paediatrics and Adolescent Medicine, Division of Paediatric Epidemiology, Ludwig-Maximilians-University Munich, Germany" - }, - { - "author_name": "Markus Hufnagel", - "author_inst": "Division of Pediatric Infectious Diseases and Rheumatology, Department of Pediatrics and Adolescent Medicine, University Medical Center, Medical Faculty, Univer" - }, - { - "author_name": "Maren Doenhardt", - "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany" - }, - { - "author_name": "Natalie Diffloth", - "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany" - }, - { - "author_name": "Horst Schroten", - "author_inst": "Pediatric Infectious Diseases, Department of Pediatrics, Medical Faculty Mannheim, Heidelberg University, Germany" - }, - { - "author_name": "Ruediger von Kries", - "author_inst": "Institute of Social Paediatrics and Adolescent Medicine, Division of Paediatric Epidemiology, Ludwig-Maximilians-University Munich, Germany" - }, - { - "author_name": "Reinhard Berner", - "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany" - }, - { - "author_name": "Jakob Peter Armann", - "author_inst": "Department of Pediatrics, University Hospital and Medical Faculty Carl Gustav Carus, Technische Universitaet Dresden, Dresden, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.30.21267063", "rel_title": "On the Role of Financial Support Programs in Mitigating the Sars-CoV-2 Spread in Brazil", @@ -480399,6 +483361,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.25.21266875", + "rel_title": "COVID-19 trends and severity among symptomatic children aged 0 to 17 years in ten EU countries, 3 August 2020 to 3 October 2021", + "rel_date": "2021-11-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.25.21266875", + "rel_abs": "To guide evidence-based prevention of COVID-19 in children, we estimated risks of severe outcomes in 820,404 symptomatic paediatric cases reported by 10 EU Member States between August 2020 and October 2021. Case and hospitalisation rates rose as overall transmission increased but severe outcomes were rare: 9,611 (1.2%) were hospitalised, 640 (0.08%) required intensive care and 84 (0.01%) died. Despite increased individual risk (aOR; 95% CI for hospitalisation: 7.3; 3.3 - 16.2, ICU: 8.7; 6.2 - 12.3) in cases with comorbidities such as cancer, diabetes, cardiac or lung disease, most (83.7%) hospitalised children had no reported comorbidity.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nick Bundle", + "author_inst": "European Centre for Disease Prevention and Control (ECDC)" + }, + { + "author_name": "Nishi Dave", + "author_inst": "European Centre for Disease Prevention and Control (ECDC)" + }, + { + "author_name": "Anastasia Pharris", + "author_inst": "European Centre for Disease Prevention and Control" + }, + { + "author_name": "Gianfranco Spiteri", + "author_inst": "European Centre for Disease Prevention and Control (ECDC)" + }, + { + "author_name": "Charlotte Deogan", + "author_inst": "European Centre for Disease Prevention and Control (ECDC)" + }, + { + "author_name": "Jonathan E. Suk", + "author_inst": "European Centre for Disease Prevention and Control" + }, + { + "author_name": "- Study group members", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.29.21266976", "rel_title": "Impact of the COVID-19 pandemic on the malaria burden in northern Ghana: Analysis of routine surveillance data", @@ -480532,229 +483537,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.29.21266109", - "rel_title": "A case series of SARS-CoV-2 reinfections caused by the variant of concern Gamma in Brazil", - "rel_date": "2021-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.29.21266109", - "rel_abs": "The rapid spread of the SARS-CoV-2 Variant of Concern (VOC) Gamma during late 2020 and early 2021 in Brazilian settings with high seroprevalence raised some concern about the potential role of reinfections in driving the epidemic. Very few cases of reinfection associated with the VOC Gamma, however, have been reported. Here we describe 25 cases of SARS-CoV-2 reinfection confirmed by real-time RT-PCR twice within months apart in Brazil. SARS-CoV-2 genomic analysis confirmed that individuals were primo-infected between March and December 2020 with distinct viral lineages, including B.1.1, B.1.1.28, B.1.1.33, B.1.195 and P.2, and then reinfected with the VOC Gamma between 3 to 12 months after primo-infection. The overall mean cycle threshold (Ct) value of the first (25.7) and second (24.5) episodes were roughly similar for the whole group and 14 individuals displayed mean Ct values < 25.0 at reinfection. Sera of 14 patients tested by plaque reduction neutralization test after reinfection displayed detectable neutralizing antibodies against Gamma and other SARS-CoV-2 variants (B.1.33, B.1.1.28 and Delta). All individuals have milder or no symptoms after reinfection and none required hospitalization. The present study demonstrates that the VOC Gamma was associated with reinfections during the second Brazilian epidemic wave in 2021 and raised concern about the potential infectiousness of reinfected subjects. Although individuals here analyzed failed to mount a long-term sterilizing immunity, they developed a high anti-Gamma neutralizing antibody response after reinfection that may provide some protection against severe disease.", - "rel_num_authors": 52, - "rel_authors": [ - { - "author_name": "Felipe Gomes Naveca", - "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia, Instituto Leonidas e Maria Deane, Fiocruz, Manaus, Brazil" - }, - { - "author_name": "Valdinete Alves Nascimento", - "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia, Instituto Leonidas e Maria Deane, Fiocruz, Manaus, Brazil" - }, - { - "author_name": "Fernanda Nascimento", - "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia, Instituto Leonidas e Maria Deane, Fiocruz, Manaus, Brazil" - }, - { - "author_name": "Maria Ogrzewalska", - "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Alex Pauvolid-Correa", - "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil; Department of Veteri" - }, - { - "author_name": "Mia Ferreira Araujo", - "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Ighor Arantes", - "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil; Laboratorio de AIDS " - }, - { - "author_name": "Erika Lopes Rocha Batista", - "author_inst": "Secretaria de Saude de Aparecida de Goiania, Goias, Brazil" - }, - { - "author_name": "Alessandro Leonardo lvares Magalhaes", - "author_inst": "Secretaria de Saude de Aparecida de Goiania, Goias, Brazil" - }, - { - "author_name": "Fernando Vinhal", - "author_inst": "Laboratory HLAGYN, Goiania, Goias, Brazil" - }, - { - "author_name": "Tirza Peixoto Mattos", - "author_inst": "Laboratorio Central de Saude Publica do Amazonas (LACEN-AM) Manaus, Amazonas, Brazil" - }, - { - "author_name": "Irina Riediger", - "author_inst": "Laboratorio Central de Saude Publica de Parana (LACEN-PR) Curitiba, Parana, Brazil" - }, - { - "author_name": "Maria do Carmo Debur", - "author_inst": "Laboratorio Central de Saude Publica de Parana (LACEN-PR) Curitiba, Parana, Brazil" - }, - { - "author_name": "Beatriz Grinsztejn", - "author_inst": "Instituto Nacional de Infectologia Evandro Chagas (INI), Fiocruz, Rio de Janeiro, Brazil" - }, - { - "author_name": "ValdilEa G Veloso", - "author_inst": "Instituto Nacional de Infectologia Evandro Chagas (INI), Fiocruz, Rio de Janeiro, Brazil" - }, - { - "author_name": "Patricia Brasil", - "author_inst": "Instituto Nacional de Infectologia Evandro Chagas (INI), Fiocruz, Rio de Janeiro, Brazil" - }, - { - "author_name": "Rodrigo Ribeiro Rodrigues", - "author_inst": "Laboratorio Central de Saude Publica do Espirito Santo (LACEN-ES), Vitoria, Espirito Santo, Brazil" - }, - { - "author_name": "Darcita Buerger Rovaris", - "author_inst": "Laboratorio Central de Saude Publica do Estado de Santa Catarina (LACEN-SC), Florianopolis, Santa Catarina, Brazil" - }, - { - "author_name": "Sandra Bianchini Fernandes", - "author_inst": "Laboratorio Central de Saude Publica do Estado de Santa Catarina (LACEN-SC), Florianopolis, Santa Catarina, Brazil" - }, - { - "author_name": "Cristiano Fernandes", - "author_inst": "Fundacao de Vigilancia em Saude do Amazonas - Dra Rosemary Costa Pinto, Manaus, Amazonas, Brazil" - }, - { - "author_name": "Joao Hugo Abdalla Santos", - "author_inst": "Hospital Adventista de Manaus, Manaus, Amazonas, Brazil" - }, - { - "author_name": "Ligia Fernandes Abdalla", - "author_inst": "Universidade do Estado do Amazonas, Manaus, Brazil" - }, - { - "author_name": "Rubens Costa-Filho", - "author_inst": "Hospital Pro Cardiaco - Rede Americas UHG" - }, - { - "author_name": "Marineide Silva", - "author_inst": "Laboratorio Central de Saude Publica do Amazonas (LACEN-AM) Manaus, Amazonas, Brazil" - }, - { - "author_name": "Victor Souza", - "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia, Instituto Leonidas e Maria Deane, Fiocruz, Manaus, Brazil" - }, - { - "author_name": "gatha Araujo Costa", - "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia, Instituto Leonidas e Maria Deane, Fiocruz, Manaus, Brazil" - }, - { - "author_name": "Matilde Mejia", - "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia, Instituto Leonidas e Maria Deane, Fiocruz, Manaus, Brazil" - }, - { - "author_name": "Maria Julia Brandao", - "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia, Instituto Leonidas e Maria Deane, Fiocruz, Manaus, Brazil" - }, - { - "author_name": "Luciana FE Goncalves", - "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia, Instituto Leonidas e Maria Deane, Fiocruz, Manaus, Brazil" - }, - { - "author_name": "George Allan Silva", - "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia, Instituto Leonidas e Maria Deane, Fiocruz, Manaus, Brazil" - }, - { - "author_name": "Michele Silva de Jesus", - "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia, Instituto Leonidas e Maria Deane, Fiocruz, Manaus, Brazil" - }, - { - "author_name": "Karina Pessoa", - "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia, Instituto Leonidas e Maria Deane, Fiocruz, Manaus, Brazil" - }, - { - "author_name": "AndrE de Lima Guerra Corado", - "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia, Instituto Leonidas e Maria Deane, Fiocruz, Manaus, Brazil" - }, - { - "author_name": "Debora Camila Gomes Duarte", - "author_inst": "Laboratorio de Ecologia de Doencas Transmissiveis na Amazonia, Instituto Leonidas e Maria Deane, Fiocruz, Manaus, Brazil" - }, - { - "author_name": "Ana Beatriz Machado", - "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Ketiuce de Azevedo Zukeram", - "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Natalia Valente", - "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Renata Serrano Lopes", - "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Elisa Cavalcante Pereira", - "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Luciana Reis Appolinario", - "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Alice Sampaio Rocha", - "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Luis Fernando Lopez Tort", - "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil; Laboratory of Molecu" - }, - { - "author_name": "Tsuyoshi Sekizuka", - "author_inst": "Pathogen Genomics Center, National Institute of Infectious Diseases 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan" - }, - { - "author_name": "Kentaro Itokawa", - "author_inst": "Pathogen Genomics Center, National Institute of Infectious Diseases 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan" - }, - { - "author_name": "Masanori Hashino", - "author_inst": "Pathogen Genomics Center, National Institute of Infectious Diseases 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan" - }, - { - "author_name": "Makoto Kuroda", - "author_inst": "Pathogen Genomics Center, National Institute of Infectious Diseases 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan" - }, - { - "author_name": "Gabriel Luz Wallau", - "author_inst": "Instituto Aggeu Magalhaes, Fundacao Oswaldo Cruz, Recife, Pernambuco, Brazil" - }, - { - "author_name": "Edson Delatorre", - "author_inst": "Departamento de Biologia Centro de Ciencias Exatas, Naturais e da Saude, Universidade Federal do Espirito Santo, Alegre, Brazil" - }, - { - "author_name": "Tiago Graf", - "author_inst": "Instituto Goncalo Moniz, Fundacao Oswaldo Cruz, Salvador, Brazil" - }, - { - "author_name": "Marilda Mendonca Siqueira", - "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Gonzalo Bello", - "author_inst": "Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil" - }, - { - "author_name": "Paola Cristina Resende", - "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.29.21266996", "rel_title": "Deficits in planned hospital care for vulnerable adolescents in England during the COVID-19 pandemic: analysis of linked administrative data", @@ -482221,6 +485003,125 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.11.24.21266812", + "rel_title": "SARS-CoV-2 Convalescent Sera Binding and Neutralizing Antibody Concentrations Compared with COVID-19 Vaccine Efficacy Estimates Against Symptomatic Infection", + "rel_date": "2021-11-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.24.21266812", + "rel_abs": "Previous vaccine efficacy (VE) studies have estimated neutralizing and binding antibody concentrations that correlate with protection from symptomatic infection; how these estimates compare to those generated in response to SARS-CoV-2 infection is unclear. Here, we assessed quantitative neutralizing and binding antibody concentrations using standardized SARS-CoV-2 assays on 3,067 serum specimens collected during July 27, 2020-August 27, 2020 from COVID-19 unvaccinated persons with detectable anti-SARS-CoV-2 antibodies using qualitative antibody assays. Quantitative neutralizing and binding antibody concentrations were strongly positively correlated (r=0.76, p<0.0001) and were noted to be several fold lower in the unvaccinated study population as compared to published data on concentrations noted 28 days post-vaccination. In this convenience sample, [~]88% of neutralizing and [~]63-86% of binding antibody concentrations met or exceeded concentrations associated with 70% COVID-19 VE against symptomatic infection from published VE studies; [~]30% of neutralizing and 1-14% of binding antibody concentrations met or exceeded concentrations associated with 90% COVID-19 VE. These data support observations of infection-induced immunity and current recommendations for vaccination post infection to maximize protection against symptomatic COVID-19.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Amy J. Schuh", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Panayampalli S. Satheshkumar", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Stephanie Dietz", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Lara Bull-Otterson", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Myrna Charles", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Chris Edens", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Jefferson M. Jones", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Kristina L. Bajema", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Kristie E.N. Clarke", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "L. Clifford McDonald", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Sadhna Patel", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Kendra Cuffe", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Natalie J. Thornburg", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Jarad Schiffer", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Kelly Chun", + "author_inst": "Labcorp" + }, + { + "author_name": "Monique Bastidas", + "author_inst": "Labcorp" + }, + { + "author_name": "Manory Fernando", + "author_inst": "Labcorp" + }, + { + "author_name": "Christos J. Petropoulos", + "author_inst": "Labcorp" + }, + { + "author_name": "Terri Wrin", + "author_inst": "Labcorp" + }, + { + "author_name": "Suqin Cai", + "author_inst": "Labcorp" + }, + { + "author_name": "Dot Adcock", + "author_inst": "Labcorp" + }, + { + "author_name": "Deborah Sesok-Pizzini", + "author_inst": "Labcorp" + }, + { + "author_name": "Stanley Letovsky", + "author_inst": "Labcorp" + }, + { + "author_name": "Alicia M. Fry", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Aron J. Hall", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Adi V. Gundlapalli", + "author_inst": "United States Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.21.21266633", "rel_title": "SARS-CoV-2 vaccination predicts COVID-19 progression and outcomes in hospitalized patients", @@ -482398,49 +485299,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.24.21266831", - "rel_title": "Germany's current COVID-19 crisis is mainly driven by the unvaccinated", - "rel_date": "2021-11-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.24.21266831", - "rel_abs": "Vaccines are the most powerful pharmaceutical tool to combat the COVID-19 pandemic. While the majority (about 65%) of the German population were fully vaccinated, incidence started growing exponentially in October 2021 with about 41% of recorded new cases aged twelve or above being symptomatic breakthrough infections, presumably also contributing to the dynamics. At the time, it (i) remains elusive how significant this contribution is and (ii) whether targeted non-pharmaceutical interventions (NPIs) may stop the amplification of the ongoing crisis. Here, we estimate that about 67%-76% of all new infections are caused by unvaccinated individuals, implying that only 24%-33% are caused by the vaccinated. Furthermore, we estimate 38%-51% of new infections to be caused by unvaccinated individuals infecting other unvaccinated individuals. In total, unvaccinated individuals are expected to be involved in 8-9 of 10 new infections. We further show that decreasing the transmissibility of the unvaccinated by, e. g. targeted NPIs, causes a steeper decrease in the effective reproduction number [R] than decreasing the transmissibility of vaccinated individuals, potentially leading to temporary epidemic control. Furthermore, reducing contacts between vaccinated and unvaccinated individuals serves to decrease [R] in a similar manner as increasing vaccine uptake. Taken together, our results contribute to the public discourse regarding policy changes in pandemic response and highlight the importance of combined measures, such as vaccination campaigns and contact reduction, to achieve epidemic control and preventing an overload of public health systems.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Benjamin F Maier", - "author_inst": "Humboldt University of Berlin" - }, - { - "author_name": "Marc Wiedermann", - "author_inst": "Humboldt University of Berlin" - }, - { - "author_name": "Angelique Burdinski", - "author_inst": "Humboldt University of Berlin" - }, - { - "author_name": "Pascal Klamser", - "author_inst": "Humboldt University of Berlin" - }, - { - "author_name": "Mirjam A Jenny", - "author_inst": "Humboldt University of Berlin" - }, - { - "author_name": "Cornelia Betsch", - "author_inst": "Humboldt University of Berlin" - }, - { - "author_name": "Dirk Brockmann", - "author_inst": "Humboldt University of Berlin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.24.21266748", "rel_title": "COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: two prospective observational cohort studies", @@ -484135,6 +486993,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.22.21266692", + "rel_title": "Serological responses to COVID-19 booster vaccine in England", + "rel_date": "2021-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266692", + "rel_abs": "IntroductionThere are limited data on immune responses after COVID-19 vaccine boosters in individuals receiving primary immunisation with BNT162b2 (Pfizer-BioNTech) or AZD1222 (AstraZeneca).\n\nMethodsA prospective, cohort study to assess SARS-CoV-2 antibody responses before and after booster vaccination with BNT162b2 in adults receiving either (i) two BNT162b2 doses <30 days apart (BNT162b2-control), (ii) two BNT162b2 doses [≥]30 days apart (BNT162b2-extended) or (iii) two AZD1222 doses [≥]30 days apart (AZD1222-extended) in London, England. SARS-CoV-2 spike protein antibody geometric mean titres (GMTs) before and 2-4 weeks after booster were compared.\n\nResultsOf 750 participants, 626 provided serum samples for up to 38 weeks after their second vaccine dose. Antibody GMTs peaked at 2-4 weeks after the second dose, before declining by 68% at 36-38 weeks after dose 2 for BNT162b2-control participants, 85% at 24-29 weeks for BNT162b2-extended participants and 78% at 24-29 weeks for AZD1222-extended participants. Antibody GMTs was highest in BNT162b2-extended participants (942 [95%CI, 797-1113]) than AZD1222-extended (183 [124-268]) participants at 24-29 weeks or BNT162b2-control participants at 36-38 weeks (208; 95%CI, 150-289). At 2-4 weeks after booster, GMTs were significantly higher than after primary vaccination in all three groups: 18,104 (95%CI, 13,911-23,560; n=47) in BNT162b2-control (76.3-fold), 13,980 (11,902-16,421; n=118) in BNT162b2-extended (15.9-fold) and 10,799 (8,510-13,704; n=43) in AZD1222-extended (57.2-fold) participants. BNT162b2-control participants (median:262 days) had a longer interval between primary and booster doses than BNT162b2-extended or AZD1222-extended (both median:186 days) participants.\n\nConclusionsWe observed rapid serological responses to boosting with BNT162b2, irrespective of vaccine type or schedule used for primary immunisation, with higher post-booster responses with longer interval between primary immunisation and boosting. Boosters will not only provide additional protection for those at highest risk of severe COVID-19 but also prevent infection and, therefore, interrupt transmission, thereby reducing infections rates in the population. Ongoing surveillance will be important for monitoring the duration of protection after the booster.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Georgina Ireland", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Heather Whitaker", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Shamez N Ladhani", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Frances Baawuah", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Vani Subbarao", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Ezra Linley", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Lenesha Warrener", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Michelle O'Brien", + "author_inst": "Brondesbury Medical Centre, Kilburn, London, United Kingdom" + }, + { + "author_name": "Corrine Whillock", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Paul Moss", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Mary E Ramsay", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Gayatri Amirthalingam", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Kevin E Brown", + "author_inst": "UK Health Security Agency" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.22.21266713", "rel_title": "In Vitro Nasal Tissue Model for the Validation of Nasopharyngeal and Mid-turbinate Swabs for SARS-CoV-2 Testing", @@ -484324,25 +487249,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.11.22.21266721", - "rel_title": "Simulating the impact of vaccination rates on the initial stages of a COVID-19 outbreak in New Zealand (Aotearoa) with a stochastic model", - "rel_date": "2021-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266721", - "rel_abs": "AimThe August 2021 COVID-19 outbreak in Auckland has caused the New Zealand government to transition from an elimination strategy to suppression, which relies heavily on high vaccination rates in the population. As restrictions are eased and as COVID-19 leaks through the Auckland boundary, there is a need to understand how different levels of vaccination will impact the initial stages of COVID-19 outbreaks that are seeded around the country.\n\nMethodA stochastic branching process model is used to simulate the initial spread of a COVID-19 outbreak for different vaccination rates.\n\nResultsHigh vaccination rates are effective at minimizing the number of infections and hospitalizations. Increasing vaccination rates from 20% (approximate value at the start of the August 2021 outbreak) to 80% (approximate proposed target) of the total population can reduce the median number of infections that occur within the first four weeks of an outbreak from 1011 to 14 (25th and 75th quantiles of 545-1602 and 2-32 for V=20% and V=80%, respectively). As the vaccination rate increases, the number of breakthrough infections (infections in fully vaccinated individuals) and hospitalizations of vaccinated individuals increases. Unvaccinated individuals, however, are 3.3x more likely to be infected with COVID-19 and 25x more likely to be hospitalized.\n\nConclusionThis work demonstrates the importance of vaccination in protecting individuals from COVID-19, preventing high caseloads, and minimizing the number of hospitalizations and hence limiting the pressure on the healthcare system.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Leighton M Watson", - "author_inst": "University of Oregon" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.22.21266683", "rel_title": "Final sizes and durations of new COVID-19 pandemic waves in Ukraine and around the world predicted by generalized SIR model", @@ -485849,6 +488755,69 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.11.24.21266401", + "rel_title": "Effectiveness of BNT162b2 and ChAdOx1 against SARS-CoV-2 household transmission - a prospective cohort study in England", + "rel_date": "2021-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.24.21266401", + "rel_abs": "BackgroundThe ability of SARS-CoV-2 vaccines to protect against infection and onward transmission determines whether immunisation can control global circulation. We estimated effectiveness of BNT162b2 and ChAdOx1 vaccines against acquisition and transmission of the Alpha and Delta variants in a prospective household study in England.\n\nMethodsAdult index cases in the community and their household contacts took oral-nasal swabs on days 1, 3 and 7 after enrolment. Swabs were tested by RT-qPCR with genomic sequencing conducted on a subset. We used Bayesian logistic regression to infer vaccine effectiveness against acquisition and transmission, adjusted for age, vaccination history and variant.\n\nFindingsBetween 2 February 2021 and 10 September 2021 213 index cases and 312 contacts were followed up. After excluding households lacking genomic proximity (N=2) or with unlikely serial intervals (N=16), 195 households with 278 contacts remained of whom 113 (41%) became PCR positive. Delta lineages had 1.64 times the risk (95% Credible Interval: 1.15 - 2.44) of transmission than Alpha; contacts older than 18 years were 1.19 times (1.04 - 1.52) more likely to acquire infection than children. Effectiveness of two doses of BNT162b2 against transmission of Delta was 31% (-3%, 61%) and 42% (14%, 69%) for ChAdOx1, similar to their effectiveness for Alpha. Protection against infection with Alpha was higher than for Delta, 71% (12%,95%) vs 24% (-2%, 64%) respectively for BNT162b2 and 26% (-39%, 73%) vs 14% (-5%, 46%) respectively for ChAdOx1.\n\nInterpretationBNT162b2 and ChAdOx1 reduce transmission of the Delta variant from breakthrough infections in the household setting though their protection against infection is low.\n\nFundingThis study was funded by the UK Health Security Agency (formerly Public Health England) as part of the COVID-19 response.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Samuel Clifford", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Pauline Waight", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Jada Hackman", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Stephane Hue", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Charlotte M Gower", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Freja CM Kirsebom", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Catriona Skarnes", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Louise Letley", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Jamie Lopez Bernal", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Nick Andrews", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Stefan Flasche", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Elizabeth Miller", + "author_inst": "London School of Hygiene and Tropical Medicine, UK Health Security Agency" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.22.21266599", "rel_title": "Modeling on Wastewater Treatment Process in Saudi Arabia: a perspective of Covid-19", @@ -485982,33 +488951,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.23.21266775", - "rel_title": "Recurring Spatiotemporal Patterns of COVID-19 in the United States", - "rel_date": "2021-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.23.21266775", - "rel_abs": "We analyzed the waxing and waning patterns (\"surges\") of reported SARS-CoV-2 cases from January 1, 2020 through Oct 31, 2021 in all states and provinces (n = 93) in the USA, Mexico, and Canada, and across all counties (N = 3142) in the USA. A correlation matrix of the 576 x 576 daily case incidence rates in the 50 US states generates a distinctive \"checkerboard\" pattern showing that the epidemic has consisted of seven distinct internally coherent spatiotemporal wave patterns, four in the first year of the epidemic, and three thus far in the second year. Geoclustering of state case rate trajectories reveals three dominant co-varying spatial clusters of similar case rate trajectories, in the northeastern, southeastern and central/western regions of the USA. The spatiotemporal patterns of epidemic year 1 have thus far been repeated (p<.001) in epidemic year 2. The \"checkerboard\" pattern of the correlation matrix of case trajectories can be closely simulated as three sets of interacting sine waves with annual frequencies of 1:1:2 major cycles per year, corresponding to the northeastern, central/western, and southeastern state clusters. Case incidence patterns in Mexico and Canada have been similar to nearby regions in the southern US and the northern US, respectively. Time lapse videos allow visualization of the wave patterns. These highly structured geographical and temporal patterns, coupled with emerging evidence of annual repetition of these same patterns, show that SARS-CoV-2 case rates are driven at least in part by predictable seasonal factors.\n\nSignificance StatementLocal COVID-19 rates wax and wane. Often these epidemic changes are attributed to localized human behavioral factors. Our finding of highly structured continental scale spatiotemporal patterns that cross state and national boundaries, coupled with emerging evidence of annual repetition of these same patterns, shows that COVID-19 transmission is driven at least in part by seasonal factors. Other epidemic factors such as vaccine coverage rates, or emergence of new strains like the Delta variant of SARS-CoV-2 appear to modify, but not totally eclipse, these underlying seasonal patterns. COVID-19 seasonal transmission patterns are associated with, and may be driven by, seasonal weather patterns. Predictability of these patterns can provide opportunities for forecasting the epidemic and for guiding public health preparedness and control efforts.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Hawre Jalal", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Kyueun Lee", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Donald S Burke", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.21.21266484", "rel_title": "Durability of SARS-CoV-2 Antibodies from Natural Infection in Children and Adolescents", @@ -487663,6 +490605,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.19.21266580", + "rel_title": "COVID-19 cases and hospitalizations averted by case investigation and contact tracing in the United States", + "rel_date": "2021-11-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.19.21266580", + "rel_abs": "ImportanceEvidence of the impact of COVID-19 Case Investigation and Contact Tracing (CICT) programs is lacking. Policymakers need this evidence to assess its value.\n\nObjectiveEstimate COVID-19 cases and hospitalizations averted nationwide by US states CICT programs.\n\nDesignWe combined data from US CICT programs (e.g., proportion of cases interviewed, contacts notified or monitored, and days to case and contact notification) with incidence data to model CICT impacts over 60 days period (November 25, 2020 to January 23, 2021) during the height of the pandemic. We estimated a range of impacts by varying assumed compliance with isolation and quarantine recommendations.\n\nSettingUS States and Territories\n\nParticipantsFifty-nine state and territorial health departments that received federal funding supporting COVID-19 pandemic response activities were eligible for inclusion. Of these, 22 states and 1 territory reported all measures necessary for the analysis. These 23 jurisdictions covered 42.5% of the US population (140 million persons), spanned all 4 census regions, and reported data that reflected all 59 federally funded CICT programs.\n\nInterventionPublic health case investigation and contact tracing\n\nMain Outcomes and MeasuresCases and hospitalizations averted; percent of cases averted among cases not prevented by vaccination and other non-pharmaceutical interventions (other NPIs).\n\nResultsWe estimated 1.11 million cases and 27,231 hospitalizations were averted by CICT programs under a scenario where 80% of interviewed cases and monitored contacts, and 30% of notified contacts fully complied with isolation and quarantine guidance, eliminating their contributions to future transmission. As many as 1.36 million cases and 33,527 hospitalizations could have been prevented if all interviewed cases and monitored contacts had entered into and fully complied with isolation and quarantine guidelines upon being interviewed or notified. Across all scenarios and jurisdictions, CICT averted a median of 21.2% (range: 1.3% - 65.8%) of the cases not prevented by vaccination and other NPIs.\n\nConclusions and RelevanceCICT programs likely had a substantial role in curtailing the pandemic in most jurisdictions during the winter 2020-2021 peak. Differences in impact across jurisdictions indicate an opportunity to further improve CICT effectiveness. These estimates demonstrate the potential benefits from sustaining and improving these programs.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSWhat were the health impacts of COVID-19 case investigation and contact tracing programs (CICT) in the US?\n\nFindingsBy combining CICT program data from 22 states and 1 territory with mathematical modeling, we estimate CICT averted between 1.11 to 1.36 million cases and 27,231 to 33,527 hospitalizations over 60 days during the height of the pandemic (winter 2020-21). The upper estimate assumes all interviewed cases and monitored contacts complied with isolation and quarantine guidelines, while the lower estimate assumes fractions of interviewed cases and monitored or notified contacts did so.\n\nMeaningCICT programs likely played a critical role in curtailing the pandemic.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Gabriel Rainisch", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Seonghye Jeon", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Danielle Pappas", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Kimberly Spencer", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Leah S Fischer", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Bishwa Adhikari", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Melanie Taylor", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Bradford Greening Jr.", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Patrick Moonan", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "John Oeltmann", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Emily B Kahn", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Michael Washington", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Martin I Meltzer", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.11.19.21266581", "rel_title": "Baseline hypocapnia is associated with intubation in COVID-19 diagnosed patients", @@ -487808,137 +490817,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.19.21266588", - "rel_title": "Longitudinal SARS-CoV-2 RNA Wastewater Monitoring Across a Range of Scales Correlates with Total and Regional COVID-19 Burden in a Well-Defined Urban Population", - "rel_date": "2021-11-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.19.21266588", - "rel_abs": "Wastewater-based epidemiology (WBE) is an emerging surveillance tool that has been used to monitor the ongoing COVID-19 pandemic by tracking SARS-CoV-2 RNA shed into wastewater. WBE was performed to monitor the occurrence and spread of SARS-CoV-2 from three wastewater treatment plants (WWTP) and six neighborhoods in the city of Calgary, Canada (population 1.3 million). A total of 222 WWTP and 192 neighborhood samples were collected from June 2020 to May 2021, encompassing the end of the first-wave (June 2020), the second-wave (November end to December, 2020) and the third-wave of the COVID-19 pandemic (mid-April to May, 2021). Flow-weighted 24-hour composite samples were processed to extract RNA that was then analyzed for two SARS-CoV-2-specific regions of the nucleocapsid gene, N1 and N2, using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Using this approach SARS-CoV-2 RNA was detected in 98.06 % (406/414) of wastewater samples. SARS-CoV-2 RNA abundance was compared to clinically diagnosed COVID-19 cases organized by the three-digit postal code of affected individuals primary residences, enabling correlation analysis at neighborhood, WWTP and city-wide scales. Strong correlations were observed between N1 & N2 gene signals in wastewater and new daily cases for WWTPs and neighborhoods. Similarly, when flow rates at Calgarys three WWTPs were used to normalize observed concentrations of SARS-CoV-2 RNA and combine them into a city-wide signal, this was strongly correlated with regionally diagnosed COVID-19 cases and clinical test percent positivity rate. Linked census data demonstrated disproportionate SARS-CoV-2 in wastewater from areas of the city with lower socioeconomic status and more racialized communities. WBE across a range of urban scales was demonstrated to be an effective mechanism of COVID-19 surveillance.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Nicole Acosta", - "author_inst": "University of Calgary" - }, - { - "author_name": "Maria Bautista", - "author_inst": "University of Calgary" - }, - { - "author_name": "Barbara J Waddell", - "author_inst": "University of Calgary" - }, - { - "author_name": "Janine McCalder", - "author_inst": "University of Calgary" - }, - { - "author_name": "Alex Buchner Beaudet", - "author_inst": "University of Calgary" - }, - { - "author_name": "Lawrence Man", - "author_inst": "University of Calgary" - }, - { - "author_name": "Puja Pradhan", - "author_inst": "University of Calgary" - }, - { - "author_name": "Navid Sedaghat", - "author_inst": "University of Calgary" - }, - { - "author_name": "Chloe Papparis", - "author_inst": "University of Calgary" - }, - { - "author_name": "Andra Bacanu", - "author_inst": "University of Calgary" - }, - { - "author_name": "Jordan Hollman", - "author_inst": "University of Calgary" - }, - { - "author_name": "Alexander Krusina", - "author_inst": "University of Calgary" - }, - { - "author_name": "Danielle Southern", - "author_inst": "University of Calgary" - }, - { - "author_name": "Tyler Williamson", - "author_inst": "University of Calgary" - }, - { - "author_name": "Carmen Li", - "author_inst": "University of Calgary" - }, - { - "author_name": "Srijak Bhatnagar", - "author_inst": "Athabasca University" - }, - { - "author_name": "Sean Murphy", - "author_inst": "University of Calgary" - }, - { - "author_name": "Jianwei Chen", - "author_inst": "University of Calgary" - }, - { - "author_name": "Darina Kuzma", - "author_inst": "University of Calgary" - }, - { - "author_name": "Jon Meddings", - "author_inst": "University of Calgary" - }, - { - "author_name": "Jia Hu", - "author_inst": "Alberta Health Services" - }, - { - "author_name": "Jason Cabaj", - "author_inst": "University of Calgary" - }, - { - "author_name": "John Conly", - "author_inst": "University of Calgary" - }, - { - "author_name": "Norma Ruecker", - "author_inst": "City of Calgary" - }, - { - "author_name": "Gopal Achari", - "author_inst": "University of Calgary" - }, - { - "author_name": "Cathryn M Ryan", - "author_inst": "University of Calgary" - }, - { - "author_name": "Kevin Frankowski", - "author_inst": "University of Calgary" - }, - { - "author_name": "Casey Hubert", - "author_inst": "University of Calgary" - }, - { - "author_name": "Michael Parkins", - "author_inst": "University of Calgary" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.19.21266406", "rel_title": "Transmission of B.1.617.2 Delta Variant between vaccinated healthcare workers in Delhi, India", @@ -489369,6 +492247,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.17.21266488", + "rel_title": "Enoxaparin for thromboprophylaxis in hospitalized COVID-19 patients: comparison of 40 mg o.d. vs 40 mg b.i.d. The X-COVID19 Randomized Clinical Trial", + "rel_date": "2021-11-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266488", + "rel_abs": "It is uncertain whether higher doses of anticoagulants than recommended for thromboprophylaxis are necessary in COVID-19 patients hospitalized in general wards. This is a multicentre, open-label, randomized trial performed in 9 Italian centres, comparing 40 mg b.i.d. vs 40 mg o.d. enoxaparin in COVID-19 patients, between April 30, 2020 and April 25, 2021. Primary efficacy outcome was in-hospital incidence of venous thromboembolism (VTE): asymptomatic or symptomatic proximal deep vein thrombosis (DVT) diagnosed by serial compression ultrasonography (CUS), and/or symptomatic pulmonary embolism (PE) diagnosed by computed tomography angiography (CTA). Secondary endpoints included each individual component of the primary efficacy outcome and a composite of death, VTE, mechanical ventilation, stroke, myocardial infarction, admission to ICU. Safety outcomes included major bleeding. The study was interrupted prematurely due to slow recruitment. We included 183 (96%) of the 189 enrolled patients in the primary analysis (91 in b.i.d., 92 in o.d.). Primary efficacy outcome occurred in 6 patients (6{middle dot}5%, 0 DVT, 6 PE) in the o.d. group and 0 in the b.id. group (ARR 6{middle dot}5, 95% CI, 1{middle dot}5-11{middle dot}6). Absence of concomitant DVT and imaging characteristics suggest that most pulmonary artery occlusions were actually caused by local thrombi rather than PE. Statistically non-significant differences in secondary and safety endpoints were observed, with two major bleeding events in each arm. In conclusion, no DVT developed in COVID-19 patients hospitalized in general wards, independently of enoxaparin dosing used for thromboprophylaxis. Pulmonary artery occlusions developed only in the o.d. group. Our trial is underpowered and with few events.\n\nREGISTRATIONClinicalTrials.gov Identifier: NCT04366960\n\nEthics Commettee approvation number75/2020", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Nuccia Morici", + "author_inst": "ASST GRANDE OSPEDALE METROPOLITANO NIGUARDA" + }, + { + "author_name": "Gian Marco Podda", + "author_inst": "University of Milan; Medicina 2, ASST Santi Paolo e Carlo, Milan, Italy" + }, + { + "author_name": "Simone Birocchi", + "author_inst": "Medicina 2, ASST Santi Paolo e Carlo, Milan, Italy" + }, + { + "author_name": "Luca Bonacchini", + "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" + }, + { + "author_name": "Marco Merli", + "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" + }, + { + "author_name": "Michele Trezzi", + "author_inst": "Struttura Operativa Complessa (SOC) Malattie Infettive II, AUSL Toscana Centro, Ospedale San Jacopo, Pistoia, Italy" + }, + { + "author_name": "Gianluca Massaini", + "author_inst": "Struttura Operativa Semplice (SOS) Chirurgia vascolare, AUSL Toscana Centro, Ospedale San Jacopo, Pistoia, Italy" + }, + { + "author_name": "Marco Agostinis", + "author_inst": "Emergency Department, Ospedale San Carlo Borromeo, ASST Santi Paolo e Carlo, Milano, Italy" + }, + { + "author_name": "Giulia Carioti", + "author_inst": "Emergency Department, Ospedale San Carlo Borromeo, ASST Santi Paolo e Carlo, Milano, Italy" + }, + { + "author_name": "Francesco Saverio Serino", + "author_inst": "ASL 4 Veneto, Covid Hospital, Jesolo, Italy" + }, + { + "author_name": "Gianluca Gazzaniga", + "author_inst": "Postgraduate School of Clinical Pharmacology and Toxicology, Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy" + }, + { + "author_name": "Daniela Barberis", + "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" + }, + { + "author_name": "Laura Antolini", + "author_inst": "Center of Bioinformatics, Biostatistics and Bioimaging, School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy" + }, + { + "author_name": "Maria Grazia Valsecchi", + "author_inst": "Center of Bioinformatics, Biostatistics and Bioimaging, School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy" + }, + { + "author_name": "Marco Cattaneo", + "author_inst": "University of Milan; Medicina 2, ASST Santi Paolo e Carlo, Milan, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.17.21266367", "rel_title": "A prospective study of asymptomatic SARS-CoV-2 infection among individuals involved in academic research under limited operations during the COVID-19 pandemic", @@ -489534,49 +492487,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.15.21266335", - "rel_title": "A SARS-CoV-2 Delta Variant Containing Mutation in the Probe Binding Region Used for qRT-PCR Test in Japan Exhibited Atypical PCR Amplification and Might Induce False Negative Result", - "rel_date": "2021-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.15.21266335", - "rel_abs": "A recent pandemic of SARS-CoV-2 infection has caused severe health problems and substantially restricted social and economic activities. To cope with such an outbreak, the identification of infected individuals with high accuracy is vital. qRT-PCR plays a key role in the diagnosis of SARS-CoV-2 infection. The N protein-coding region is widely analyzed in qRT-PCR for the diagnosis of SARS-CoV-2 infection in Japan. We recently encountered two cases of SARS-CoV-2-positive specimens showing atypical amplification curves in the qRT-PCR. We performed whole-genome sequencing and found that the virus was a Delta-type variant of SARS-CoV-2 with a single nucleotide mutation in the probe-binding site. To evaluate the extent of spread of the variant in the area, we performed whole viral genome sequencing of samples collected from 61 patients infected with SARS-CoV-2 during the same time and in the same area. There were no other cases with the same mutation, indicating that the variant had not spread in the area. Furthermore, we performed phylogenetic analysis with various SARS-CoV-2 sequences deposited in the public database. Hundreds of variants were reported globally, and one in Japan were found to contain the same mutation. Phylogenetic analysis showed that the variant was very close to other Delta variants endemic in Japan but quite far from the variants containing the same mutation reported from outside Japan, suggesting that the variant would have been sporadically generated in some domestic areas. These findings propose two key points: i) mutations in the region used for SARS-CoV-2 qRT-PCR can cause abnormal amplification curves; therefore, the qRT-PCR result should not just be judged in an automated manner, but also manually checked by the examiner to prevent false-negative results, and ii) various mutations can be generated sporadically and unpredictably; therefore, efficient and robust screening systems are needed to promptly monitor the emergence of de novo variants.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Samiul Alam Rajib", - "author_inst": "Division of Genomics & Transcriptomics, The Joint Research Center for Human Retrovirus Infection, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, " - }, - { - "author_name": "Yasuhiro Ogi", - "author_inst": "Kumamoto City Medical Association Inspection Center, 2-3-40 Minami Kumamoto, Chuo-ku, Kumamoto 860-0812, Japan" - }, - { - "author_name": "Md Belal Hossain", - "author_inst": "Division of Genomics & Transcriptomics, The Joint Research Center for Human Retrovirus Infection, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, " - }, - { - "author_name": "Terumasa Ikeda Ph.D", - "author_inst": "Division of Molecular Virology and Genetics, The Joint Research Center for Human Retrovirus Infection, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0" - }, - { - "author_name": "Eiichi Tanaka MD", - "author_inst": "Kumamoto City Medical Association Inspection Center, 2-3-40 Minami Kumamoto, Chuo-ku, Kumamoto 860-0812, Japan" - }, - { - "author_name": "Tatsuya Kawaguchi MD, Ph.D", - "author_inst": "Department of Medical Technology, Kumamoto Health Science University, 325 Izumi-machi, Kita-ku, Kumamoto 861-5598, Japan." - }, - { - "author_name": "Yorifumi Satou MD, Ph.D", - "author_inst": "Division of Genomics & Transcriptomics, The Joint Research Center for Human Retrovirus Infection, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, " - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.18.21266442", "rel_title": "Immunoglobulin G1 Fc glycosylation as an early hallmark of severe COVID-19", @@ -490951,6 +493861,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.14.21266334", + "rel_title": "Attenuation of antibody titres during 3-6 months after the second dose of the BNT162b2 vaccine depends on sex, with age and smoking as risk factors for lower antibody titres at 6 months", + "rel_date": "2021-11-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.14.21266334", + "rel_abs": "ObjectiveWe aimed to determine antibody titres at 6 months and their rate of change during 3-6 months after the second dose of the BNT162b2 coronavirus disease 2019 (COVID-19) mRNA vaccine (Pfizer/BioNTech) and to explore clinical variables associated with titres in Japan.\n\nMethodsWe enrolled 365 healthcare workers (250 women, 115 men) whose 3-month antibody titres were analyzed in our previous study and whose blood samples were collected 183 {+/-} 15 days after the second dose. Participant characteristics collected previously were used. The relationships of these factors with antibody titres at 6 months and rates of change in antibody titres during 3-6 months were analyzed.\n\nResultsMedian age was 44 years. Median antibody titre at 6 months was 539 U/mL. Older participants had significantly lower antibody titres (20s, 752 U/mL; 60s-70s, 365 U/mL). In age-adjusted analysis, smoking was the only factor associated with lower antibody titres. Median rate of change in antibody titres during 3-6 months was -29.4%. The only factor significantly associated with the rate of change in Ab titres was not age or smoking, but sex (women, -31.6%; men, -25.1%).\n\nConclusionThe most important factors associated with lower antibody titres at 6 months were age and smoking, as at 3 months, probably reflecting their effect on peak antibody titres. However, antibody titres significantly attenuated during 3-6 months in women alone, which reduced the sex difference in antibody titres seen during the first 3 months. Antibody titres may be affected by different factors at different time points.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yushi Nomura", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + }, + { + "author_name": "Michiru Sawahata", + "author_inst": "Jichi Medical University" + }, + { + "author_name": "Yosikazu Nakamura", + "author_inst": "Jichi Medical University" + }, + { + "author_name": "Ryousuke Koike", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + }, + { + "author_name": "Otohiro Katsube", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + }, + { + "author_name": "Koichi Hagiwara", + "author_inst": "Jichi Medical University" + }, + { + "author_name": "Seiji Niho", + "author_inst": "Dokkyo Medical University" + }, + { + "author_name": "Norihiro Masuda", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + }, + { + "author_name": "Takaaki Tanaka", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + }, + { + "author_name": "Kumiya Sugiyama", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.16.21266414", "rel_title": "Unraveling the spatiotemporal spread of COVID-19 in Brazil through spatial network connectivity", @@ -491196,45 +494161,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.17.21266455", - "rel_title": "Estimating COVID-19-induced Excess Mortality in Lombardy", - "rel_date": "2021-11-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266455", - "rel_abs": "We compare the expected all-cause mortality with the observed one for different age classes during the pandemic in Lombardy, which was the epicenter of the epidemic in Italy and still is the region most affected by the pandemic. A generalized linear mixed model is introduced to model weekly mortality from 2011 to 2019, taking into account seasonal patterns and year-specific trends. Based on the 2019 year-specific conditional best linear unbiased predictions, a significant excess of mortality is estimated in 2020, leading to approximately 35000 more deaths than expected, mainly arising during the first wave. In 2021, instead, the excess mortality is not significantly different from zero, for the 85+ and 15-64 age classes, and significant reductions with respect to the 2020 estimated excess mortality are estimated for other age classes.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Antonello Maruotti", - "author_inst": "LUMSA University" - }, - { - "author_name": "Giovanna Jona-Lasinio", - "author_inst": "Sapienza University of Roma" - }, - { - "author_name": "Fabio Divino", - "author_inst": "University of Molise" - }, - { - "author_name": "Gianfranco Lovison", - "author_inst": "University of Palermo" - }, - { - "author_name": "Massimo Ciccozzi", - "author_inst": "Campus Biomedical University of Rome" - }, - { - "author_name": "Alessio Farcomeni", - "author_inst": "University of Roma \"Tor Vergata\"" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.16.21266360", "rel_title": "Impact of SARS-CoV-2 Vaccines on Covid-19 Incidence and Mortality in the United States", @@ -492661,6 +495587,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2021.11.15.21265526", + "rel_title": "COVID-19 in the Republic of Belarus: pandemic features and the interim safety and efficacy assessment of the Gam-COVID-Vac vaccine", + "rel_date": "2021-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.15.21265526", + "rel_abs": "ObjectiveTo study the COVID-19 pandemic features among the population of the Republic of Belarus from February 2020 to September 2021 and assess the safety (tolerance) and epidemiological efficacy of the Gam-COVID-Vac vaccine (Sputnik V).\n\nMaterials and methodsA retrospective analysis of COVID-19 cases in the Republic of Belarus from the beginning of registration (February 28, 2020) to September 12, 2021 was performed. To assess the COVID-19 case detection dynamics, official registration data available on the website of the Ministry of Health of the Republic of Belarus were used.\n\nVaccine safety (tolerance) and efficacy were assessed in an observational study. Safety (tolerance) was assessed by presence/absence of adverse reactions: general and local ones.\n\nThe efficacy rate (E) and the epidemiological efficacy index (K) was calculated according to the formula: E(%)=100*(b-a)/b, K=b/a.\n\nResultsOur data show that The COVID-19 pandemic in the Republic of Belarus is characterized by successive development stages: the first is the absence of COVID-19 cases in the country; the second is the registration of individual infection cases that came from abroad followed by local pathogen spread among the countrys population; the third is a local spread of COVID-19 among individuals who had contact with infected people; the fourth is the detection of cases where patients had no history of exposure to COVID-19 patients.\n\nAs of calendar week 26, 2021 Delta variant of SARS-CoV-2 has become the prevalent in the country.\n\nFollow-up results in January-August 2021 showed that the Sputnik V vaccine was well tolerated, with 80,832 adverse reactions reported (2.99% (95% CI 2.9-3.0) of the total number of vaccine doses administered). In terms of severity, adverse reactions were mild (91.4% (95% CI 91.2-91.6)) and moderate (8.6% (95% CI 8.6-8.8)). The epidemiological efficacy rate was 96.3%, the epidemiological efficacy index was 26.7. Thus, the results obtained testify to high prophylactic efficacy of the Sputnik V vaccine.\n\nConclusionsThe COVID-19 pandemic in the Republic of Belarus is characterized by successive development stages: from no cases in early 2020 to detected cases where most individuals had no history of contact with COVID-19 patients; periods of rising and falling incidence. The Sputnik V vaccine has demonstrated a high safety profile and epidemiological efficacy throughout mass vaccination in the Republic of Belarus.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ala M Dashkevich", + "author_inst": "Republican Centre of Hygiene, Epidemiology and Public Health" + }, + { + "author_name": "Veronika S Vysotskaya", + "author_inst": "Republican Centre of Hygiene, Epidemiology and Public Health" + }, + { + "author_name": "Iryna N Hlinskaya", + "author_inst": "Republican Centre of Hygiene, Epidemiology and Public Health" + }, + { + "author_name": "Anzhela L Skuranovich", + "author_inst": "Republican Centre of Hygiene, Epidemiology and Public Health" + }, + { + "author_name": "Aliaksandr A Tarasenka", + "author_inst": "Ministry of Health of the Republic of Belarus" + }, + { + "author_name": "Inna A Karaban", + "author_inst": "Ministry of Health of the Republic of Belarus" + }, + { + "author_name": "Natalia D Kolomiets", + "author_inst": "Belarusian Medical Academy of Postgraduate Education" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.16.21266391", "rel_title": "From online data collection to identification of disease mechanisms: The IL-1beta, IL-6 and TNF-alpha; cytokine triad is associated with post-acute sequelae of COVID-19 in a digital research cohort", @@ -492814,25 +495783,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.15.21266317", - "rel_title": "Effect of COVID-19 vaccination on menstrual periods in a retrospectively recruited cohort", - "rel_date": "2021-11-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.15.21266317", - "rel_abs": "Surveillance schemes are receiving increasing numbers of reports from people who have noticed a change to their period following COVID-19 vaccination. In order to investigate this, we retrospectively recruited 1273 people who have a record of their menstrual cycle and vaccination dates and used their reports to explore hypotheses about how COVID-19 vaccination and menstrual changes could be linked. In this dataset, we were unable to detect strong signals to support the idea that COVID-19 vaccination is linked to menstrual changes. However, larger, prospectively recruited studies may be able to find associations that we were not powered to detect.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Victoria Male", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "sexual and reproductive health" - }, { "rel_doi": "10.1101/2021.11.15.21266338", "rel_title": "Comparative analysis of antibody production by mRNA 1273, AZD 1222 and BBIBP-CorV on elderly people suffering from different co-morbidity in Bangladesh", @@ -494863,6 +497813,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.11.12.21266292", + "rel_title": "Covid-19 Pandemic and its Effect on Residents' Mental Well-Being", + "rel_date": "2021-11-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.12.21266292", + "rel_abs": "Concerns about COVID-19s long-term consequences on the mental health of frontline health professionals are mounting as the entire world strives anew to contain it. The primary objective of this research is to describe the impact of working during the COVID-19 pandemic on junior doctors mental health and to investigate the effect of the COVID-19 pandemic on junior doctors training and professional performance. A cross-sectional online survey using the Google Forms platform was conducted from May 1st to May 30th, 2021, in 311 healthcare workers who were currently enrolled in a residency program at the Kuwait Institutional of Medical Specialization (KIMS). Socio-demographic details of each health worker were collected and the scores related to depression, anxiety, and stress were measured using the previously validated depression anxiety stress scale-21 (DASS-21). Higher stress scores were seen in those who were devoid of the option to work with COVID-19 patients (adjusted {beta} 5.1 (95%CI:1.2-9);p=0.01), who reported that working during the pandemic affected their study schedule (adjusted {beta} 4.8 (95%CI:1.6-8.1);p= 0.004), and who lost off service training time (adjusted {beta} 2.7 (95%CI:0.13-5.2); p=0.034). Further, the anxiety scores were significantly higher in females. The impact of the ongoing pandemic on residents mental health is grave, necessitating psychological treatment and support. The study discovered various factors linked to depression, anxiety, and stress. As a result, these aspects must be regarded to protect the residents mental health.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Anwar Yazdani", + "author_inst": "Anesthesia and ICU Department, AlSabah Hospital, Kuwait" + }, + { + "author_name": "Hend Esmaeili", + "author_inst": "Department of Anesthesia and Critical Care, Farwaniya Hospital, Kuwait" + }, + { + "author_name": "Abdulla K AlSaleh", + "author_inst": "Anesthesia and ICU Department, Amiri Hospital, Kuwait" + }, + { + "author_name": "Ahmed Sultan", + "author_inst": "Anesthesia and ICU Department, Amiri Hospital, Kuwait" + }, + { + "author_name": "Esam Alamad", + "author_inst": "Anesthesia and ICU Department, Al Adan Hospital, Kuwait" + }, + { + "author_name": "Ali Bandar", + "author_inst": "Department of Anesthesia and critical care, Jaber Hospital, Kuwait" + }, + { + "author_name": "Hanouf Rawdhan", + "author_inst": "Department of Anesthesia Kuwait Cancer Control Center" + }, + { + "author_name": "Mariam Ayed", + "author_inst": "Ministry of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.11.10.21266063", "rel_title": "Case Series of Thrombosis with Thrombocytopenia Syndrome following COVID-19 vaccination--United States, December 2020-August 2021", @@ -495100,41 +498097,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.10.21265739", - "rel_title": "Limited impact of contact tracing in a University setting for COVID-19 due to asymptomatic transmission and social distancing", - "rel_date": "2021-11-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.10.21265739", - "rel_abs": "Contact tracing is an important tool for controlling the spread of infectious diseases, including COVID-19. Here, we investigate the spread of COVID-19 and the effectiveness of contact tracing in a university population, using a data-driven ego-centric network model constructed with social contact data collected during 2020 and similar data collected in 2010. We find that during 2020, university staff and students consistently reported fewer social contacts than in 2010, however those contacts occurred more frequently and were of longer duration. We find that contact tracing in the presence of social distancing is less impactful than without social distancing. By combining multiple data sources, we show that University-aged populations are likely to develop asymptomatic COVID-19 infections. We find that asymptomatic index cases cannot be reliably back-traced through contact tracing and consequently transmission in their social network is not significantly reduced through contact tracing. In summary, social distancing restrictions had a large impact on limiting COVID-19 outbreaks in universities; to reduce transmission further contact tracing should be used in conjunction with alternative interventions.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Daniel A Stocks", - "author_inst": "University of Bristol" - }, - { - "author_name": "Emily J Nixon", - "author_inst": "University of Bristol" - }, - { - "author_name": "Adam Trickey", - "author_inst": "University of Bristol" - }, - { - "author_name": "Martin Homer", - "author_inst": "University of Bristol" - }, - { - "author_name": "Ellen Brooks-Pollock", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.12.21266271", "rel_title": "AI/ML Models to Aid in the Diagnosis of COVID-19 Illness from Forced Cough Vocalizations: Results and Challenges of a Systematic Review of the Relevant Literature", @@ -496737,6 +499699,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.11.21266216", + "rel_title": "Effectiveness of non-pharmaceutical measures (NPIs) on COVID-19 in Europe: A systematic literature review", + "rel_date": "2021-11-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.11.21266216", + "rel_abs": "BackgroundThe study objective was to conduct a systematic review to assess the effectiveness of non-pharmaceutical interventions (NPIs) to reduce the transmission of SARS-CoV-2 in Europe during the first wave of the pandemic.\n\nMethodsWe searched OVID Medline, EMBASE, and the Cochrane and Campbell Databases for Systematic Reviews published up to April 15th 2021. Focusing on community (meso-level) and society (macro-level) level NPIs, we included all study designs, while a geographic restriction was limited to the EU, UK and European Economic Area (EEA) countries. Using the PICO framework, two reviewers independently extracted data and assessed quality using appropriate quality appraisal tools. A qualitative synthesis was performed, with NPIs grouped initially by a) Physical Distancing measures, b) Case detection and management measures, and c) hygiene measures and subsequently by country.\n\nResultsOf 17,692 studies initially assessed, 45 met all inclusion criteria. Most studies (n=30) had a modelling study design, while 13 were observational, one quasi-experimental and one experimental. Evidence from across the European continent, presented by country, indicates that the implementations of physical distancing measures (i.e., lockdowns/quarantines), preferably earlier in the pandemic, reduce the number of cases and hospitalisation across settings and for which the timing and duration are essential parameters. Case detection and management measures were also identified as effective measures at certain levels of testing and incidence, while hygiene and safety measures complemented the implementation of physical distancing measures.\n\nConclusionsThis literature review represents a comprehensive assessment of the effectiveness of NPIs in Europe up to April 2021. Despite heterogeneity across studies, NPIs, as assessed within the context of this systematic review at the macro and meso level, are effective in reducing SARS-CoV-2 transmission rates and COVID-19 hospitalisation rates and deaths in the European Region and may be applied as response strategies to reduce the burden of COVID-19 in forthcoming waves.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Constantine Vardavas", + "author_inst": "University of Crete" + }, + { + "author_name": "Katerina Nikitara", + "author_inst": "University of Crete" + }, + { + "author_name": "Katerina Aslanoglou", + "author_inst": "University of Crete" + }, + { + "author_name": "Michele Hilton Boon", + "author_inst": "WISE Centre for Economic Justice, Glasgow Caledonian University" + }, + { + "author_name": "Revati Phalkey", + "author_inst": "Climate Change and Health Group, Public Health England, United Kingdom" + }, + { + "author_name": "Jo Leonardi-Bee", + "author_inst": "Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, UK" + }, + { + "author_name": "Gkikas Magiorkinis", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Paraskevi Katsaounou", + "author_inst": "Department of Respiratory Medicine, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Anastasia Pharris", + "author_inst": "European Centre for Disease Prevention and Control" + }, + { + "author_name": "Ettore Severi", + "author_inst": "European Centre for Disease Prevention and Control" + }, + { + "author_name": "Jonathan E. Suk", + "author_inst": "European Centre for Disease Prevention and Control" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.11.10.21266124", "rel_title": "Differences in COVID-19 vaccination coverage by occupation in England: a national linked data study", @@ -496866,29 +499887,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.10.21266188", - "rel_title": "A study of the benefits of vaccine mandates and vaccine passports for SARS-CoV-2", - "rel_date": "2021-11-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.10.21266188", - "rel_abs": "ObjectiveTo evaluate the benefits of vaccine mandates and vaccine passports (VMVP) for SARS-CoV-2 by estimating the benefits of vaccination and exclusion of unvaccinated people from different settings.\n\nMethodsQuantified the benefits of vaccination using meta-analyses of randomized controlled trials (RCTs), cohort studies, and transmission studies to estimate the relative risk reduction (RRR), absolute risk reduction (ARR), and number needed to vaccinate (NNV) for transmission, infection, and severe illness/hospitalization. Estimated the baseline infection risk and the baseline transmission risks for different settings. Quantified the benefits of exclusion using these data to estimate the number of unvaccinated people needed to exclude (NNE) to prevent one transmission in different settings. Modelled how the benefits of vaccination and exclusion change as a function of baseline infection risk. Studies were identified from recent systematic reviews and a search of MEDLINE, MEDLINE In-Process, Embase, Global Health, and Google Scholar.\n\nResultsData on infection and severe illness/hospitalization were obtained from 10 RCTs and 19 cohort studies of SARS-CoV-2 vaccines, totalling 5,575,049 vaccinated and 4,341,745 unvaccinated participants. Data from 7 transmission studies were obtained, totalling 557,020 index cases, 49,328 contacts of vaccinated index cases, and 1,294,372 contacts of unvaccinated index cases. The estimated baseline infection risk in the general population is 3.04%. The estimated breakthrough infection risk in the vaccinated population is 0.57%. Vaccines are very effective at reducing the risk of infection (RRR=88%, ARR=2.59%, NNV=39) and severe illness/hospitalization (RRR=89%, ARR=0.15%, NNV=676) in the general population. While the latter effect is small, vaccines nearly eliminate the baseline risk of severe illness/hospitalization (0.16%). Among an infected persons closest contacts (primarily household members), vaccines reduce transmission risk (RRR=41%, ARR=11.04%, NNV=9). In the general population, the effect of vaccines on transmission risk is likely very small for most settings and baseline infection risks (NNVs [≥] 1,000). Infected vaccinated people have a nontrivial transmission risk for their closest contacts (14.35%), but it is less than unvaccinated people (23.91%). The transmission risk reduction gained by excluding unvaccinated people is very small for most settings: healthcare (NNE=4,699), work/study places (NNE=2,193), meals/gatherings (NNE=531), public places (NNE=1,731), daily conversation (NNE=587), and transportation (NNE=4,699). Exclusion starts showing benefits on transmission risk for some settings when the baseline infection risk is between 10% to 20%.\n\nConclusionsThe benefits of VMVP are clear: the coercive element to these policies will likely lead to increased vaccination levels. Our study shows that higher vaccination levels will drive infections lower and almost eliminate severe illness/hospitalization from the general population. This will substantially lower the burden on healthcare systems. The benefits of exclusion are less clear. The NNEs suggest that hundreds, and even thousands, of unvaccinated people may need to be excluded from various settings to prevent one SARS-CoV-2 transmission from unvaccinated people. Therefore, consideration of the costs of exclusion is warranted, including staffing shortages from losing unvaccinated healthcare workers, unemployment/unemployability, financial hardship for unvaccinated people, and the creation of a class of citizens who are not allowed to fully participate in many areas of society.\n\nRegistrationThis study is not registered.\n\nFundingThis study received no grant from any funding agency, commercial, or not-for-profit sectors. It has also received no support of any kind from any individual or organization.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Aaron Prosser", - "author_inst": "Department of Psychiatry and Behavioural Neurosciences, McMaster University" - }, - { - "author_name": "David L. Streiner", - "author_inst": "Department of Psychiatry and Behavioural Neurosciences, McMaster University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.08.21265944", "rel_title": "Mapping the human genetic architecture of COVID-19: an update", @@ -498659,6 +501657,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.09.21266145", + "rel_title": "Viral kinetic modeling and clinical trial simulation predicts disruption of respiratory disease trials by non-pharmaceutical COVID-19 interventions", + "rel_date": "2021-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.09.21266145", + "rel_abs": "Clinical research in infectious respiratory diseases has been profoundly affected by non-pharmaceutical interventions (NPIs) against COVID-19. On top of trial delays or even discontinuation which have been observed in all disease areas, NPIs altered transmission pattern of many seasonal respiratory viruses which followed regular patterns for decades before the pandemic. Clinical trial design based on pre-pandemic historical data therefore needs to be put in question. In this article, we show how knowledge-based mathematical modeling can be used to address this issue. We set up an epidemiological model of respiratory tract infection (RTI) sensitive to a time dependent between-host transmission rate and coupled this model to a mechanistic description of viral RTI episodes in an individual patient. By reducing the transmission rate when the lockdown was introduced in the United Kingdom in March 2020, we were able to reproduce the perturbed 2020 RTI disease burden data. Using this setup, we simulated several NPIs scenarios of various strength (none, mild, medium, strong) and conducted placebo-controlled in silico clinical trials in pediatric patients with recurrent RTIs (RRTI) quantifying annual RTI rate distributions. In interventional arms, virtual patients aged 1-5 years received the bacterial lysate OM-85 (approved in several countries for the prevention of pediatric RRTIs) through a pro-type I immunomodulation mechanism of action described by a physiologically based pharmacokinetics and pharmacodynamics approach (PBPK/PD). Our predictions showed that sample size estimates based on the ratio of RTI rates (or the post-hoc power of fixed sample size trials) are not majorly impacted under NPIs which are less severe (none, mild and medium NPIs) than a strict lockdown (strong NPI). However, NPIs show a stronger impact on metrics more relevant for assessing the clinical relevance of the effect such as absolute benefit. This dichotomy shows the risk that successful trials (even with their primary endpoints being met) still get challenged in risk benefit assessment during the review of market authorization. Furthermore, we found that a mild NPI scenario already affected the time to recruit significantly when sticking to eligibility criteria complying with historical data. In summary, our model predictions can help rationalize and forecast post-COVID-19 trial feasibility. They advocate for gauging absolute and relative benefit metrics as well as clinical relevance for assessing efficacy hypotheses in trial design and they question eligibility criteria misaligned with the actual disease burden.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Simon Ars\u00e8ne", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Claire Couty", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Igor Faddeenkov", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Natacha Go", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Sol\u00e8ne Granjeon-Noriot", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Daniel \u0160m\u00edt", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Riad Kahoul", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Ben Illigens", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Jean-Pierre Boissel", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Aude Chevalier", + "author_inst": "OM Pharma" + }, + { + "author_name": "Lorenz Lehr", + "author_inst": "OM Pharma" + }, + { + "author_name": "Christian Pasquali", + "author_inst": "OM Pharma" + }, + { + "author_name": "Alexander Kulesza", + "author_inst": "Novadiscovery" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.09.467827", "rel_title": "A novel histone deacetylase inhibitor-based approach to eliminate microglia and retain astrocyte properties in glial cell culture.", @@ -498848,20 +501913,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.11.10.468037", - "rel_title": "Potent antibody immunity to SARS-CoV-2 variants elicited by a third dose of inactivated vaccine", - "rel_date": "2021-11-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.10.468037", - "rel_abs": "SARS-CoV-2 variants are still prevalent worldwide and continue to pose a challenge to the effectiveness of current vaccines. It remains unknown whether a third dose of inactivated vaccine elicits immune potential against SARS-CoV-2 variants. Here, we showed a significant decline in plasma neutralization against SARS-CoV-2 at seven months after a second dose of the inactivated vaccine in a large-scale cohort. However, we also found that a third vaccination with an inactivated vaccine largely increased plasma neutralization against variants including Beta, Delta, and Lambda. More importantly, the high-affinity anti-RBD memory B cells were also generated by the third vaccination, suggesting a more potent and longer protection. These findings highlighted the importance and effectiveness of a third dose of inactivated vaccine in conferring higher protection against the emerging variants in populations.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.11.10.21266141", "rel_title": "PBPK modelling of dexamethasone in patients with COVID-19 and liver disease", @@ -500248,6 +503299,37 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.11.09.21266122", + "rel_title": "The effects of the first national lockdown in England on geographical inequalities in the evolution of COVID-19 case rates: An ecological study", + "rel_date": "2021-11-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.09.21266122", + "rel_abs": "BackgroundSocio-economic inequalities in COVID-19 case rates have been noted worldwide. Previous studieshave compared case rates over set phases. There has been no analysis of how inequalities in cases changed overtime and were shaped by national mitigation strategies (e.g. lock downs). This paper provides the first analysis of the evolution of area-level inequalities in COVID-19 cases by deprivation levels in the first wave of the pandemic (January to July 2020) in England - with a focus on the effects of the first national lockdown (March - July 2020).\n\nMethodsWeekly case rates per Middle Super Output Area (MSOA, n=4412) in England from 2020-03-15 to 2020-07-04 were obtained, and characteristics of local epidemics were calculated, e.g. the highest case rate per area. Simple linear and logistic regression analyses were employed to assess the association of these metrics with index of multiple deprivation (IMD). Local authority-level (n=309) cases were used similarly in a sensitivity analysis, as these data were available daily and extended further back in time. The impact of lockdown was assessed by comparing the cumulative case rate in the most deprived 20% of MSOAs to the least deprived 20%, for the periods before the lockdown, and by the end of lockdown.\n\nFindingsLess deprived areas began recording COVID-19 cases earlier than more deprived areas and were more likely to have peaked by March 2020. More deprived areas case rates grew faster and peaked higher than less deprived areas. During the first national lockdown in the UK, the relative excess in case rates in the most deprived areas increased to 130% of that of the least deprived ones.\n\nInterpretationThe pattern of disease spread in England confirm the hypothesis that initial cases of a novel infectious disease are likely to occur in more affluent communities, but more deprived areas will overtake them once national mitigation strategies begin, and bear the brunt of the total case load. The strict first national lockdown served to increase case rate inequalities in England.\n\nFundingThis work was supported by a grant from The Health Foundation (Ref: 2211473), who took no part in the design, analysis or writing of this study.\n\nResearch in Context\n\nEvidence before this studyThe magnitude and distribution of deprivation-related inequalities in COVID-19 cases have been reported for England and many other countries, however, none have yet investigated the initial evolution of these inequalities, nor the effects of the first national lockdown.\n\nAdded value of this studyWe leverage the benefits of two separate datasets of COVID-19 case counts to investigate the initiation and evolution in inequalities in disease burden by deprivation. We found that cases were first recorded in less deprived areas before rising faster in more deprived areas. The first national lockdown led to an increase in these geographical inequalities.\n\nImplications of all the available evidenceNational lockdowns are an important tool in the armoury of pandemic control, but their timing and duration must be carefully decided and be locally specific. Because case rate inequalities were already present before lockdown in England, movement restrictions served to further increase them.\n\nSummary Box\n\nSection 1: What is already known on this subjectGeographical inequalities in COVID-19 case rates have been noted worldwide, and in England. However, how these inequalities were affected by policy responses - such as national lockdowns - has yet to be investigated.\n\nSection 2: What this study addsWe examined geographical inequalities in COVID-19 case rates by deprivation during the first English lock down (March - July, 2020). We find that cases were first reported in the less deprived areas of England, but this pattern quickly reversed and large excesses of cases occurred in the most deprived areas during the first national lockdown. Case rates in more deprived areas also rose more sharply, peaked higher, and then dropped faster than in less deprived areas. Inequality in cumulative case rates grew over the lockdown, increasing inequalities in disease burden.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Claire E Welsh", + "author_inst": "Newcastle University" + }, + { + "author_name": "Viviana Albani", + "author_inst": "Newcastle University" + }, + { + "author_name": "Fiona E Matthews", + "author_inst": "Newcastle University" + }, + { + "author_name": "Clare Bambra", + "author_inst": "Newcastle University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.08.21266055", "rel_title": "Immunity to COVID-19 in India through vaccination and natural infection", @@ -500373,113 +503455,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.11.08.21265312", - "rel_title": "Understanding COVID-19 trajectories from a nationwide linked electronic health record cohort of 56 million people: phenotypes, severity, waves & vaccination", - "rel_date": "2021-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.08.21265312", - "rel_abs": "BackgroundUpdatable understanding of the onset and progression of individuals COVID-19 trajectories underpins pandemic mitigation efforts. In order to identify and characterize individual trajectories, we defined and validated ten COVID-19 phenotypes from linked electronic health records (EHR) on a nationwide scale using an extensible framework.\n\nMethodsCohort study of 56.6 million people in England alive on 23/01/2020, followed until 31/05/2021, using eight linked national datasets spanning COVID-19 testing, vaccination, primary & secondary care and death registrations data. We defined ten COVID-19 phenotypes reflecting clinically relevant stages of disease severity using a combination of international clinical terminologies (e.g. SNOMED-CT, ICD-10) and bespoke data fields; positive test, primary care diagnosis, hospitalisation, critical care (four phenotypes), and death (three phenotypes). Using these phenotypes, we constructed patient trajectories illustrating the transition frequency and duration between phenotypes. Analyses were stratified by pandemic waves and vaccination status.\n\nFindingsWe identified 3,469,528 infected individuals (6.1%) with 8,825,738 recorded COVID-19 phenotypes. Of these, 364,260 (11%) were hospitalised and 140,908 (4%) died. Of those hospitalised, 38,072 (10%) were admitted to intensive care (ICU), 54,026 (15%) received non-invasive ventilation and 21,404 (6%) invasive ventilation. Amongst hospitalised patients, first wave mortality (30%) was higher than the second (23%) in non-ICU settings, but remained unchanged for ICU patients. The highest mortality was for patients receiving critical care outside of ICU in wave 1 (51%). 13,083 (9%) COVID-19 related deaths occurred without diagnoses on the death certificate, but within 30 days of a positive test while 10,403 (7%) of cases were identified from mortality data alone with no prior phenotypes recorded. We observed longer patient trajectories in the second pandemic wave compared to the first.\n\nInterpretationOur analyses illustrate the wide spectrum of severity that COVID-19 displays and significant differences in incidence, survival and pathways across pandemic waves. We provide an adaptable framework to answer questions of clinical and policy relevance; new variant impact, booster dose efficacy and a way of maximising existing data to understand individuals progression through disease states.\n\nResearch in ContextO_ST_ABSEvidence before the studyC_ST_ABSWe searched PubMed on October 14, 2021, for publications with the terms \"COVID-19\" or \"SARS-CoV-2\", \"severity\", and \"electronic health records\" or \"EHR\" without date or language restrictions. Multiple studies explore factors associated with severity of COVID-19 infection, and model predictions of outcome for hospitalised patients. However, most work to date focused on isolated facets of the healthcare system, such as primary or secondary care only, was conducted in subpopulations (e.g. hospitalised patients) of limited sample size, and often utilized dichotomised outcomes (e.g. mortality or hospitalisation) ignoring the full spectrum of disease. We identified no studies which comprehensively detailed severity of infections while describing disease severity across pandemic waves, vaccination status, and patient trajectories.\n\nAdded value of this studyTo our knowledge, this is the first study providing a comprehensive view of COVID-19 across pandemic waves using national data and focusing on severity, vaccination, and patient trajectories. Drawing on linked electronic health record (EHR) data on a national scale (56.6 million people alive and registered with GP in England), we describe key demographic factors, frequency of comorbidities, impact of the two main waves in England, and effect of full vaccination on COVID-19 severities. Additionally, we identify and describe patient trajectory networks which illustrate the main transition pathways of COVID-19 patients in the healthcare system. Finally, we provide reproducible COVID-19 phenotyping algorithms reflecting clinically relevant stages of disease severity i.e. positive tests, primary care diagnoses, hospitalisation, critical care treatments (e.g. ventilatory support) and mortality.\n\nImplications of all the available evidenceThe COVID-19 phenotypes and trajectory analysis framework outlined produce a reproducible, extensible and repurposable means to generate national-scale data to support critical policy decision making. By modelling patient trajectories as a series of interactions with healthcare systems, and linking these to demographic and outcome data, we provide a means to identify and prioritise care pathways associated with adverse outcomes and highlight healthcare system touch points which may act as tangible targets for intervention.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Johan H Thygesen", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Christopher R Tomlinson", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Sam Hollings", - "author_inst": "NHS Digital, Leeds, UK" - }, - { - "author_name": "Mehrdad A Mizani", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Alex Handy", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Ashley Akbari", - "author_inst": "Population Data Science and Health Data Research UK, Swansea University, Swansea, UK" - }, - { - "author_name": "Amitava Banerjee", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Jennifer A Cooper", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK" - }, - { - "author_name": "Alvina G Lai", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Kezhi Li", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Bilal A Mateen", - "author_inst": "The Wellcome Trust, London, UK" - }, - { - "author_name": "Naveed Sattar", - "author_inst": "Institute of Cardiovascular & Medical Sciences, University of Glasgow, Glasgow, UK" - }, - { - "author_name": "Reecha Sofat", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Ana Torralbo", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Honghan Wu", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Angela Wood", - "author_inst": "British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK" - }, - { - "author_name": "Jonathan AC Sterne", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK" - }, - { - "author_name": "Christina Pagel", - "author_inst": "Clinical Operational Research Unit, University College London, London, UK" - }, - { - "author_name": "William Whiteley", - "author_inst": "Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Cathie Sudlow", - "author_inst": "Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Harry Hemingway", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Spiros Denaxas", - "author_inst": "Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "- CVD-COVID-UK Consortium", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.08.21266049", "rel_title": "Ad26.COV2.S breakthrough infections induce high titers of antibodies capable of neutralizing variants of concern", @@ -502150,6 +505125,101 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.11.03.21265533", + "rel_title": "Effect of the Neutralizing SARS-CoV-2 Antibody Sotrovimab in Preventing Progression of COVID-19: A Randomized Clinical Trial", + "rel_date": "2021-11-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.03.21265533", + "rel_abs": "ImportanceOlder patients and those with underlying comorbidities infected with SARS-CoV-2 may be at increased risk of hospitalization and death from COVID-19. Sotrovimab is a neutralizing antibody designed for treatment of high-risk patients to prevent COVID-19 progression.\n\nObjectiveTo evaluate the efficacy and safety of sotrovimab in preventing progression of mild to moderate COVID-19 to severe disease.\n\nDesignRandomized, double-blind, multicenter, placebo-controlled, phase 3 study.\n\nSetting57 centers in 5 countries.\n\nParticipantsNonhospitalized patients with symptomatic, mild to moderate COVID-19 and at least 1 risk factor for disease progression.\n\nInterventionPatients were randomized (1:1) to an intravenous infusion of sotrovimab 500 mg or placebo.\n\nMain Outcomes and MeasuresThe primary efficacy outcome was the proportion of patients with COVID-19 progression, defined as all-cause hospitalization longer than 24 hours for acute illness management or death through day 29. Key secondary outcomes included the proportion of patients with COVID-19 progression, defined as emergency room visit, hospitalization of any duration, or death, and proportion of patients developing severe/critical respiratory COVID-19 requiring supplemental oxygen.\n\nResultsAmong 1057 patients randomized (sotrovimab, 528; placebo, 529), all-cause hospitalization longer than 24 hours or death was significantly reduced with sotrovimab (6/528 [1%]) vs placebo (30/529 [6%]) by 79% (95% CI, 50% to 91%; P<.001). Secondary outcome results further demonstrated the effect of sotrovimab in reducing emergency room visits, hospitalization of any duration, or death, which was reduced by 66% (95% CI, 37% to 81%; P<.001), and severe/critical respiratory COVID-19, which was reduced by 74% (95% CI, 41% to 88%; P=.002). No patients receiving sotrovimab required high-flow oxygen, oxygen via nonrebreather mask, or mechanical ventilation compared with 14 patients receiving placebo. The proportion of patients reporting adverse events was similar between treatment groups; sotrovimab was well tolerated, and no safety concerns were identified.\n\nConclusions and RelevanceAmong nonhospitalized patients with mild to moderate COVID-19, a single 500-mg intravenous dose of sotrovimab prevented progression of COVID-19, with a reduction in hospitalization and need for supplemental oxygen. Sotrovimab is a well-tolerated, effective treatment option for patients at high risk for severe morbidity and mortality from COVID-19.\n\nTrial RegistrationClinicalTrials.gov Identifier: NCT04545060", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Anil Gupta", + "author_inst": "Albion Finch Medical, William Osler Health Centre" + }, + { + "author_name": "Yaneicy Gonzalez-Rojas", + "author_inst": "Optimus U, Corp." + }, + { + "author_name": "Erick Juarez", + "author_inst": "Florida International Medical Research" + }, + { + "author_name": "Manuel Crespo", + "author_inst": "Alvaro Cunqueiro Hospital, IIS Galicia Sur" + }, + { + "author_name": "Jaynier Moya", + "author_inst": "Pines Care Research Center" + }, + { + "author_name": "Diego Falci", + "author_inst": "Hospital de Clinicas de Porto Alegre" + }, + { + "author_name": "Elias Sarkis", + "author_inst": "Sarkis Clinical Trials" + }, + { + "author_name": "Joel Solis", + "author_inst": "Centex Studies" + }, + { + "author_name": "Hanzhe Zheng", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Nicola Scott", + "author_inst": "GlaxoSmithKline" + }, + { + "author_name": "Andrea L. Cathcart", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Sergio Parra", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Jennifer E. Sager", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Daren J Austin", + "author_inst": "GlaxoSmithKline" + }, + { + "author_name": "Amanda Peppercorn", + "author_inst": "GlaxoSmithKline" + }, + { + "author_name": "Elizabeth Alexander", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Wendy W. Yeh", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Cynthia Brinson", + "author_inst": "Central Texas Clinical Research" + }, + { + "author_name": "Melissa Aldinger", + "author_inst": "Vir Biotechnology, Inc." + }, + { + "author_name": "Adrienne E Shapiro", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.05.21265763", "rel_title": "Surveillance of COVID-19 in a Vaccinated Population: A Rapid Literature Review", @@ -502391,33 +505461,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.11.07.21266027", - "rel_title": "Ethnicity and outcomes in COVID-19 in the United Kingdom: a systematic review and meta-analysis", - "rel_date": "2021-11-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.07.21266027", - "rel_abs": "This systematic review and meta-analysis evaluated the clinical outcomes of COVID-19 disease in the ethnic minorities of the UK in comparison to the White ethnic group. Medline, Embase, Cochrane, MedRxiv, and Prospero were searched for articles published between May 2020 to April 2021. PROSPERO ID: CRD42021248117. Fourteen studies (767177 participants) were included in the review. In the adjusted analysis, the pooled Odds Ratio (OR) for the mortality outcome was higher for the Black (1.83, 95% CI: 1.21-2.76), Asian (1.16, 95% CI: 0.85-1.57), and Mixed and Other (MO) groups (1.12, 95% CI: 1.04-1.20) compared to the White group. The adjusted and unadjusted ORs of intensive care admission were more than double for all ethnicities (OR Black 2.32, 95% CI: 1.73-3.11, Asian 2.34, 95% CI: 1.89-2.90, MO group 2.26, 95% CI: 1.64-3.11). In the adjusted analysis of mechanical ventilation need the ORs were similarly significantly raised (Black group 2.03, 95% CI: 1.80-2.29, Asian group 1.84, 95% CI: 1.20-2.80, MO 2.09, 95% CI: 1.35-3.22). This review confirmed that all ethnic groups in the UK suffered from increased disease severity and mortality with regards to COVID-19. This has urgent public health and policy implications to reduce the health disparities.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Sania Siddiq", - "author_inst": "University of Manchester" - }, - { - "author_name": "Saima Ahmed", - "author_inst": "University of Manchester" - }, - { - "author_name": "Irfan Akram", - "author_inst": "Royal College of General Practitioners" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.05.467523", "rel_title": "SARS-COV-2 Delta variant displays moderate resistance to neutralizing antibodies and spike protein properties of higher soluble ACE2 sensitivity, enhanced cleavage and fusogenic activity", @@ -503968,6 +507011,33 @@ "type": "new results", "category": "synthetic biology" }, + { + "rel_doi": "10.1101/2021.11.04.21265937", + "rel_title": "Estimation of the basic reproduction number of COVID-19 from the incubation period distribution", + "rel_date": "2021-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.04.21265937", + "rel_abs": "BackgroundThe estimates of future course of spreading of the SARS-CoV-2 virus are frequently based on Markovian models in which the transitions between the compartments are exponentially distributed. Specifically, the basic reproduction number R0 is also determined from formulae where it is related to the parameters of such models. The observations show that the start of infectivity of an individual appears nearly at the same time as the onset of symptoms, while the distribution of the incubation period is not an exponential.\n\nMethodsWe propose a method for estimation of R0 for COVID-19 based on the empirical incubation period distribution and assumed very short infectivity period that lasts only few days around the onset of symptoms. It is tested on daily new cases in six major countries in Europe, in the first wave of epidemic in spring, 2020.\n\nResultsThe calculations show that even if the infectivity starts two days before the onset of symptoms and stops immediately when they appear, the value of R0 is larger than that from the classical, Markovian approach. For more realistic cases, when only individuals with mild symptoms spread the virus for few days after onset of symptoms, the respective values are even larger.\n\nConclusionsThe calculations of R0 and other characteristics of spreading of COVID-19 based on the classical, Markovian approaches should be taken very cautiously. Instead, non-Markovian models with general distribution functions of transition between compartments should be considered as more appropriate.\n\nKey messagesO_LIAlthough formulae for estimate of the basic reproduction number R0, by using general-form functions of infectivity are known since the earliest works in epidemiology, majority of studies are based on exponential distribution function.\nC_LIO_LIWe introduce a new methodology of calculating R0 with an infectivity function obtained by combining empirical incubation period distribution with infectivity window function that is localized around the onset of symptoms.\nC_LIO_LIEstimates of R0 for the first wave of COVID - 19 in the spring 2020, by the proposed methodology are larger than those from the classical SIR model.\nC_LIO_LIWhen possible, the estimates of R0 should be based on empirical distributions of the infectivity functions, while the values obtained with the conventional epidemic spreading models should be taken with caution.\nC_LI", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Lasko Basnarkov", + "author_inst": "SS Cyril and Methodius University in Skopje, Macedonia" + }, + { + "author_name": "Igor Tomovski", + "author_inst": "Macedonian Academy of Sciences and Arts" + }, + { + "author_name": "Florin Avram", + "author_inst": "Universite de Pau, France" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.04.21265910", "rel_title": "SARS-CoV-2 Aerosol Transmission Indoors: A Closer Look at Viral Load, Infectivity, the Effectiveness of Preventive Measures and a Simple Approach for Practical Recommendations", @@ -504257,49 +507327,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.03.21265791", - "rel_title": "Cohort study of Covid-19 vaccine effectiveness among healthcare workers in Finland, December 2020 - October 2021", - "rel_date": "2021-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.03.21265791", - "rel_abs": "Recently, Covid-19 vaccine effectiveness has decreased especially against mild disease due to emergence of the Delta variant and waning protection. In this register-based study among healthcare workers in Finland, the vaccine effectiveness of two-dose mRNA vaccine series against SARS-CoV-2 infection decreased from 82% (95% CI 79-85%) 14-90 days after vaccination to 53% (43-62%) after 6 months. Similar trend was observed for other series. Waning was not observed against Covid-19 hospitalization. These results facilitate decision-making of booster doses for healthcare workers.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Eero Poukka", - "author_inst": "Finnish institute for Health and Welfare" - }, - { - "author_name": "Ulrike Baum", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Arto A Palmu", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Toni O Lehtonen", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Heini Salo", - "author_inst": "Finnish Institute for Health and Welfare (THL)" - }, - { - "author_name": "Hanna Nohynek", - "author_inst": "Finnish Institute for Health and Welfare" - }, - { - "author_name": "Tuija Leino", - "author_inst": "Finnish Institute for Health and Welfare" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.04.21265886", "rel_title": "The United States COVID-19 Forecast Hub dataset", @@ -505846,6 +508873,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.02.466951", + "rel_title": "Drug targeting Nsp1-ribosomal complex shows antiviral activity against SARS-CoV-2", + "rel_date": "2021-11-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.02.466951", + "rel_abs": "The SARS-Cov-2 non-structural protein 1 (Nsp1) contains an N-terminal domain and C-terminal helices connected by a short linker region. The C-terminal helices of Nsp1 (Nsp1-C-ter) from SARS-Cov-2 bind in the mRNA entry channel of the 40S ribosomal subunit and block the entry of mRNAs thereby shutting down host protein synthesis. Nsp1 suppresses the host immune function and is vital for viral replication. Hence, Nsp1 appears to be an attractive target for therapeutics. In this study, we have in silico screened Food and Drug Administration (FDA)-approved drugs against Nsp1-C-ter and find that montelukast sodium hydrate binds to Nsp1-C-ter with a binding affinity (KD) of 10.8{+/-}0.2 M in vitro and forms a stable complex with it in simulation runs with a binding energy of -76.71{+/-}8.95 kJ/mol. The drug also rescues the inhibitory effect of Nsp1 in host protein synthesis as demonstrated by the expression of firefly luciferase reporter gene in cells. Importantly, montelukast sodium hydrate demonstrates antiviral activity against SARS-CoV-2 with reduced viral replication in HEK cells expressing ACE2 and Vero-E6 cells. We therefore propose montelukast sodium hydrate may help in combatting SARS-CoV-2 infection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tanweer Hussain", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Mohammad Afsar", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Rohan Narayan", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Md Noor Akhtar", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Huma Rahil", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Sandeep Eswarappa", + "author_inst": "Indian Institute of Science Bangalore" + }, + { + "author_name": "Shashank Tripathi", + "author_inst": "Indian Institute of Science" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.11.03.21265876", "rel_title": "Investigating the relationship between interventions, contact patterns, and SARS-CoV-2 transmissibility", @@ -506019,77 +509089,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.29.466402", - "rel_title": "Inhibition of SAR S-CoV-2 infection and replication by lactoferrin, MUC1 and \u03b1-lactalbumin identified in human breastmilk", - "rel_date": "2021-11-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.29.466402", - "rel_abs": "The global pandemic of COVID-19 caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection confers great threat to the public health. Human breastmilk is an extremely complex with nutritional composition to nourish infants and protect them from different kinds of infection diseases and also SARS-CoV-2 infection. Previous studies have found that breastmilk exhibited potent antiviral activity against SARS-CoV-2 infection. However, it is still unknown which component(s) in the breastmilk is responsible for its antiviral activity. Here, we identified Lactoferrin (LF), MUC1 and -Lactalbumin (-LA) from human breastmilk by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and in vitro confirmation that inhibited SARS-CoV-2 infection and analyzed their antiviral activity using the SARS-CoV-2 pseudovirus system and transcription and replication-competent SARS-CoV-2 virus-like-particles (trVLP) in the Huh7.5, Vero E6 and Caco-2-N cell lines. Additionally, we found that LF and MUC1 could inhibit viral attachment, entry and post-entry replication, while -LA just inhibit viral attachment and entry. Importantly, LF, MUC1 and -LA possess potent antiviral activities towards not only wild-type but also variants such as B.1.1.7 (alpha), B.1.351 (beta), P.1 (gamma) and B.1.617.1 (kappa). Moreover, LF from other species (e.g., bovine and goat) is still capable of blocking viral attachment to cellular heparan sulfate. Taken together, our study provided the first line of evidence that human breastmilk components (LF, MUC1 and -LA) are promising therapeutic candidates warranting further development or treatingVID-19 given their exceedingly safety levels.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Kuanhui Xiang", - "author_inst": "Peking University Health Science Center" - }, - { - "author_name": "Xinyuan Lai", - "author_inst": "Peking University" - }, - { - "author_name": "Yanying Yu", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Wei Xian", - "author_inst": "Peking University" - }, - { - "author_name": "Fei Ye", - "author_inst": "China CDC" - }, - { - "author_name": "Xiaohui Ju", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Yuqian Luo", - "author_inst": "Nanjing University" - }, - { - "author_name": "Huijun Dong", - "author_inst": "Peking University" - }, - { - "author_name": "Yihua Zhou", - "author_inst": "Najing University" - }, - { - "author_name": "Wenjie Tan", - "author_inst": "China CDC" - }, - { - "author_name": "Hui Zhuang", - "author_inst": "Peking University" - }, - { - "author_name": "Tong Li", - "author_inst": "Peking University" - }, - { - "author_name": "Xiaoyun Liu", - "author_inst": "Peking University Health Science Center" - }, - { - "author_name": "Qiang Ding", - "author_inst": "Tsinghua University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.11.01.21265764", "rel_title": "Equipment-free detection of SARS-CoV-2 and Variants of Concern using Cas13", @@ -508224,6 +511223,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.01.21265653", + "rel_title": "Modelling COVID-19 Pandemic Dynamics Using Transparent, Interpretable, Parsimonious and Simulatable (TIPS) Machine Learning Models: A Case Study from Systems Thinking and System Identification Perspectives", + "rel_date": "2021-11-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.01.21265653", + "rel_abs": "Since the outbreak of COVID-19, an astronomical number of publications on the pandemic dynamics appeared in the literature, of which many use the susceptible infected removed (SIR) and susceptible exposed infected removed (SEIR) models, or their variants, to simulate and study the spread of the coronavirus. SIR and SEIR are continuous-time models which are a class of initial value problems (IVPs) of ordinary differential equations (ODEs). Discrete-time models such as regression and machine learning have also been applied to analyze COVID-19 pandemic data (e.g. predicting infection cases), but most of these methods use simplified models involving a small number of input variables pre-selected based on a priori knowledge, or use very complicated models (e.g. deep learning), purely focusing on certain prediction purposes and paying little attention to the model interpretability. There have been relatively fewer studies focusing on the investigations of the inherent time-lagged or time-delayed relationships e.g. between the reproduction number (R number), infection cases, and deaths, analyzing the pandemic spread from a systems thinking and dynamic perspective. The present study, for the first time, proposes using systems engineering and system identification approach to build transparent, interpretable, parsimonious and simulatable (TIPS) dynamic machine learning models, establishing links between the R number, the infection cases and deaths caused by COVID-19. The TIPS models are developed based on the well-known NARMAX (Nonlinear AutoRegressive Moving Average with eXogenous inputs) model, which can help better understand the COVID-19 pandemic dynamics. A case study on the UK COVID-19 data is carried out, and new findings are detailed. The proposed method and the associated new findings are useful for better understanding the spread dynamics of the COVID-19 pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hua-Liang Wei", + "author_inst": "The University Of Sheffield" + }, + { + "author_name": "Stephen A Billings", + "author_inst": "The University of Sheffield" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.01.21265729", "rel_title": "Quantifying the effects of non-pharmaceutical and pharmaceutical interventions against COVID-19 epidemic in the Republic of Korea: Mathematical model-based approach considering age groups and the Delta variant", @@ -508353,153 +511375,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.10.31.21265703", - "rel_title": "Efficacy and Safety of SOBERANA 02, a COVID-19 conjugate vaccine in heterologous three doses combination", - "rel_date": "2021-11-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.31.21265703", - "rel_abs": "BackgroundSOBERANA-02 is a COVID-19 conjugate vaccine (recombinant RBD conjugated to tetanus toxoid). Phases 1/2 clinical trials demonstrated high immunogenicity, promoting neutralizing IgG and specific T-cell response. A third heterologous dose of SOBERANA-Plus (RBD-dimer) further increased neutralizing antibodies.\n\nMethodsFrom March 8th to September 30th, 2021 we conducted in Havana, Cuba a multicentre randomized, double-blind, placebo-controlled, phase-3 trial evaluating two doses of SOBERANA-02 and a heterologous scheme with one dose SOBERANA-Plus added to it. Participants 19-80 years were randomly assigned to receiving 28 days apart either the two or three dose scheme or placebo. The main endpoint was vaccine efficacy in preventing the occurrence of RT-PCR confirmed symptomatic COVID-19 occurring at least 14 days after the second or third dose in the per-protocol population. We also assessed efficacy against severe disease and, in all participants receiving at least one vaccine/placebo dose, safety for 28 days after each dose.\n\nFindingWe included 44{middle dot}031 participants in a context of Beta VOC predominance, with this variant being gradually replaced by Delta near the trial end. Vaccine efficacy in the heterologous combination was 92{middle dot}0% (95%CI 80{middle dot}4-96{middle dot}7) against symptomatic and 100% against severe COVID-19. Two doses of SOBERANA-02 was 69{middle dot}7% (95%CI 56{middle dot}5-78{middle dot}9) and 74{middle dot}9% (95%CI 33{middle dot}7-90{middle dot}5) efficacious to protect against symptomatic and severe COVID-19, respectively. The occurrence of serious and severe AEs was very rare and equally distributed between placebo and vaccine groups. Solicited AEs were slightly more frequent in the vaccine group but predominantly local and mostly mild and transient.\n\nInterpretationOur results indicate that the straightforward to manufacture SOBERANA vaccines are efficacious in a context of Beta and Delta VOC dominance and that they constitute an attractive, feasible option for low- and middle-income countries, where besides financial constraints ease of vaccine storage and distribution is of concern.\n\nFundingThis study received funds from Finlay Vaccine Institute and National Fund for Science and Technology (FONCI-CITMA-Cuba, contract 2020-20). of Ministry of Science, Technology and the Environment (Contract Project-2020-20) in Cuba.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Maria Eugenia Toledo-Romani", - "author_inst": "Pedro Kouri Tropical Medicine Institute, Havana" - }, - { - "author_name": "Mayra Garcia-Carmenate", - "author_inst": "Havana Hygiene and Epidemiological Center" - }, - { - "author_name": "Carmen Valenzuela Silva", - "author_inst": "Institute of Cybernetics, Mathematics and Physics, Havana" - }, - { - "author_name": "Waldemar Baldoquin-Rodriguez", - "author_inst": "Pedro Kouri Tropical Medicine Institute" - }, - { - "author_name": "Marisel Martinez Perez", - "author_inst": "Finlay Vaccine Institute" - }, - { - "author_name": "Meiby C Rodriguez Gonzalez", - "author_inst": "Finlay Vaccine Institute, Havana,Cuba" - }, - { - "author_name": "Beatriz Paredes Moreno", - "author_inst": "Finlay Vaccine Institute, Havana, Cuba" - }, - { - "author_name": "Ivis Mendoza Hernandez", - "author_inst": "Center for Coordination of Clinical Trial, Havana" - }, - { - "author_name": "Raul Gonzalez-Mujica Romero", - "author_inst": "Finlay Vaccine Institute, Havana, Cuba" - }, - { - "author_name": "Oscar Samon Tabio", - "author_inst": "Technological Havana University Jose Antonio Echevarria" - }, - { - "author_name": "Pablo Velazco Villares", - "author_inst": "UCT Geocuba Research and consultation, Havana" - }, - { - "author_name": "Juan Pablo Bacallao Castillo", - "author_inst": "UCT Geocuba Research and consultation, Havana" - }, - { - "author_name": "Ernesto Licea Martin", - "author_inst": "Finlay Vaccine Institute, Havana, Cuba" - }, - { - "author_name": "Misladys Rodriguez Ortega,", - "author_inst": "Pedro Kouri Tropical Medicine Institute, Havana" - }, - { - "author_name": "Nuris Liem Herrera Marrero", - "author_inst": "Pedro Kouri Tropical Medicine Institute, Havana" - }, - { - "author_name": "Esperanza Caballero Gonzalez", - "author_inst": "Finlay Vaccine Institute, Havana,Cuba" - }, - { - "author_name": "Liudmila Ibelin Egues Torres", - "author_inst": "Havana Hygiene and Epidemiological Center" - }, - { - "author_name": "Reinaldo Duarte Gonzalez", - "author_inst": "Havana Hygiene and Epidemiological Center" - }, - { - "author_name": "Serguey Garcia Blanco", - "author_inst": "Havana Hygiene and Epidemiological Center" - }, - { - "author_name": "Suzette Perez Cabrera", - "author_inst": "Havana Hygiene and Epidemiological Center" - }, - { - "author_name": "Santos Huete Ferreira", - "author_inst": "Havana Hygiene and Epidemiological Center" - }, - { - "author_name": "Kirenia Idalmis Idalmis Cisnero", - "author_inst": "Havana Hygiene and Epidemiological Center" - }, - { - "author_name": "Omaida Fonte Galindo", - "author_inst": "Havana Hygiene and Epidemiological Center" - }, - { - "author_name": "Dania Melia Perez", - "author_inst": "Havana Hygiene and Epidemiological Center" - }, - { - "author_name": "Ivonne Rojas Remedios", - "author_inst": "Havana Hygiene and Epidemiological Center" - }, - { - "author_name": "Delaram Doroud", - "author_inst": "Pasteur Institute of Iran, Teheran, Iran" - }, - { - "author_name": "Alireza Biglari", - "author_inst": "Pasteur Institute of Iran, Teheran, Iran" - }, - { - "author_name": "Mohammad Mehdi Gouya", - "author_inst": "Center for Disease Control, Ministery of Health, Teheran, Iran" - }, - { - "author_name": "Sonsire Fernandez Castillo", - "author_inst": "Finlay Vaccine Institute, Havana, Cuba" - }, - { - "author_name": "Yanet Climent Ruiz", - "author_inst": "Finlay Vaccine Institute, Havana, Cuba" - }, - { - "author_name": "Yury Valdes Balbin", - "author_inst": "Finlay Vaccine Institute, Havana, Cuba" - }, - { - "author_name": "Dagmar Garcia Rivera", - "author_inst": "Finlay Vaccine Institute, Havana, Cuba" - }, - { - "author_name": "vicente Verez-Bencomo", - "author_inst": "Finlay Vaccine Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.29.466470", "rel_title": "Allosteric modulation of the SARS-CoV-2 spike conformation", @@ -509898,6 +512773,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.10.28.21265499", + "rel_title": "Time of day of vaccination affects SARS-CoV-2 antibody responses in an observational study of healthcare workers", + "rel_date": "2021-10-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.28.21265499", + "rel_abs": "The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global crisis with unprecedented challenges for public health. Vaccinations against SARS-CoV-2 have slowed the incidence of new infections and reduced disease severity. As the time-of-day of vaccination has been reported to influence host immune responses to multiple pathogens, we quantified the influence of SARS-CoV-2 vaccination time, vaccine type, age, sex, and days post-vaccination on anti-Spike antibody responses in healthcare workers. The magnitude of the anti-Spike antibody response associated with the time-of-day of vaccination, vaccine type, participant age, sex, and days post vaccination. These results may be relevant for optimizing SARS-CoV-2 vaccine efficacy.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Wei Wang", + "author_inst": "Division of Sleep and Circadian Disorders, Brigham and Womens Hospital; Division of Sleep Medicine, Harvard Medical School, US." + }, + { + "author_name": "Peter Balfe", + "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "David W Eyre", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sheila F Lumley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Denise O'Donnell", + "author_inst": "Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK" + }, + { + "author_name": "Fiona Warren", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK" + }, + { + "author_name": "Derrick W Crook", + "author_inst": "NIHR Oxford Biomedical Research Centre" + }, + { + "author_name": "Katie Jeffery", + "author_inst": "Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, and\tRadcliffe Department of Medic" + }, + { + "author_name": "Philippa C Matthews", + "author_inst": "Nuffield Department of Medicine, and 4.\tDepartment of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hos" + }, + { + "author_name": "Elizabeth B Klerman", + "author_inst": "Massachusetts General Hospital/Harvard Medical School" + }, + { + "author_name": "Jane McKeating", + "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.28.21265544", "rel_title": "In vitro characterisation and clinical evaluation of the diagnostic accuracy of a new antigen test for SARS-CoV-2 detection.", @@ -510067,53 +513001,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2021.10.28.21265604", - "rel_title": "Transferability of Psychological Interventions from Disaster-Exposed Employees to Healthcare Workers Working during the COVID-19 Pandemic", - "rel_date": "2021-10-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.28.21265604", - "rel_abs": "BackgroundThe COVID-19 Pandemic had a significant negative impact on the mental health of healthcare workers. Evidence-based interventions that could be used to mitigate this impact are lacking in the literature. This review aims to evaluate psychological interventions used for employees following previous disasters and assess the transferability of these interventions to a healthcare setting during the COVID-19 pandemic.\n\nMethodsIntervention information from a previously published systematic review of the literature published up to 2015 was extracted, and an additional search of studies published from 2015-2020 was conducted. Studies were assessed for transferability using a checklist derived from the PIET-T process model.\n\nResultsInterventions from eighteen studies were assessed for transferability (including three studies identified in an updated literature search). Interventions established as most transferable included resilience training, meditation/mindfulness interventions, and cognitive behavioural therapy. Psychological debriefing was transferable but as it is contrary to current recommendations is not deemed appropriate for adoption.\n\nImplicationsSeveral existing interventions have the potential to be utilised within the COVID-19 context/pandemic. More research needs to be undertaken in this area to assess these interventions upon transfer.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sean Treacy", - "author_inst": "Department of Child and Adolescent Psychiatry, School of Medicine, University College Dublin, Ireland" - }, - { - "author_name": "Shane O Donnell", - "author_inst": "Department of Child and Adolescent Psychiatry, School of Medicine, University College Dublin, Ireland" - }, - { - "author_name": "Blanaid Gavin", - "author_inst": "Department of Child and Adolescent Psychiatry, School of Medicine, University College Dublin, Ireland" - }, - { - "author_name": "Tamara Schloemer", - "author_inst": "Maastricht University, The Netherlands;" - }, - { - "author_name": "Etain Quigley", - "author_inst": "Department of Law, Maynooth University, Ireland" - }, - { - "author_name": "Dimitrios Adamis", - "author_inst": "Sligo Mental Health Services, Health Service Executive, Ireland" - }, - { - "author_name": "Fiona Mc Nicholas", - "author_inst": "Department of Child and Adolescent Psychiatry, School of Medicine, University College Dublin, Ireland" - }, - { - "author_name": "John Hayden", - "author_inst": "RCSI University of Medicine and Health Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.10.28.21265596", "rel_title": "A Novel Indicator for COVID-19 Pandemic Assessment and Comparison", @@ -511764,6 +514651,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.27.21265574", + "rel_title": "Boosting of Cross-Reactive Antibodies to Endemic Coronaviruses by SARS-CoV-2 Infection but not Vaccination with Stabilized Spike", + "rel_date": "2021-10-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.27.21265574", + "rel_abs": "Pre-existing antibodies to endemic coronaviruses (CoV) that cross-react with SARS-CoV-2 have the potential to influence the antibody response to COVID-19 vaccination and infection for better or worse. In this observational study of mucosal and systemic humoral immunity in acutely infected, convalescent, and vaccinated subjects, we tested for cross reactivity against endemic CoV spike (S) protein at subdomain resolution. Elevated responses, particularly to the {beta}-CoV OC43, were observed in all natural infection cohorts tested and were correlated with the response to SARS-CoV-2. The kinetics of this response and isotypes involved suggest that infection boosts preexisting antibody lineages raised against prior endemic CoV exposure that cross react. While further research is needed to discern whether this recalled response is desirable or detrimental, the boosted antibodies principally targeted the better conserved S2 subdomain of the viral spike and were not associated with neutralization activity. In contrast, vaccination with a stabilized spike mRNA vaccine did not robustly boost cross-reactive antibodies, suggesting differing antigenicity and immunogenicity. In sum, this study provides evidence that antibodies targeting endemic CoV are robustly boosted in response to SARS-CoV-2 infection but not to vaccination with stabilized S, and that depending on conformation or other factors, the S2 subdomain of the spike protein triggers a rapidly recalled, IgG-dominated response that lacks neutralization activity.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC=\"FIGDIR/small/21265574v1_figA1.gif\" ALT=\"Figure 1\">\nView larger version (22K):\norg.highwire.dtl.DTLVardef@168d38aorg.highwire.dtl.DTLVardef@1183afcorg.highwire.dtl.DTLVardef@1c88b77org.highwire.dtl.DTLVardef@13c6e0a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO Antibody responses to SARS-CoV-2 and endemic CoV spike proteins were measured in diverse cohorts. While antibodies to SARS-CoV-2 were induced across all isotypes, only IgA and IgG responses to endemic CoV were robustly boosted, and only among naturally-infected but not vaccinated individuals. These recalled, cross-reactive responses to endemic CoV primarily recognized the better conserved S2 domain and were non-neutralizing. While other antiviral activities of broadly cross-reactive S2-specifc antibodies are not known, the differing antigenicity of natural infection and vaccination with stabilized pre-fusion spike has potential implications for the breadth and level of protection afforded by each.\n\nC_FIG", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Andrew R Crowley", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Harini Natarajan", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Andrew P Hederman", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Carly A Bobak", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Joshua A Weiner", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Wendy F. Wieland-Alter", + "author_inst": "Dartmouth Hitchcock Medical Center" + }, + { + "author_name": "Jiwon Lee", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Evan M Bloch", + "author_inst": "Johns Hopkins Medicine" + }, + { + "author_name": "Aaron AR Tobian", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Andrew Redd", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Joel N. Blankson", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Dana Wolf", + "author_inst": "Hadassah University Medical Center" + }, + { + "author_name": "Tessa Goetghebuer", + "author_inst": "CHU St. Pierre" + }, + { + "author_name": "Arnaud Marchant", + "author_inst": "Universite libre de Bruxelles" + }, + { + "author_name": "Ruth I Connor", + "author_inst": "Dartmouth Hitchcock Medical Center" + }, + { + "author_name": "Peter F Wright", + "author_inst": "Dartmouth Hitchcock Medical Center" + }, + { + "author_name": "Margaret E Ackerman", + "author_inst": "Dartmouth College" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.27.21265591", "rel_title": "How many lives do COVID vaccines save? Evidence from Israel.", @@ -511973,65 +514943,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.10.26.21265531", - "rel_title": "Boosting of the SARS-CoV-2-specific immune response after vaccination with single-dose Sputnik Light vaccine", - "rel_date": "2021-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.26.21265531", - "rel_abs": "Despite the measures taken worldwide, COVID-19 pandemic still progresses. While efficient antiviral drugs are not yet widely available, vaccination is the best option to control the infection rate. Although this option is obvious in case of COVID-19-naive individuals, it is still unclear when individuals who have recovered from a previous SARS-CoV-2 infection should be vaccinated and whether the vaccination raises immune responses against the coronavirus and its novel variants. Here we measured the dynamics of the antibody and T-cell responses, as well as virus neutralizing activity (VNA) in serum against two SARS-CoV-2 variants, B.1.1.1 and B.1.617.2, among 84 individuals with different COVID-19 status who were vaccinated with Sputnik Light vaccine. We showed that vaccination of individuals previously exposed to the virus considerably boosts the existing immune response. In these individuals, RBD-specific IgG titers and VNA in serum were already elevated on the 7th day after vaccination, while COVID-19-naive individuals developed the antibody response and VNA mainly 21 days post-vaccination. Additionally, we found a strong correlation between RBD-specific IgG titers and VNA in serum, and according to these data vaccination may be recommended if the RBD-specific IgG titers drop to 142.7 BAU/mL or below. In summary, the results of the study demonstrate that vaccination is beneficial both for COVID-19-naive and recovered individuals, especially since it raises serum VNA against the B.1.617.2 variant - one of four the SARS-CoV-2 variants of concern.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Alexey Komissarov", - "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia" - }, - { - "author_name": "Inna Dolzhikova", - "author_inst": "Federal State Budget Institution \"National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya\" of the Ministry of H" - }, - { - "author_name": "Grigory Efimov", - "author_inst": "National Research Center for Hematology, 125167, 4a Novozykovskii proezd, Moscow, Russia" - }, - { - "author_name": "Denis Logunov", - "author_inst": "Federal State Budget Institution \"National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya\" of the Ministry of H" - }, - { - "author_name": "Olga Mityaeva", - "author_inst": "Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia" - }, - { - "author_name": "Ivan Molodtsov", - "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia" - }, - { - "author_name": "Nelli Naigovzina", - "author_inst": "A.I. Yevdokimov Moscow State University of Medicine and Dentistry, 127473, 20 Delegatskaya str., Moscow, Russia" - }, - { - "author_name": "Iuliia Peshkova", - "author_inst": "National Research Center for Hematology, 125167, 4a Novozykovskii proezd, Moscow, Russia" - }, - { - "author_name": "Dmitry Shcheblyakov", - "author_inst": "Federal State Budget Institution \"National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya\" of the Ministry of H" - }, - { - "author_name": "Pavel Volchkov", - "author_inst": "Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia" - }, - { - "author_name": "Elena Vasilieva", - "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.26.21265488", "rel_title": "Mobility network reveals the impact of geographic vaccination heterogeneity on COVID-19", @@ -513542,6 +516453,97 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.10.25.465714", + "rel_title": "Nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants", + "rel_date": "2021-10-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.25.465714", + "rel_abs": "We are in the midst of the historic coronavirus infectious disease 2019 (COVID-19) pandemic caused by severe respiratory syndrome coronavirus 2 (SARS-CoV-2). Although countless efforts to control the pandemic have been attempted--most successfully, vaccination1-3--imbalances in accessibility to vaccines, medicines, and diagnostics among countries, regions, and populations have been problematic. Camelid variable regions of heavy chain-only antibodies (VHHs or nanobodies)4 have unique modalities: they are smaller, more stable, easier to customize, and, importantly, less expensive to produce than conventional antibodies5, 6. We present the sequences of nine alpaca nanobodies that detect the spike proteins of four SARS-CoV-2 variants of concern (VOCs)--namely, the alpha, beta, gamma, and delta variants. We show that they can quantify or detect spike variants via ELISA and lateral flow, kinetic, flow cytometric, microscopy, and Western blotting assays7. The panel of nanobodies broadly neutralized viral infection by pseudotyped SARS-CoV-2 VOCs. Structural analyses showed that a P86 clone targeted epitopes that were conserved yet unclassified on the receptor-binding domain (RBD) and located inside the N-terminal domain (NTD). Human antibodies have hardly accessed both regions; consequently, the clone buries hidden crevasses of SARS-CoV-2 spike proteins undetected by conventional antibodies and maintains activity against spike proteins carrying escape mutations.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Ryota Maeda", + "author_inst": "Kyoto University & COGNANO Inc." + }, + { + "author_name": "Junso Fujita", + "author_inst": "Osaka University" + }, + { + "author_name": "Yoshinobu Konishi", + "author_inst": "Kyoto University" + }, + { + "author_name": "Yasuhiro Kazuma", + "author_inst": "Kyoto University" + }, + { + "author_name": "Hiroyuki Yamazaki", + "author_inst": "COGNANO Inc." + }, + { + "author_name": "Itsuki Anzai", + "author_inst": "Osaka University" + }, + { + "author_name": "Keishi Yamaguchi", + "author_inst": "Osaka University" + }, + { + "author_name": "Kazuki Kasai", + "author_inst": "Kyoto University & COGNANO Inc." + }, + { + "author_name": "Kayoko Nagata", + "author_inst": "Kyoto University" + }, + { + "author_name": "Yutaro Yamaoka", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Kei Miyakawa", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Akihide Ryo", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Kotaro Shirakawa", + "author_inst": "Kyoto University" + }, + { + "author_name": "Fumiaki Makino", + "author_inst": "Osaka University & JEOL Ltd." + }, + { + "author_name": "Yoshiharu Matsuura", + "author_inst": "Osaka University" + }, + { + "author_name": "Tsuyoshi Inoue", + "author_inst": "Osaka University" + }, + { + "author_name": "Akihiro Imura", + "author_inst": "COGNANO Inc." + }, + { + "author_name": "Keiichi Namba", + "author_inst": "Osaka University & JEOL YOKOGUSHI Research Alliance Laboratories & RIKEN Center for Biosystems Dynamics Research and SPring-8 Center" + }, + { + "author_name": "Akifumi Takaori-Kondo", + "author_inst": "Kyoto University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.10.22.21265188", "rel_title": "Response to the coronavirus disease 2019 (COVID-19) pandemic at private retail pharmacies in Kenya: a mixed methods study", @@ -513719,77 +516721,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.22.21265255", - "rel_title": "Clinical performance characteristics of the Swift Normalase Amplicon Panel for sensitive recovery of SARS-CoV-2 genomes", - "rel_date": "2021-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.22.21265255", - "rel_abs": "Amplicon-based sequencing methods have been central in characterizing the diversity, transmission and evolution of SARS-CoV-2, but need to be rigorously assessed for clinical utility. Here, we validated the Swift Biosciences SARS-CoV-2 Swift Normalase Amplicon Panels using remnant clinical specimens. High quality genomes meeting our established library and sequence quality criteria were recovered from positive specimens with a 95% limit of detection of [≥] 40.08 SARS-CoV-2 copies/PCR reaction. Breadth of genome recovery was evaluated across a range of Ct values (11.3 - 36.7, median 21.6). Out of 428 positive samples, 406 (94.9%) generated genomes with < 10% Ns, with a mean genome coverage of 13,545X {+/-} SD 8,382X. No genomes were recovered from PCR-negative specimens (n = 30), or from specimens positive for non-SARS-CoV-2 respiratory viruses (n = 20). Compared to whole-genome shotgun metagenomic sequencing (n = 14) or Sanger sequencing for the spike gene (n = 11), pairwise identity between consensus sequences was 100% in all cases, with highly concordant allele frequencies (R2 = 0.99) between Swift and shotgun libraries. When samples from different clades were mixed at varying ratios, expected variants were detected even in 1:99 mixtures. When deployed as a clinical test, 268 tests were performed in the first 23 weeks with a median turnaround time of 11 days, ordered primarily for outbreak investigations and infection control.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Lasata Shrestha", - "author_inst": "University of Washington" - }, - { - "author_name": "Michelle J. Lin", - "author_inst": "University of Washington" - }, - { - "author_name": "Hong Xie", - "author_inst": "University of Washington" - }, - { - "author_name": "Margaret G. Mills", - "author_inst": "University of Washington" - }, - { - "author_name": "Shah A.M. Bakhash", - "author_inst": "University of Washington" - }, - { - "author_name": "Vinod P. Gaur", - "author_inst": "University of Washington" - }, - { - "author_name": "Robert J. Livingston", - "author_inst": "University of Washington" - }, - { - "author_name": "Jared Castor", - "author_inst": "University of Washington" - }, - { - "author_name": "Emily A. Bruce", - "author_inst": "University of Vermont" - }, - { - "author_name": "Jason W. Botten", - "author_inst": "University of Vermont" - }, - { - "author_name": "Meei-Li Huang", - "author_inst": "University of Washington" - }, - { - "author_name": "Keith R. Jerome", - "author_inst": "University of Washington" - }, - { - "author_name": "Alexander L. Greninger", - "author_inst": "University of Washington" - }, - { - "author_name": "Pavitra Roychoudhury", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.24.21265170", "rel_title": "Optimizing Social Distancing Policies: A Dynamic Programming Approach for Coupled High and Low Risk Populations", @@ -515468,6 +518399,189 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.10.18.21264530", + "rel_title": "Integrated Genomic Surveillance reveals extensive onward transmission of travel-imported SARS-CoV-2 infections in the community", + "rel_date": "2021-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.18.21264530", + "rel_abs": "Integration of genomic surveillance with contact tracing provides a powerful tool for the reconstruction of person-to-person pathogen transmission chains. We report two large clusters of SARS-CoV-2 cases (\"Delta\" clade, 110 cases combined) detected in July 2021 by Integrated Genomic Surveillance in Dusseldorf. Structured interviews and deep contact tracing demonstrated an association to a single SARS-CoV-2 infected return traveller (Cluster 1) and to return travel from Catalonia and other European countries (Cluster 2), highlighting the importance of containing travel-imported SARS-CoV-2 infections.", + "rel_num_authors": 42, + "rel_authors": [ + { + "author_name": "Torsten Houwaart", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Samir Belhaj", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Emran Tawalbeh", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Dirk Nagels", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Patrick Finzer", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany; Zotz | Klimas, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Lisa Stiller", + "author_inst": "Medizinische Laboratorien D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Jacqueline Blum", + "author_inst": "Medizinische Laboratorien D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Christian Lange", + "author_inst": "Medizinische Laboratorien D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Yara Fr\u00f6hlich", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Assia Benmoumene", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Dounia Asskali", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Hussein Haidar", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Janina von Dahlen", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Carla Adelmann", + "author_inst": "Solingen Health Authority (Gesundheitsamt Solingen)" + }, + { + "author_name": "Britta Schroer", + "author_inst": "Solingen Health Authority (Gesundheitsamt Solingen)" + }, + { + "author_name": "Ute Osmers", + "author_inst": "MVZ SYNLAB Leverkusen GmbH" + }, + { + "author_name": "Christiane Grice", + "author_inst": "MVZ SYNLAB Leverkusen GmbH" + }, + { + "author_name": "Phillipp P. Kirfel", + "author_inst": "MVZ SYNLAB Leverkusen GmbH" + }, + { + "author_name": "Hassan Jomaa", + "author_inst": "MVZ SYNLAB Leverkusen GmbH" + }, + { + "author_name": "Moritz Pigulla", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Pascal Kreuzer", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Alona Tyshaieva", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Jonas Weber", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Daniel Strelow", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Jessica Nicolai", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Tobias Wienemann", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Malte Kohns Vasconcelos", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Lisanna H\u00fclse", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Katrin Hoffmann", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Nadine L\u00fcbke", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Sandra Hauka", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Marcel Andree", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Claus J\u00fcrgen Scholz", + "author_inst": "Labor Dr. Wisplinghoff, Cologne, Germany" + }, + { + "author_name": "Nathalie Jazmati", + "author_inst": "Labor Dr. Wisplinghoff, Cologne, Germany" + }, + { + "author_name": "Klaus G\u00f6bels", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Rainer Zotz", + "author_inst": "Zotz | Klimas, D\u00fcsseldorf, Germany; Labor Dr. Wisplinghoff, Cologne, Germany" + }, + { + "author_name": "Klaus Pfeffer", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "J\u00f6rg Timm", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Lutz Ehlkes", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Andreas Walker", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Alexander T. Dilthey", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "- German COVID-19 OMICS Initiative (DeCOI)", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.24.465626", "rel_title": "SARS-CoV-2 infects human adipose tissue and elicits an inflammatory response consistent with severe COVID-19", @@ -515653,61 +518767,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2021.10.21.21265318", - "rel_title": "The impact of vaccinating adolescents and children on COVID-19 disease outcomes", - "rel_date": "2021-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.21.21265318", - "rel_abs": "IntroductionDespite the high COVID-19 vaccination coverage among adults, there is concern over a peak in SARS-CoV-2 infections in the coming months. To help ensure that healthcare systems are not overwhelmed in the event of a new wave of SARS-CoV-2 infections, many countries have extended vaccination to adolescents (those aged 12-17 years) and may consider further extending to children aged 5-11 years. However, there is considerable debate about whether or not to vaccinate healthy adolescents and children against SARS-CoV-2 because, while vaccination of children and adolescents may limit transmission from these groups to other, more vulnerable groups, adolescents and children themselves have limited risk of severe disease if infected and may experience adverse events from vaccination. To quantify the benefits of extending COVID-19 vaccination beyond adults we compare daily cases, hospital admissions, and intensive care (IC) admissions for vaccination in adults only, those 12 years and above, and those 5 years and above.\n\nMethods and FindingsWe developed a deterministic, age-structured susceptible-exposed-infectious-recovered (SEIR) model to simulate disease outcomes (e.g., cases, hospital admissions, IC admissions) under different vaccination scenarios. The model is partitioned into 10-year age bands (0-9, 10-19, ..., 70-79, 80+) and accounts for differences in susceptibility and infectiousness by age group, seasonality in transmission rate, modes of vaccine protection (e.g., infection, transmission), and vaccine characteristics (e.g., vaccine effectiveness). Model parameters are estimated by fitting the model piecewise to daily cases from the Dutch notification database Osiris from 01 January 2020 to 22 June 2021. Forward simulations are performed from 22 June 2021 to 31 March 2022. We performed sensitivity analyses in which vaccine-induced immunity waned.\n\nWe found that upon relaxation of all non-pharmaceutical control measures a large wave occurred regardless of vaccination strategy. We found overall reductions of 5.7% (4.4%, 6.9%) of cases, 2.0% (0.7%, 3.2%) of hospital admissions, and 1.7% (0.6%, 2.8%) of IC admissions when those 12 years and above were vaccinated compared to vaccinating only adults. When those 5 years and above were vaccinated we observed reductions of 8.7% (7.5%, 9.9%) of cases, 3.2% (2.0%, 4.5%) of hospital admissions, and 2.4% (1.2%, 3.5%) of IC admissions compared to vaccination in adults only. Benefits of extending vaccination were larger within the age groups included in the vaccination program extension than in other age groups. The benefits of vaccinating adolescents and children were smaller if vaccine protection against infection, hospitalization, and transmission (once infected) wanes.\n\nDiscussionOur results highlight the benefits of extending COVID-19 vaccination programs beyond adults to reduce infections and severe outcomes in adolescents and children and in the wider population. A reduction of infections in school-aged children/adolescents may have the added benefit of reducing the need for school closures during a new wave. Additional control measures may be required in future to prevent a large wave despite vaccination program extensions. While the results presented here are based on population characteristics and the COVID-19 vaccination program in The Netherlands, they may provide valuable insights for other countries who are considering COVID-19 vaccination program extensions.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Kylie E. C. Ainslie", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Jantien A. Backer", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Pieter de Boer", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Albert Jan van Hoek", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Don Klinkenberg", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Hester Korthals Altes", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Ka Yin Leung", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Hester de Melker", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Fuminari Miura", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Jacco Wallinga", - "author_inst": "National Institute for Public Health and the Environment" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.21.21265289", "rel_title": "Geographic Disparities and Predictors of COVID-19 Hospitalization Risk in the St. Louis Area, Missouri (USA).", @@ -517446,6 +520505,145 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.10.22.465476", + "rel_title": "The humanized nanobody RBD-1-2G tolerates the spike N501Y mutation to neutralize SARS-CoV-2", + "rel_date": "2021-10-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.22.465476", + "rel_abs": "Neutralizing antibodies targeting the SARS-CoV-2 spike protein have shown a great preventative/therapeutic potential. Here, we report a rapid and efficient strategy for the development and design of SARS-CoV-2 neutralizing humanized nanobody constructs with sub-nanomolar affinities and nanomolar potencies. CryoEM-based structural analysis of the nanobodies in complex with spike revealed two distinct binding modes. The most potent nanobody, RBD-1-2G(NCATS-BL8125), tolerates the N501Y RBD mutation and remains capable of neutralizing the B.1.1.7 (Alpha) variant. Molecular dynamics simulations provide a structural basis for understanding the neutralization process of nanobodies exclusively focused on the spike-ACE2 interface with and without the N501Y mutation on RBD. A primary human airway air-lung interface (ALI) ex vivo model showed that RBD-1-2G-Fc antibody treatment was effective at reducing viral burden following WA1 and B.1.1.7 SARS-CoV-2 infections. Therefore, this presented strategy will serve as a tool to mitigate the threat of emerging SARS-CoV-2 variants.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Ying Fu", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Juliana da Fonseca Rezende e Mello", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Bryan D Fleming", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Alex Renn", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Catherine Z. Chen", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Xin Hu", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Miao Xu", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Kirill Gorshkov", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Quinlin Hanson", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Wei Zheng", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Emily M Lee", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Lalith Perera", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Robert Petrovich", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Manisha Pradhan", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Richard T Eastman", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Zina Itkin", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Thomas Stanley", + "author_inst": "National Institute of Environmental Health Services" + }, + { + "author_name": "Allen Hsu", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Venkata Dandey", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "William Gillette", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Troy Taylor", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Nitya Ramakrishnan", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Shelley Perkins", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Dominic Esposito", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Eunkeu Oh", + "author_inst": "Naval Research Laboratory" + }, + { + "author_name": "Kimihiro Susumu", + "author_inst": "Jacobs Corporation" + }, + { + "author_name": "Mason Wolak", + "author_inst": "Naval Research Laboratory" + }, + { + "author_name": "Marc Ferrer", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Matthew D. Hall", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Mario J Borgnia", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Anton Simeonov", + "author_inst": "National Center for Advancing Translational Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "synthetic biology" + }, { "rel_doi": "10.1101/2021.10.23.465542", "rel_title": "Protection from SARS-CoV-2 Delta one year after mRNA-1273 vaccination in nonhuman primates is coincident with an anamnestic antibody response in the lower airway", @@ -517831,25 +521029,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.10.19.21265093", - "rel_title": "The Mask-Wearing Bias In The Estimates Of Vaccine Efficacy", - "rel_date": "2021-10-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.19.21265093", - "rel_abs": "In the United States mask wearing is positively correlated with vaccine acceptance. This correlation introduces an important bias into real-world estimates of vaccine efficacy. I derive the formulae for vaccine efficacy that correct for this phenomenon and show that such biases explain some of the differences between higher estimates of vaccine efficacy observed in the US studies, on one hand, and lower estimates from Israel and Pfizer trials, on the other hand. Control for such biases is important for currently-debated public health decisions regarding COVID19 vaccine booster doses.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Andrew Matytsin", - "author_inst": "None" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.18.21264686", "rel_title": "Regional excess mortality during the 2020 COVID-19 pandemic: a study of five European countries", @@ -519395,6 +522574,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.10.20.21265149", + "rel_title": "Differences in COVID-19 Risk by Race and County-Level Social Determinants of Health Among Veterans", + "rel_date": "2021-10-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.20.21265149", + "rel_abs": "COVID-19 disparities by area-level social determinants of health (SDH) may be impacting U.S. Veterans. This retrospective analysis utilized COVID-19 data from the U.S. Department of Veterans Affairs (VA)s EHR and geographically linked county-level data from 18 area-based socioeconomic measures. The risk of testing positive with Veterans county-level SDHs adjusting for demographics, comorbidities, and facility characteristics was calculated using generalized linear models. We found an exposure-response relationship whereby individual COVID-19 infection risk increased with each increasing quartile of adverse county-level SDH such as the percentage of residents in a county without a college degree, eligible for Medicaid, and living in crowded housing.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Hoda S. Abdel Magid", + "author_inst": "Stanford University; Veterans Affairs Palo Alto Healthcare System" + }, + { + "author_name": "Jacqueline M Ferguson", + "author_inst": "Stanford University; Veterans Affairs Palo Alto Healthcare System" + }, + { + "author_name": "Raymond V Cleve", + "author_inst": "Stanford University; Veterans Affairs Palo Alto Healthcare System" + }, + { + "author_name": "Amanda Purnell", + "author_inst": "Veterans Affairs Central Office" + }, + { + "author_name": "Thomas F Osborne", + "author_inst": "Stanford University; Veterans Affairs Palo Alto Healthcare System" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.21.21265133", "rel_title": "Post COVID-19 in children, adolescents, and adults: results of a matched cohort study including more than 150,000 individuals with COVID-19", @@ -519684,25 +522898,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.10.22.465411", - "rel_title": "Underlying selection for the diversity of Spike protein sequences of SARS-CoV-2", - "rel_date": "2021-10-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.22.465411", - "rel_abs": "The global spread of SARS-CoV-2 is fast moving and has caused a worldwide public health crisis. In the present manuscript we analyzed spike protein sequences of SARS-CoV-2 genomes to assess the impact of mutational diversity. We observed from amino acid usage patterns that spike proteins are associated with a diversity of mutational changes and most important underlying cause of variation of amino acid usage is the changes in hydrophobicity of spike proteins. The changing patterns of hydrophobicity of spike proteins over time and its influence on the receptor binding affinity provides crucial information on the SARS-CoV-2 interaction with human receptor. Our results also show that spike proteins have evolved to prefer more hydrophobic residues over time. The present study provides a comprehensive analysis of molecular sequence data to consider that mutational variants might play a crucial role in modulating the virulence and spread of the virus and has immediate implications for therapeutic strategies.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Surajit Basak", - "author_inst": "ICMR-NICED" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.10.22.465272", "rel_title": "Molecular Insights into the Differential Dynamics of SARS-CoV-2 Variants of Concern (VOCs)", @@ -521541,6 +524736,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.18.21265057", + "rel_title": "Impact of routine asymptomatic screening on COVID-19 incidence in a highly vaccinated university population", + "rel_date": "2021-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.18.21265057", + "rel_abs": "BackgroundWith the return of in-person classes, an understanding of COVID-19 transmission in vaccinated university campuses is essential. Given the context of high anticipated vaccination rates and other measures, there are outstanding questions of the potential impact of campus-based asymptomatic screening.\n\nMethodsWe estimated the expected number of cases and hospitalizations in one semester using rates derived for British Columbia (BC), Canada up to September 15th, 2021 and age-standardizing to a University population. To estimate the expected number of secondary cases averted due to routine tests of unvaccinated individuals in a BC post-secondary institution, we used a probabilistic model based on the incidence, vaccination effectiveness, vaccination coverage and R0. We examined multiple scenarios of vaccine coverage, screening frequency, and pre-vaccination R0.\n\nResultsFor one 12 week semester, the expected number of cases is 67 per 50,000 for 80% vaccination coverage and 37 per 50,000 for 95% vaccination coverage. Screening of the unvaccinated population averts an expected 6-16 cases per 50,000 at 80% decreasing to 1-2 averted cases per 50,000 at 95% vaccination coverage for weekly to daily screening. Further scenarios can be explored using a web-based application.\n\nInterpretationRoutine screening of unvaccinated individuals may be of limited benefit if vaccination coverage is 80% or greater within a university setting.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Rebeca Cardim Falcao", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Michael Otterstatter", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "May A. Ahmed", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Michelle Spencer", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Sarafa Iyaniwura", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Naveed Z. Janjua", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Geoff McKee", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Michael A. Irvine", + "author_inst": "BC Centre for Disease Control" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.15.21265037", "rel_title": "Extreme COVID-19 waves reveal hyperexponential growth and finite-time singularity", @@ -521838,33 +525080,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.10.20.21265279", - "rel_title": "Factors affecting the mental health of pregnant women using UK maternity services during the COVID-19 pandemic: A qualitative interview study.", - "rel_date": "2021-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.20.21265279", - "rel_abs": "BackgroundPeople using maternity services in the United Kingdom (UK) have faced significant changes brought on by the COVID-19 pandemic and social distancing regulations. We focused on the experiences of pregnant women using UK maternity services during the pandemic and the impact of social distancing rules on their mental health and wellbeing.\n\nMethodsWe conducted 23 qualitative semi-structured interviews from June 2020 to August 2021, with women from across the UK who experienced a pregnancy during the pandemic. Nineteen women in the study carried their pregnancy to term and four women experienced a miscarriage during the pandemic. Interviews took place remotely over video or telephone call, discussing topics such as mental health during pregnancy and use of UK maternity services. We used reflexive thematic analysis to analyse interview transcripts.\n\nResultsWe generated six higher order themes: (1) Some pregnancy discomforts alleviated by social distancing measures, (2) The importance of relationships that support coping and adjustment, (3) Missed pregnancy and parenthood experiences, (4) The mental health consequences of birth partner and visitor restrictions, (5) Maternity services under pressure, and (6) Lack of connection with staff. Many participants felt a sense of loss over a pregnancy experience that differed so remarkably to what they had expected because of the pandemic. Supportive relationships were important to help cope with pregnancy and pandemic-related changes; but feelings of isolation were compounded for some participants because opportunities to build social connections through face-to-face parent groups were unavailable. Participants also described feeling alone due to restrictions on partners being present when accessing UK maternity services.\n\nConclusionsOur findings highlight some of the changes that may have affected pregnant womens mental health during the COVID-19 pandemic. Reduced social support and being unable to have a partner or support person present during maternity service use were the greatest concerns reported by women in this study, as this absence removed a protective buffer in times of uncertainty and distress. This suggests that the availability of a birth partner or support person must be prioritised wherever possible to protect the mental health of women experiencing pregnancy and miscarriage in times of pandemics.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Alison Ruth McKinlay", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - }, - { - "author_name": "Alexandra Burton", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.10.20.21265245", "rel_title": "Comparative effectiveness of allocation strategies of COVID-19 vaccines and antivirals against emerging SARS-CoV-2 variants of concern in East Asia and Pacific region", @@ -523346,6 +526561,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.13.21264919", + "rel_title": "Agile design and development of a high throughput cobas(R) SARS-CoV-2 RT-PCR diagnostic test", + "rel_date": "2021-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264919", + "rel_abs": "Diagnostic testing is essential for management of the COVID-19 pandemic. An agile assay design methodology, optimized for the cobas(R) 6800/8800 system, was used to develop a dual-target, qualitative SARS-CoV-2 RT-PCR test using commercially available reagents and existing sample processing and thermocycling profiles. The limit of detection was 0.004 to 0.007 TCID50/mL for USA-WA1/2020. Assay sensitivity was confirmed for SARS-CoV-2 variants Alpha, Beta, Gamma, Delta and Kappa. The coefficients of variation of the cycle threshold number (Ct) were between 1.1 and 2.2%. There was no difference in Ct using nasopharyngeal compared to oropharyngeal swabs in universal transport medium (UTM). A small increase in Ct was observed with specimens collected in cobas(R) PCR medium compared to UTM. In silico analysis indicated that the dual-target test is capable of detecting all >1,800,000 SARS-CoV-2 sequences in the GISAID database. Our agile assay design approach facilitated rapid development and deployment of this SARS-CoV-2 RT-PCR test.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Chitra Manohar", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Jingtao Sun", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Peter Schlag", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Chris Santini", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Marcel Fontecha", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Pirmin Lotscher", + "author_inst": "Roche Diagnostics International AG, Rotkreuz, Switzerland" + }, + { + "author_name": "Carolin Bier", + "author_inst": "Roche Diagnostics International AG, Rotkreuz, Switzerland" + }, + { + "author_name": "Kristina Goepfert", + "author_inst": "Roche Diagnostics International AG, Rotkreuz, Switzerland" + }, + { + "author_name": "Dana Duncan", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Gene Spier", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Daniel Jarem", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Dmitriy Kosarikov", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.14.21265010", "rel_title": "How frequent are acute reactions to COVID-19 vaccination and who is at risk?", @@ -523507,69 +526785,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.13.21264946", - "rel_title": "Clinical observation of high-flow nasal cannula (HFNC) with non-rebreather mask (NRM) use on severe or critically ill COVID-19 diabetic patients", - "rel_date": "2021-10-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264946", - "rel_abs": "Background and aimsPrevalence of diabetes is a vital factor in COVID-19s clinical prognosis. This study aimed to investigate and compare the efficacy of High-flow Nasal Cannula (HFNC) with/without non-rebreather mask (NRM) use on critical COVID-19 patients with/without diabetes.\n\nMethodsFor analysis and comparison, epidemiological, biochemical, and clinical data were collected from 240 HFNC ({+/-}NRM) treated severe and critical COVID-19 patients (diabetic = 136; non-diabetic = 104) admitted into ICUs of five hospitals in Chattogram, Bangladesh.\n\nResults59.1% of patients with fever had diabetes (p=0.012). ICU stay was longer for diabetic patients (9.06{+/-}5.70) than non-diabetic patients (7.41{+/-}5.11) (p=0.020). Majority of the hypertensive patients were diabetic (68.3%; p<0.001). Majority of diabetic patients (70.4%; p<0.005) had elevated creatinine levels. Partial pressure of oxygen (mmHg) after HFNC (only) administration was significantly (p=0.031) higher in non-diabetic patients (69.30{+/-}23.56) than in diabetic patients (61.50{+/-}14.49). Diabetic (62.64{+/-}13.05) and non-diabetic patients (59.40{+/-}13.22) had almost similar partial pressure of oxygen (mmHg) from HFNC with NRM. Patients with elevated RBS required NRM with HFNC five times (AOR=5.1, 1.2-20.8) higher than others. Besides age, and hypertension were significantly associated with the HFNC+NRM treated diabetic patients. Factors those affected the HFNC only treated patients were fever and impaired glucose tolerance.\n\nConclusionsThe results of this study imply that oxygen supply with HFNC and NRM may be beneficial for the elderly/hypertensive diabetic patients with COVID-19 associated AHRF; and that increased blood glucose level could be a determinant for the need of HFNC + NRM treatment.\n\nHighlightsO_LIElderly diabetic patients required both HFNC and NRM to increase oxygen saturation.\nC_LIO_LIHypertension may be a factor for diabetic patients with COVID-19 requiring HFNC and NRM together.\nC_LIO_LI HFNC + NRM-combination therapy might be needed when blood glucose levels rise.\nC_LI", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "AFM Tareq Bhuiyan", - "author_inst": "Department of Anesthesia and ICU, 250 Bedded General Hospital, Chattogram, 4000, Bangladesh." - }, - { - "author_name": "Sudipta Deb Nath", - "author_inst": "Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, 1000, Bangladesh." - }, - { - "author_name": "Md Jakir Hossain", - "author_inst": "Pancreatic Research Group, South Western Sydney Clinical School, Faculty of Medicine and Health, UNSW Sydney" - }, - { - "author_name": "Shuva Das", - "author_inst": "Department of Microbiology, Chittagong Medical College, Chattogram, 4203, Bangladesh." - }, - { - "author_name": "Moumita Das", - "author_inst": "Department of Anesthesia and ICU, 250 Bedded General Hospital, Chattogram, 4000, Bangladesh." - }, - { - "author_name": "Moinul Ahsan", - "author_inst": "Department of Anesthesia and ICU, 250 Bedded General Hospital, Chattogram, 4000, Bangladesh." - }, - { - "author_name": "Md. Iftekher-E-Alam Ziad", - "author_inst": "Department of Anesthesia and ICU, 250 Bedded General Hospital, Chattogram, 4000, Bangladesh." - }, - { - "author_name": "Fahmida Khatun Padma", - "author_inst": "Department of Anesthesia and ICU, Chittagong Medical College, Chattogram, 4203, Bangladesh." - }, - { - "author_name": "Rana Dey", - "author_inst": "Department of Anesthesia and ICU, Chattagram Maa-O-Shishu General Hospital, Chattogram, 4000, Bangladesh." - }, - { - "author_name": "AKM Shamsul Alam", - "author_inst": "ICU, Parkview Hospital, Chattogram, 4203, Bangladesh." - }, - { - "author_name": "Farial Hoque Zehan", - "author_inst": "Department of Anesthesia and ICU, 250 Bedded General Hospital, Chattogram, 4000, Bangladesh." - }, - { - "author_name": "Ayan Saha", - "author_inst": "Department of Genetic Engineering and Biotechnology, East West University, Dhaka, 1212, Bangladesh." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.10.14.21264897", "rel_title": "Differentiating COVID-19 and dengue from other febrile illnesses in co-epidemics: Development and internal validation of COVIDENGUE scores", @@ -524916,6 +528131,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.17.21265101", + "rel_title": "Time-varying effectiveness of the mRNA-1273, BNT162b2 and Ad26.COV2.S vaccines against SARS-CoV-2 infections and COVID-19 hospitalizations and deaths: an analysis based on observational data from Puerto Rico", + "rel_date": "2021-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.17.21265101", + "rel_abs": "BackgroundAs of October 1, 2021 2,217,547 individuals were fully vaccinated against COVID-19 in Puerto Rico. Since the vaccination process commenced on December 15, 2020 111,052 laboratory-confirmed SARS-CoV-2 infections have been reported. These data permitted us to quantify the benefits of the immunization campaign and to compare effectiveness of the mRNA-1273 (Moderna), BNT162b2 (Pfizer), and Ad26.COV2.S (J&J) vaccines.\n\nMethodsDepartment of Health databases holding vaccination status, SARS-CoV-2 test results, and COVID-19 hospitalizations and deaths were integrated. We fit a statistical model that adjusted for time-varying incidence rates and age to estimate vaccine effectiveness and hospitalization and death relative risks. Code and data are provided here: https://github.com/rafalab/vax-eff-pr.\n\nResultsAt the peak of their protection, mRNA-1273, BNT162b2, and Ad26.COV2.S had an effectiveness of 90% (88%-91%), 87% (85%-89%), and 58% (51%-65%), respectively. After four months, effectiveness waned to about 70%, 60%, and 30%. We found no evidence that effectiveness was different after the Delta variant became dominant. For those infected, the vaccines provided further protection against hospitalization and deaths across all age groups. All vaccines had a lower effectiveness for those over 85 years, with a larger decrease for the Ad26.COV2.S vaccine. Overall, thousands of hospitalizations and deaths were avoided thanks to the vaccines.\n\nConclusionsThe mRNA-1273 and BNT162b2 vaccines were highly effective across all age groups. They were still effective after four months although the protection waned. The Ad26.COV2.S vaccine was effective but to a lesser degree, especially for older age groups.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Monica M. Robles-Fontan", + "author_inst": "Departamento de Salud de Puerto Rico" + }, + { + "author_name": "Elvis G. Nieves", + "author_inst": "Departamento de Salud de Puerto Rico" + }, + { + "author_name": "Iris Cardona-Gerena", + "author_inst": "Departamento de Salud de Puerto Rico" + }, + { + "author_name": "Rafael A Irizarry", + "author_inst": "Dana-Farber Cancer Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.18.21265046", "rel_title": "Comparative assessment of methods for short-term forecasts of COVID-19 admissions in England at the local level", @@ -525045,69 +528291,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.10.17.21265123", - "rel_title": "Long-term manifestations and modifiers of prevalence estimates of the post-COVID-19 syndrome: A systematic review and meta-analysis.", - "rel_date": "2021-10-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.17.21265123", - "rel_abs": "BackgroundPost-acute COVID-19 syndrome (PACS) is a multi-system disease comprising persistent symptomatology after the acute phase of infection. Long-term PACS effects significantly impact patient outcomes, but their incidence remains uncharacterized due to high heterogeneity between studies. Therefore, we aimed to summarize published data on PACS, characterizing the clinical presentation, prevalence, and modifiers of prevalence estimates.\n\nMethodIn this systematic review and meta-analysis, we research MEDLINE for original studies published from January 1st, 2020, to January 31st, 2021, that reported proportions of PACS manifestations. Studies were eligible for inclusion if they included patients aged [≥]18 years with confirmed COVID-19 by RT-PCR or antigen testing and a minimum follow-up of 21 days. The prevalence of individual manifestations across studies was pooled using random-effects meta-analysis. For evaluating determinants of heterogeneity, meta-regression analysis was performed. This study was registered in PROSPERO (CRD42019125025).\n\nResultsAfter screening 1,235 studies, we included 29 reports for analysis. Twenty-seven meta-analyses were performed, and 61 long-term manifestations were described. The pooled prevalence of PACS was 56% (95%CI 45-66%), with the most common manifestations being diminished health status, fatigue, asthenia, dyspnea, myalgias, hyposmia and dysgeusia. Most of the included studies presented high heterogeneity. After conducting the meta-regression analysis, we identified that age, gender, number of comorbidities, and reported symptoms significantly modify the prevalence estimation of PACS long-term manifestations.\n\nConclusionPACS is inconsistently reported between studies, and population characteristics influence the prevalence estimates due to high heterogeneity. A systematized approach for the study of PACS is needed to characterize its impact adequately.\n\nFundingnone", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Daniel De-la-Rosa-Mart\u00ednez", - "author_inst": "Instituto Nacional de Canceroloria" - }, - { - "author_name": "Marco Antonio Delaye-Mart\u00ednez", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Omar Yaxmehen Bello-Chavolla", - "author_inst": "Instituto Nacional de Geriatria" - }, - { - "author_name": "Alejandro Sicilia-Andrade", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Isaac David Ju\u00e1rez-Cruz", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Carlos A Ferm\u00edn-Mart\u00ednez", - "author_inst": "Instituto Nacional de Geriatria" - }, - { - "author_name": "Alejandro M\u00e1rquez-Salinas", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Enrique C. Guerra", - "author_inst": "National Autonomous University of Mexico" - }, - { - "author_name": "Luisa Fern\u00e1ndez-Chirino", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Monica Itzel Mart\u00ednez-Guti\u00e9rrez", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Daniel Eduardo Sandoval-Colin", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Diana Vilar-Compte", - "author_inst": "Instituto Nacional de Cancerologia" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.16.464660", "rel_title": "Boosting of SARS-CoV-2 immunity in nonhuman primates using an oral rhabdoviral vaccine", @@ -526937,6 +530120,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.10.11.21264709", + "rel_title": "Quantitative chest CT combined with plasma cytokines predict outcomes in COVID-19 patients", + "rel_date": "2021-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.11.21264709", + "rel_abs": "Despite extraordinary international efforts to dampen the spread and understand the mechanisms behind SARS-CoV-2 infections, accessible predictive biomarkers directly applicable in the clinic are yet to be discovered. Recent studies have revealed that diverse types of assays bear limited predictive power for COVID-19 outcomes. Here, we harness the predictive power of chest CT in combination with plasma cytokines using a machine learning approach for predicting death during hospitalization and maximum severity degree in COVID-19 patients. Patients (n=152) from the Mount Sinai Health System in New York with plasma cytokine assessment and a chest CT within 5 days from admission were included. Demographics, clinical, and laboratory variables, including plasma cytokines (IL-6, IL-8, and TNF-) were collected from the electronic medical record. We found that chest CT combined with plasma cytokines were good predictors of death (AUC 0.78) and maximum severity (AUC 0.82), whereas CT quantitative was better at predicting severity (AUC 0.81 vs 0.70) while cytokine measurements better predicted death (AUC 0.70 vs 0.66). Finally, we provide a simple scoring system using plasma IL-6, IL-8, TNF-, GGO to aerated lung ratio and age as novel metrics that may be used to monitor patients upon hospitalization and help physicians make critical decisions and considerations for patients at high risk of death for COVID-19.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Guillermo Carbonell", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Diane Marie Del Valle", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Edgar E Gonzalez-Kozlova", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Brett Marinelli", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Emma Klein", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Maria El Homsi", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Daniel Stocker", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Michael Chung", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adam Bernheim", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Nicole Simons", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jiani Xiang", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sharon Nirenberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Patricia Kovatch", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sara Lewis", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Miriam Merad", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sacha Gnjatic", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Bachir Taouli", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2021.10.12.21264890", "rel_title": "Breastfeeding infants receive neutralizing antibodies and cytokines from mothers immunized with a COVID-19 mRNA vaccine", @@ -527114,33 +530380,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2021.10.12.21264903", - "rel_title": "Leaders gender and the fight against COVID-19: investigation, replication, and a possible explanation", - "rel_date": "2021-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.12.21264903", - "rel_abs": "ObjectivesTo investigate the alleged relationship between leaders gender and COVID-19 related cases and deaths in different countries across the globe.\n\nStudy designThe relationship between leaders gender and percent of women in parliament to COVID-19 cases and death per million was investigated in three time points (10 months) across 180 countries, controlling for possible covariates.\n\nMethodsThree different types of analyses were run: (1) Six basic t-tests; (2) Two repeated-measure ANOVA tests analyzing change over time; (3) Six stepwise regression analyses for both leaders gender and the percentage of women in parliament.\n\nResultsOur findings suggest that, contrary to some research and popular media headlines, and in-line with recent academic research, leadership gender is not a significant factor in explaining the variation between countries in the fight against the COVID-19 pandemic.\n\nConclusionsWe suggest that this alleged relationship may stem from an illusory correlation. We argue that the uncertainty, stress, and anxiety that prevail in these times of global pandemic may be the breeding ground for judgmental biases of this sort.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Yossi Maaravi", - "author_inst": "Interdisciplinary Center Herzliya" - }, - { - "author_name": "Tamar Gur", - "author_inst": "Hebrew University" - }, - { - "author_name": "Yossi Gur-Arie", - "author_inst": "Interdisciplinary Center Herzliya" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.10.13.21264967", "rel_title": "Reliability of multi-modal MRI-derived brain phenotypes for multi-site assessment of neuropsychiatric complications of SARS-CoV-2 infection", @@ -528759,6 +531998,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.10.13.21264975", + "rel_title": "Disparities in SARS-CoV-2 exposure: evidence from a citywide seroprevalence study in Holyoke, Massachusetts, USA", + "rel_date": "2021-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264975", + "rel_abs": "BackgroundSeroprevalence studies are important tools to estimate the prevalence of prior or recent SARS-CoV-2 infections, identifying hotspots and high-risk groups and informing public health responses to the COVID-19 pandemic. We conducted a city-level seroprevalence study in Holyoke, Massachusetts, USA to estimate the seroprevalence of SARS-CoV-2 antibodies and risk factors for seropositivity.\n\nMethodsWe invited inhabitants of 2,000 randomly sampled addresses between November 5 and December 31, 2020. Participants completed questionnaires measuring sociodemographic and health characteristics, and COVID-19 exposure history, and provided dried blood spots for measurement of SARS-CoV-2 IgG and IgM antibodies. We calculate total and subgroup seroprevalence estimates based on presence of IgG antibodies using a Bayesian procedure that incorporates uncertainty in antibody test sensitivity and specificity. We account for clustering by household and weighting based on demographic characteristics to ensure estimates represented the citys population.\n\nFindingsWe enrolled 280 households including 472 individuals. 328 underwent antibody testing. The citywide seroprevalence estimate of SARS-CoV-2 IgG was 13.1% (95%CI 6.9-22.3) compared to 9.8% based on publicly reported case counts. Seroprevalence was 16.1% (95%CI 6.2-31.8) among individuals identifying as Hispanic compared to 9.4% (95%CI 4.6-16.4) among those identifying as non-Hispanic white. Seroprevalence was higher among Spanish speaking households (21.9%; 95% CI 8.3-43.9) compared to English speaking households (10.2%; 95% CI 5.2-18.0) and among individuals living in high vulnerability areas (14.4%; 95% CI 7.1-25.5) compared to low vulnerability areas (8.2%; 95% CI 3.1-16.9).\n\nInterpretationThe measured SARS-CoV-2 seroprevalence of IgG antibodies in Holyoke was only 13.1% during the second surge of SARS-CoV-2 in this region, far from accepted thresholds for \"herd immunity.\" Already vulnerable communities were at highest risk of prior infection. Implementation of local serosurveys in tandem with proactive public health interventions that address disparities in SARS-CoV-2 exposure are crucial to ensure at-risk communities have appropriate educational materials and access to vaccines, testing, and timely treatment.\n\nFundingThe Sullivan Family Foundation, Harvard Data Science Institute Bias2 program, the US Centers for Disease Control and Prevention.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Wilfredo Rafael Matias", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA; Division of Infectious Diseases, Brigham and Womens Hospital, Boston, MA; Center fo" + }, + { + "author_name": "Isabel R Fulcher", + "author_inst": "Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA; Harvard Data Science Initiative, Cambridge, MA" + }, + { + "author_name": "Sara M Sauer", + "author_inst": "Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Cody P Nolan", + "author_inst": "Department of Medicine, Brigham and Womens Hospital, Boston, MA" + }, + { + "author_name": "Yodeline Guillaume", + "author_inst": "Center for Global Health, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Jack Zhu", + "author_inst": "Center for Global Health, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Francisco J Molano", + "author_inst": "Center for Global Health, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Elizabeth Uceta", + "author_inst": "Center for Global Health, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Shannon Collins", + "author_inst": "Center for Global Health, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Damien M Slater", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Vanessa M Sanchez", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Serina Moheed", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Jason B Harris", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Richelle C Charles", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA; Department of Medicine, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Ryan M Paxton", + "author_inst": "Holyoke Board of Health, Holyoke, MA" + }, + { + "author_name": "Sean F Gonsalves", + "author_inst": "Holyoke Board of Health, Holyoke, MA" + }, + { + "author_name": "Molly F Franke", + "author_inst": "Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Louise C Ivers", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA; Center for Global Health, Massachusetts General Hospital, Boston, MA; Department of" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.13.21264901", "rel_title": "Soluble angiotensin-converting enzyme 2 as a prognostic biomarker for disease progression in patients infected with SARS-CoV-2", @@ -528908,85 +532234,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.13.21264960", - "rel_title": "Evaluation of real-life use of Point-Of-Care Rapid Antigen TEsting for SARS-CoV-2 in schools for outbreak control (EPOCRATES)", - "rel_date": "2021-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264960", - "rel_abs": "AbstractO_ST_ABSBackgroundC_ST_ABSWe evaluated the use of rapid antigen detection tests (RADT) for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in school settings to determine RADTs performance compared to PCR.\n\nMethodsIn this real-world, prospective observational cohort study, high-school students and staff were recruited from two high-schools in Montreal (Canada) and followed from January 25th to June 10th, 2021. Twenty-five percent of asymptomatic participants were tested weekly by RADT (nasal) and PCR (gargle). Class contacts of cases were tested. Symptomatic participants were tested by RADT (nasal) and PCR (nasal and gargle). The number of cases and outbreaks were compared to other high schools in the same area.\n\nResultsOverall, 2,099 students and 286 school staff members consented to participate. The overall RADTs specificity varied from 99.8 to 100%, with a lower sensitivity, varying from 28.6% in asymptomatic to 83.3% in symptomatic participants. Secondary cases were identified in 10 of 35 classes. Returning students to school after a 7-day quarantine, with a negative PCR on D6-7 after exposure, did not lead to subsequent outbreaks. Of cases for whom the source was known, 37 of 57 (72.5%) were secondary to household transmission, 13 (25%) to intra-school transmission and one to community contacts between students in the same school.\n\nConclusionRADT did not perform well as a screening tool in asymptomatic individuals. Reinforcing policies for symptom screening when entering schools and testing symptomatic individuals with RADT on the spot may avoid subsequent significant exposures in class.\n\nTable of Contents SummaryRapid antigen tests were compared to standard PCR to diagnose SARS-CoV-2 infections in high-school students. They performed better in symptomatic individuals.\n\nWhats Known on This SubjectRapid antigen detection tests (RADT) are often used to diagnose respiratory pathogens at the point-of-care. Their performance characteristics vary, but they usually have high specificity and moderate sensitivity compared with PCR.\n\nWhat This Study AddsRADT sensitivity ranged from 28.6% in asymptomatic individuals to 83.3% in symptomatic individuals. Return to school after 7 days of quarantine was safe in exposed students. Secondary cases were identified in 28% of classes with an index case.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Ana C. Blanchard", - "author_inst": "CHU Sainte-Justine, University of Montreal" - }, - { - "author_name": "Marc Desforges", - "author_inst": "CHU Ste-Justine" - }, - { - "author_name": "Annie-Claude Labbe", - "author_inst": "Hopital Maisonneuve-Rosemont" - }, - { - "author_name": "Cat Tuong Nguyen", - "author_inst": "Direction regionale de sante publique de Montreal" - }, - { - "author_name": "Yves Petit", - "author_inst": "Pensionnat du Saint-Nom-de-Marie" - }, - { - "author_name": "Dominic Besner", - "author_inst": "Ecole secondaire Calixa-Lavallee" - }, - { - "author_name": "Kate Zinszer", - "author_inst": "University of Montreal" - }, - { - "author_name": "Olivier Seguin", - "author_inst": "Direction regionale de sante publique de Montreal" - }, - { - "author_name": "Zineb Laghdir", - "author_inst": "CHU Sainte-Justine" - }, - { - "author_name": "Kelsey Adams", - "author_inst": "CHU Sainte-Justine" - }, - { - "author_name": "Marie-Eve Benoit", - "author_inst": "CHU Sainte-Justine" - }, - { - "author_name": "Genevieve Leduc", - "author_inst": "CHU Sainte-Justine" - }, - { - "author_name": "Jean Longtin", - "author_inst": "Centre hospitalier universitaire (CHU) de Quebec" - }, - { - "author_name": "Ioannis Ragoussis", - "author_inst": "McGill University" - }, - { - "author_name": "David L. Buckeridge", - "author_inst": "McGill University" - }, - { - "author_name": "Caroline Quach", - "author_inst": "University of Montreal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.11.21264805", "rel_title": "Impact Of Adaptive Natural Killer Cells, KLRC2 Genotype And Cytomegalovirus Reactivation On Late Mortality In Patients With Severe Covid-19 Lung Disease", @@ -530541,6 +533788,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.10.09.21264794", + "rel_title": "Covid-19 Epidemic Prediction in France: the Multimodal Case.", + "rel_date": "2021-10-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.09.21264794", + "rel_abs": "In two previous papers we have proposed models to estimate the Covid-19 epidemic when the number of daily positive cases has a bell shaped form that we call a mode. We have observed that each Covid variant produces this type of epidemic shape at a different moment, resulting in a multimodal epidemic shape. We will show in this document that each mode can still be estimated with models described in the two previous papers provides we replace the cumulated number of positive cases y by the cumulated number of positive cases reduced by a parameter P to be estimated. Therefore denoting z the logarithm of y -P, z follows approximately the differential equation [z] = b -azr where a, b, r have also to be estimated from the observed data. We will show the obtained predictions on the four French modes April, November 2020, May and September 2021. The comparison between the prediction obtained before the containment decisions made by the French government and the observed data afterwards suggests the inefficiency of the epidemic lockdowns.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Jean-Pierre Quadrat", + "author_inst": "Retired from INRIA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.11.463917", "rel_title": "Secondary structure of subgenomic RNA M of SARS-CoV-2", @@ -530794,65 +534060,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.07.21257459", - "rel_title": "Cellular and Antibody Immunity after COVID-19 Vaccination at >4-Month Follow Up in Immunocompetent and Immunocompromised Subjects", - "rel_date": "2021-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.07.21257459", - "rel_abs": "We evaluated post-vaccination immunity after COVID-19 vaccination with serial changes in cellular and antibody responses to the spike protein S, its S2 component which is conserved between SARS-CoV-2 and human coronaviruses, and the S1 component, which is specific to SARS-CoV-2 and also contains its receptor binding domain (RBD). In 21 healthy immunocompetent subjects all of whom demonstrated circulating IgG antibodies 4 months after mRNA1273 or BNT162b vaccination, a) the strength of S-IgG was stable while RBD-IgG declined, b) S2-reactive B-cell frequencies increased progressively (p=0.002) c) S1-reactive CD8+T-cells and CD19+B-cells were undetectable after a transient increase, and d) monocytic and polymorphonuclear myeloid-derived suppressor cells (M-MDSC, PMN-MDSC) increased after the first vaccine dose. Compared with 4-month measurements from immunocompetent subjects, single samples from 20 vaccinated immunocompromised (IC) subjects revealed a) circulating S-IgG and RBD-IgG in 13 (65%) and 9 (45%) subjects, respectively, b) no differences in S2-reactive T- and B-cells, c) undetectable S1-reactive T- and B-cells, and d) fewer S-reactive CD8+T-cells and CD19+B-cells (p<0.05). Among 11 IC recipients who failed to make RBD-IgG, frequencies of PMN-MDSC were significantly higher (p<0.0004) compared with IC or immunocompetent subjects with RBD-IgG. COVID-19 vaccination induces stable antibodies to the spike protein and expands circulating B-cells reactive to the conserved spike protein sequence in immunocompetent subjects. MDSC which are known to suppress T- and B-cells, and which increase after vaccination, may limit post-vaccination responses especially among immunocompromised subjects. Antibody and cellular responses to SARS-CoV-2-specific spike antigenic sequences appear to be less durable.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Rakesh Sindhi", - "author_inst": "UPMC Children's Hospital of Pittsburgh, Hillman Center for Pediatric Transplantation, Pittsburgh, PA" - }, - { - "author_name": "Chethan Ashokkumar", - "author_inst": "UPMC Children's Hospital of Pittsburgh, Hillman Center for Pediatric Transplantation, Pittsburgh, PA" - }, - { - "author_name": "Vineeta Singh", - "author_inst": "Plexision" - }, - { - "author_name": "Brianna Spishock", - "author_inst": "Plexision" - }, - { - "author_name": "Maggie Saunders", - "author_inst": "Plexision" - }, - { - "author_name": "Angelo Mabasa", - "author_inst": "Columbia University Medical Center, New York, NY" - }, - { - "author_name": "Elizabeth Sindhi", - "author_inst": "Plexision" - }, - { - "author_name": "Pradeep Sethi", - "author_inst": "Plexision" - }, - { - "author_name": "Ashok Reddy", - "author_inst": "Plexision" - }, - { - "author_name": "Shankar Subramaniam", - "author_inst": "Department of Bioengineering, University of California San Diego, La Jolla, CA" - }, - { - "author_name": "Bobby Nibhanupudy", - "author_inst": "Advent Health Transplant Institute, Orlando, FL" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.10.21264807", "rel_title": "Level and determinants of willingness to pay for rapid COVID-19 testing delivered through private retail pharmacies in Kenya.", @@ -532470,6 +535677,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.07.21264419", + "rel_title": "Higher education responses to COVID-19 in the United States: Evidence for the impacts of university policy", + "rel_date": "2021-10-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.07.21264419", + "rel_abs": "With a dataset of testing and case counts from over 1,400 institutions of higher education (IHEs) in the United States, we analyze the number of infections and deaths from SARS-CoV-2 in the counties surrounding these IHEs during the Fall 2020 semester (August to December, 2020). We used a matching procedure designed to create groups of counties that are aligned along age, race, income, population, and urban/rural categories--socio-demographic variables that have been shown to be correlated with COVID-19 outcomes. We find that counties with IHEs that remained primarily online experienced fewer cases and deaths during the Fall 2020 semester; whereas before and after the semester, these two groups had almost identical COVID-19 incidence. Additionally, we see fewer deaths in counties with IHEs that reported conducting any on-campus testing compared to those that reported none. We complement the statistical analysis with a case study of IHEs in Massachusetts--a rich data state in our dataset--which further highlights the importance of IHE-affiliated testing for the broader community. The results in this work suggest that campus testing can itself be thought of as a mitigation policy and that allocating additional resources to IHEs to support efforts to regularly test students and staff would be beneficial to mitigating the spread of COVID-19 in the general population.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Brennan Klein", + "author_inst": "Northeastern University Network Science Institute" + }, + { + "author_name": "Nicholas Generous", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Matteo Chinazzi", + "author_inst": "Northeastern University" + }, + { + "author_name": "Zarana Bhadricha", + "author_inst": "Northeastern University" + }, + { + "author_name": "Rishab Gunashekar", + "author_inst": "Northeastern University" + }, + { + "author_name": "Preeti Kori", + "author_inst": "Northeastern University" + }, + { + "author_name": "Bodian Li", + "author_inst": "Northeastern University" + }, + { + "author_name": "Stefan McCabe", + "author_inst": "Northeastern University" + }, + { + "author_name": "Jon Green", + "author_inst": "Northeastern University" + }, + { + "author_name": "David Lazer", + "author_inst": "Northeastern University" + }, + { + "author_name": "Christopher R. Marsicano", + "author_inst": "Davidson College" + }, + { + "author_name": "Samuel V. Scarpino", + "author_inst": "The Rockefeller Foundation Pandemic Prevention Institute" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Northeastern University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.08.21264749", "rel_title": "Longitudinal changes in home confinement and mental health implications: A 17-month follow-up study in England during the COVID-19 pandemic", @@ -532667,93 +535941,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.10.08.463613", - "rel_title": "Gut Bacterial Dysbiosis and Instability is Associated with the Onset of Complications and Mortality in COVID-19", - "rel_date": "2021-10-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.08.463613", - "rel_abs": "ObjectiveThere is a growing debate about the involvement of the gut microbiome in COVID-19, although it is not conclusively understood whether the microbiome has an impact on COVID-19, or vice versa, especially as analysis of amplicon data in hospitalized patients requires sophisticated cohort recruitment and integration of clinical parameters. Here, we analyzed fecal and saliva samples from SARS-CoV-2 infected and post COVID-19 patients and controls considering multiple influencing factors during hospitalization.\n\nDesign16S rRNA gene sequencing was performed on fecal and saliva samples from 108 COVID-19 and 22 post COVID-19 patients, 20 pneumonia controls and 26 asymptomatic controls. Patients were recruited over the first and second corona wave in Germany and detailed clinical parameters were considered. Serial samples per individual allowed intra-individual analysis.\n\nResultsWe found the gut and oral microbiota to be altered depending on number and type of COVID-19-associated complications and disease severity. The occurrence of individual complications was correlated with low-risk (e.g., Faecalibacterium prausznitzii) and high-risk bacteria (e.g., Parabacteroides). We demonstrated that a stable gut bacterial composition was associated with a favorable disease progression. Based on gut microbial profiles, we identified a model to estimate mortality in COVID-19.\n\nConclusionGut microbiota are associated with the occurrence of complications in COVID-19 and may thereby influencing disease severity. A stable gut microbial composition may contribute to a favorable disease progression and using bacterial signatures to estimate mortality could contribute to diagnostic approaches. Importantly, we highlight challenges in the analysis of microbial data in the context of hospitalization.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "David Schult", - "author_inst": "Department of Internal Medicine II, Klinikum rechts der Isar, Technical University Munich" - }, - { - "author_name": "Sandra Reitmeier", - "author_inst": "ZIEL - Institute for Food & Health, Technical University Munich" - }, - { - "author_name": "Plamena Koyumdzhieva", - "author_inst": "Department of Internal Medicine II, Klinikum rechts der Isar, Technical University Munich" - }, - { - "author_name": "Moritz Middelhof", - "author_inst": "Department of Internal Medicine II, Klinikum rechts der Isar, Technical University Munich" - }, - { - "author_name": "Johanna Erber", - "author_inst": "Department of Internal Medicine II, Klinikum rechts der Isar, Technical University Munich" - }, - { - "author_name": "Jochen Schneider", - "author_inst": "Department of Internal Medicine II, Klinikum rechts der Isar, Technical University Munich" - }, - { - "author_name": "Juliane Krager", - "author_inst": "Department of Internal Medicine II, Klinikum rechts der Isar, Technical University Munich" - }, - { - "author_name": "Marina Frolova", - "author_inst": "Department of Internal Medicine II, Klinikum rechts der Isar, Technical University Munich" - }, - { - "author_name": "Julia Horstmann", - "author_inst": "Department of Internal Medicine II, Klinikum rechts der Isar, Technical University Munich" - }, - { - "author_name": "Lisa Fricke", - "author_inst": "Department of Internal Medicine II, Klinikum rechts der Isar, Technical University Munich" - }, - { - "author_name": "Katja Steiger", - "author_inst": "Technische Universitat Munchen Fakultat fur Medizin" - }, - { - "author_name": "Moritz Jesinghaus", - "author_inst": "Institute of Pathology, Technical University Munich" - }, - { - "author_name": "Klaus-Peter Janssen", - "author_inst": "Department of Surgery, Klinikum rechts der Isar, Technical University Munich" - }, - { - "author_name": "Ulrike Protzer", - "author_inst": "Technische Universitaet Muenchen / Helmholtz Zentrum Muenchen" - }, - { - "author_name": "Klaus Neuhaus", - "author_inst": "ZIEL - Institute for Food & Health, Technical University Munich" - }, - { - "author_name": "Roland M Schmid", - "author_inst": "Department of Internal Medicine II, Klinikum rechts der Isar, Technical University Munich" - }, - { - "author_name": "Dirk Haller", - "author_inst": "ZIEL - Institute for Food & Health, Technical University Munich" - }, - { - "author_name": "Michael Quante", - "author_inst": "Department of Internal Medicine II, Klinikum rechts der Isar, Technical University Munich" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.10.08.21262462", "rel_title": "Nine-month presence of SARS-CoV-2 in saliva: a case report", @@ -534376,6 +537563,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.04.21264540", + "rel_title": "Detailed reconstruction of the Iranian COVID-19 epidemic reveals high attack rates of SARS-CoV-2 in several provinces", + "rel_date": "2021-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.04.21264540", + "rel_abs": "Detailed reconstruction of the SARS-CoV-2 transmission dynamics and assessment of its burden in several parts of the world has still remained largely unknown due to the scarcity of epidemiological analyses and limited testing capacities of different countries to identify cases and deaths attributable to COVID-19 [1-4]. Understanding the true burden of the Iranian COVID-19 epidemic is subject to similar challenges with limited clinical and epidemiological studies at the subnational level [5-9]. To address this, we develop a new quantitative framework that enables us to fully reconstruct the transmission dynamics across the country and assess the level of under-reporting in infections and deaths using province-level, age-stratified all-cause mortality data. We show that excess mortality aligns with seroprevalence estimates in each province and subsequently estimate that as of 2021-10-22, only 48% (95% confidence interval: 43-55%) of COVID-19 deaths in Iran have been reported. We find that in the most affected provinces such as East Azerbaijan, Qazvin, and Qom approximately 0.4% of the population have died of COVID-19 so far. We also find significant heterogeneity in the estimated attack rates across the country with 11 provinces reaching close to or higher than 100% attack rates. Despite a relatively young age structure in Iran, our analysis reveals that the infection fatality rate in most provinces is comparable to high-income countries with a larger percentage of older adults, suggesting that limited access to medical services, coupled with undercounting of COVID-19-related deaths, can have a significant impact on accurate estimation of COVID-19 fatalities. Our estimation of high attack rates in provinces with largely unmitigated epidemics whereby, on average, between 10% to 25% individuals have been infected with COVID-19 at least twice over the course of 20 months also suggests that, despite several waves of infection, herd immunity through natural infection has not been achieved in the population.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Mahan Ghafari", + "author_inst": "University of Oxford" + }, + { + "author_name": "Oliver J Watson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ariel Karlinsky", + "author_inst": "Hebrew University of Jerusalem" + }, + { + "author_name": "Luca Ferretti", + "author_inst": "Nuffield Department of Medicine" + }, + { + "author_name": "Aris Katzourakis", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.06.21264645", "rel_title": "A joint hierarchical model for the number of cases and deaths due to COVID-19 across the boroughs of Montreal", @@ -534573,137 +537795,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.10.05.21264160", - "rel_title": "Internalizing Problems Before and During the COVID-19 Pandemic in Dutch Children and Adolescents with and without Pre-Existing Mental Health Problems", - "rel_date": "2021-10-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.05.21264160", - "rel_abs": "The aim of the study was to assess internalizing problems before and during the pandemic with data from Dutch consortium Child and adolescent mental health and wellbeing in times of the COVID-19 pandemic, consisting of two Dutch general population samples (GS) and two clinical samples (CS) referred to youth/psychiatric care. In each sample, measures of internalizing problems were obtained from ongoing data collections pre-pandemic (NGS= 35,357; NCS= 4,487) and twice during the pandemic, in Apr.-May 2020 (NGS= 3,938; clinical: NCS= 1,008) and in Nov.-Dec. 2020 (NGS= 1,489; NCS= 1,536), in children and adolescents (8-18 years) with parent- (Brief Problem Monitor) and/or child reports (Patient-Reported Outcomes Measurement Information System(R)). Results show significantly greater proportions of worrisome internalizing problems (based on validated cut-offs) and significantly higher internalizing problems mean levels from pre-pandemic to pandemic measurements in the general population. These levels stabilized or decreased over the course of the pandemic. In the clinical sample, we found an increase in child-reported internalizing problems measures over the course of the pandemic, but parents reported no differences in internalizing problems measures over the course of the pandemic, nor from pre-pandemic to during the pandemic. Overall, the findings indicate that children and adolescents of both the general and clinical population were affected negatively by the pandemic in terms of their internalizing problems. Attention is therefore warranted to investigate what long-term effects this may cause and to monitor if internalizing problems return back to pre-pandemic levels or if they remain elevated post-pandemic.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Karen Fischer", - "author_inst": "Department of Biological Psychology, Vrije Universiteit Amsterdam, The Netherlands" - }, - { - "author_name": "Jacintha Tieskens", - "author_inst": "LUMC Curium - Child and Adolescent Psychiatry, Leiden University Medical Center, The Netherlands" - }, - { - "author_name": "Michiel Luijten", - "author_inst": "Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Child and Adolescent Psychiatry & Psychosocial Care, Amsterdam Reproduct" - }, - { - "author_name": "Josjan Zijlmans", - "author_inst": "Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Department of Child and Adolescent Psychiatry & Psychosocial Care, The Netherlands" - }, - { - "author_name": "Hedy van Oers", - "author_inst": "Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Child and Adolescent Psychiatry & Psychosocial Care, Amsterdam Reproduct" - }, - { - "author_name": "Rowdy de Groot", - "author_inst": "Amsterdam University Medical Center, University of Amsterdam, Department of Medical Informatics, Amsterdam, The Netherlands" - }, - { - "author_name": "Daniel van der Doelen", - "author_inst": "Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands" - }, - { - "author_name": "Hanneke van Ewijk", - "author_inst": "LUMC Curium - Child and Adolescent Psychiatry, Leiden University Medical Center, The Netherlands" - }, - { - "author_name": "Helen Klip", - "author_inst": "Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands" - }, - { - "author_name": "Rikkert van der Lans", - "author_inst": "LUMC Curium - Child and Adolescent Psychiatry, Leiden University Medical Center, The Netherlands" - }, - { - "author_name": "Ronald de Meyer", - "author_inst": "Praktikon, Nijmegen, The Netherlands" - }, - { - "author_name": "Malindi van der Mheen", - "author_inst": "Levvel, Academic Center for Child and Adolescent Psychiatry, Amsterdam, The Netherlands" - }, - { - "author_name": "Maud van Muilekom", - "author_inst": "Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Child and Adolescent Psychiatry & Psychosocial Care, Amsterdam Reproduct" - }, - { - "author_name": "Hyun Ruisch", - "author_inst": "University of Groningen, University Medical Center Groningen, Department of Child and Adolescent Psychiatry, Groningen, The Netherlands" - }, - { - "author_name": "Lorynn Teela", - "author_inst": "Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Child and Adolescent Psychiatry & Psychosocial Care, Amsterdam Reproduct" - }, - { - "author_name": "Germie van den Berg", - "author_inst": "Netherlands Youth Institute, Utrecht, The Netherlands" - }, - { - "author_name": "Hilgo Bruining", - "author_inst": "Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Department of Child and Adolescent Psychiatry & Psychosocial Care, The Netherlands" - }, - { - "author_name": "Rachel van der Rijken", - "author_inst": "Praktikon, Nijmegen, The Netherlands" - }, - { - "author_name": "Jan Buitelaar", - "author_inst": "Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands" - }, - { - "author_name": "Pieter Hoekstra", - "author_inst": "University of Groningen, University Medical Center Groningen, Department of Child and Adolescent Psychiatry, Groningen, The Netherlands" - }, - { - "author_name": "Ramon Lindauer", - "author_inst": "Levvel, Academic Center for Child and Adolescent Psychiatry, Amsterdam, The Netherlands" - }, - { - "author_name": "Kim Oostrom", - "author_inst": "Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Child and Adolescent Psychiatry & Psychosocial Care, Amsterdam Reproduct" - }, - { - "author_name": "Wouter Staal", - "author_inst": "Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands" - }, - { - "author_name": "Robert Vermeiren", - "author_inst": "LUMC Curium - Child and Adolescent Psychiatry, Leiden University Medical Center, The Netherlands" - }, - { - "author_name": "Ronald Cornet", - "author_inst": "Amsterdam University Medical Center, University of Amsterdam, Department of Medical Informatics, Amsterdam, The Netherlands" - }, - { - "author_name": "Lotte Haverman", - "author_inst": "Emma Children's Hospital, Amsterdam University Medical Center, University of Amsterdam, Child and Adolescent Psychiatry & Psychosocial Care, Amsterdam Reproduct" - }, - { - "author_name": "Meike Bartels", - "author_inst": "Department of Biological Psychology, Vrije Universiteit Amsterdam, The Netherlands" - }, - { - "author_name": "Tinca Polderman", - "author_inst": "Amsterdam Public Health Research Institute, Amsterdam University Medical Centres, Amsterdam, The Netherlands" - }, - { - "author_name": "Arne Popma", - "author_inst": "Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Department of Child and Adolescent Psychiatry & Psychosocial Care, The Netherlands" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.10.07.21264655", "rel_title": "The consequences of a year of the COVID-19 pandemic for the mental health of young adult twins in England and Wales", @@ -536534,6 +539625,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.10.05.21264548", + "rel_title": "Feasibility and acceptability of daily testing at school as an alternative to self-isolation following close contact with a confirmed case of COVID-19: A qualitative analysis", + "rel_date": "2021-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.05.21264548", + "rel_abs": "BackgroundDaily testing using a rapid Lateral Flow Device (LFD) has been suggested as an alternative to self-isolation. A randomised trial comparing daily contact testing (DCT) in schools with self-isolation found that SARS-CoV-2 transmission within school was comparable and low in both groups. However, if this approach is to be adopted widely, it is critical that we understand the perspective of those who will be delivering and receiving DCT. The aim of this qualitative process study embedded in the randomised controlled trial (RCT) was to improve understanding of a range of behavioural factors that could influence implementation.\n\nMethodsInterviews were conducted with 63 participants, including staff, students, and parents of students who had been identified as being in close contact with someone with COVID-19. The topic guide explored perceptions of daily testing, understanding of positive and negative test results, and adherence to guidance. Data were analysed using an inductive thematic approach.\n\nResultsResults were organised under three main headings: (1) factors influencing daily testing (2) interpretation of test results (3) behaviour during testing period. Participants recognized that daily testing may allow students to remain in school, which was viewed as necessary for both education and social needs. Whilst some felt safer as a result of daily testing, others raised concerns about safety. Participants did not always understand how to interpret and respond to test results, and although participants reported high levels of adherence to the guidance, improved communications were desired.\n\nConclusionDaily testing may be a feasible and acceptable alternative to self-isolation among close contacts of people who test positive. However, improved communications are needed to ensure that all students and parents have a good understanding of the rationale for testing, what test results mean, how test results should be acted on, and how likely students are to test positive following close contact. Support is needed for students and parents of students who have to self-isolate and for those who have concerns about the safety of daily testing.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sarah Denford", + "author_inst": "University of Bristol" + }, + { + "author_name": "Lauren Towler", + "author_inst": "University of Southampton" + }, + { + "author_name": "Behiye Ali", + "author_inst": "University of Bristol" + }, + { + "author_name": "Georgia Treneman-Evans", + "author_inst": "University of Bristol" + }, + { + "author_name": "Rachael Bloomer", + "author_inst": "University of Bristol" + }, + { + "author_name": "Tim E Peto", + "author_inst": "oxford university" + }, + { + "author_name": "Bernadette C Young", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lucy Yardley", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.10.05.463205", "rel_title": "SARS-CoV-2 causes human BBB injury and neuroinflammation indirectly in a linked organ chip platform", @@ -536687,133 +539825,6 @@ "type": "new results", "category": "synthetic biology" }, - { - "rel_doi": "10.1101/2021.10.05.463271", - "rel_title": "Clinical and immunological signatures of severe COVID-19 in previously healthy patients with clonal hematopoiesis", - "rel_date": "2021-10-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.05.463271", - "rel_abs": "Identifying additional risk factors for COVID-19 severity in numerous previously healthy patients without canonical clinical risk factors remains challenging. In this study, we investigate whether clonal hematopoiesis of indeterminate potential (CHIP), a common aging-related process that predisposes various inflammatory responses, may exert COVID-19 severity. We examine the clinical impact of CHIP in 143 laboratory-confirmed COVID-19 patients. Both stratified analyses and logistic regression including the interaction between canonical risk factors and CHIP show that CHIP is an independent risk factor for severe COVID-19, especially in previously healthy patients. Analyses of 60,310 single-cell immune transcriptome profiles identify distinct immunological signatures for CHIP (+) severe COVID-19 patients, particularly in classical monocytes, with a marked increase in pro-inflammatory cytokine responses and potent IFN-{gamma} mediated hyperinflammation signature. We further demonstrate that the enhanced expression of CHIP (+) specific IFN-{gamma} response genes is attributed to the CHIP mutation-dependent epigenetic reprogramming of poised or bivalent cis-regulatory elements. Our results highlight a unique immunopathogenic mechanism of CHIP in the progression of severe COVID-19, which could be extended to elucidate how CHIP contributes to a variety of human infectious diseases.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Chang Kyung Kang", - "author_inst": "Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea." - }, - { - "author_name": "Baekgyu Choi", - "author_inst": "Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea" - }, - { - "author_name": "Sugyeong Kim", - "author_inst": "Genome Opinion Inc., Seoul 04799, Republic of Korea" - }, - { - "author_name": "Seongwan Park", - "author_inst": "Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea" - }, - { - "author_name": "Soon Ho Yoon", - "author_inst": "Department of Radiology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea." - }, - { - "author_name": "Dohoon Lee", - "author_inst": "Bioinformatics Institute, Seoul National University, Seoul 08826, Republic of Korea" - }, - { - "author_name": "Andrew Lee", - "author_inst": "Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea" - }, - { - "author_name": "Yuji Ko", - "author_inst": "Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea" - }, - { - "author_name": "Euijin Chang", - "author_inst": "Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea." - }, - { - "author_name": "Jongtak Jung", - "author_inst": "Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea. Department of Internal Medicine, Seoul National" - }, - { - "author_name": "Pyoeng Gyun Choe", - "author_inst": "Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea." - }, - { - "author_name": "Wan Beom Park", - "author_inst": "Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea." - }, - { - "author_name": "Eu Suk Kim", - "author_inst": "Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea." - }, - { - "author_name": "Hong Bin Kim", - "author_inst": "Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea. Department of Internal Medicine, Seoul National" - }, - { - "author_name": "Nam Joong Kim", - "author_inst": "Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea." - }, - { - "author_name": "Myoung-don Oh", - "author_inst": "Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea." - }, - { - "author_name": "Sun Kim", - "author_inst": "Department of Computer Science and Engineering, College of Engineering, Seoul National University, Seoul 08826, Republic of Korea Interdisciplinary Program in B" - }, - { - "author_name": "Hogune Im", - "author_inst": "Genome Opinion Inc., Seoul 04799, Republic of Korea" - }, - { - "author_name": "Joohae Kim", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, National Medical Center, Seoul 04564, Republic" - }, - { - "author_name": "Kyuho Kang", - "author_inst": "Department of Biology, Chungbuk National University, Cheongju, 28644, Republic of Korea" - }, - { - "author_name": "Suk-Jo Kang", - "author_inst": "Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea" - }, - { - "author_name": "Yong Hoon Lee", - "author_inst": "Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea" - }, - { - "author_name": "Jaehee Lee", - "author_inst": "Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University," - }, - { - "author_name": "Ji Yeon Lee", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, National Medical Center, Seoul 04564, Republic of Korea" - }, - { - "author_name": "Joon Ho Moon", - "author_inst": "Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea" - }, - { - "author_name": "Kyoung-Ho Song", - "author_inst": "Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea. Department of Internal Medicine, Seoul National" - }, - { - "author_name": "Youngil Koh", - "author_inst": "Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea. Genome Opinion Inc., Seoul 04799, Republic of K" - }, - { - "author_name": "Inkyung Jung", - "author_inst": "KAIST" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.10.05.463150", "rel_title": "Single-cell profiling in COVID-19 associated acute kidney injury reveals patterns of tubule injury and repair in human", @@ -538932,6 +541943,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.10.02.21264210", + "rel_title": "SARS-CoV-2 multi-variant graphene biosensor based on engineered dimeric ACE2 receptor", + "rel_date": "2021-10-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.02.21264210", + "rel_abs": "Fast, reliable and point-of-care systems to detect the SARS-CoV-2 infection are crucial to contain viral spreading and to adopt timely clinical treatments. Many of the rapid detection tests currently in use are based on antibodies that bind viral proteins1. However, newly appearing virus variants accumulate mutations in their RNA sequence and produce proteins, such as Spike, that may show reduced binding affinity to these diagnostic antibodies, resulting in less reliable tests and in the need for continuous update of the sensing systems2. Here we propose a graphene field-effect transistor (gFET) biosensor which exploits the key interaction between the Spike protein and the human ACE2 receptor. This interaction is one of the determinants of host infections and indeed recently evolved Spike variants were shown to increase affinity for ACE2 receptor3. Through extensive computational analyses we show that a chimeric ACE2-Fc construct mimics the ACE2 dimer, normally present on host cells membranes, better than its soluble truncated form. We demonstrate that ACE2-Fc functionalized gFET is effective for in vitro detection of Spike and outperforms the same chip functionalized with either a diagnostic antibody or the soluble ACE2. Our sensor is implemented in a portable, wireless, point-of-care device and successfully detected both alpha and gamma virus variants in patients clinical samples. As incomplete immunization, due to vaccine roll-out, may offer new selective grounds for antibody-escaping virus variants4, our biosensor opens to a class of highly sensitive, rapid and variant-robust SARS-CoV-2 detection systems.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Mattia D'Agostino", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Eleonora Pavoni", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Alice Romagnoli", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy. New York-Marche Structural Biology Ce" + }, + { + "author_name": "Chiara Ardiccioni", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy. New York-Marche Structural Biology Ce" + }, + { + "author_name": "Stefano Motta", + "author_inst": "Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy." + }, + { + "author_name": "Paolo Crippa", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Giorgio Biagetti", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Valentina Notarstefano", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Simone Barocci", + "author_inst": "Department of Clinical Pathology, ASUR Marche AV1, Urbino, PU, Italy." + }, + { + "author_name": "Brianna K Costabile", + "author_inst": "Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA." + }, + { + "author_name": "Gabriele Colasurdo", + "author_inst": "OMME GEARS, Falconara M.am, Zona Ind. CIAF, 60015, Ancona, Italy." + }, + { + "author_name": "Sara Caucci", + "author_inst": "Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy." + }, + { + "author_name": "Davide Mencarelli", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Claudio Turchetti", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Marco Farina", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Luca Pierantoni", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Anna La Teana", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy. New York-Marche Structural Biology Ce" + }, + { + "author_name": "Richard Al Hadi", + "author_inst": "Alcatera Inc, Los Angeles, CA 90024, USA." + }, + { + "author_name": "Mauro Chinappi", + "author_inst": "Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy." + }, + { + "author_name": "Emiliano Trucchi", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Filippo Mancia", + "author_inst": "Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA." + }, + { + "author_name": "Blasco Morozzo della Rocca", + "author_inst": "Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy." + }, + { + "author_name": "Ilda D'Annessa", + "author_inst": "Institute of Chemical Science and Technologies, SCITEC-CNR, Via Mario Bianco 9, 20131, Milan, Italy." + }, + { + "author_name": "Daniele Di Marino", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy. New York-Marche Structural Biology Ce" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.01.452232", "rel_title": "Characterization and Structural Prediction of ORF10, ORF7b, ORF7a, ORF6, Membrane Glycoprotein, and Envelope Protein in SARS-CoV-2 Bangladeshi Variant through Bioinformatics Approach", @@ -539021,29 +542143,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.10.01.21262806", - "rel_title": "Frequency of surveillance testing necessary to reduce transmission of the Delta variant of SARS-CoV-2", - "rel_date": "2021-10-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.01.21262806", - "rel_abs": "We estimate the reduction in transmission of SARS-CoV-2 achievable by surveillance testing of a susceptible population at different frequencies, comparing the cases of both the original Wuhan strain and the Delta variant. We estimate the viral dynamics using viral copy number at first detection combined with considerations arising from aerosol transmission. We take into account the recent findings that infected vaccinated adults may have live viral loads at the same level as infected unvaccinated adults. Our estimates suggest that twice weekly testing, which was adequate for the original strains of SARS-CoV-2 will be insufficient on its own to contain the spread of the Delta variant of concern. We exclude consideration of contact tracing since the rapidity of the onset of viral titre in the case of the Delta variant suggests that unless contact tracing and quarantine are performed very rapidly (i.e., much less than a day), these mitigations will be of minimal impact in reducing transmission. These crude estimates do not take into account heterogeneity of susceptibility, social activity, and compliance, nor do they include the additional reduction in transmission that could be achieved by masking and social distancing. In the setting of a large public university, these considerations suggest that risk-targeted testing of vaccinated students, staff and faculty combined with surveillance testing of all unvaccinated individuals is the most efficient way to reduce transmission of COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ahmed Elbanna", - "author_inst": "University of Illinois Urbana Champaign" - }, - { - "author_name": "Nigel Goldenfeld", - "author_inst": "University of Illinois at Urbana-Champaign" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.01.462840", "rel_title": "Structure selected RBM immunogens prime polyclonal memory responses that neutralize SARS-CoV-2 variants of concern", @@ -540518,6 +543617,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.01.21264412", + "rel_title": "Initial SARS-CoV-2 viral load is associated with disease severity: a retrospective cohort study", + "rel_date": "2021-10-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.01.21264412", + "rel_abs": "BackgroundWe aimed to assess the association between initial SARS-CoV-2 viral load and the subsequent hospital and intensive care unit (ICU) admission and overall survival.\n\nMethodsAll persons with a positive SARS-CoV-2 RT-PCR result from a combined nasopharyngeal (NP) and oropharyngeal (OP) swab (first samples from unique persons only) that was collected between March 17, 2020, and March 31, 2021, in Public Health testing facilities in the region Kennemerland, province of North Holland, the Netherlands were included. Data on hospital (and ICU) admission were collected from the two large teaching hospitals in the region Kennemerland.\n\nResultsIn total, 20,207 SARS-CoV-2 positive persons were included in this study, of whom 310 (1.5%) were hospitalized in a regional hospital within 30 days of their positive SARS-CoV-2 RT-PCR test. When persons were categorized in three SARS-CoV-2 viral load groups, the high viral load group (Cp < 25) was associated with an increased risk of hospitalization as compared to the low viral load group (Cp > 30) (ORadjusted [95%CI]: 1.57 [1.11-2.26], p-value=0.012), adjusted for age and sex. The same association was seen for ICU admission (ORadjusted [95%CI]: 7.06 [2.15-43.57], p-value=0.007). For a subset of 243 of the 310 hospitalized patients, the association of initial SARS-CoV-2 Cp-value with in-hospital mortality was analyzed. The initial SARS-CoV-2 Cp-value of the 17 patients who deceased in the hospital was significantly lower (indicating a higher viral load) compared to the 226 survivors: median Cp-value [IQR]: 22.7 [3.4] vs. 25.0 [5.2], OR[95%CI]: 0.81 [0.68-0.94], p-value = 0.010.\n\nConclusionsOur data show that higher initial SARS-CoV-2 viral load is associated with an increased risk of hospital admission, ICU admission, and in-hospital mortality. We believe that our findings emphasize the added value of reporting SARS-CoV-2 viral load based on Cp-values to identify persons who are at the highest risk of adverse outcomes such as hospital or ICU admission and who therefore may benefit from more intensive monitoring.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Dennis Souverein", + "author_inst": "Regional Public Health Laboratory Kennemerland" + }, + { + "author_name": "Karlijn van Stralen", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Steven van Lelyveld", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Claudia van Gemeren", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Milly Haverkort", + "author_inst": "Public Health Service Kennemerland" + }, + { + "author_name": "Dominic Snijders", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Robin Soetekouw", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Erik Kapteijns", + "author_inst": "Rode Kruis Ziekenhuis" + }, + { + "author_name": "Evelien de Jong", + "author_inst": "Rode Kruis Ziekenhuis" + }, + { + "author_name": "Gonneke Hermanides", + "author_inst": "Rode Kruis Ziekenhuis" + }, + { + "author_name": "Sem Aronson", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Alex Wagemakers", + "author_inst": "Regional Public Health Laboratory Kennemerland" + }, + { + "author_name": "Sjoerd Euser", + "author_inst": "Regional Public Health Laboratory Kennemerland" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.01.21264428", "rel_title": "Risk factors for infection, predictors of severe disease and antibody response to COVID-19 in patients with rheumatic diseases in Portugal - a multicentre, nationwide study", @@ -540719,53 +543885,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.28.21264245", - "rel_title": "Disproportionality analysis of adverse neurological and psychiatric reactions with the ChAdOx1 (Oxford-AstraZeneca) and BNT162b2 (Pfizer-BioNTech) COVID-19 vaccines in the United Kingdom", - "rel_date": "2021-10-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.28.21264245", - "rel_abs": "ObjectiveThe information on neurologic or psychiatric adverse reactions to the COVID-19 vaccines is limited. Our objective was to examine the odds of neurological and psychiatric adverse reactions to BNT162b2 (Pfizer-BioNTech) and ChAdOx1 (Oxford-AstraZeneca) COVID-19 vaccines.\n\nMethodsWe analyzed all Adverse Vaccine Reaction reports to the United Kingdom Medicines and Healthcare products Regulatory Agency between December 9, 2020 and June 30, 2021 that mentioned the BNT162b2 or ChAdOx1 vaccines. We compared the rates of adverse neurological and psychiatric reactions with ChAdOx1 to those with BNT162b2. P-values were obtained by a Bonferroni-adjusted Z-test for proportions.\n\nResultsAs of June 30, 2021, 53.2 M doses of ChAdOx1 and 46.1 M doses of BNT162b2 had been administered. We extracted information from 300,518 distinct reports. The number of individual adverse neurologic or psychiatric reaction reports were less than 200/M doses administered, except headache which was reported in 1,550 and 395 cases/M doses of ChAdOx1 and BNT162b2, respectively. Compared to BNT162b2, cerebral hemorrhagic or thrombotic events, headaches and migraines, Guillain-Barre syndrome and paresthesias, tremor and freezing, delirium, hallucinations, nervousness, poor sleep quality, and postural dizziness were more frequently reported with ChAdOx1. Reactions more frequently reported with BNT162b2 than ChAdOx1 were Bells palsy, facial paralysis, dysgeusia, anxiety, and presyncope or syncope.\n\nConclusionSignificant differences in the neurologic and psychiatric adverse event profiles of the ChAdOx1 and BNT162b2 vaccines may exist, emphasizing the need for additional research. The beneficial and protective effects of the COVID-19 vaccines far outweigh the low potential risk of neurologic and psychiatric reactions.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Santiago Perez-Lloret", - "author_inst": "National Research Council of Argentina" - }, - { - "author_name": "Nikolai Petrovsky", - "author_inst": "Vaxine Pty Ltd" - }, - { - "author_name": "Abdallah Alami", - "author_inst": "McLaughlin Centre for Population Health Risk Assessment, Faculty of Medicine University of Ottawa Ottawa,Canada" - }, - { - "author_name": "James Crispo", - "author_inst": "School of Mathematics and Statistics, Carleton University, Ottawa, Canada" - }, - { - "author_name": "Donald Mattison", - "author_inst": "McLaughlin Centre for Population Health Risk Assessment, Faculty of Medicine University of Ottawa Ottawa,Canada" - }, - { - "author_name": "Matilde Otero-Losadsa", - "author_inst": "National Research Council of Argentina" - }, - { - "author_name": "Francisco Capani", - "author_inst": "National Research Council of Argentina" - }, - { - "author_name": "Daniel Krewski", - "author_inst": "McLaughlin Centre for Population Health Risk Assessment, Faculty of Medicine University of Ottawa Ottawa,Canada" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/276683", "rel_title": "The importance of semantic network brain regions in integrating prior knowledge with an ongoing dialogue", @@ -542240,6 +545359,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.10.01.21264382", + "rel_title": "COVID-19 Pandemic Response in a Migrant Farmworker Community: Excess Mortality, Testing Access and Contact Tracing in Immokalee, Florida", + "rel_date": "2021-10-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.01.21264382", + "rel_abs": "IntroductionWe aim to estimate the impact of COVID-19 in Immokalee, FL and assess community experiences with workplace conditions, access to testing, sources of information, and contact tracing to inform and strengthen local public health sector efforts in reaching and providing high-quality care to the community.\n\nMethodsWe conducted a descriptive analysis of data on COVID-19 deaths for Collier County from May-August 2020. We surveyed a cross-sectional, randomized representative sample of 318 adults living in Immokalee from March-November 2020 to assess socio-demographics, sources of information, ability to follow guidelines, and experiences with local programs. Results were compared across language groups.\n\nResultsAverage excess mortality in Collier County was 108%. The majority surveyed in Immokalee had socio-demographic factors associated with higher COVID risk. Non-English speakers had higher workplace risk due to less ability to work from home. Haitian Creole speakers were less likely to be tested, though all participants were willing to get symptomatic testing and quarantine. Those participants who tested positive or had COVID-19 exposures had low engagement with the contact tracing program, and Spanish-speakers reported lower quality of contact tracing than English speakers.\n\nConclusionsThe community of Immokalee, FL is a vulnerable population that suffered disproportionate deaths from COVID-19. This study reveals language inequities in COVID testing and contact tracing should be targeted in future pandemic response in Immokalee and other migrant farmworker communities.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Neha Limaye", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Brennan Ninesling", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Frantzso Marcelin", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Cody Nolan", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Walter Sobba", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Matthew Hing", + "author_inst": "David Geffen School of Medicine at UCLA" + }, + { + "author_name": "Emily Ptaszek", + "author_inst": "Healthcare Network of Southwest Florida" + }, + { + "author_name": "Fernet Leandre", + "author_inst": "Partners in Health" + }, + { + "author_name": "Daniel Palazuelos", + "author_inst": "Brigham and Women's Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.10.01.462460", "rel_title": "ZBP1 induces inflammatory signaling via RIPK3 and promotes SARS-CoV-2-induced cytokine expression", @@ -542413,29 +545583,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.28.21263671", - "rel_title": "Standardized incidence ratio of the COVID-19 pandemic: a case study in a Midwestern state", - "rel_date": "2021-09-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.28.21263671", - "rel_abs": "MotivationThe Coronavirus disease 2019 (COVID-19) has made a dramatic impact around the world, with some communities facing harsher outcomes than others. We sought to understand how counties in the state of South Dakota (SD) fared compared to expected based on a reference population and what factors contributed to negative outcomes from the pandemic in SD.\n\nMethodsThe Standardized Incidence Ratios (SIR) of all counties, using age-adjusted and crude adjusted hospitalization and death rates were computed using the SD age-adjusted rate as a reference population. In addition, a penalized generalized linear regression model was used to identify factors that are associated with COVID-19 hospitalization and death rates. This model was then used to compute a new SIR after controlling for other socio-demographic and -economic factors.\n\nResultsWe identified counties that had more or less severe outcomes than what would be expected based on the rate of SD after age adjustment. Additionally, race, education, and testing rate were some of the significant factors associated with the outcome. The SIR values after controlling for these additional factors showed change in magnitude from the range of 4 times more severe to 1.5 times more severe out-come than what is expected. Interestingly the lower end of this interval did not have a major change.\n\nConclusionThe age adjusted SIR model used in this study allowed for the identification of counties with more or less severe than what is expected based on the state rate. These counties tended to be those with high nonwhite percentage, which mostly included counties with American Indian reservations. Although several predictors are associated with hospitalization and deaths, the penalized model confirmed what is already reported in literature that race and education level have a very high association with the outcome variables. As can be expected the further adjusted SIR mostly changed in those counties with higher than expected outcomes. We believe that these results may provide useful information to improve the implementation of mitigation strategies to curb the damage of this or future pandemics by providing a way for data-driven resource allocation.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Emma Spors", - "author_inst": "South Dakota State University" - }, - { - "author_name": "Semhar Michael", - "author_inst": "South Dakota State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.09.28.21263801", "rel_title": "Analysis of overdispersion in airborne transmission of Covid-19", @@ -544502,6 +547649,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.27.21264174", + "rel_title": "Counter-intuitive COVID-19 Trajectories - Explanations, Early Warning Indicator and Mitigation Strategies", + "rel_date": "2021-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.27.21264174", + "rel_abs": "The COVID-19 trajectories worldwide have shown several surprising features which are outside the purview of classical epidemiological models. These include (a) almost constant and low daily case rates over extended periods of time, (b) sudden waves emerging from the above solution despite no or minimal change in the level of non-pharmaceutical interventions (NPI), and (c) reduction or flattening of case counts even after relaxation of NPI. To explain these phenomena, we add contact tracing to our recently developed cluster seeding and transmission (CST) model, which is predicated on heterogeneous rather than homogeneous mixing of people in society. With this addition, we find no fewer than four effects which make prediction of epidemic trajectories uncertain. These are (a) cryptogenic instability, where a small increase in population-averaged contact rate causes a large increase in cases, (b) critical mass effect, where a wave can manifest after weeks of quiescence with no change in parameter values, (c) knife-edge effect, where a small change in parameter across a critical value can cause a huge change in the response of the system, and (d) hysteresis effect, where the timing and not just the strength of a particular NPI determines the subsequent evolution of the epidemic. Despite these effects however, it is a robust conclusion that a good contact tracing program can effectively substitute for much more invasive measures. We further find that the contact tracing capacity ratio - a metric of the stress to which the tracers are subject - can act as a reliable early warning indicator of an imminent epidemic wave. Extensive simulations demonstrate that whenever there is a drop in capacity ratio during a period of low daily infections, there is a very high probability of the case counts rising significantly in the immediate future.\n\nAuthor summaryClose to two years into the pandemic, the trajectories of COVID-19 in different places and at different times have shown wild variations and confounded modeling and forecasting efforts. Our new mathematical model can help to explain these variations. Some solutions of our model are non-standard but realistic. For example, we find an epidemic curve where daily cases remain on a plateau for a long time before suddenly exploding into a wave, despite interventions remaining constant throughout. We also find solutions showing that a specific intervention, for example capacity reduction at public gatherings, is very effective if implemented early on in a wave but useless if implemented a little later. Our proposed early warning indicator can be a game-changer for epidemic forecasting and model-based intervention strategies. Current forecasting algorithms have the weakest performance at the inflection points where there is an abrupt change in trend in the daily infection rates. The early warning indicator can give us advance notice of an approaching inflection point, and enable the authorities to take preventive measures before a wave actually arrives. Our results indicate that close communication between contact tracing personnel and public health authorities can achieve synergistic mitigation of the pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "B Shayak", + "author_inst": "Cornell University" + }, + { + "author_name": "Mohit Manoj Sharma", + "author_inst": "Weill Cornell Medicine" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.29.21264261", "rel_title": "World Science against COVID-19: Gender and Geographical Distribution of Research.", @@ -544595,41 +547765,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.09.28.21264265", - "rel_title": "How a positive COVID-19 diagnosis affects the physical, social and psychological wellbeing of people in the United Arab Emirates? An Explorative Qualitative Study", - "rel_date": "2021-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.28.21264265", - "rel_abs": "PurposeExploring the effect of COVID-19 diagnosis on the individual has not been explored through an exploratory qualitative approach. This study aims to explore the physical, social, and psychological impact of the diagnosis on the individual through online interviews.\n\nMethodA qualitative study approach using online interviews was conducted. A sample of 30 participants of different age groups, gender, and nationalities were interviewed to explore the impact of a positive COVID-19 diagnosis on their physical, mental, social, psychological health, and lifestyle practices. An interview guide was created based on coping strategy model and conceptual framework of coping strategies. All interviews were recorded then transcribed after obtaining written consent from participants. Ethics approval was obtained from the United Arab Emirates Social Science Ethics Committee. NVIVO software was used for thematic analysis based on both identified coping models to highlight the most important feelings and emotions, family support, and changes in lifestyle that may impact the COVID-19 patient and family. Researchers identified the themes separately and then verified themes in one meeting.\n\nResultsMajor themes include the physical effects, social effects, psychological effects, spiritual effects, and lifestyle effects. Emerging themes include coping mechanisms, trust in authorities and health care system, appreciation of the role of the government, conspiracy theories, and media roles. Those who had a positive infection towards the end of 2020 and in 2021 described having fewer negative emotions and better psychological resilience.\n\nConclusionThe findings of this study indicate that people diagnosed with COVID-19 have perceived a very good support in terms of their physical health from the government and health authorities, but require social, psychological, and educational support during the infection period and post-recovery.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mouza Alkuwaiti", - "author_inst": "Institute of Public Health, College of Medicine and Health Sciences, United Arab Emirates University" - }, - { - "author_name": "Bayan Abu Hamda", - "author_inst": "Institute of Public Health , College of MedicIne and Health Sciences, United Arab Emirates University" - }, - { - "author_name": "Noof Aljneibi", - "author_inst": "Emirates Centre for Happiness Research, United Arab Emirates University" - }, - { - "author_name": "Marilia Silva Paulo", - "author_inst": "Institute of Public Health, College of Medicine and Health Sciences, United Arab Emirates University" - }, - { - "author_name": "Iffat Elbarazi", - "author_inst": "United Arab Emirates University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.27.21264156", "rel_title": "Inequalities in COVID-19 inequalities research: who had the capacity to respond?", @@ -546644,6 +549779,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.09.27.21264044", + "rel_title": "Sub-Saharan African Countries' COVID-19 Research: An analysis of the External and Internal Contributions, Collaboration Patterns and Funding Sources", + "rel_date": "2021-09-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.27.21264044", + "rel_abs": "This study aims at providing some evidence-based insight into Sub-Saharan Africas first eighteen months of COVID-19 research by evaluating its research contributions, patterns of collaboration, and funding sources. Eighteen months (2020 January 1-2021 June 30) COVID-19 publication data of 46 Sub-Saharan African countries was collected from Scopus for analysis. Country of affiliation of the authors and funding agencies data was analyzed to understand country contributions, collaboration pattern and funding sources. USA (23.08%) and the UK (19.63%), the top two external contributors, collaborated with Sub-Saharan African countries about three times more than other countries. Collaborative papers between Sub-Saharan African countries - without contributions from outside the region-made up less than five percent of the sample, whereas over 50% of the papers were written in collaboration with researchers from outside the region. Organizations that are in USA and the UK funded 45% of all the COVID-19 research from Sub-Saharan Africa. 53.44% of all the funding from Sub-Saharan African countries came from South African organizations. This study provides evidence that pan-African COVID-19 research collaboration is low, perhaps due to poor funding and lack of institutional support within Sub-Saharan Africa. This mirrors the collaborative features of science in Sub-Saharan Africa before the COVID-19 pandemic. The high volume of international collaboration during the pandemic is a good development. There is also a strong need to forge more robust pan-African research collaboration networks, through funding from Africas national and regional government organizations, with the specific objective of meeting local COVID-19 and other healthcare needs.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Toluwase Victor Asubiaro", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Hafsah Shaik", + "author_inst": "Independent Researcher" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.27.21264130", "rel_title": "Effectiveness of the mRNA BNT162b2 vaccine against SARS-CoV-2 severe infections in the Israeli over 60 population: a temporal analysis done by using the national surveillance data.", @@ -546725,49 +549883,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.09.27.21264188", - "rel_title": "Bayesian Inference of State-Level COVID-19 Basic Reproduction Numbers across the United States", - "rel_date": "2021-09-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.27.21264188", - "rel_abs": "Although many persons in the United States have acquired immunity to COVID-19, either through vaccination or infection with SARS-CoV-2, COVID-19 will pose an ongoing threat to non-immune persons so long as disease transmission continues. We can estimate when sustained disease transmission will end in a population by calculating the population-specific basic reproduction number [R]0, the expected number of secondary cases generated by an infected person in the absence of any interventions. The value of [R]0 relates to a herd immunity threshold (HIT), which is given by 1 - 1/[R]0. When the immune fraction of a population exceeds this threshold, sustained disease transmission becomes exponentially unlikely (barring mutations allowing SARS-CoV-2 to escape immunity). Here, we report state-level [R]0 estimates obtained using Bayesian inference. Maximum a posteriori estimates range from 7.1 for New Jersey to 2.3 for Wyoming, indicating that disease transmission varies considerably across states and that reaching herd immunity will be more difficult in some states than others. [R]0 estimates were obtained from compartmental models via the next-generation matrix approach after each model was parameterized using regional daily confirmed case reports of COVID-19 from 21-January-2020 to 21-June-2020. Our [R]0 estimates characterize infectiousness of ancestral strains, but they can be used to determine HITs for a distinct, currently dominant circulating strain, such as SARS-CoV-2 variant Delta (lineage B.1.617.2), if the relative infectiousness of the strain can be ascertained. On the basis of Delta-adjusted HITs, vaccination data, and seroprevalence survey data, we find that no state has achieved herd immunity as of 20-September-2021.\n\nSignificance StatementCOVID-19 will continue to threaten non-immune persons in the presence of ongoing disease transmission. We can estimate when sustained disease transmission will end by calculating the population-specific basic reproduction number [R]0, which relates to a herd immunity threshold (HIT), given by 1 - 1/[R]0. When the immune fraction of a population exceeds this threshold, sustained disease transmission becomes exponentially unlikely. Here, we report state-level [R]0 estimates indicating that disease transmission varies considerably across states. Our [R]0 estimates can also be used to determine HITs for the Delta variant of COVID-19. On the basis of Delta-adjusted HITs, vaccination data, and serological survey results, we find that no state has yet achieved herd immunity.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Abhishek Mallela", - "author_inst": "University of California Davis" - }, - { - "author_name": "Jacob Neumann", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "Ely F Miller", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "Ye Chen", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "Richard G Posner", - "author_inst": "Northern Arizona University" - }, - { - "author_name": "Yen Ting Lin", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "William S Hlavacek", - "author_inst": "Los Alamos National Laboratory" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.27.21264163", "rel_title": "Four SARS-CoV-2 vaccines induce quantitatively different antibody responses against SARS-CoV-2 variants", @@ -548194,6 +551309,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.25.21264082", + "rel_title": "Contact surveys reveal heterogeneities in age-group contributions to SARS-CoV-2 dynamics in the United States", + "rel_date": "2021-09-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.25.21264082", + "rel_abs": "SARS-CoV-2 is spread primarily through person-to-person contacts. Quantifying population contact rates is important for understanding the impact of physical distancing policies and for modeling COVID-19, but contact patterns have changed substantially over time due to shifting policies and behaviors. There are surprisingly few empirical estimates of age-structured contact rates in the United States both before and throughout the COVID-19 pandemic that capture these changes. Here, we use data from six waves of the Berkeley Interpersonal Contact Survey (BICS), which collected detailed contact data between March 22, 2020 and February 15, 2021 across six metropolitan designated market areas (DMA) in the United States. Contact rates were low across all six DMAs at the start of the pandemic. We find steady increases in the mean and median number of contacts across these localities over time, as well as a greater proportion of respondents reporting a high number of contacts. We also find that young adults between ages 18 and 34 reported more contacts on average compared to other age groups. The 65 and older age group consistently reported low levels of contact throughout the study period. To understand the impact of these changing contact patterns, we simulate COVID-19 dynamics in each DMA using an age-structured mechanistic model. We compare results from models that use BICS contact rate estimates versus commonly used alternative contact rate sources. We find that simulations parameterized with BICS estimates give insight into time-varying changes in relative incidence by age group that are not captured in the absence of these frequently updated estimates. We also find that simulation results based on BICS estimates closely match observed data on the age distribution of cases, and changes in these distributions over time. Together these findings highlight the role of different age groups in driving and sustaining SARS-CoV-2 transmission in the U.S. We also show the utility of repeated contact surveys in revealing heterogeneities in the epidemiology of COVID-19 across localities in the United States.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Taylor Chin", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Dennis M. Feehan", + "author_inst": "UC Berkeley" + }, + { + "author_name": "Caroline O. Buckee", + "author_inst": "Harvard School of Public Health" + }, + { + "author_name": "Ayesha S. Mahmud", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.26.21264145", "rel_title": "Racial and ethnic inequalities in COVID-19 mortality within carceral settings: An analysis of Texas prisons and jails", @@ -548287,45 +551433,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2021.09.26.21264152", - "rel_title": "Intravenous Immunoglobulin (IVIG) in Treating Non-ventilated COVID-19 Patients with Moderate to Severe Hypoxia is Pharmacoeconomically Favorable When Appropriately Targeted", - "rel_date": "2021-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.26.21264152", - "rel_abs": "BackgroundPrior studies have shown that intravenous immunoglobulin (IVIG) can improve outcomes in patients with COVID-19, but the high costs of IVIG leave questions as to its pharmacoeconomic value.\n\nMethodsThe hospital costs of 2 IVIG vs. non-IVIG COVID-19 patient groups were compared. The first cohort was a case-control analysis of 10 non-ventilated moderately to severely hypoxic COVID-19 patients who received IVIG (Privigen) matched 1:2 with 20 control patients of similar age, body mass index (BMI), degree of hypoxemia, and co-morbidities. The second cohort consisted of patients enrolled in a previously published randomized open-label prospective study of 14 COVID-19 patients receiving standard of care (SOC) versus 13 patients who received SOC plus IVIG (Octagam 10%).\n\nResultsAmong the first case control population, mean total direct costs including IVIG for the treatment group was $21,982 per IVIG-treated case versus $42,431 per case for matched non-IVIG receiving controls, representing a net cost reduction of $20,449 (48%) per case. For the second (randomized) group, mean total direct costs including IVIG for the treatment group was $28,268 per case versus $62,707 per case for untreated controls, representing a net cost reduction of $34,439 (55%) per case. 24% of the non-IVIG patients had hospital costs exceeded $80,000, as compared to none of the IVIG patient host (p=0.016, Fisher exact test).\n\nConclusionWhen allocated to the appropriate patient type (moderate to severe illness without end-organ comorbidities and age <70 years), IVIG can significantly reduce hospital costs in COVID-19 care. More importantly, it may reduce the demand on scare critical care resources during the COVID-19 pandemic.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Matthew Poremba", - "author_inst": "Sharp Memorial Hospital" - }, - { - "author_name": "Matthew Dehner", - "author_inst": "Sharp Memorial Hospital" - }, - { - "author_name": "Alexandra Perreiter", - "author_inst": "Sharp Memorial Hospital" - }, - { - "author_name": "Ashley Semma", - "author_inst": "Sharp Memorial Hospital" - }, - { - "author_name": "Kimbery Mills", - "author_inst": "Sharp Memorial Hospital" - }, - { - "author_name": "George Sakoulas", - "author_inst": "UCSD School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2021.09.26.21264067", "rel_title": "Effect of different disease-modifying therapies on humoral response to BNT162b2 vaccine in Sardinian multiple sclerosis patients", @@ -550328,6 +553435,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.23.21264014", + "rel_title": "Neutralizing efficacy of vaccines against the SARS-CoV-2 Mu variant", + "rel_date": "2021-09-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.23.21264014", + "rel_abs": "The rise of mutant strains of SARS-CoV-2 poses an additional problem to the existing pandemic of COVID-19. There are rising concerns about the Mu variant which can escape humoral immunity acquired from infections from previous strains or vaccines. We examined the neutralizing efficacy of the BNT162b2 mRNA vaccine against the Mu variant and report that the vaccine has 76% neutralizing effectiveness against the Mu compared to 96% with the original strain. We also show that Mu, similar to the Delta variant, causes cell-to-cell fusion which can be an additional factor for the variant to escape vaccine-mediated humoral immunity. Despite the rise in vaccine escape strains, the vaccine still possesses adequate ability to neutralize majority of the mutants.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kei Miyakawa", + "author_inst": "Yokohama City University School of Medicine" + }, + { + "author_name": "Sundararaj Stanleyraj Jeremiah", + "author_inst": "Yokohama City University School of Medicine" + }, + { + "author_name": "Hideaki Kato", + "author_inst": "Yokohama City University Hospital" + }, + { + "author_name": "Akihide Ryo", + "author_inst": "Yokohama City University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.21.21263902", "rel_title": "Quantification and prognostic significance of interferon-\u03b3 secreting SARS-CoV-2 responsive T cells in hospitalised patients with acute COVID-19", @@ -550569,53 +553707,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.22.21263944", - "rel_title": "The importance of sustained compliance with physical distancing during COVID-19 vaccination rollout", - "rel_date": "2021-09-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.22.21263944", - "rel_abs": "Mass vaccination campaigns against SARS-CoV-2 are ongoing in many countries with increasing vaccination coverage enabling relaxation of lockdowns. Vaccination rollout is frequently supplemented with advisory from public health authorities for continuation of physical distancing measures. Compliance with these measures is waning while more transmissible virus variants such as Alpha (B.1.1.7) and Delta (B.1.617.2) have emerged. In this work, we considered a population where the waning of compliance depends on vaccine coverage. We used a SARS-CoV-2 transmission model which captures the feedback between compliance, infection incidence, and vaccination coverage to investigate factors that contribute to the increase of the prevalence of infection during the initial stages of the vaccination rollout as compared to no vaccination scenario. We analysed how the vaccine uptake rate affects cumulative numbers of new infections three and six months after the start of vaccination. Our results suggest that the combination of fast waning compliance in non-vaccinated population, low compliance in vaccinated population and more transmissible virus variants may result in a higher cumulative number of new infections than in a situation without vaccination. These adverse effects can be alleviated if vaccinated individuals do not revert to pre-pandemic contact rates, and if non-vaccinated individuals remain compliant with physical distancing measures. Both require convincing, clear and appropriately targeted communication strategies by public health authorities.\n\nSignificance StatementSARS-CoV-2 vaccination campaigns are in progress in many countries around the world. As the vaccination coverage increases, the compliance with physical distancing measures aimed at reducing virus transmission may decline. Using a socio-epidemiological model we identify factors that are the drivers of increased transmission when SARS-CoV-2 prevalence is higher than the projected prevalence without vaccination. To maximize the benefits of vaccination campaigns, compliance in vaccinated and non-vaccinated groups should be targeted prioritizing one group over the other depending on the vaccination rate, the efficacy of vaccine in blocking the infection, and the circulating variant.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Alexandra Teslya", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Ganna Rozhnova", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Thi Mui Pham", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Daphne A van Wees", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Hendrik Nunner", - "author_inst": "Utrecht University" - }, - { - "author_name": "Noortje G. Godijk", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Martin CJ Bootsma", - "author_inst": "Utrecht University" - }, - { - "author_name": "Mirjam E Kretzschmar", - "author_inst": "University Medical Center Utrecht" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.23.21264009", "rel_title": "Cross-sectional assessment of predictors for COVID-19 vaccine uptake: an online survey in Greece", @@ -552046,6 +555137,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.09.23.461605", + "rel_title": "Apixaban, an orally available anticoagulant, inhibits SARS-CoV-2 replication by targeting its major protease in a non-competitive way", + "rel_date": "2021-09-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.23.461605", + "rel_abs": "Anticoagulants are associated with clinical benefit against the 2019 coronavirus disease (COVID-19), preventing COVID-19 associated coagulopathy. Blood coagulation factor Xa (FXa) and SARS-CoV-2 major protease (Mpro) share over 80% homology at the three-dimensional protein level. Thus, it is worth interrogating whether there is crosstalk between inhibitors and substrates between these enzymes. Here, we found that the clinically-approved FXa inhibitor apixaban targets SARS-CoV-2 Mpro with a 21-fold higher potency than boceprevir (GC376). Apixaban displayed a non-competitive mechanism of inhibition towards Mpro, since it targets the enzyme/substrate complex and the allosteric site onto the viral protease. Enzymatic assays were further validated in infected Calu-3 cells, which reveal that apixaban decreases the production of infectious viral particles in a dose-dependent manner, with an inhibitory potency in the micromolar range. Our results are in line with the proposed early use of anticoagulants, including FXa inhibitors, to improve clinical outcome of COVID-19 patients. In this context, apixaban may display a dual mechanism of action by targeting FXa to prevent coagulopathy and, at some level, SARS-CoV-2 Mpro.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Otavio Augusto Chaves", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Carolina Q. Sacramento", + "author_inst": "FIOCRUZ" + }, + { + "author_name": "Natalia Fintelman-Rodrigues", + "author_inst": "FIOCRUZ" + }, + { + "author_name": "Jairo Ramos Temerozo", + "author_inst": "Oswaldo Cruz Institute" + }, + { + "author_name": "Filipe Pereira-Dutra", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Daniella M. Mizurini", + "author_inst": "UFRJ" + }, + { + "author_name": "Robson Q. Monteiro", + "author_inst": "UFRJ" + }, + { + "author_name": "Leonardo Vazquez", + "author_inst": "Fiocruz" + }, + { + "author_name": "Patricia T. Bozza", + "author_inst": "Lab Imunofarmacologia, Instituto Oswaldo Cruz, FIOCRUZ" + }, + { + "author_name": "Hugo Caire Castro-Faria-Neto", + "author_inst": "Fiocruz" + }, + { + "author_name": "Thiago Moreno L. Souza", + "author_inst": "Oswaldo Cruz Foundation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.09.23.21262822", "rel_title": "Plasma S-Adenosylmethionine is Associated with Lung Injury in COVID-19", @@ -552263,89 +555413,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.21.21262619", - "rel_title": "Saliva-based detection of COVID-19 infection in a real-world setting using reagent-free Raman spectroscopy and machine learning", - "rel_date": "2021-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.21.21262619", - "rel_abs": "SignificanceThe primary method of COVID-19 detection is reverse transcription polymerase chain reaction (RT-PCR) testing. PCR test sensitivity may decrease as more variants of concern arise.\n\nAimWe aimed to develop a reagent-free way to detect COVID-19 in a real-world setting with minimal constraints on sample acquisition.\n\nApproachWe present a workflow for collecting, preparing and imaging dried saliva supernatant droplets using a non-invasive, label-free technique - Raman spectroscopy - to detect changes in the molecular profile of saliva associated with COVID-19 infection.\n\nResultsUsing machine learning and droplet segmentation, amongst all confounding factors, we discriminated between COVID-positive and negative individuals yielding receiver operating coefficient (ROC) curves with an area under curve (AUC) of 0.8 in both males (79% sensitivity, 75% specificity) and females (84% sensitivity, 64% specificity). Taking the sex of the saliva donor into account increased the AUC by 5%.\n\nConclusionThese findings may pave the way for new rapid Raman spectroscopic screening tools for COVID-19 and other infectious diseases.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Katherine J I Ember", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Fran\u00e7ois Daoust", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Myriam Mahfoud", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Fr\u00e9d\u00e9rick Dallaire", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Esmat Zamani", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Trang Tran", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Arthur Plante", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Mame-Kany Diop", - "author_inst": "Center de recherche du Center hospitalier de l Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Tien Nguyen", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Am\u00e9lie St-Georges-Robillard", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Nassim Ksantini", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Julie Lanthier", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Antoine Filiatrault", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Guillaume Sheehy", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Caroline Quach", - "author_inst": "Research Center, CHU Sainte-Justine, Montreal, Canada; Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada" - }, - { - "author_name": "Dominique Trudel", - "author_inst": "Center de recherche du CHUM; Institut du cancer de Montreal; Department of Pathology and Cellular Biology, Universite de Montreal; Department of Pathology, CHUM" - }, - { - "author_name": "Fr\u00e9d\u00e9ric Leblond", - "author_inst": "Polytechnique Montreal" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.12.21263442", "rel_title": "Financial and Non-financial Conflicts of Interest Among the Japanese Government Advisory Board Members Concerning Coronavirus Disease 2019", @@ -553756,6 +556823,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.09.18.21263773", + "rel_title": "COVID-19 Acceleration and Vaccine Status in France - August 2021", + "rel_date": "2021-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.18.21263773", + "rel_abs": "ObjectivesThis note provides an assessment of COVID-19 acceleration among groups with different vaccine status in France.\n\nMethodsWe assess viral acceleration using a novel indicator introduced in Baunez et al. (2021). The acceleration index relates the percentage change of tests that have been performed on a given day to the percentage change in the associated positive cases that same day. We compare viral acceleration among vaccinated and unvaccinated individuals in France over the period May 31st - August 29, 2021.\n\nResultsOnce the state of the epidemic within each groups is accounted for, it turns out that viral acceleration has since mid-July converged to similar levels among vaccinated and unvaccinated individuals in France, even though viral speed is larger for the latter group compared to the former.\n\nConclusionOur results call for an increasing testing effort for both vaccinated and unvaccinated individuals, in view of the fact that viral circulation is currently accelerating at similar levels for both groups in France.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Christelle Baunez", + "author_inst": "Institut Neurosciences Timone" + }, + { + "author_name": "Mickael Degoulet", + "author_inst": "Institut Neurosciences Timone" + }, + { + "author_name": "Stephane Luchini", + "author_inst": "Aix-Marseille School of Economics" + }, + { + "author_name": "Patrick Pintus", + "author_inst": "Aix-Marseille University and CNRS" + }, + { + "author_name": "Miriam Teschl", + "author_inst": "Aix-Marseille School of Economics" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.09.19.21262487", "rel_title": "Genomic analysis of SARS-CoV-2 breakthrough infections from Varanasi, India", @@ -553977,37 +557079,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2021.09.18.21263783", - "rel_title": "The Delta Variant Had Negligible Impact on COVID-19 Vaccine Effectiveness in the USA", - "rel_date": "2021-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.18.21263783", - "rel_abs": "The SARS-CoV-2 Delta variant (B.1.617.2) was initially identified in India in December 2020. Due to its high transmissibility, its prevalence in the U.S.A. grew from a near-zero baseline in early May 2021 to nearly 100% by late August 2021, according to CDC tracking. We accessed openly available data sources from the public health authorities of seven U.S. states, five U.S. counties, and the District of Columbia on RT-PCR COVID-19 tests split by the COVID-19 vaccination status of individuals tested during this period. Together, these time series enable estimation and tracking of COVID-19 vaccine effectiveness (VE*) (against RT-PCR diagnosed infection) concurrently with the growth of Delta variant prevalence in those locations. Our analyses reveal that in each locality the VE* for the combined set of all three US vaccines remained relatively stable and quite well-performing, despite the dramatic concurrent rise of Delta variant prevalence. We conclude that the Delta variant does not significantly evade vaccine-induced immunity. The variations in our measured VE* appear to be driven by demographic factors affecting the composition of the vaccinated cohorts, particularly as pertains to age distribution. We report that the measured VE*, aggregated across the collected sites, began at a value of about 0.9 in mid-May, declined to about 0.76 by mid-July, and recovered to about 0.9 by mid-September.\n\nSummaryWe estimated local COVID-19 vaccine effectiveness using RT-PCR COVID-19 test data broken out by vaccination status from select localities in the U.S.A. between 15 May and 15 September 2021 while the SARS-CoV-2 Delta variant (B.1.617.2) was ascending from essentially zero prevalence to total dominance of the genome, and showed that the rise of the Delta variant had negligible effect on vaccine effectiveness.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ben Blaiszik", - "author_inst": "Argonne National Laboratory, Argonne, IL, USA" - }, - { - "author_name": "Carlo Graziani", - "author_inst": "Argonne National Laboratory, Argonne, IL, USA" - }, - { - "author_name": "James L. Olds", - "author_inst": "Schar School of Policy and Government, George Mason University, Arlington, VA, USA" - }, - { - "author_name": "Ian Foster", - "author_inst": "Argonne National Laboratory, Argonne, IL, USA" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.19.21263805", "rel_title": "Identifying At-Risk Communities and Key Vulnerability Indicators in the COVID-19 Pandemic", @@ -555722,6 +558793,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.09.16.21263576", + "rel_title": "Impact of prior SARS-CoV-2 infection on post-vaccination SARS-CoV-2 spike IgG antibodies in a longitudinal cohort of healthcare workers", + "rel_date": "2021-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.16.21263576", + "rel_abs": "Waning serum antibodies against SARS-CoV-2 have sparked discussions about long-term immunity and need for vaccine boosters. We examined SARS-CoV-2 spike IgG antibodies in a longitudinal cohort, comparing antibody decay in individuals who received an mRNA SARS-CoV-2 vaccine, with and without prior SARS-CoV-2 infection. We completed a longitudinal cohort of healthcare workers (HWs) between June 2020 and September 2021. HWs were included if they had a serum sample collected after SARS-CoV-2 infection and/or a serum sample collected [≥] 14 days after second dose of an mRNA SARS-CoV-2 vaccine. Linear regression models adjusting for vaccine type, age, and sex were used to compare post-vaccination antibody levels between 1) HWs with and without prior SARS-CoV-2 infection and 2) HWs with prior SARS-CoV-2 infection [≤] 90 days and > 90 days prior to first vaccine. Serum was collected from 98 HWs after SARS-CoV-2 infection and before vaccine, and 1960 HWs [≥] 14 days following second vaccine dose. Serum spike antibody levels were higher after vaccination than after natural infection. Compared to SARS-CoV-2 naive individuals, those with prior infection maintained higher post-vaccination mean spike IgG values at 1, 3, and 6 months, after adjusting for age, sex, and vaccine type. Individuals with PCR-confirmed infection > 90 days before vaccination had higher post-vaccination antibody levels than individuals infected [≤] 90 days before vaccination. Individuals with three exposures to spike protein maintain the highest antibody levels particularly when first and second exposures were greater than 90 days apart. A booster dose provides a third exposure and may similarly induce a more durable antibody response.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Diana Zhong", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Shaoming Xiao", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Amanda K Debes", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Emily R Egbert", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Patrizio Caturegli", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Elizabeth Colantuoni", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Aaron M Milstone", + "author_inst": "Johns Hopkins University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.20.21263875", "rel_title": "Comparative single-dose mRNA and ChAdOx1 vaccine effectiveness against SARS-CoV-2, including early variants of concern: a test-negative design, British Columbia, Canada", @@ -555863,20 +558977,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.09.18.21263775", - "rel_title": "Detection of COVID-19 in smartphone-based breathing recordings using CNN-BiLSTM: a pre-screening deep learning tool", - "rel_date": "2021-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.18.21263775", - "rel_abs": "This study was sought to investigate the feasibility of using smartphone-based breathing sounds within a deep learning framework to discriminate between COVID-19, including asymptomatic, and healthy subjects. A total of 480 breathing sounds (240 shallow and 240 deep) were obtained from a publicly available database named Coswara. These sounds were recorded by 120 COVID-19 and 120 healthy subjects via a smartphone microphone through a website application. A deep learning framework was proposed herein the relies on hand-crafted features extracted from the original recordings and from the mel-frequency cepstral coefficients (MFCC) as well as deep-activated features learned by a combination of convolutional neural network and bi-directional long short-term memory units (CNN-BiLSTM). Analysis of the normal distribution of the combined MFCC values showed that COVID-19 subjects tended to have a distribution that is skewed more towards the right side of the zero mean (shallow: 0.59{+/-}1.74, deep: 0.65{+/-}4.35). In addition, the proposed deep learning approach had an overall discrimination accuracy of 94.58% and 92.08% using shallow and deep recordings, respectively. Furthermore, it detected COVID-19 subjects successfully with a maximum sensitivity of 94.21%, specificity of 94.96%, and area under the receiver operating characteristic (AUROC) curves of 0.90. Among the 120 COVID-19 participants, asymptomatic subjects (18 subjects) were successfully detected with 100.00% accuracy using shallow recordings and 88.89% using deep recordings. This study paves the way towards utilizing smartphone-based breathing sounds for the purpose of COVID-19 detection. The observations found in this study were promising to suggest deep learning and smartphone-based breathing sounds as an effective pre-screening tool for COVID-19 alongside the current reverse-transcription polymerase chain reaction (RT-PCR) assay. It can be considered as an early, rapid, easily distributed, time-efficient, and almost no-cost diagnosis technique complying with social distancing restrictions during COVID-19 pandemic.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.09.17.21263748", "rel_title": "Impact of COVID 19 on the quality of life OF LIFE (QoL) of patients living with Sickle Cell Disorder (SCD) in Lagos Nigeria", @@ -557185,6 +560285,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.17.21263723", + "rel_title": "Optimized Post-Vaccination Strategies and Preventative Measures for SARS-CoV-2", + "rel_date": "2021-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.17.21263723", + "rel_abs": "IntroductionSince March of 2020, over 210 million SARS-CoV-2 cases have been reported and roughly five billion doses of a SARS-CoV-2 vaccine have been delivered. The rise of the more infectious delta variant has recently indicated the value of reinstating previously relaxed non-pharmacological and test-driven preventative measures. These efforts have been met with resistance, due, in part, to a lack of site-specific quantitative evidence which can justify their value. As vaccination rates continue to increase, a gap in knowledge exists regarding appropriate thresholds for escalation and de-escalation of COVID-19 preventative measures.\n\nMethodsWe conducted a series of simulation experiments, trialing the spread of SARS-CoV-2 virus in a hypothesized working environment that is subject to COVID-19 infections from the surrounding community. We established cohorts of individuals who would, in simulation, work together for a set period of time. With these cohorts, we tested the rates of workplace and community acquired infections based on applied isolation strategies, community infection rates (CIR), scales of testing, non-pharmaceutical interventions, variant predominances and testing strategies, vaccination coverages, and vaccination efficacies of the members included. Permuting through each combination of these variables, we estimated expected case counts for 33,462 unique workplace scenarios.\n\nResultsWhen the CIR is 5 new confirmed cases per 100,000 or fewer, and at 50% of the workforce is vaccinated with a 95% efficacious vaccine, then testing daily with an antigen-based or PCR based test in only unvaccinated workers will result in less than one infection through 4,800 person weeks. When the community infection rate per 100,000 persons is less than or equal to 60, and the vaccination coverage of the workforce is 100% with 95% vaccine efficacy then no masking or routine testing + isolation strategies are needed to prevent workplace acquired infections regardless of variant predominance. Identifying and isolating workers with antigen-based SARS-CoV-2 testing methods results in the same or fewer workplace acquired infections than testing with polymerase chain reaction (PCR) methods.\n\nConclusionsSpecific scenarios exist in which preventative measures taken to prevent SARS-CoV-2 spread, including masking, and testing plus isolation strategies can safely be relaxed. Further, efficacious testing with quarantine strategies exist for implementation in only unvaccinated cohorts in a workplace. Due to shorter turnaround time, antigen-based testing with lower sensitivity is more effective than PCR testing with higher sensitivities in comparable testing strategies. The general reference interactive heatmap we provide can be used for site specific, immediate, parameter-based case count predictions to inform appropriate institutional policy making.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Rowland W Pettit", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Bo Peng", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Patrick Yu", + "author_inst": "Corporate Medical Advisors, Houston, Texas, USA" + }, + { + "author_name": "Peter Matos", + "author_inst": "Corporate Medical Advisors, Houston, Texas, USA" + }, + { + "author_name": "Alexander L. Greninger", + "author_inst": "Laboratory Medicine, University of Washington" + }, + { + "author_name": "Julie McCashin", + "author_inst": "International S.O.S., Houston, TX" + }, + { + "author_name": "Christopher Ian Amos", + "author_inst": "Baylor College of Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.09.16.21263714", "rel_title": "The Relationship of Vaccine Uptake and COVID-19 Infections among Nursing Home Staff and Residents in Missouri", @@ -557282,37 +560425,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.09.19.460950", - "rel_title": "IL13Pred: A method for predicting immunoregulatory cytokine IL-13 inducing peptides for managing COVID-19 severity.", - "rel_date": "2021-09-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.19.460950", - "rel_abs": "Interleukin 13 (IL-13) is an immunoregulatory cytokine that is primarily released by activated T-helper 2 cells. It induces the pathogenesis of many allergic diseases, such as airway hyperresponsiveness, glycoprotein hypersecretion and goblet cell hyperplasia. IL-13 also inhibits tumor immunosurveillance, which leads to carcinogenesis. In recent studies, elevated IL-13 serum levels have been shown in severe COVID-19 patients. Thus it is important to predict IL-13 inducing peptides or regions in a protein for designing safe protein therapeutics particularly immunotherapeutic. This paper describes a method developed for predicting, designing and scanning IL-13 inducing peptides. The dataset used in this study contain experimentally validated 313 IL-13 inducing peptides and 2908 non-inducing homo-sapiens peptides extracted from the immune epitope database (IEDB). We have extracted 95 key features using SVC-L1 technique from the originally generated 9165 features using Pfeature. Further, these key features were ranked based on their prediction ability, and top 10 features were used for building machine learning prediction models. In this study, we have deployed various machine learning techniques to develop models for predicting IL-13 inducing peptides. These models were trained, test and evaluated using five-fold cross-validation techniques; best model were evaluated on independent dataset. Our best model based on XGBoost achieves a maximum AUC of 0.83 and 0.80 on the training and independent dataset, respectively. Our analysis indicate that certain SARS-COV2 variants are more prone to induce IL-13 in COVID-19 patients. A standalone package as well as a web server named IL-13Pred has been developed for predicting IL-13 inducing peptides (https://webs.iiitd.edu.in/raghava/il13pred/).\n\nKey PointsO_LIInterleukin-13, an immunoregulatory cytokine plays an important role in increasing severity of COVID-19 and other diseases.\nC_LIO_LIIL-13Pred is a highly accurate in-silico method developed for predicting the IL-13 inducing peptides/ epitopes.\nC_LIO_LIIL-13 inducing peptides are reported in various SARS-CoV2 strains/variants proteins.\nC_LIO_LIThis method can be used to detect IL-13 inducing peptides in vaccine candidates.\nC_LIO_LIUser friendly web server and standalone software is freely available for IL-13Pred\nC_LI\n\nAuthors BiographyO_LIShipra Jain is currently working as Ph.D. in Computational Biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.\nC_LIO_LIAnjali Dhall is currently working as Ph.D. in Computational Biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.\nC_LIO_LISumeet Patiyal is currently working as Ph.D. in Computational Biology from Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.\nC_LIO_LIGajendra P. S. Raghava is currently working as Professor and Head of Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Shipra Jain", - "author_inst": "Indraprastha Institute of Information Technology, Delhi" - }, - { - "author_name": "Anjali Dhall", - "author_inst": "Indraprastha Institute of Information Technology, Delhi" - }, - { - "author_name": "Sumeet Patiyal", - "author_inst": "Indraprastha Institute of Information Technology, Delhi" - }, - { - "author_name": "Gajendra P.S. Raghava", - "author_inst": "Indraprastha Institute of Information Technology" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.09.20.461041", "rel_title": "Mechanistic Insights into the Effects of Key Mutations on SARS-CoV-2 RBD-ACE2 Binding", @@ -558795,6 +561907,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.14.21262977", + "rel_title": "Spatiotemporal analyses illuminate the competitive advantage of a SARS-CoV-2 variant of concern over a variant of interest", + "rel_date": "2021-09-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.14.21262977", + "rel_abs": "The emergence of novel SARS-CoV-2 variants in late 2020 and early 2021 raised alarm worldwide and prompted reassessment of the management, surveillance, and projected future of COVID-19. Mutations that confer competitive advantages by increasing transmissibility or immune evasion have been associated with the localized dominance of single variants. Thus, elucidating the evolutionary and epidemiological dynamics among novel variants is essential for understanding the trajectory of the COVID-19 pandemic. Here we show the interplay between B.1.1.7 (Alpha) and B.1.526 (Iota) in New York (NY) from December 2020 to April 2021 through phylogeographic analyses, space-time scan statistics, and cartographic visualization. Our results indicate that B.1.526 likely evolved in the Bronx in late 2020, providing opportunity for an initial foothold in the heavily interconnected New York City (NYC) region, as evidenced by numerous exportations to surrounding locations. In contrast, B.1.1.7 became dominant in regions of upstate NY where B.1.526 had limited presence, suggesting that B.1.1.7 was able to spread more efficiently in the absence of B.1.526. Clusters discovered from the spatial-time scan analysis supported the role of competition between B.1.526 and B.1.1.7 in NYC in March 2021 and the outsized presence of B.1.1.7 in upstate NY in April 2021. Although B.1.526 likely delayed the rise of B.1.1.7 in NYC, B.1.1.7 became the dominant variant in the Metro region by the end of the study period. These results reveal the advantages endemicity may grant to a variant (founder effect), despite the higher fitness of an introduced lineage. Our research highlights the dynamics of inter-variant competition at a time when B.1.617.2 (Delta) is overtaking B.1.1.7 as the dominant lineage worldwide. We believe our combined spatiotemporal methodologies can disentangle the complexities of shifting SARS-CoV-2 variant landscapes at a time when the evolution of variants with additional fitness advantages is impending.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Alexis Russell", + "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "Collin O'Connor", + "author_inst": "Division of Epidemiology, New York State Department of Health" + }, + { + "author_name": "Erica Lasek-Nesselquist", + "author_inst": "Bioinformatics Core, Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "Jonathan Plitnick", + "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "John P Kelly", + "author_inst": "Applied Genomic Technology Core, Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "Daryl M Lamson", + "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "Kirsten St George", + "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.14.21263153", "rel_title": "Evolution of COVID-19 mortality over time: results from the Swiss hospital surveillance system (CH-SUR)", @@ -559244,45 +562399,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.09.15.21263628", - "rel_title": "COVID-19 Vaccination and Healthcare Demand", - "rel_date": "2021-09-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.15.21263628", - "rel_abs": "One of the driving concerns during any epidemic is the strain on the healthcare system. As we have seen many times over the globe with the COVID-19 pandemic, hospitals and ICUs can quickly become overwhelmed by cases. While strict periods of public health mitigation have certainly helped decrease incidence and thus healthcare demand, vaccination is the only clear long-term solution. In this paper, we develop a two-module model to forecast the effects of relaxation of non-pharmaceutical intervention and vaccine uptake on daily incidence, and the cascade effects on healthcare demand. The first module is a simple epidemiological model which incorporates non-pharmaceutical intervention, the relaxation of such measures and vaccination campaigns to predict caseloads into the the Fall of 2021. This module is then fed into a healthcare module which can forecast the number of doctor visits, the number of occupied hospital beds, number of occupied ICU beds and any excess demand of these. From this module we can also estimate the length of stay of individuals in ICU. For model verification and forecasting, we use the four most populous Canadian provinces as a case study.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Matthew Betti", - "author_inst": "Mount Allison University" - }, - { - "author_name": "Amira Hassan Abouleish", - "author_inst": "Mount Allison University" - }, - { - "author_name": "Victoria Spofford", - "author_inst": "Health Canada" - }, - { - "author_name": "Cory Peddigrew", - "author_inst": "Health Canada" - }, - { - "author_name": "Alan Diener", - "author_inst": "Health Canada" - }, - { - "author_name": "Jane M Heffernan", - "author_inst": "York University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2021.09.18.460926", "rel_title": "A Genotype-to-Phenotype Modeling Framework to Predict Human Pathogenicity of Novel Coronaviruses", @@ -561197,6 +564313,101 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.09.13.21263487", + "rel_title": "SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population", + "rel_date": "2021-09-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263487", + "rel_abs": "We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Jia Wei", + "author_inst": "University of Oxford" + }, + { + "author_name": "Koen B. Pouwels", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nicole Stoesser", + "author_inst": "University of Oxford" + }, + { + "author_name": "Philippa C. Matthews", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ian Diamond", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Ruth Studley", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Emma Rourke", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Duncan Cook", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "John I Bell", + "author_inst": "University of Oxford" + }, + { + "author_name": "John N Newton", + "author_inst": "Public Health England" + }, + { + "author_name": "Jeremy Farrar", + "author_inst": "Wellcome Trust" + }, + { + "author_name": "Alison Howarth", + "author_inst": "University of Oxford" + }, + { + "author_name": "Brian D. Marsden", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sarah Hoosdally", + "author_inst": "University of Oxford" + }, + { + "author_name": "E Yvonne Jones", + "author_inst": "University of Oxford" + }, + { + "author_name": "David I Stuart", + "author_inst": "University of Oxford" + }, + { + "author_name": "Derrick W. Crook", + "author_inst": "University of Oxford" + }, + { + "author_name": "Tim E.A. Peto", + "author_inst": "University of Oxford" + }, + { + "author_name": "A.Sarah Walker", + "author_inst": "University of Oxford" + }, + { + "author_name": "David W. Eyre", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.09.21263348", "rel_title": "Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multi-target approach", @@ -561406,101 +564617,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.09.13.21263365", - "rel_title": "High Seroconversion Rates Amongst Black and Hispanics With Hematologic Malignancies after SARS-CoV-2 Vaccination", - "rel_date": "2021-09-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263365", - "rel_abs": "It is well established that COVID-19 carries a higher risk of morbidity and mortality in patients with hematologic malignancies, however, very little data on ethnicity specific responses in this particular patient population currently exist. We established a program of rapid vaccination and evaluation of antibody-mediated response to all EUA COVID-19 vaccines in an inner city minority population to determine the factors that contribute to the poor seroconversion to COVID-19 vaccination in this population. We conducted a cross-sectional cohort study of 126 patients with hematologic malignancies in the outpatient practices of our institution who completed their vaccination series with one of the three FDA EUA COVID-19 vaccines, Moderna, Pfizer, or Johnson & Johnson (J&J). We qualitatively measured Spike IgG production in all patients using the AdviseDx SARS-CoV-2 IgG II assay and quantitatively in 106 patients who completed their vaccination series with at least 14 days after the 2nd dose of the Moderna or Pfizer vaccines or 28d after the single J&J vaccine. Patient characteristics were analyzed using standard descriptive statistics and associations between patient characteristics, cancer subtypes, treatments, and vaccine response were assessed using Fisher Exact test or Kruskal-Wallis Rank Sum test. The majority of patients (74%) were minorities. Seventy patients (60%) received Pfizer, 36 patients (31%) Moderna, and 10 patients (9%) J&J. We observed a high-rate of seropositivity (86%) with 16 pts (14%) having a negative Spike IgG. Of the 86 minority patients included, 94% Blacks (30/32) and 87% (39/45) Hispanics showed seropositivity. The factors that contributed to significantly lower seroconversion rates included patients with Non-Hodgkin lymphoma (p=0.005), those who received cytotoxic chemotherapy (p=0.002), IVIG (p=0.01), CAR-T cell therapy (p=0.00002), and CD20 monoclonal antibodies (Ab) (p=0.0000008). Plasma cell neoplasms (p=0.02), immunomodulatory agents (p=0.01), and proteasome inhibitors (p=0.01) had significantly higher seroconversion rates, and those with a history of prior COVID-19 (11%, 12/106) had significantly higher antibody titers (p=0.0003). The positivity rate was 86% (37 seropositive, 6 seronegative) for autologous HSCT and 75% (3 seropositive, 1 seronegative) for allogeneic HSCT. No life-threatening AE were observed. We show high seroconversion rates after SARS-CoV-2 vaccination in non-White patients with hematologic malignancies treated with a wide spectrum of therapeutic modalities. Vaccination is safe, effective, and should be encouraged in most patients with hematologic malignancies. Our minorities based study could be employed as an educational tool to dispel myths and provide data driven evidence to overcome vaccine hesitancy.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Lauren C Shapiro", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Astha Thakkar", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Radhika Gali", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Jesus D Gonzalez-Lugo", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Abdul-Hamid Bazarbachi", - "author_inst": "Jacobi Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Shafia Rahman", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Kith Pradhan", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Karen Fehn", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Michelly Abreu", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Noah Kornblum", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Kira Gritsman", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Mendel Goldfinger", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Aditi Shastri", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Ioannis Mantzaris", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Ira Braunschweig", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Balazs Halmos", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Amit Verma", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Margaret McCort", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "Lizamarie Bachier-Rodriguez", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - }, - { - "author_name": "R Alejandro Sica", - "author_inst": "Montefiore Medical Center/Albert Einstein College of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2021.09.13.21263543", "rel_title": "Social Capital Dimensions are Differentially Associated with COVID-19 Vaccinations, Masks, and Physical Distancing", @@ -563239,6 +566355,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.10.21263072", + "rel_title": "VALIDATION OF A SALIVA-BASED TEST FOR THE MOLECULAR DIAGNOSIS OF SARS-CoV-2 INFECTION", + "rel_date": "2021-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.10.21263072", + "rel_abs": "BackgroundSince the beginning of the pandemic, clinicians and researchers have been searching for alternative tests to improve screening and diagnosis of SARS-CoV-2 infection (Y. Yang et al., medRxiv 2020; W. Wang et al., 2020.3786; A Senok et al., Infect Drug Resist 2020). Currently, the gold standard for virus identification is the nasopharyngeal (NP) swab (N. Sethuraman et al., JAMA 2020; A.J. Jamal et al Clinical Infect Disease 2021). Saliva samples, however, offer clear practical and logistical advantages (K.K.W To et al, Clinical Microb and Infect; A.L. Wylle et al. N Engl J Med 2020; N. Matic et al, Eur J Clin 2021) but due to lack of collection, transport, and storage solutions, high-throughput saliva-based laboratory tests are difficult to scale up as a screening or diagnostic tool (D. Esser et al., Biomark Insights 2008; E. Kaufman et al., Crit Rev Oral Biol Med2002). With this study, we aimed to validate an intra-laboratory molecular detection method for SARS-CoV-2 on saliva samples collected in a new storage saline solution, comparing the results to NP swabs to determine the difference in sensitivity between the two tests.\n\nMethodsIn this study, 156 patients (cases) and 1005 asymptomatic subjects (controls) were enrolled and tested simultaneously for the detection of the SARS-CoV-2 viral genome by RT-PCR on both NP swab and saliva samples. Saliva samples were collected in a preservative and inhibiting saline solution (Biofarma Srl). Internal method validation was performed to standardize the entire workflow for saliva samples.\n\nResultsThe identification of SARS-CoV-2 conducted on saliva samples showed a clinical sensitivity of 95.1% and specificity of 97.8% compared to NP swabs. The positive predictive value (PPV) was 81% while the negative predictive value (NPV) was 99.5%. Test concordance was 97.6% (Cohens Kappa=0.86; 95% CI 0.81-0.91). The LoD of the test was 5 viral copies for both samples.\n\nConclusionsRT-PCR assays conducted on a stored saliva sample achieved similar performance to those on NP swabs and this may provide a very effective tool for population screening and diagnosis. Collection of saliva in a stabilizing solution makes the test more convenient and widely available; furthermore, the denaturing properties of the solution reduce the infective risks belonging to sample manipulation.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Michela Bulfoni", + "author_inst": "Department of Medicine, University of Udine, Udine, Italy; Institute of Pathology, ASU FC, Udine, Italy" + }, + { + "author_name": "Emanuela Sozio", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Barbara Marcon", + "author_inst": "Department of Laboratory Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Maria De Martino", + "author_inst": "Department of Medicine, University of Udine, Udine, Italy" + }, + { + "author_name": "Daniela Cesselli", + "author_inst": "Department of Medicine, University of Udine, Udine, Italy; Institute of Pathology, ASU FC, Udine, Italy" + }, + { + "author_name": "Chiara De Carlo", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Romina Martinella", + "author_inst": "Department of Laboratory Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Angelica Migotti", + "author_inst": "Department of Laboratory Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Eleonora Vania", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Agnese Zanus-Fortes", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Jessica De Piero", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Emanuele Nencioni", + "author_inst": "Biofarma Srl" + }, + { + "author_name": "Carlo Tascini", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy; Department of Medicine, University of Udine, Udine, Italy" + }, + { + "author_name": "Miriam Isola", + "author_inst": "Department of Medicine, University of Udine, Udine, Italy" + }, + { + "author_name": "Francesco Curcio", + "author_inst": "Department of Laboratory Medicine, ASU FC, Udine, Italy; Department of Medicine, University of Udine, Udine, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.14.460356", "rel_title": "Rapid Identification of Neutralizing Antibodies against SARS-CoV-2 Variants by mRNA Display", @@ -563392,49 +566583,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.07.21263194", - "rel_title": "COVID-19 convalescent plasma and randomized clinical trials: rebuilding confidence by explaining failures and finding signals of efficacy.", - "rel_date": "2021-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.07.21263194", - "rel_abs": "Convalescent plasma (CP) recurs as a frontline treatment in epidemics because it is available as soon as there are survivors. The COVID-19 pandemic represented the first large-scale opportunity to shed light into mechanisms of action, safety and efficacy of CP using modern evidence-based medicine approaches. Studies ranging from observational case series to randomized controlled trials (RCT) have reported highly variable efficacy results for COVID-19 CP (CCP), resulting in uncertainty. Reasons for CCP success and failure may be hidden in study details, which are usually difficult to explain to physicians and the public but provide fertile ground for designing next-generation studies. We analyzed variables associated with efficacy such as clinical settings, disease severity, CCP SARS-CoV-2 antibody levels and function, dose, timing of administration (variously defined as time from onset of symptoms, molecular diagnosis, diagnosis of pneumonia, or hospitalization, or by serostatus), outcomes (defined as hospitalization, requirement for ventilation, clinical improvement or mortality), CCP provenance and time for collection, and criteria for efficacy. Focusing only on the results from the 30 available RCTs we noted that these were more likely to show signals of efficacy, including reductions in mortality, if the plasma neutralizing titer was [≥] 160 and the time to randomization was [≤] 9 days, consistent with passive antibody therapy efficacy requiring dosing with sufficient antibody. The fact that most studies revealed signals of efficacy despite variability in CCP and its use suggest likely therapeutic effects that become apparent despite the data noise. Despite the recent WHO guidelines discouraging CCP usage, the Omicron variant of concern is reminding us the superiority of polyclonal antibody therapies over monoclonal antibodies, and CCP from vaccinated convalescents is likely to be evaluated soon", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Daniele Focosi", - "author_inst": "Pisa University Hospital, Italy" - }, - { - "author_name": "Massimo Franchini", - "author_inst": "Carlo Poma Hospital, Mantua, Italy" - }, - { - "author_name": "Liise-anne Pirofski", - "author_inst": "Albert Einstein College of Medicine, New York, USA" - }, - { - "author_name": "Thierry Burnouf", - "author_inst": "Taipei Medical University, Taiwan" - }, - { - "author_name": "Nigel Paneth", - "author_inst": "Michigan State University, East Lansing, USA" - }, - { - "author_name": "Michael J Joyner", - "author_inst": "Mayo Clinic, Rochester, USA" - }, - { - "author_name": "Arturo Casadevall", - "author_inst": "Johns Hopkins School of Public Health, Baltimore, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.14.460265", "rel_title": "The snoGloBe interaction predictor enables a broader study of box C/D snoRNA functions and mechanisms", @@ -564953,6 +568101,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.07.21262725", + "rel_title": "SARS-COV2 mutant-specific T cells and neutralizing antibodies after vaccination and up to 1 year after infection", + "rel_date": "2021-09-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.07.21262725", + "rel_abs": "ObjectiveWe investigated blood samples from fully SARS-CoV2-vaccinated subjects and from previously positive tested patients up to one year after infection with SARS-CoV2, and compared short- and long-term T cell and antibody responses, with a special focus on the recently emerged delta variant (B.1.617.2).\n\nMethods and ResultsIn 23 vaccinated subjects, we documented high anti-SARS-CoV2 spike protein receptor binding domain (RBD) antibody titers. Average virus neutralization by antibodies, assessed as inhibition of ACE2 binding to RBD, was 2.2-fold reduced for delta mutant vs. wild type (wt) RBD. The mean specific antibody titers were lower one year after natural infection than after vaccination; ACE2 binding to delta mutant vs. wt RBD was 1.65-fold reduced. In an additional group, omicron RBD binding was reduced compared to delta.\n\nSpecific CD4+ T cell responses were measured after stimulation with peptides pools from wt, alpha, beta, gamma, or delta variant SARS-CoV2 spike proteins by flow cytometric intracellular cytokine staining. There was no significant difference in cytokine production of IFN-{gamma}, TNF-, or IL-2 between vaccinated subjects. T cell responses to wt or mutant SARS-CoV2 spike were significantly weaker after natural occurring infections compared to those in vaccinated individuals.\n\nConclusionAntibody neutralisation of the delta mutant was reduced compared to wt, as assessed in a novel inhibition assay with a finger prick blood drop. Strong CD4 T cell responses were present against wt and mutant SARS-CoV2 variants, including the delta (B.1.617.2) strain, in fully vaccinated individuals, whereas they were partly weaker 1 year after natural infection. Hence, immune responses after vaccination are stronger compared to those after naturally occurring infection, pointing out the need of the vaccine to overcome the pandemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jennifer R Richardson", + "author_inst": "ISAR Bioscience" + }, + { + "author_name": "Ralph Goetz", + "author_inst": "ISAR Bioscience" + }, + { + "author_name": "Vanessa Mayr", + "author_inst": "ISAR Bioscience" + }, + { + "author_name": "Martin J Lohse", + "author_inst": "ISAR Bioscience" + }, + { + "author_name": "Hans-Peter Holthoff", + "author_inst": "ISAR Bioscience" + }, + { + "author_name": "Martin Ungerer", + "author_inst": "ISAR Bioscience" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.09.10.21262710", "rel_title": "Antibody responses to BNT162b2 mRNA vaccine: infection-naive individuals with abdominal obesity warrant attention", @@ -565150,153 +568337,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "palliative medicine" }, - { - "rel_doi": "10.1101/2021.09.03.21262841", - "rel_title": "COVID-19 Bimodal Clinical and Pathological Phenotypes", - "rel_date": "2021-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21262841", - "rel_abs": "BackgroundPatients with coronavirus disease-2019 (COVID-19) present varying clinical complications. Different viral load and host response related to genetic and immune background are probably the reasons for these differences. We aimed to sought clinical and pathological correlation that justifies the different clinical outcomes among COVID-19 autopsies cases.\n\nMethodsMinimally invasive autopsy was performed on forty-seven confirmed COVID-19 patients from May-July, 2020. Electronic medical record of all patients was collected and a comprehensive histopathological evaluation was performed. Immunohistochemistry, immunofluorescence, special stain, western blotting and post-mortem real-time reverse transcriptase polymerase chain reaction on fresh lung tissue were performed.\n\nResultsWe show that 5/47 (10,6%) patients present a progressive decline in oxygenation index for acute respiratory distress syndrome (PaO2/FiO2 ratio), low compliance levels, interstitial fibrosis, high -SMA+ cells/protein expression, high collagens I/III deposition and NETs(P<0.05), named as fibrotic phenotype (N=5). Conversely, 10/47 (21,2%) patients demonstrated progressive increase in PaO2/FiO2 ratio, high pulmonary compliance levels, preserved elastic framework, increase thrombus formation and high platelets and D-dimer levels at admission (P<0.05), named as thrombotic phenotype. While 32/47 (68,1%) had a mixed phenotypes between both ones.\n\nConclusionsWe believe that categorization of patients based on these two phenotypes can be used to develop prognostic tools and potential therapies since the PaO2/FiO2 ratio variation and D-dimer levels correlate with the underlying fibrotic or thrombotic pathologic process, respectively; which may indicate possible clinical outcome of the patient.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Sabrina Batah", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Maira Benatti", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Li Siyuan", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Wagner Telini", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Jamile Barbosa", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Marcelo Menezes", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Tales Nadai", - "author_inst": "Hospital Estadual de Bauru" - }, - { - "author_name": "Keyla S", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Chirag Vaswani", - "author_inst": "Keenan Research Centre for Biomedical Science, St. Michaels Hospital" - }, - { - "author_name": "Sahil Gupta", - "author_inst": "Keenan Research Centre for Biomedical Science, St. Michaels Hospital" - }, - { - "author_name": "Dario Zamboni", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Danilo Wada", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Rodrigo Calado", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Rene Oliveira", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Paulo Louzada-Junior", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Maria Auxiliadora-Martins", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Flavio Veras", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Larissa Cunha", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Thiago Cunha", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Rodrigo Luppino-Assad", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Marcelo Balancin", - "author_inst": "Faculty of Medicine, University of Sao Paulo" - }, - { - "author_name": "Sirlei Morais", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Ronaldo Martins", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Eurico Arruda", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Fernando Chahud", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Marcel Koenigkam-Santos", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Andrea Cetlin", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Fernando Cunha", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - }, - { - "author_name": "Claudia Santos", - "author_inst": "Keenan Research Centre for Biomedical Science, St. Michaels Hospital" - }, - { - "author_name": "Vera Capelozzi", - "author_inst": "Faculty of Medicine, University of Sao Paulo" - }, - { - "author_name": "Junya Fukuoka", - "author_inst": "Nagasaki University / Kameda Medical Center" - }, - { - "author_name": "Rosane Duarte-Achcar", - "author_inst": "National Jewish Health" - }, - { - "author_name": "Alexandre Fabro", - "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.09.03.21262611", "rel_title": "Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity.", @@ -567135,6 +570175,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.13.460111", + "rel_title": "Therapeutic efficacy of an oral nucleoside analog of remdesivir against SARS-CoV-2 pathogenesis in mice.", + "rel_date": "2021-09-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.13.460111", + "rel_abs": "The COVID-19 pandemic remains uncontrolled despite the rapid rollout of safe and effective SARS-CoV-2 vaccines, underscoring the need to develop highly effective antivirals. In the setting of waning immunity from infection and vaccination, breakthrough infections are becoming increasingly common and treatment options remain limited. Additionally, the emergence of SARS-CoV-2 variants of concern with their potential to escape therapeutic monoclonal antibodies emphasizes the need to develop second-generation oral antivirals targeting highly conserved viral proteins that can be rapidly deployed to outpatients. Here, we demonstrate the in vitro antiviral activity and in vivo therapeutic efficacy of GS-621763, an orally bioavailable prodrug of GS-441524, the parental nucleoside of remdesivir, which targets the highly conserved RNA-dependent RNA polymerase. GS-621763 exhibited significant antiviral activity in lung cell lines and two different human primary lung cell culture systems. The dose-proportional pharmacokinetic profile observed after oral administration of GS-621763 translated to dose-dependent antiviral activity in mice infected with SARS-CoV-2. Therapeutic GS-621763 significantly reduced viral load, lung pathology, and improved pulmonary function in COVID-19 mouse model. A direct comparison of GS-621763 with molnupiravir, an oral nucleoside analog antiviral currently in human clinical trial, proved both drugs to be similarly efficacious. These data demonstrate that therapy with oral prodrugs of remdesivir can significantly improve outcomes in SARS-CoV-2 infected mice. Thus, GS-621763 supports the exploration of GS-441524 oral prodrugs for the treatment of COVID-19 in humans.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Alexandra Schafer", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "David R Martinez", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "John J Won", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Fernanado R Moreira", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Ariane J Brown", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Kendra L Gully", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Rao Kalla", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Kwon Chun", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Venice Du Pont", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Darius Babusis", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Jennifer Tang", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Eisuke Murakami", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Raju Subramanian", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Kimberly T Barrett", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Blake J. Bleier", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Roy Bannister", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Joy Y. Feng", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "John P. Bilello", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Tomas Cihlar", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Richard L. Mackman", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Stephanie A. Montgomery", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Timothy P. Sheahan", + "author_inst": "University of North Carolina at Chapel Hill" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.09.13.460130", "rel_title": "Elucidation of the interactions between SARS-CoV-2 Spike protein and wild and mutant types of IFITM proteins by in silico methods", @@ -567268,49 +570415,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.09.11.459879", - "rel_title": "Ultrafast, one-step, and microwave heating-based synthesis of DNA/RNA-AuNP conjugates", - "rel_date": "2021-09-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.11.459879", - "rel_abs": "DNA/RNA-gold nanoparticle (DNA/RNA-AuNP) nanoprobes have been widely employed for nanobiotechnology applications. Here we discovered that both thiolated and non-thiolated DNA/RNA can be efficiently attached to AuNPs to achieve high-stable spherical nucleic acid (SNA) within minutes under a domestic microwave (MW)-assisted heating-dry circumstance. Further studies showed that for non-thiolated DNA/RNA the conjugation is poly (T/U) tag dependent. Spectroscopy, test strip hybridization, and loading counting experiments indicate that low-affinity poly (T/U) tag mediates the formation of a standing-up conformation, which is distributed in the outer layer of such a SNA structure. In further applications study, CRISPR/Cas9-sgRNA (135 bp), RNA from Nucleocapsid (N) gene of SARS-CoV-2 (1279 bp), and rolling circle amplification (RCA) DNA products (over 1000 bp) could be successfully attached on AuNPs, which overcomes the routine methods in long-chain nucleic acid-AuNP conjugation, exhibiting great promise in novel biosensing and nucleic acids delivery strategy. This novel heating-dry strategy has improved the traditional DNA/RNA-AuNP conjugation methods in simplicity, rapidity, cost, and universality.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Mengqi Huang", - "author_inst": "South China Normal University" - }, - { - "author_name": "Erhu Xiong", - "author_inst": "South China Normal University" - }, - { - "author_name": "Menglu Hu", - "author_inst": "South China Normal University" - }, - { - "author_name": "Huahua Yue", - "author_inst": "South China Normal University" - }, - { - "author_name": "Tian Tian", - "author_inst": "South China Normal University" - }, - { - "author_name": "Debin Zhu", - "author_inst": "South China Normal University" - }, - { - "author_name": "Xiaoming Zhou", - "author_inst": "South China Normal University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.09.06.21262986", "rel_title": "Rehabilitation in Survivors of COVID-19 (RE2SCUE): a nonrandomized, controlled, and open protocol", @@ -568741,6 +571845,33 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.09.11.459891", + "rel_title": "Phylogenetic evidence for asparagine to aspartic acid protein editing of N-glycosylated SARS-CoV-2 viral proteins by NGLY1 deglycosylation/deamidation suggests an unusual vaccination strategy", + "rel_date": "2021-09-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.11.459891", + "rel_abs": "Many viral proteins, including multiple SARS-CoV-2 proteins, are secreted via the endoplasmic reticulum, and viral particles are assembled and exported in ER-associated replication compartments. Viral coat proteins such as the SARS-CoV-2 Spike protein are N-glycosylated at NxS/T sites as they enter the ER. N-glycosylated sites in many eukaryotic proteins are deglycosylated by the NGLY1/PNG-1 deglycosylation enzyme which also deamidates the N-glycosylated asparagine to aspartic acid, thus editing the target protein sequence. Proteomic analysis of mammalian cell lines has revealed deamidation of many host N-glycosylated asparagines to aspartic acid by NGLY1/PNG-1 on peptides that are presented by mammalian HLA for immune surveillance. The key client protein for NGLY1/PNG-1 deglycosylation and N to D protein editing was revealed by genetic analysis of C. elegans proteasome regulation to be the intact endoplasmic reticulum-transiting SKN-1A transcription factor. Strikingly, an analysis of cancer cell genetic dependencies for growth revealed that the mammalian orthologue of SKN-1A, NRF1 (also called NFE2L1) is required by a highly correlated set of cell lines as NGLY1/PNG-1, supporting that NGLY1/PNG-1 and NRF1 act in the same pathway. NGLY1/PNG-1 edits N-glycosylated asparagines on the intact SKN-1 protein as it is retrieved by ERAD from the ER to in turn activate the transcription of target proteasomal genes. The normal requirement for NGLY1/PNG-1 editing of SKN-1A can be bypassed by a genomic substituion of N to D in four NxS/T N-glycosylation motifs of SKN-1A. Thus NGLY1/PNG-1-mediated N to D protein editing is more than a degradation step for the key client protein for proteasomal homeostasis in C. elegans or tumor growth in particular mammalian cell lines, SKN-1A/NRF1. In addition, such N to D substitutions in NxS/T N-glycosylation motifs occur in evolution: N to D substitutions are observed in phylogenetic comparisons of SKN-1A between nematode species that diverged hundreds of millions of years ago or of the vertebrate NRF1 between disparate vertebrates. Genomic N to D mutations bypass the many steps in N-glycosylation in the ER and deglycosylation-based editing of N to D, perhaps based on differences in the competency of divergent species for various N-glycosylation or deglycosylation steps.\n\nWe surveyed the N-glycosylation sites in coronavirus proteins for such phylogenetic evidence for N to D protein editing in viral life cycles, and found evidence for preferential N to D residue substitutions in NxS/T N-glycosylation sites in comparisons of the genome sequences of hundreds of coronaviruses. This suggests that viruses use NGLY1/PNG-1 in some hosts, for example humans, to edit particular N-glycosylated residues to aspartic acid, but that in other hosts, often in bats, an N to D substitution mutation in the virus genome is selected. Single nucleotide mutations in Asp or Asn codons can produce viruses with N to D or D to N substitutions that might be selected in different animal hosts from the population of viral variants produced in any previous host. NGLY1/PNG-1 has been implicated in viral immunity in mammalian cell culture, favoring this hypothesis.\n\nBecause of the phylogenetic evidence that the NGLY1/PNG-1 editing of protein sequences has functional importance for SKN-1A/NRF1 and viruses, and because most immunization protocols do not address the probable editing and functional importance of N-glycosylated aspargines to aspartic acid in normal viral infections, we suggest that immunization with viral proteins engineered to substitute D at genomically encoded NxS/T sites of N-glycosylated viral proteins that show a high frequency of N to D substitution in viral phylogeny may enhance immunological response to peptide antigens. Such genomically-edited peptides would not require ER-localization for N-glycosylation or other cell compartment localization for NGLY1/PNG-1 N to D protein editing. In addition, such N to D edited protein vaccines could be produced in bacteria since N-glycosylation and deglycosylation which do not occur in bacteria would no longer be required to immunize with a D-substituted peptide. Bacterially-expressed vaccines would be much lower cost and with fewer failure modes than attenuated viral vaccines or recombinant animal viruses produced in chicken eggs, mammalian tissue culture cells, or delivered by mRNA vectors to the patient directly. Because N to D edited peptides are clearly produced by NGLY1/PNG-1, and may be and presented by mammalian HLA, such peptides may more robustly activate T-cell killing or B-cell maturation to mediate more robust viral immunity.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Gary Ruvkun", + "author_inst": "Massachusetts General Hospital and Harvard Medical School" + }, + { + "author_name": "Ruslan Sadreyev", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Fei Ji", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2021.09.06.21263168", "rel_title": "Coronavirus disease (COVID-19) associated Mucormycosis: An Anaesthesiologist's Perspective", @@ -568874,25 +572005,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.09.07.21263236", - "rel_title": "Change in Measles Vaccine Coverage and Estimated Impact on Measles Mortality in Low and Middle Income Countries, 2020: An Investigation into Secondary Public Health Effects of the COVID-19 Pandemic Using the Lives Saved Tool", - "rel_date": "2021-09-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.07.21263236", - "rel_abs": "With the global COVID-19 pandemic, many public health services were severely disrupted. Estimating the overall health effects of this is difficult as most disease surveillance systems have also been substantially affected during the pandemic. For some diseases, this effect is mitigated by the methods enacted to fight the pandemic, such as use of facial coverings, social distancing and quarantine, but measles is infectious to the degree that this mitigation is likely to be limited. Thus, outbreaks and an increase in global measles mortality are expected. However, the severity of this impact is not yet known.\n\nIn early 2020, a study by Roberton and colleagues predicted an additional 12,360 to 37,920 deaths in children under-five worldwide from measles over the coming year based on three potential levels of vaccine coverage reductions ranging from 18.5 to 51.9%. Our study investigates the magnitude of the increase in measles mortality due to decreased vaccine coverage because of COVID-19, based on official estimates of 2020 measles vaccine coverage from WHO/UNICEF released in July 2021. Using the Lives Saved Tool (LiST), an interventions modeling program, we estimated measles mortality for low/middle income countries (LMICs) based on the 2020 WHO/UNICEF estimates of national immunization coverage (WUENIC). Because these calculations use actual reported vaccine coverage, they provide a more accurate picture of measles mortality related to COVID-19 disruptions in 2020.\n\nUsing the WUENIC data, LiST predicted fewer additional deaths in 2020 due to decreases in measles vaccine coverage than estimations made by LiST based on Roberton, 2020 due to remarkable recovery efforts by national immunization programmes in the second half of 2020.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Lucy Claire Gregory", - "author_inst": "Poudre High School" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.07.21263221", "rel_title": "Serial evaluation of anti-SARS-CoV-2 IgG antibody and breakthrough infections in BNT162b2 Vaccinated migrant workers from Bangladesh", @@ -570799,6 +573911,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.02.21263033", + "rel_title": "Epidemic Models for COVID-19 during the First Wave from February to May 2020: a Methodological Review", + "rel_date": "2021-09-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.02.21263033", + "rel_abs": "We review epidemiological models for the propagation of the COVID-19 pandemic during the early months of the outbreak: from February to May 2020. The aim is to propose a methodological review that highlights the following characteristics: (i) the epidemic propagation models, (ii) the modeling of intervention strategies, (iii) the models and estimation procedures of the epidemic parameters and (iv) the characteristics of the data used. We finally selected 80 articles from open access databases based on criteria such as the theoretical background, the reproducibility, the incorporation of interventions strategies, etc. It mainly resulted to phenomenological, compartmental and individual-level models. A digital companion including an online sheet, a Kibana interface and a markdown document is proposed. Finally, this work provides an opportunity to witness how the scientific community reacted to this unique situation.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Marie Garin", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli, F-91190 Gif-sur-Yvette, France" + }, + { + "author_name": "Myrto Limnios", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli, F-91190 Gif-sur-Yvette, France" + }, + { + "author_name": "Alice Nicolai", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Ioannis Bargiotas", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Olivier Boulant", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Stephen E. Chick", + "author_inst": "INSEAD, Boulevard de Constance, 77300 Fontainebleau, France" + }, + { + "author_name": "Amir Dib", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Theodoros Evgeniou", + "author_inst": "INSEAD, Boulevard de Constance, 77300 Fontainebleau, France" + }, + { + "author_name": "Mathilde Fekom", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Argyris Kalogeratos", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Christophe Labourdette", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Anton Ovchinnikov", + "author_inst": "INSEAD, Boulevard de Constance, 77300 Fontainebleau, France and Smith School of Business, Queen's University, Kingston, ON, K7L3N6, Canada" + }, + { + "author_name": "Rapha\u00ebl Porcher", + "author_inst": "Universit\u00e9 de Paris CRESS, INSERM, INRA, 75004 Paris, France" + }, + { + "author_name": "Camille Pouchol", + "author_inst": "MAP5 Laboratory, FP2M, CNRS FR 2036, Universit\u00e9 de Paris, 75006 Paris, France" + }, + { + "author_name": "Nicolas Vayatis", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.09.21263328", "rel_title": "COVID-19 Vaccine Concerns about Safety, Effectiveness and Policies in the United States, Canada, Sweden, and Italy among Unvaccinated Individuals", @@ -570948,33 +574135,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2021.09.09.459504", - "rel_title": "Differential antibody dynamics to SARS-CoV-2 infection and vaccination", - "rel_date": "2021-09-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.09.459504", - "rel_abs": "Optimal immune responses furnish long-lasting (durable) antibodies protective across dynamically mutating viral variants (broad). To assess robustness of mRNA vaccine-induced immunity, we compared antibody durability and breadth after SARS-CoV-2 infection and vaccination. While vaccination delivered robust initial virus-specific antibodies with some cross-variant coverage, pre-variant SARS-CoV-2 infection-induced antibodies, while modest in magnitude, showed highly stable long-term antibody dynamics. Vaccination after infection induced maximal antibody magnitudes with enhanced longitudinal stability while infection-naive vaccinee antibodies fell with time to post-infection-alone levels. The composition of antibody neutralizing activity to variant relative to original virus also differed between groups, with infection-induced antibodies demonstrating greater relative breadth. Differential antibody durability trajectories favored COVID-19-recovered subjects with dual memory B cell features of greater early antibody somatic mutation and cross-coronavirus reactivity. By illuminating an infection-mediated antibody breadth advantage and an anti-SARS-CoV-2 antibody durability-enhancing function conferred by recalled immunity, these findings may serve as guides for ongoing vaccine strategy improvement.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Tianshu Xiao", - "author_inst": "Laboratory of Molecular Medicine, Boston Childrens Hospital; Department of Pediatrics, Harvard Medical School, Boston, MA" - }, - { - "author_name": "Yongfei Cai", - "author_inst": "Laboratory of Molecular Medicine, Boston Childrens Hospital; Department of Pediatrics, Harvard Medical School, Boston, MA" - }, - { - "author_name": "Bing Chen", - "author_inst": "Laboratory of Molecular Medicine, Boston Childrens Hospital; Department of Pediatrics, Harvard Medical School, Boston, MA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.09.10.459749", "rel_title": "Intranasal administration of a VLP-based vaccine against COVID-19 induces neutralizing antibodies against SARS-CoV-2 and Variants of Concerns", @@ -572909,6 +576069,137 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.09.08.459480", + "rel_title": "Targeted isolation of panels of diverse human broadly neutralizing antibodies against SARS-like viruses", + "rel_date": "2021-09-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.08.459480", + "rel_abs": "The emergence of current SARS-CoV-2 variants of concern (VOCs) and potential future spillovers of SARS-like coronaviruses into humans pose a major threat to human health and the global economy 1-7. Development of broadly effective coronavirus vaccines that can mitigate these threats is needed 8, 9. Notably, several recent studies have revealed that vaccination of recovered COVID-19 donors results in enhanced nAb responses compared to SARS-CoV-2 infection or vaccination alone 10-13. Here, we utilized a targeted donor selection strategy to isolate a large panel of broadly neutralizing antibodies (bnAbs) to sarbecoviruses from two such donors. Many of the bnAbs are remarkably effective in neutralization against sarbecoviruses that use ACE2 for viral entry and a substantial fraction also show notable binding to non-ACE2-using sarbecoviruses. The bnAbs are equally effective against most SARS-CoV-2 VOCs and many neutralize the Omicron variant. Neutralization breadth is achieved by bnAb binding to epitopes on a relatively conserved face of the receptor binding domain (RBD) as opposed to strain-specific nAbs to the receptor binding site that are commonly elicited in SARS-CoV-2 infection and vaccination 14-18. Consistent with targeting of conserved sites, select RBD bnAbs exhibited in vivo protective efficacy against diverse SARS-like coronaviruses in a prophylaxis challenge model. The generation of a large panel of potent bnAbs provides new opportunities and choices for next-generation antibody prophylactic and therapeutic applications and, importantly, provides a molecular basis for effective design of pan-sarbecovirus vaccines.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Wan-ting He", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Rami Musharrafieh", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Ge Song", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Katharina Dueker", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Longping V. Tse", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "David R. Martinez", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Alexandra Schafer", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Sean Callaghan", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Peter Yong", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Nathan Beutler", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Jonathan L. Torres", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Reid M. Volk", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Panpan Zhou", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Meng Yuan", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Hejun Liu", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Fabio Anzanello", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Tazio Capozzola", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Mara Parren", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Elijah Garcia", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Stephen A. Rawlings", + "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." + }, + { + "author_name": "Davey M. Smith", + "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." + }, + { + "author_name": "Ian A. Wilson", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Yana Safonova", + "author_inst": "Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA" + }, + { + "author_name": "Andrew B. Ward", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Thomas Rogers", + "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Lisa E. Gralinski", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Dennis R. Burton", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Raiees Andrabi", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.09.08.459260", "rel_title": "Artemisia annua hot-water extracts show potent activity in vitro against Covid-19 variants including delta", @@ -573070,73 +576361,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.03.21263083", - "rel_title": "Suicide and self-harm in low- and middle- income countries during the COVID-19 pandemic: A systematic review", - "rel_date": "2021-09-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21263083", - "rel_abs": "There is widespread concern over the potential impact of the COVID-19 pandemic on suicide and self-harm globally, particularly in low- and middle-income countries (LMIC) where the burden of these behaviours is greatest. We synthesised the evidence from the published literature on the impact of the pandemic on suicide and self-harm in LMIC.\n\nThis review is nested within a living systematic review that continuously identifies published evidence (all languages) through a comprehensive automated search of multiple databases (PubMed; Scopus; medRxiv, PsyArXiv; SocArXiv; bioRxiv; the WHO COVID-19 database; and the COVID-19 Open Research Dataset by Semantic Scholar (up to 11/2020), including data from Microsoft Academic, Elsevier, arXiv and PubMed Central.) All articles identified by the 4th August 2021 were screened. Papers reporting on data from a LMIC and presenting evidence on the impact of the pandemic on suicide or self-harm were included.\n\nA total of 22 studies from LMIC were identified representing data from 12 countries. There was an absence of data from Africa. The reviewed studies mostly report on the early months of COVID-19 and were generally methodologically poor. Few studies directly assessed the impact of the pandemic. The most robust evidence, from time-series studies, indicate either a reduction or no change in suicide and self-harm behaviour.\n\nAs LMIC continue to experience repeated waves of the virus and increased associated mortality, against a backdrop of vaccine inaccessibility and limited welfare support, continued efforts are needed to track the indirect impact of the pandemic on suicide and self-harm in these countries.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Duleeka Kniipe", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; South Asian Clinical Toxicology Research Collaboration, Faculty of Medic" - }, - { - "author_name": "Ann John", - "author_inst": "Population Data Science, Swansea University Medical School, Swansea, UK" - }, - { - "author_name": "Prianka Padmanathan", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK." - }, - { - "author_name": "Emily Eyles", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK." - }, - { - "author_name": "Dana Dekel", - "author_inst": "Population Data Science, Swansea University Medical School, Swansea, UK" - }, - { - "author_name": "Julian Higgins", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; National Institute of Health Research Biomedical Research Centre, Unive" - }, - { - "author_name": "Jason Bantjes", - "author_inst": "Institute for Life Course Health Research, Department of Global Health, Faculty of medicine and Health Sciences, Stellenbosch University, South Africa." - }, - { - "author_name": "Rakhi Dandona", - "author_inst": "Public Health Foundation of India, Gurugram, India; Institute for Health Metrics and Evaluation, University of Washington, Seattle, USA" - }, - { - "author_name": "Catherine Macleod-Hall", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK." - }, - { - "author_name": "Luke A McGuinness", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK." - }, - { - "author_name": "Lena Schmidt", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; Sciome LLC, Research Triangle Park, NC, United States." - }, - { - "author_name": "Roger Webb", - "author_inst": "Division of Psychology & Mental Health, University of Manchester, Manchester, UK; National Institute of Health Research Greater Manchester Patient Safety Transl" - }, - { - "author_name": "David Gunnell", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.; National Institute of Health Research Biomedical Research Centre, Unive" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.03.21263086", "rel_title": "Unraveling the COVID-19 hospitalization dynamics in Spain using publicly available data", @@ -574599,6 +577823,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.03.21257002", + "rel_title": "Long COVID: Assessment of Neuropsychiatric Symptoms in Children and Adolescents - A Clinical Data Analysis", + "rel_date": "2021-09-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21257002", + "rel_abs": "COVID-19 infections in adults often result in medical, neuropsychiatric, and unspecific symptoms, called Long COVID, and the premorbid functional status cannot be achieved. Regarding the course in children and adolescents, however, reliable data are not yet available.\n\nObjective380 children and adolescents/young adults aged between 6 and 21 years, being treated for various psychiatric diseases in an outpatient clinical service, were examined for COVID-19 infections and Long COVID symptoms following a structured protocol.\n\nResultsThree patients had COVID-19; one patient had symptoms of Long COVID in his medical history, but they could not be objectivized in an in-depth neuropsychiatric and neuropsychological assessment.\n\nConclusionsLong COVID seems to occur rarely in children and adolescents. Objectivizing the symptoms is a difficult task that requires various diagnostic considerations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jan Froelich", + "author_inst": "Central Institute of Mental Health Department of Child and Adolescent Psychiatry, University of Heidelberg - Faculty of Medicine Mannheim" + }, + { + "author_name": "Tobias Banaschewski", + "author_inst": "Central Institute of Mental Health Department of Child and Adolescent Psychiatry, University of Heidelberg - Faculty of Medicine Mannheim" + }, + { + "author_name": "Annabelle Ulmer", + "author_inst": "Practice for Child and Adolescent Psychiatry and Psychotherapy Dr. Dr. Jan Froelich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.09.02.21263038", "rel_title": "COVID-19 Vaccine Efficacy in a Diverse Urban Healthcare Worker Population", @@ -574732,77 +577983,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.09.02.21263042", - "rel_title": "Local SARS-CoV-2 peptide-specific Immune Responses in Convalescent and Uninfected Human Lung Tissue Models", - "rel_date": "2021-09-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.02.21263042", - "rel_abs": "Multi-specific and long-lasting T cell immunity have been recognized as indicators for long term protection against pathogens including the novel coronavirus SARS-CoV-2, the causative agent of the COVID-19 pandemic. Functional significance of peripheral memory T cells in individuals recovering from COVID-19 (COVID-19+) are beginning to be appreciated; but little is known about lung resident memory T cells (lung TRM) in SARS-CoV-2 infection. Here, we utilize a perfused three dimensional (3D) human lung tissue model and identify pre-existing local T cell immunity against SARS-CoV-2 proteins in lung tissues. We report ex vivo maintenance of functional multi-specific IFN-{gamma} secreting lung TRM in COVID-19+ and their induction in lung tissues of vaccinated COVID-19+. Importantly, we identify SARS-CoV-2 peptide-responding B cells and IgA+ plasma cells in lung tissues of COVID-19+ in ex vivo 3D-tissue models. Our study highlights the importance of balanced and local anti-viral immune response in the lung with persistent induction of TRM and IgA+ plasma cells for future protection against SARS-CoV-2 infection. Further, our data suggest that inclusion of multiple viral antigens in vaccine approaches may broaden the functional profile of memory T cells to combat the severity of coronavirus infection.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Kayla F. Goliwas", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Anthony M. Wood", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Christopher S. Simmons", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Rabisa J. Khan", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Saad A. Khan", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Yong Wang", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Joel L. Berry", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Mohammad Athar", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "James A Mobley", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Young-il Kim", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Victor J Thannickal", - "author_inst": "Tulane University" - }, - { - "author_name": "Kevin S Harrod", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "James M Donahue", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Jessy S. Deshane", - "author_inst": "University of Alabama at Birmingham" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.02.21262832", "rel_title": "The missing microbes: Bifidobacterium and Faecalibacterium depletion and loss of microbiome diversity as potential susceptibility markers for SARS-CoV-2 infection and severity", @@ -576117,6 +579297,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.09.03.458854", + "rel_title": "The genetics of eating behaviors: research in the age of COVID-19", + "rel_date": "2021-09-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.03.458854", + "rel_abs": "How much pleasure we take in eating is more than just how much we enjoy the taste of food. Food involvement - the amount of time we spend on food beyond the immediate act of eating and tasting - is key to the human food experience. We took a biological approach to test whether food-related behaviors, together capturing food involvement, have genetic components and are partly due to inherited variation. We collected data via an internet survey from a genetically informative sample of 419 adult twins (114 monozygotic twin pairs, 31 dizygotic twin pairs, and 129 singletons). Because we conducted this research during the pandemic, we also ascertained how many participants had experienced COVID-19-associated loss of taste and smell. Since these respondents had previously participated in research in person, we measured their level of engagement to evaluate the quality of their online responses. Additive genetics explained 16-44% of the variation in some measures of food involvement, most prominently various aspects of cooking, suggesting some features of the human food experience may be inborn. Other features reflected shared (early) environment, captured by respondents twin status. About 6% of participants had a history of COVID-19 infection, many with transitory taste and smell loss, but all but one had recovered before the survey. Overall, these results suggest that people may have inborn as well as learned variations in their involvement with food. We also learned to adapt to research during a pandemic by considering COVID-19 status and measuring engagement in online studies of human eating behavior.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Mackenzie E. Hannum", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Cailu Lin", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Katherine A Bell", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Aurora K Toskala", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Riley R Koch", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Tharaka Galaniha", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Alissa Nolden", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Danielle R. Reed", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Paule Valery Joseph", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2021.08.27.21262422", "rel_title": "Characteristics associated with COVID-19 vaccine uptake among adults in England (08 December to 17 May 2021)", @@ -576294,53 +579525,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.09.03.458953", - "rel_title": "An Extended Coatomer Binding Motif in the SARS-CoV-2 Spike Protein", - "rel_date": "2021-09-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.03.458953", - "rel_abs": "{beta}-Coronaviruses such as SARS-CoV-2 hijack coatomer protein-I (COPI) for spike protein retrograde trafficking to the progeny assembly site in endoplasmic reticulum-Golgi intermediate compartment (ERGIC). However, limited residue-level details are available into how the spike interacts with COPI. Here we identify an extended COPI binding motif in the spike that encompasses the canonical K-x-H dibasic sequence. This motif demonstrates selectivity for COPI subunit. Guided by an in silico analysis of dibasic motifs in the human proteome, we employ mutagenesis and binding assays to show that the spike motif terminal residues are critical modulators of complex dissociation, which is essential for spike release in ERGIC. COPI residues critical for spike motif binding are elucidated by mutagenesis and crystallography and found to be conserved in the zoonotic reservoirs, bats, pangolins, camels, and in humans. Collectively, our investigation on the spike motif identifies key COPI binding determinants with implications for retrograde trafficking.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Debajit Dey", - "author_inst": "University of Maryland Baltimore" - }, - { - "author_name": "Suruchi Singh", - "author_inst": "University of Maryland Baltimore" - }, - { - "author_name": "Saif Khan", - "author_inst": "University of Iowa" - }, - { - "author_name": "Matthew Martin", - "author_inst": "University of Maryland Baltimore" - }, - { - "author_name": "Nicholas Schnicker", - "author_inst": "University of Iowa" - }, - { - "author_name": "Lokesh Gakhar", - "author_inst": "University of Iowa" - }, - { - "author_name": "Brian Pierce", - "author_inst": "Institute for Bioscience and Biotechnology Research, University of Maryland" - }, - { - "author_name": "S Saif Hasan", - "author_inst": "University of Maryland Baltimore" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.08.27.21262450", "rel_title": "Wastewater-Based Epidemiology and Whole-Genome Sequencing for Community-Level Surveillance of SARS-CoV-2 in Selected Urban Communities of Davao City, Philippines: A Pilot Study", @@ -578111,6 +581295,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.30.21262341", + "rel_title": "Modelling the potential role of super spreaders on COVID-19 transmission dynamics", + "rel_date": "2021-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.30.21262341", + "rel_abs": "Superspreading phenomenon has been observed in many infectious diseases and contributes significantly to public health burden in many countries. Superspreading events have recently been reported in the transmission of the COVID-19 pandemic. The present study uses a set of nine ordinary differential equations to investigate the impact of superspreading on COVID-19 dynamics. The model developed in this study addresses the heterogeineity in infectiousness by taking into account two forms of transmission rate functions for superspreaders based on clinical (infectivity level) and social or environmental (contact level). The basic reproduction number has been derived and the contribution of each infectious compartment towards the generation of new COVID-19 cases is ascertained. Data fitting was performed and parameter values were estimated within plausible ranges. Numerical simulations performed suggest that control measures that decrease the effective contact radius and increase the transmission rate exponent will be greatly beneficial in the control of COVID-19 in the presence of superspreading phenomena.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Josiah Mushanyu", + "author_inst": "University of zimbabwe" + }, + { + "author_name": "Williams Chukwu", + "author_inst": "University of Johannesburg" + }, + { + "author_name": "Farai Nyabadza", + "author_inst": "University of Johannesburg" + }, + { + "author_name": "Gift Muchatibaya", + "author_inst": "university of Zimbabwe" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.01.458644", "rel_title": "Co-expression analysis to identify key modules and hub genes associated with COVID19 in Platelets", @@ -578240,49 +581455,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.09.01.458653", - "rel_title": "Nanobody-Functionalized Cellulose for Capturing and Containing SARS-CoV-2", - "rel_date": "2021-09-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.01.458653", - "rel_abs": "The highly transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than 217 million people, claiming ~ 4.5 million lives to date. Although mandatory quarantines, lockdowns, and vaccinations help curb viral transmission, safe and effective preventative measures remain urgently needed. Here, we present a generic strategy for containing SARS-CoV-2 by cellulose materials. Specifically, we developed a bifunctional fusion protein consisting of a cellulose-binding domain and a nanobody (Nb) targeting the receptor-binding domain of SARS-CoV-2. The immobilization of the fusion proteins on cellulose substrates enhanced the capture efficiency of Nbs against SARS-CoV-2 pseudoviruses of the wildtype and the D614G variant, the latter of which has been shown to confer higher infectivity. Furthermore, the fusion protein was integrated into a customizable chromatography with highly porous cellulose for neutralizing virus from contaminated fluids in a continuous and cost-effective fashion. Taken together, our work leverages low-cost cellulose materials and recently developed Nbs to provide a complementary approach to addressing the pandemic.\n\nIMPORTANCEThe ongoing efforts to address the COVID-19 pandemic center around the development of point-of-care diagnostics, preventative measures, and therapeutic strategies against COVID-19. In contrast to existing work, we have provided a complementary approach to target and contain SARS-CoV-2 from contaminated fluids and surfaces. Specifically, we present a generic strategy for the capture and containing of SARS-CoV-2 by cellulose-based substrates. This was archived by developing a bifunctional fusion protein consisting of both a cellulose-binding domain and a nanobody specific for the receptor-binding domain of SARS-CoV-2. As a proof-of-concept, our fusion protein-coated cellulose substrates exhibited enhanced capture efficiency against SARS-CoV-2 pseudovirus of both wildtype and the D614G mutant variants, the latter of which has been shown to confer higher infectivity. Furthermore, the fusion protein was integrated into a customizable chromatography with highly porous cellulose for neutralizing the virus from contaminated fluids in a highly continuous and cost-effective fashion.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Xin Sun", - "author_inst": "Northeastern University" - }, - { - "author_name": "Shaobo Yang", - "author_inst": "Northeastern University" - }, - { - "author_name": "Amal Al-Dossary", - "author_inst": "Imam Abdulrahman Bin Faisal University" - }, - { - "author_name": "Shana Broitman", - "author_inst": "Northeastern University" - }, - { - "author_name": "Yun Ni", - "author_inst": "Northeastern University" - }, - { - "author_name": "Mengdi Yang", - "author_inst": "Northeastern University" - }, - { - "author_name": "Jiahe Li", - "author_inst": "Northeastern University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2021.08.31.21262713", "rel_title": "Deep immune profiling reveals early-stage and highly coordinated immune responses in mild COVID-19 patients", @@ -580077,6 +583249,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.24.21262245", + "rel_title": "Symptomatology associated with the diffusion of the SARS-CoV-2 Lambda variant in Peru: An infodemiologic analysis", + "rel_date": "2021-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.24.21262245", + "rel_abs": "The SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) Lambda variant rapidly diffused across Peru following its identification in December 2020, and had now spread worldwide. In this study, we investigated infodemiologic trends in symptomatology associated with the Coronavirus Disease 2019 (COVID-19) following the spread of SARS-CoV-2 Lambda variant in Peru, enabling infodemiologic surveillance of SARS-CoV-2 in regions with high circulation of this new variant. Weekly Google Trends scores were obtained for key symptom keywords between March 1st, 2020 and July 4th, 2021, whilst case count data were obtained from Peruvian Ministry of Health. Multiple time series linear regression was used to assess trends in each score series, using the week of December 27th as cutoff for emergence of the Lambda variant. The significance of such trends was tested for each time period, before and after the cutoff date. A total 2,075,484 confirmed SARS-CoV-2 infections in Peru in relation to Google Trends data were analyzed. After Lambda variant emergence, searches for \"diarrhea\" demonstrated a change from a negative to positive correlation with weekly case counts and anticipated dynamic changes in case counts by 1-5 weeks. Searches for \"shortness of breath\" and \"headache\" remained consistently positively correlated to weekly case counts before and after Lambda emergence. No changes in searches for other common cold symptoms were observed, while no specific trends were observed for \"taste loss\" or \"smell loss\". Diarrhea, headache, and shortness of breath appear to be the most important symptoms for infodemiologic tracking the current outbreak in Peru and other regions with high circulation of SARS-CoV-2 Lambda variant.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Brandon Michael Henry", + "author_inst": "Clinical Laboratory, Division of Nephrology and Hypertension, Cincinnati Children Hospital Medical Center, Cincinnati, OH, USA" + }, + { + "author_name": "Maria Helena Santos de Oliveira", + "author_inst": "Department of Biostatistics, State University of Maringa, Maringa, Brazil" + }, + { + "author_name": "Thais Barbosa de Oliveira", + "author_inst": "Department of Biostatistics, State University of Maringa, Maringa, Brazil" + }, + { + "author_name": "Kin Israel Notarte", + "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila 1008, Philippines" + }, + { + "author_name": "Giuseppe Lippi", + "author_inst": "Section of Clinical Biochemistry, Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.23.21262413", "rel_title": "Towards the global equilibrium of COVID-19: statistical analysis of country-level data", @@ -580190,37 +583397,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.08.26.21262647", - "rel_title": "Spatial equity of COVID-19 vaccination services in Aotearoa", - "rel_date": "2021-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.26.21262647", - "rel_abs": "AimThis research examines the spatial equity, and associated health equity implications, of the geographic distribution of Covid-19 vaccination services in Aotearoa New Zealand.\n\nMethodWe mapped the distribution of Aotearoas population and used the enhanced-two-step-floating-catchment-method (E2SFCA) to estimate spatial access to vaccination services, taking into account service supply, population demand, and distance between populations and services. We used the Gini coefficient and both global and local measures of spatial autocorrelation to assess the spatial equity of vaccination services across Aotearoa. Additional statistics included an analysis of spatial accessibility for priority populations, including M[a]ori (Indigenous people of Aotearoa), Pacific, over 65-year-olds, and people living in areas of high socioeconomic deprivation. We also examined vaccination service access according to rurality, and by District Health Board region.\n\nResultsSpatially accessibility to vaccination services varies across Aotearoa, and appears to be better in major cities than rural regions. A Gini coefficient of 0.426 confirms that spatial accessibility scores are not shared equally across the vaccine-eligible population. Furthermore, priority populations including M[a]ori, older people, and residents of areas with socioeconomic constraint have, on average, statistically significantly lower spatial access to vaccination services. This is also true for people living in rural areas. Spatial access to vaccination services, also varies significantly by District Health Board (DHB) region as does equality of access, and the proportion of DHB priority population groups living in areas with poor access to vaccination services. A strong and significant positive correlation was identified between average spatial accessibility and the M[a]ori vaccination rate ratio of DHBs.\n\nConclusionCovid-19 vaccination services in Aotearoa are not equitably distributed. Priority populations, with the most pressing need to receive Covid-19 vaccinations, have the worst access to vaccination services.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jesse Whitehead", - "author_inst": "University of Waikato" - }, - { - "author_name": "Polly Atatoa Carr", - "author_inst": "University of Waikato" - }, - { - "author_name": "Nina Scott", - "author_inst": "Waikato District Health Board" - }, - { - "author_name": "Ross Lawrenson", - "author_inst": "University of Waikato" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.08.26.21258418", "rel_title": "Hybrid immunity versus vaccine-induced immunity against SARS CoV2 in Patients with Autoimmune Rheumatic Diseases", @@ -582227,6 +585403,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.08.20.21261687", + "rel_title": "Randomized trials on non-pharmaceutical interventions for COVID-19 as of August 2021: a meta-epidemiological analysis", + "rel_date": "2021-08-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.20.21261687", + "rel_abs": "BackgroundNumerous non-pharmaceutical interventions (NPIs) were taken worldwide to contain the spread of the COVID-19 pandemic. We aimed at providing an overview of randomized trials assessing NPIs to prevent COVID-19.\n\nMethodsWe included all randomized trials assessing NPIs to prevent COVID-19 in any country and setting registered in ClinicalTrials.gov and the World Health Organization International Clinical Trials Registry Platform using the COVID-evidence platform (until 17 August 2021). We searched for corresponding publications in MEDLINE/PubMed, Google Scholar, the Living Overview of Evidence platform (L-OVE), and the Cochrane COVID-19 registry as well as for results posted in registries.\n\nResultsWe identified 41 randomized trials. Of them, 11 were completed (26.8%) including 7 with published results. The 41 trials planned to recruit a median of 1,700 participants (IQR, 588 to 9,500, range 30 to 35,256,399) with a median planned duration of 8 months (IQR, 3 to 14, range 1 to 24). Most came from the United States (n=11, 26.8%). The trials mostly assessed protective equipment (n=11, 26.8%), COVID-19-related information and education programs (n=9, 22.0%), access to mass events under specific safety measures (n=5, 12.2%), testing and screening strategies (n=5, 12.2%), and hygiene management (n=5, 12.2%).\n\nConclusionsWorldwide, 41 randomized trials assessing NPIs have been initiated with published results available to inform policy decisions for only 7 of them. A long-term research agenda including behavioral, environmental, social, and systems level interventions is urgently needed to guide policies and practices in the current and future public health emergencies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Julian Hirt", + "author_inst": "Department of Clinical Research, University Hospital Basel, University of Basel" + }, + { + "author_name": "Perrine Janiaud", + "author_inst": "Department of Clinical Research, University Hospital Basel, University of Basel" + }, + { + "author_name": "Lars G. Hemkens", + "author_inst": "Department of Clinical Research, University Hospital Basel, University of Basel" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.29.458083", "rel_title": "Allosteric regulation of 3CL protease of SARS-CoV-2 and SARS-CoV observed in the crystal structure ensemble", @@ -582328,61 +585531,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.08.24.21262423", - "rel_title": "Waning immunity of the BNT162b2 vaccine: A nationwide study from Israel", - "rel_date": "2021-08-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.24.21262423", - "rel_abs": "BackgroundStarting December 2020, Israel began a mass vaccination campaign against coronavirus administering the Pfizer BNT162b2 vaccine, which led to a sharp curtailing of the outbreak. After a period with almost no SARS-CoV-2 infections, a resurgent COVID-19 outbreak initiated mid June 2021. Possible reasons for the breakthrough were reduced vaccine effectiveness against the Delta variant, and waning immunity. The aim of this study was to quantify the extent of waning immunity using Israels national-database.\n\nMethodsData on all PCR positive test results between July 11-31, 2021 of Israeli residents who became fully vaccinated before June 2021 were used in this analysis. Infection rates and severe COVID-19 outcomes were compared between individuals who were vaccinated in different time periods using a Poisson regression, stratifying by age group and adjusting for possible confounding factors.\n\nResultsThe rates of both documented SARS-CoV-2 infections and severe COVID-19 exhibit a statistically significant increase as time from second vaccine dose elapsed. Elderly individuals (60+) who received their second dose in March 2021 were 1.6 (CI: [1.3, 2]) times more protected against infection and 1.7 (CI: [1.0, 2.7]) times more protected against severe COVID-19 compared to those who received their second dose in January 2021. Similar results were found for different age groups.\n\nConclusionsThese results indicate a strong effect of waning immunity in all age groups after six months. Quantifying the effect of waning immunity on vaccine effectiveness is critical for policy makers worldwide facing the dilemma of administering booster vaccinations.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Yair Goldberg", - "author_inst": "Technion - Israel Institute of Technology" - }, - { - "author_name": "Micha Mandel", - "author_inst": "The Hebrew University of Jerusalem, Israel" - }, - { - "author_name": "Yinon M. Bar-On", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Omri Bodenheimer", - "author_inst": "Israel Ministry of Health, Israel" - }, - { - "author_name": "Laurence S Freedman", - "author_inst": "The Gertner Institute for Epidemiology & Health Policy Research, Sheba Medical Center, Israel" - }, - { - "author_name": "Eric Haas", - "author_inst": "Israel Ministry of Health, Israel" - }, - { - "author_name": "Ron Milo", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Sharon Alroy-Preis", - "author_inst": "Israel Ministry of Health, Israel" - }, - { - "author_name": "Nachman Ash", - "author_inst": "Israel Ministry of Health, Israel" - }, - { - "author_name": "Amit Huppert", - "author_inst": "The Gertner Institute for Epidemiology & Health Policy Research" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.23.21262489", "rel_title": "The COVID-19 Pandemic and Mental Health Concerns on Twitter in the United States", @@ -583933,6 +587081,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.08.25.21262636", + "rel_title": "Impact of Covid-19 Pandemic on Racial/Ethnic Differences in Mortality by Cause of Death", + "rel_date": "2021-08-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.25.21262636", + "rel_abs": "ObjectivesTo quantify changes in all-cause and cause-specific mortality by race and ethnicity between 2019 and 2020.\n\nMethodsUsing 2019 and 2020 provisional death counts from the National Center for Health Statistics and population estimates from the US Census Bureau, we estimate age-standardized death rates by race/ethnicity and attribute changes in mortality to various causes of death. We also examine how patterns of change across racial/ethnic groups vary by age and sex.\n\nResultsCovid-19 death rates in 2020 were highest in the Hispanic community whereas Black individuals had the largest increase in all-cause mortality between 2019 and 2020. Increases in mortality from heart disease, diabetes, and external causes of death accounted for the adverse trend in all-cause mortality within the Black population. Percentage increases in all-cause mortality were similar for men and women and for ages 25-64 and 65+ for Black and White populations, but increases were greatest for working-aged men among the Hispanic population.\n\nConclusionsExamining increases in non-Covid-19 causes of death is essential for fully capturing both the direct and indirect impact of the Covid-19 pandemic on racial/ethnic mortality disparities.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Anneliese N. Luck", + "author_inst": "Department of Sociology and Population Studies Center, University of Pennsylvania, Philadelphia, PA, USA" + }, + { + "author_name": "Samuel H. Preston", + "author_inst": "Department of Sociology and Population Studies Center, University of Pennsylvania, Philadelphia, PA, USA" + }, + { + "author_name": "Irma T. Elo", + "author_inst": "Department of Sociology and Population Studies Center, University of Pennsylvania, Philadelphia, PA, USA" + }, + { + "author_name": "Andrew C. Stokes", + "author_inst": "Department of Global Health, Boston University School of Public Health, Boston, MA, USA" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.08.25.21262614", "rel_title": "Democratic governance and excess mortality during the COVID-19 pandemic", @@ -584122,29 +587301,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2021.08.26.21262694", - "rel_title": "When do we need massive computations to perform detailed COVID-19 simulations?", - "rel_date": "2021-08-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.26.21262694", - "rel_abs": "The COVID-19 pandemic has infected over 200 million people worldwide and killed more than 4 million as of August 2021. Many intervention strategies have been utilized by governments around the world, including masks, social distancing, and vaccinations. However, officials making decisions regarding interventions may have a limited time to act. Computer simulations can aid them by predicting future disease outcomes, but they also have limitations due to requirements on processing power or time. This paper examines whether a machine learning model can be trained on a small subset of simulation runs to inexpensively predict future disease trajectories very close to the original simulation results. Using four previously published agent-based models for COVID-19, this paper analyzes the predictions of decision tree regression machine learning models and compares them to the results of the original simulations. The results indicate that accurate machine learning meta-models can be generated from simulation models with no strong interventions (e.g., vaccines, lockdowns) using small amounts of simulation data. However, meta-models for simulation models that include strong interventions required much more training data to achieve a similar accuracy. This indicates that machine learning meta-models could be used in some scenarios to assist in faster decision making.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Christopher B Lutz", - "author_inst": "Miami University" - }, - { - "author_name": "Philippe J. Giabbanelli", - "author_inst": "Miami University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.08.26.21262661", "rel_title": "A Learning Health System Approach to the COVID-19 Pandemic: System-Wide Changes in Clinical Practice and 30-Day Mortality Among Hospitalized Patients", @@ -586175,6 +589331,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.23.21262477", + "rel_title": "Low risk of SARS-CoV-2 transmission via fomite, even in cold-chain", + "rel_date": "2021-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.23.21262477", + "rel_abs": "BackgroundCountries continue to debate the need for decontamination of cold-chain food packaging to reduce possible SARS-CoV-2 fomite transmission among workers. While laboratory-based studies demonstrate persistence of SARS-CoV-2 on surfaces, the likelihood of fomite-mediated transmission under real-life conditions is uncertain.\n\nMethodsUsing a quantitative risk assessment model, we simulated in a frozen food packaging facility 1) SARS-CoV-2 fomite-mediated infection risks following worker exposure to contaminated plastic packaging; and 2) reductions in these risks attributed to masking, handwashing, and vaccination.\n\nFindingsIn a representative facility with no specific interventions, SARS-CoV-2 infection risk to a susceptible worker from contact with contaminated packaging was 2{middle dot}8 x 10-3 per 1h-period (95%CI: 6{middle dot}9 x 10-6, 2{middle dot}4 x 10-2). Implementation of standard infection control measures, handwashing and masks (9{middle dot}4 x 10-6 risk per 1h-period, 95%CI: 2{middle dot}3 x 10-8, 8{middle dot}1 x 10-5), substantially reduced risk (99{middle dot}7%). Vaccination of the susceptible worker (two doses Pfizer/Moderna, vaccine effectiveness: 86-99%) combined with handwashing and masking reduced risk to less than 1{middle dot}0 x 10-6. Simulating increased infectiousness/transmissibility of new variants (2-, 10-fold viral shedding) among a fully vaccinated workforce, handwashing and masks continued to mitigate risk (2{middle dot}0 x 10-6 -1{middle dot}1 x 10-5 risk per 1h-period). Decontamination of packaging in addition to these interventions reduced infection risks to below the 1{middle dot}0 x 10-6 risk threshold.\n\nInterpretationFomite-mediated SARS-CoV-2 infection risks were very low under cold-chain conditions. Handwashing and masking provide significant protection to workers, especially when paired with vaccination.\n\nFundingU.S. Department of Agriculture", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Julia S. Sobolik", + "author_inst": "Emory University" + }, + { + "author_name": "Elizabeth T. Sajewski", + "author_inst": "Emory University" + }, + { + "author_name": "Lee-Ann Jaykus", + "author_inst": "North Carolina State University" + }, + { + "author_name": "D. Kane Cooper", + "author_inst": "Emory University" + }, + { + "author_name": "Ben A. Lopman", + "author_inst": "Emory University" + }, + { + "author_name": "Alicia NM. Kraay", + "author_inst": "Emory University" + }, + { + "author_name": "P. Barry Ryan", + "author_inst": "Emory University" + }, + { + "author_name": "Jodie L. Guest", + "author_inst": "Emory University" + }, + { + "author_name": "Amy Webb-Girard", + "author_inst": "Emory University" + }, + { + "author_name": "Juan S. Leon", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.08.23.21262499", "rel_title": "Comparative analyses of all FDA EUA-approved rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolation", @@ -586352,53 +589563,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.08.24.21262535", - "rel_title": "Correlation between Proinflammatory cytokines and severity of COVID-19 within Palestinian Population", - "rel_date": "2021-08-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.24.21262535", - "rel_abs": "COVID-19 was characterized by cytokine storm and endothelial dysfunction in severely ill patients. As the severity of the infection was corelated with ethnicity, this study aimed to assess the correlation of proinflammatory cytokine serum level and COVID-19 symptoms within the Palestinian population. In cross-sectional study, serum samples of 27 non-hospitalized patients and 63 hospitalized patients SARS-CoV-2 infected patients, were tested for total antibodies, IL-6, TNF-, IFN-{gamma} and IL-1{beta} using the ELISA test. Results showed that most common symptoms within patients were Joint pain, cough, and fever (73.3%, 69.7% and 50% respectively). Serum total antibodies (IGs) levels in non-hospitalized patients were higher than hospitalized patients ((44.7 COI and 9.2 COI). TNF- and IL-6 were lower in non-hospitalized patients compared to hospitalized patients (48{+/-}17.9 pg/ml, 193.3{+/-}350.5 pg/ml respectively). On the other hand, IFN-{gamma}, in non-hospitalized patients (1{+/-}2 IU/ml) was significantly higher than hospitalized patients (0.4{+/-}0.26 IU/ml). IL-1{beta} was slightly lower in hospitalized patients (8.8{+/-}13.6 pg/ml) compared to non-hospitalized patients (12.5{+/-}24.5 pg/ml). Common mild symptoms of COVID-10 were negatively associated with proinflammatory cytokines serum level. In conclusion as it with other populations worldwide, IL-6 and TNF- are playing a major role in the complications of SARS-CoV-2 infection. Monitoring the two cytokines is crucial for management and treatment of complicated consequence of COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Walid Basha", - "author_inst": "Faculty of Medicine and Health Sciences-An-Najah National University" - }, - { - "author_name": "Zaher Nazzal", - "author_inst": "Faculty of Medicine and Health Sciences- An-Najah National university" - }, - { - "author_name": "Yousef El-Hamshary", - "author_inst": "Palestinian Ministry of Health" - }, - { - "author_name": "Anwar Odeh", - "author_inst": "Faculty of Medicine and Health Sciences-An-Najah National University" - }, - { - "author_name": "Lama Hijjawi", - "author_inst": "Faculty of Medicine and Health Sciences-An-Najah National University" - }, - { - "author_name": "Mahmoud Doden", - "author_inst": "Faculty of Medicine and Health Sciences-An-Najah National University" - }, - { - "author_name": "Ahmad Musa", - "author_inst": "Faculty of Medicine and Health Sciences-An-Najah National University" - }, - { - "author_name": "Saad Ruzzeh", - "author_inst": "Palestinian Ministry of Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.25.21262569", "rel_title": "Durability of antibody responses elicited by a single dose of Ad26.COV2.S and substantial increase following late boosting", @@ -588265,6 +591429,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.19.21262139", + "rel_title": "Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California", + "rel_date": "2021-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.19.21262139", + "rel_abs": "Associations between vaccine breakthrough cases and infection by SARS coronavirus 2 (SARS-CoV-2) variants have remained largely unexplored. Here we analyzed SARS-CoV-2 whole-genome sequences and viral loads from 1,373 persons with COVID-19 from the San Francisco Bay Area from February 1 to June 30, 2021, of which 125 (9.1%) were vaccine breakthrough infections. Fully vaccinated were more likely than unvaccinated persons to be infected by variants carrying mutations associated with decreased antibody neutralization (L452R, L452Q, E484K, and/or F490S) (78% versus 48%, p = 1.96e-08), but not by those associated with increased infectivity only (N501Y) (85% versus 77%, p = 0.092). Differences in viral loads were non-significant between unvaccinated and fully vaccinated persons overall (p = 0.99) and according to lineage (p = 0.09 - 0.78). Viral loads were significantly higher in symptomatic as compared to asymptomatic vaccine breakthrough cases (p < 0.0001), and symptomatic vaccine breakthrough infections had similar viral loads to unvaccinated infections (p = 0.64). In 5 cases with available longitudinal samples for serologic analyses, vaccine breakthrough infections were found to be associated with low or undetectable neutralizing antibody levels attributable to immunocompromised state or infection by an antibody-resistant lineage. Taken together, our results suggest that vaccine breakthrough infecions are overrepresnted by circulating antibody-resistant SARS-CoV-2 variants, and that symptomatic breakthrough infections may potentially transmit COVID-19 as efficiently as unvaccinated infections, regardless of the infecting lineage.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Venice Servellita", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alicia Sotomayor-Gonzalez", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Amelia Gliwa", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Erika Torres", + "author_inst": "Color Genomics" + }, + { + "author_name": "Noah Brazer", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alicia Zhou", + "author_inst": "Color Genomics" + }, + { + "author_name": "Katherine Hernandez", + "author_inst": "San Francisco Department of Public Health" + }, + { + "author_name": "Madeline Sankaran", + "author_inst": "San Francisco Department of Public Health" + }, + { + "author_name": "Baolin Wang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Daniel Wong", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Candace Wang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Yueyuan Zhang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kevin Reyes", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Dustin Glasner", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Wayne Deng", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jessica Streithorst", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Steve Miller", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Edwin Frias", + "author_inst": "Abbott Laboratories" + }, + { + "author_name": "John Hackett", + "author_inst": "Abbott Laboratories" + }, + { + "author_name": "Susan Philip", + "author_inst": "San Francisco Department of Public Health" + }, + { + "author_name": "Scott Topper", + "author_inst": "Color Genomics" + }, + { + "author_name": "Darpun Sachdev", + "author_inst": "San Francisco Department of Public Health" + }, + { + "author_name": "Charles Y Chiu", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.24.21262415", "rel_title": "Comparing SARS-CoV-2 natural immunity to vaccine-induced immunity: reinfections versus breakthrough infections", @@ -588402,33 +591673,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.08.23.21262469", - "rel_title": "The impact of the COVID-19 pandemic on adult mental health in the UK: A rapid systematic review", - "rel_date": "2021-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.23.21262469", - "rel_abs": "BackgroundThere is evidence that the COVID-19 pandemic has affected the mental health of the UK population, but this needs synthesising to guide effective policy recommendations and ensure support is targeted to populations most at risk. We conducted a rapid systematic review of the evidence of the impact of COVID-19 and associated restrictions on the mental health of UK adults, including risk and protective factors.\n\nMethodA range of databases were searched to identify eligible studies. Studies were eligible if they reported primary quantitative or qualitative research on the mental health of UK adults between March 2020 and March 2021. Journal publications and pre-prints were included. Reviews, position papers, protocol papers and studies published in languages other than English were excluded. The study authors screened papers for eligibility and included 102 papers in the analysis.\n\nResultsThe evidence from this review indicates that the mental health of UK adults has declined since the start of the pandemic, with different populations being unequally affected. Populations particularly affected are women, young adults, ethnic minorities, people from lower socio-economic backgrounds, people with pre-existing conditions and people who have had COVID-19. Other risk factors include having to isolate and time spent watching pandemic related news. Protective factors include social contact and maintaining healthy behaviours, such as physical activity.\n\nConclusionsPolicy should aim to discourage risky behaviours while ensuring support is available for people to engage in protective behaviours. Interventions should be directed towards populations that have been most adversely affected. Addressing the decline in mental health across the UK population since the COVID-19 pandemic will require increasing mental health provision and ensuring equitable access to support.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Eleonore Batteux", - "author_inst": "Public Health England" - }, - { - "author_name": "Jo Taylor", - "author_inst": "Public Health England" - }, - { - "author_name": "Holly Carter", - "author_inst": "Public Health England" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.08.18.21262046", "rel_title": "Reduction in initiations of HIV treatment in South Africa during the COVID pandemic", @@ -590018,6 +593262,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.16.21262150", + "rel_title": "The IHME vs Me: Modeling USA CoVID-19 Spread, Early Data to the Fifth Wave", + "rel_date": "2021-08-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.16.21262150", + "rel_abs": "Epidemiologists have never had such high-quality real-time pandemic data. Modeling CoVID-19 pandemic data became a predictive tool in-stead of an afterwards analysis. How early CoVID-19 model predictions impacted US Government policies and practices is first reviewed here as an important part of the pandemic history. It spurred independent modeling efforts, such as this, to help develop a better understanding of CoVID-19 spread, and to provide a substitute for the IHME (Institute for Health Metrics & Evaluation, U. Washington) 4-month predictions for the expected pandemic evolution, which they had to revise every couple of weeks. Our alternative model, which was developed over the course of several earlier medrxiv.org preprints, is shown here to provide a good description for the entire USA CoVID-19 pandemic to date, covering: (1) the original CoVID-19 wave [3/21/20-6/07/20], (2) the Summer 2020 Resurgence [6/07/20-9/25/20], (3) the large Winter 2020 Resurgence [9/25/20-3/19/21], (4) a small Spring 2021 \"Fourth Wave\", [3/19/21-6/07/21], and (5) the present-day Summer 2021 \"Fifth Wave\" [6/07/21-present], which the USA is now in the midst of. Our analysis of the initial \"Fifth Wave\" data shows that this wave presently has the capacity to infect virtually all susceptible non-vaccinated persons who practice NO Mask-Wearing and minimal Social Distancing.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Genghmun Eng", + "author_inst": "Retired Scientist" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.18.21262061", "rel_title": "Closed Doors: Predictors of Stress, Anxiety, Depression, and PTSD During the Onset of COVID-19 Pandemic in Brazil", @@ -590259,37 +593522,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.08.23.457434", - "rel_title": "Structure-based design of antisense oligonucleotides that inhibit SARS-CoV-2 replication", - "rel_date": "2021-08-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.23.457434", - "rel_abs": "Antisense oligonucleotides (ASOs) are an emerging class of drugs that target RNAs. Current ASO designs strictly follow the rule of Watson-Crick base pairing along target sequences. However, RNAs often fold into structures that interfere with ASO hybridization. Here we developed a structure-based ASO design method and applied it to target severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our method makes sure that ASO binding is compatible with target structures in three-dimensional (3D) space by employing structural design templates. These 3D-ASOs recognize the shapes and hydrogen bonding patterns of targets via tertiary interactions, achieving enhanced affinity and specificity. We designed 3D-ASOs that bind to the frameshift stimulation element and transcription regulatory sequence of SARS-CoV-2 and identified lead ASOs that strongly inhibit viral replication in human cells. We further optimized the lead sequences and characterized structure-activity relationship. The 3D-ASO technology helps fight coronavirus disease-2019 and is broadly applicable to ASO drug development.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Yan Li", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Gustavo Garcia Jr.", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Vaithilingaraja Arumugaswami", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Feng Guo", - "author_inst": "University of California, Los Angeles" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.08.24.457448", "rel_title": "Mutation Y453F in the spike protein of SARS-CoV-2 enhances interaction with the mink ACE2 receptor for host adaption", @@ -592100,6 +595332,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.08.23.457408", + "rel_title": "Deep immune profiling of the maternal-fetal interface with mild SARS-CoV-2 infection", + "rel_date": "2021-08-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.23.457408", + "rel_abs": "Pregnant women are an at-risk group for severe COVID-19, though the majority experience mild/asymptomatic disease. Although severe COVID-19 has been shown to be associated with immune activation at the maternal-fetal interface even in the absence of active viral replication, the immune response to asymptomatic/mild COVID-19 remains unknown. Here, we assessed immunological adaptations in both blood and term decidua from 9 SARS-exposed pregnant women with asymptomatic/mild disease and 15 pregnant SARS-naive women. In addition to selective loss of tissue-resident decidual macrophages, we report attenuation of antigen presentation and type I IFN signaling but upregulation of inflammatory cytokines and chemokines in blood monocyte derived decidual macrophages. On the other hand, infection was associated with remodeling of the T cell compartment with increased frequencies of activated CD69+ tissue-resident T cells and decreased abundance of Tregs. Interestingly, frequencies of cytotoxic CD4 and CD8 T cells increased only in the blood, while CD8 effector memory T cells were expanded in the decidua. In contrast to decidual macrophages, signatures of type I IFN signaling were increased in decidual T cells. Finally, T cell receptor diversity was significantly reduced with infection in both compartments, albeit to a much greater extent in the blood. The resulting aberrant immune activation in the placenta, even with asymptomatic disease may alter the exquisitely sensitive developing fetal immune system, leading to long-term adverse outcomes for offspring.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Suhas Sureshchandra", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Michael Z. Zulu", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Brianna Doratt", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Allen Jankeel", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Delia Tifrea", + "author_inst": "University of California,Irvine" + }, + { + "author_name": "Robert A Edwards", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Monica Rincon", + "author_inst": "Oregon Health and Sciences University" + }, + { + "author_name": "Nicole E. Marshall", + "author_inst": "Oregon Health and Science University" + }, + { + "author_name": "Ilhem Messaoudi", + "author_inst": "University of California Irvine" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.08.23.457328", "rel_title": "Presence and Stability of SARS-CoV-2 on Environmental Currency and Money Cards", @@ -592309,257 +595592,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.19.21262278", - "rel_title": "A prospective study of the protective effect of SARS-CoV-2-specific antibodies and T cells in Moscow residents", - "rel_date": "2021-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.19.21262278", - "rel_abs": "Rapid spread of COVID-19 pandemic made a substantial share of the world population immunised by SARS-CoV-2 antigens. Infection induces the development of virus-specific antibodies and T cells. Ample evidence on the antibody-mediated protection is contrasted by the elusive role of T cells in preventing infection. To explore the impact of T cells and to quantify the protective levels of the immune responses we conducted a large prospective study: 5,340 Moscow residents were evaluated for the antibody and cellular immune responses to SARS-CoV-2 and monitored for COVID-19 up to 300 days. The antibody and cellular responses were tightly interconnected, their magnitude inversely correlated with infection probability. Similar maximal level of protection was reached by individuals positive for both types of responses and by individuals with antibodies alone. Meanwhile, T cells in the absence of antibodies provided an intermediate level of protection. The real-world data on the protective effects of T cells have important implications for T cell immunology and development of the strategies to fight the pandemic.", - "rel_num_authors": 59, - "rel_authors": [ - { - "author_name": "Ivan Molodtsov", - "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia" - }, - { - "author_name": "Evgenii Kegeles", - "author_inst": "Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia" - }, - { - "author_name": "Alexander Mitin", - "author_inst": "National Research Center Institute of Immunology Federal MedicalBiological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia" - }, - { - "author_name": "Olga Mityaeva", - "author_inst": "Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia" - }, - { - "author_name": "Oksana Musatova", - "author_inst": "ShemyakinOvchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, 16/10 MiklukhoMaklaya str., Moscow, Russia" - }, - { - "author_name": "Anna Panova", - "author_inst": "National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str.," - }, - { - "author_name": "Mikhail Pashenkov", - "author_inst": "National Research Center Institute of Immunology Federal MedicalBiological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia" - }, - { - "author_name": "Iuliia Peshkova", - "author_inst": "National Research Center for Hematology, 125167, 4a Novozykovskii proezd, Moscow, Russia" - }, - { - "author_name": "Alsalloum Almaqdad", - "author_inst": "Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia" - }, - { - "author_name": "Walaa Asaad", - "author_inst": "Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia" - }, - { - "author_name": "Anna Budikhina", - "author_inst": "National Research Center Institute of Immunology Federal MedicalBiological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia" - }, - { - "author_name": "Aleksander Deryabin", - "author_inst": "ShemyakinOvchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, 16/10 MiklukhoMaklaya str., Moscow, Russia" - }, - { - "author_name": "Inna Dolzhikova", - "author_inst": "Federal State Budget Institution \"National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya\" of the Ministry of H" - }, - { - "author_name": "Ioanna Filimonova", - "author_inst": "ShemyakinOvchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, 16/10 MiklukhoMaklaya str., Moscow, Russia" - }, - { - "author_name": "Alexandra Gracheva", - "author_inst": "National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str.," - }, - { - "author_name": "Oxana Ivanova", - "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia" - }, - { - "author_name": "Anastasia Kizilova", - "author_inst": "Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia" - }, - { - "author_name": "Viktoria Komogorova", - "author_inst": "National Research Center Institute of Immunology Federal MedicalBiological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia" - }, - { - "author_name": "Anastasia Komova", - "author_inst": "Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia" - }, - { - "author_name": "Natalia Kompantseva", - "author_inst": "National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str.," - }, - { - "author_name": "Denis Lagutkin", - "author_inst": "National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str.," - }, - { - "author_name": "Yakov Lomakin", - "author_inst": "ShemyakinOvchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, 16/10 MiklukhoMaklaya str., Moscow, Russia" - }, - { - "author_name": "Alexandra Maleeva", - "author_inst": "National Research Center for Hematology, 125167, 4a Novozykovskii proezd, Moscow, Russia" - }, - { - "author_name": "Elena Maryukhnich", - "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia" - }, - { - "author_name": "Afraa Mohammad", - "author_inst": "Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia" - }, - { - "author_name": "Vladimir Murugin", - "author_inst": "National Research Center Institute of Immunology Federal MedicalBiological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia" - }, - { - "author_name": "Nina Murugina", - "author_inst": "National Research Center Institute of Immunology Federal MedicalBiological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia" - }, - { - "author_name": "Anna Navoikova", - "author_inst": "Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia" - }, - { - "author_name": "Margarita Nikonova", - "author_inst": "National Research Center Institute of Immunology Federal MedicalBiological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia" - }, - { - "author_name": "Leila Ovchinnikova", - "author_inst": "ShemyakinOvchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, 16/10 MiklukhoMaklaya str., Moscow, Russia" - }, - { - "author_name": "Natalia Pinegina", - "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia" - }, - { - "author_name": "Daria Potashnikova", - "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia" - }, - { - "author_name": "Elizaveta Romanova", - "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia" - }, - { - "author_name": "Aleena Saidova", - "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia" - }, - { - "author_name": "Nawar Sakr", - "author_inst": "Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia" - }, - { - "author_name": "Anastasia Samoilova", - "author_inst": "National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str.," - }, - { - "author_name": "Yana Serdyuk", - "author_inst": "National Research Center for Hematology, 125167, 4a Novozykovskii proezd, Moscow, Russia" - }, - { - "author_name": "Naina Shakirova", - "author_inst": "National Research Center for Hematology, 125167, 4a Novozykovskii proezd, Moscow, Russia" - }, - { - "author_name": "Nina Sharova", - "author_inst": "National Research Center Institute of Immunology Federal MedicalBiological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia" - }, - { - "author_name": "Savely Sheetikov", - "author_inst": "National Research Center for Hematology, 125167, 4a Novozykovskii proezd, Moscow, Russia" - }, - { - "author_name": "Anastasia Shemetova", - "author_inst": "National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str.," - }, - { - "author_name": "Liudmila Shevkova", - "author_inst": "Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia" - }, - { - "author_name": "Alexander Shpektor", - "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia" - }, - { - "author_name": "Anna Trufanova", - "author_inst": "Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia" - }, - { - "author_name": "Anna Tvorogova", - "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia" - }, - { - "author_name": "Valeria Ukrainskaya", - "author_inst": "ShemyakinOvchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, 16/10 MiklukhoMaklaya str., Moscow, Russia" - }, - { - "author_name": "Anatoliy Vinokurov", - "author_inst": "National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str.," - }, - { - "author_name": "Daria Vorobyeva", - "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia" - }, - { - "author_name": "Ksenia Zornikova", - "author_inst": "National Research Center for Hematology, 125167, 4a Novozykovskii proezd, Moscow, Russia" - }, - { - "author_name": "Grigory Efimov", - "author_inst": "National Research Center for Hematology, 125167, 4a Novozykovskii proezd, Moscow, Russia" - }, - { - "author_name": "Musa Khaitov", - "author_inst": "National Research Center Institute of Immunology Federal MedicalBiological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia" - }, - { - "author_name": "Ilya Kofiadi", - "author_inst": "National Research Center Institute of Immunology Federal MedicalBiological Agency of Russia, 115522, 24 Kashirskoye shosse, Moscow, Russia" - }, - { - "author_name": "Alexey Komissarov", - "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia" - }, - { - "author_name": "Denis Logunov", - "author_inst": "Federal State Budget Institution \"National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya\" of the Ministry of H" - }, - { - "author_name": "Nelli Naigovzina", - "author_inst": "A.I. Yevdokimov Moscow State University of Medicine and Dentistry, 127473, 20 Delegatskaya str., Moscow, Russia" - }, - { - "author_name": "Yury Rubtsov", - "author_inst": "ShemyakinOvchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997, 16/10 MiklukhoMaklaya str., Moscow, Russia" - }, - { - "author_name": "Irina Vasilyeva", - "author_inst": "National Medical Research Center for Phthisiopulmonology and Infectious Diseases of the Ministry of Health of the Russian Federation, 127473, 4 Dostoevsky str.," - }, - { - "author_name": "Pavel Volchkov", - "author_inst": "Genome Engineering lab, Moscow Institute of Physics and Technology, 141700, 9 Institutskiy per., Dolgoprudniy, Russia" - }, - { - "author_name": "Elena Vasilieva", - "author_inst": "Clinical City Hospital named after I.V. Davydovsky, Moscow Department of Healthcare, 109240, 11/6 Yauzskaya str., Moscow, Russia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.20.21262347", "rel_title": "Virtual Delivery of Simulation Education to Undergraduate Medical Students During the COVID-19 Pandemic", @@ -593882,6 +596914,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.14.21262042", + "rel_title": "Longitudinal monitoring of SARS-CoV-2-specific immune responses", + "rel_date": "2021-08-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.14.21262042", + "rel_abs": "The Lower Austrian Wachau region was an early COVID-19 hotspot of infection. As previously reported, in June 2020, after the first peak of infections, we determined that 8.5% and 9.0% of the participants in Wei{beta}enkirchen and surrounding communities in the Wachau region were positive for SARS-CoV-2-specific immunoglobulin G (IgG) and immunoglobulin A (IgA) antibodies, respectively. Here, we present novel data obtained eight months later (February 2021) from Wei{beta}enkirchen, after the second peak of infection, with 25.0% (138/552) and 23.6% (130/552) of participants that are positive for IgG and IgA, respectively. In participants with previous IgG/IgA positivity (June 2020), we observed a 24% reduction in IgG levels, whereas the IgA levels remained stable in February 2021. This subgroup was further analyzed for SARS-CoV-2-induced T cell activities. Although 76% (34/45) and 76% (34/45) of IgG positive and IgA positive participants, respectively, showed specific T cell activities, those were not significantly correlated with the levels of IgG or IgA. Thus, the analyses of antibodies cannot surrogate the measurement of T cell activities. For a comprehensive view on SARS-CoV-2-triggered immune responses, the measurement of different classes of antibodies should be complemented with the determination of T cell activities.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Heike Rebholz", + "author_inst": "Danube Private University" + }, + { + "author_name": "Ralf J. Braun", + "author_inst": "Danube Private University" + }, + { + "author_name": "Titas Saha", + "author_inst": "Danube Private University" + }, + { + "author_name": "Oliver Harzer", + "author_inst": "Danube Private University" + }, + { + "author_name": "Miriam Schneider", + "author_inst": "Danube Private University" + }, + { + "author_name": "Dennis Ladage", + "author_inst": "Danube Private University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.15.21262087", "rel_title": "The impact of ongoing COVID-19 lockdown on family finances and mental health", @@ -594063,41 +597134,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.15.21262097", - "rel_title": "Association of COVID-19 vaccination with risks of hospitalization and mortality due to cardiovascular and other diseases: A study of the UK Biobank", - "rel_date": "2021-08-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.15.21262097", - "rel_abs": "BackgroundVaccines for COVID-19 represent a major breakthrough. However, worries about adverse effects led to vaccine hesitancy in some people. On the other hand, as COVID-19 may be associated with various sequelae, vaccination may protect against such sequelae via prevention of infections and severe disease.\n\nMethodsWe leveraged the UK-Biobank (UKBB) and studied associations of at least one dose of COVID-19 vaccination (BioNTech-BNT162b2 or Oxford-AstraZeneca-ChAdOx1) with short-term hospitalizations from cardiovascular and other selected diseases (N=393,544; median follow-up=54 days among vaccinated). Multivariable Cox and Poisson regression analyses were performed. We also performed adjustment using prescription-time distribution matching (PTDM) and prior-event rate ratio (PERR). PERR minimizes unmeasured confounding by comparing event hazards before introduction of vaccination.\n\nResultsWe observed that COVID-19 vaccination(at least one dose), when compared to no vaccination, was associated with reduced short-term risks of hospitalizations from stroke(hazard ratio[HR]=0.178, 95% CI: 0.127-0.250, P=1.50e-23), venous thromboembolism (VTE) (HR=0.426, CI: 0.270-0.673, P=2.51e-4), dementia(HR=0.114, CI: 0.060-0.216; P=2.24e-11), non-COVID-19 pneumonia(NCP) (HR=0.108, CI: 0.080-0.145; P=2.20e-49), coronary artery disease (CAD) (HR=0.563, CI: 0.416-0.762; P=2.05e-4), chronic obstructive pulmonary disease (COPD) (HR=0.212, CI: 0.126-0.357; P=4.92e-9), type-2 diabetes (T2DM) (HR=0.216, CI: 0.096-0.486, P=2.12e-4), heart failure (HR=0.174, CI: 0.118-0.256, P=1.34e-18) and renal failure (HR=0.415, CI: 0.255-0.677, P=4.19e-4), based on Cox regression models. Among the above results, reduced hospitalizations for stroke, heart failure, NCP and dementia were consistently observed across all analyses, including regression/PTDM/PERR.\n\nConclusionsTaken together, this study provides further support to the safety and benefits of COVID-19 vaccination, and such benefits may extend beyond reduction of infection risk or severity per se. However, causal relationships cannot be concluded and further studies are required to verify the findings.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yong XIANG", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Yaning FENG", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Jinghong QIU", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Ruoyu ZHANG", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Hon-Cheong So", - "author_inst": "Chinese University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.16.21261912", "rel_title": "Genomic profiles of Covishield and Covaxin breakthrough SARS-CoV-2 strains from Odisha, India", @@ -595740,6 +598776,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.13.21262039", + "rel_title": "A sensitive and rapid wastewater test for SARS-COV-2 and its use for the early detection of a cluster of cases in a remote community", + "rel_date": "2021-08-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.13.21262039", + "rel_abs": "Throughout the COVID-19 pandemic, wastewater surveillance has been used to monitor trends in SARS-CoV-2 prevalence in the community. A major challenge in establishing wastewater surveillance programs, especially in remote areas, is the need for a well-equipped laboratory for sample analysis. Currently, no options exist for rapid, sensitive, mobile, and easy-to-use wastewater tests for SARS-CoV-2. The performance of the GeneXpert System, which offers cartridge-based, rapid molecular clinical testing for SARS-CoV-2 in a portable platform, was evaluated using wastewater as the input. The GeneXpert demonstrated a SARS-CoV-2 limit of detection in wastewater below 32 copies/mL with a sample processing time of less than an hour. Using wastewater samples collected from multiple sites across Canada during February and March 2021, a high overall agreement (97.8%) was observed between the GeneXpert assay and laboratory-developed tests regarding the presence or absence of SARS-CoV-2. Additionally, with the use of centrifugal filters the detection threshold of the GeneXpert system was improved to <10 copies/mL in wastewater. Finally, to support on-site wastewater surveillance, GeneXpert testing was implemented in Yellowknife, a remote community in Northern Canada where its use successfully alerted public health authorities to undetected transmission of COVID-19. The identification of SARS-CoV-2 in wastewater triggered clinical testing of recent travelers and identification of new COVID-19 cases/clusters. Taken together, these results suggest the GeneXpert is a viable option for surveillance of SARS-CoV-2 in wastewater in locations that do not have access to established testing laboratories.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Jade Daigle", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Kathleen Racher", + "author_inst": "Government of the Northwest Territories" + }, + { + "author_name": "Justin Hazenberg", + "author_inst": "Government of the Northwest Territories" + }, + { + "author_name": "Allan Yeoman", + "author_inst": "Government of the Northwest Territories" + }, + { + "author_name": "Heather Hannah", + "author_inst": "Government of the Northwest Territories" + }, + { + "author_name": "Diep Duong", + "author_inst": "Government of the Northwest Territories" + }, + { + "author_name": "Umar Mohammed", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Dave Spreitzer", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Branden S. J. Gregorchuk", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Breanne M. Head", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Adrienne F. A. Meyers", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Paul A. Sandstrom", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Anil Nichani", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "James I. Brooks", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Michael R. Mulvey", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Chand S. Mangat", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Michael G. Becker", + "author_inst": "Public Health Agency of Canada" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.14.21261996", "rel_title": "Association between interruption to medical care and sickness presenteeism during the COVID-19 pandemic: a cross-sectional study in Japan", @@ -595921,37 +599040,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.13.21262052", - "rel_title": "Lessons Learned From the Implementation of a Participant-Collected, Mail-Based SARS-CoV-2 Serological Survey in Massachusetts, USA", - "rel_date": "2021-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.13.21262052", - "rel_abs": "The rapid spread of SARS-CoV-2 is largely driven by pre-symptomatic or mildly symptomatic individuals who transmit the virus. Serological tests to identify antibodies against SARS-CoV-2 are an important tool to characterize subclinical infection exposure, which is critical in determining transmission trajectories and consequent population immunity. During the summer of 2020, a mail-based serological survey with self-collected dried blood spot (DBS) samples was implemented among university affiliates and their household members in Massachusetts, USA. Described here are some of the challenges faced and novel procedures used during the implementation of this study to assess the prevalence of SARS-CoV-2 antibodies amid the global pandemic. Important challenges included remote and contact-minimized participant recruitment, limited availability of commodities and laboratory capacity, a potentially biased sample population, and policy changes impacting the distribution of clinical results to study participants. Methods used to surmount these challenges and lessons learned are presented to inform similar studies. Key lessons relate to the acceptability and feasibility of DBS sampling, supply requirements, the logistics of packing and shipping packages, data linkages to enrolled household members, and the utility of having an on-call nurse available for participant concerns during sample collection.\n\nFuture studies might consider additional recruitment techniques such as conducting studies during academic semesters when recruiting in a university setting, partnerships with supply and shipping specialists, and using a stratified sampling approach to minimize potential biases in recruitment. This study design highlights the feasibility and acceptability of self-collected bio-samples and has broad applicability for other serological surveys for a range of pathogens.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Estee Y. Cramer", - "author_inst": "University of Massachusetts - Amherst" - }, - { - "author_name": "Teah Snyder", - "author_inst": "University of Massachusetts-Amherst" - }, - { - "author_name": "Johanna Ravenhurst", - "author_inst": "University of Massachusetts-Amherst" - }, - { - "author_name": "Andrew A. Lover", - "author_inst": "University of Massachusetts- Amherst" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.15.21262025", "rel_title": "The mental state of inpatients with COVID-19: a computational psychiatry approach", @@ -597314,6 +600402,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.10.21261836", + "rel_title": "Efficacy and Safety of Ayurveda Intervention AYUSH 64 as add-on therapy for patients with COVID 19 infections: An open labelled, Parallel Group, Randomized controlled clinical trial", + "rel_date": "2021-08-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.10.21261836", + "rel_abs": "The authors have withdrawn this manuscript because they found a serious issue in data-analysis which leads to wrong interpretation of the results. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Pankaj Bhardwaj", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Pawan Kumar Godatwar", + "author_inst": "National Institute of Ayurveda, Jaipur, Rajasthan" + }, + { + "author_name": "Jaykaran Charan", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Sanjeev Sharma", + "author_inst": "National Institute of Ayurveda, Jaipur, Rajasthan" + }, + { + "author_name": "Shazia Shafi", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Nishant Chauhan", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Pratibha Vyas", + "author_inst": "NIIR NCD Jodhpur" + }, + { + "author_name": "Naveen Dutt", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Naresh Midha", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Ramniwas Jalandra", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Meenakshi Sharma", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Vijaya Lakshmi Nag", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Suman Sharma", + "author_inst": "National Institute of Ayurveda, Jaipur, Rajasthan" + }, + { + "author_name": "Sarvesh Kumar Singh", + "author_inst": "National Institute of Ayurveda Jaipur" + }, + { + "author_name": "Praveen Sharma", + "author_inst": "All India Institute of Medical Sciences Jodhpur" + }, + { + "author_name": "Sanjeev Misra", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.15.21262000", "rel_title": "Seasonal betacoronavirus antibodies expansion post BNT161b2 vaccination associates with reduced SARS-CoV-2 VoCs neutralization", @@ -597559,81 +600726,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.08.17.456606", - "rel_title": "Pseudotyped Bat Coronavirus RaTG13 is efficiently neutralised by convalescent sera from SARS-CoV-2 infected Patients", - "rel_date": "2021-08-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.17.456606", - "rel_abs": "RaTG13 is a close relative of SARS-CoV-2, the virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic, sharing 96% sequence similarity at the genome-wide level. The spike receptor binding domain (RBD) of RaTG13 contains a large number of amino acid substitutions when compared to SARS-CoV-2, likely impacting affinity for the ACE2 receptor. Antigenic differences between the viruses are less well understood, especially whether RaTG13 spike can be efficiently neutralised by antibodies generated from infection with, or vaccination against, SARS-CoV-2. Using RaTG13 and SARS-CoV-2 pseudotypes we compared neutralisation using convalescent sera from previously infected patients as well as vaccinated healthcare workers. Surprisingly, our results revealed that RaTG13 was more efficiently neutralised than SARS-CoV-2. In addition, neutralisation assays using spike chimeras and mutants harbouring single amino acid substitutions within the RBD demonstrated that both spike proteins can tolerate multiple changes without dramatically reducing how efficiently they are neutralised. Moreover, introducing the 484K mutation into RaTG13 resulted in increased neutralisation, in contrast to the same mutation in SARS-CoV-2 (E484K). This is despite E484K having a well-documented role in immune evasion in variants of concern (VOC) such as B.1.351 (Beta). These results indicate that the immune-escape mutations found in SARS-CoV-2 VOCs might be driven by strong antibody pressures, and that the future spill-over of RaTG13 and/or related sarbecoviruses could be mitigated using current SARS-CoV-2-based vaccination strategies.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Diego Cantoni", - "author_inst": "Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent & Greenwich, Chatham, United Kingdom" - }, - { - "author_name": "Martin Mayora-Neto", - "author_inst": "Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent & Greenwich, Chatham, United Kingdom" - }, - { - "author_name": "Nazia Thakur", - "author_inst": "The Pirbright Institute, Guildford, Surrey, GU24 0NF, United Kingdom" - }, - { - "author_name": "Ahmed ME Elrefaey", - "author_inst": "The Pirbright Institute, Guildford, Surrey, GU24 0NF, United Kingdom" - }, - { - "author_name": "Joseph Newman", - "author_inst": "The Pirbright Institute, Guildford, Surrey, GU24 0NF, United Kingdom" - }, - { - "author_name": "Sneha Vishwanath", - "author_inst": "Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Angalee Nadesalingam", - "author_inst": "Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Andrew Chan", - "author_inst": "Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Peter Smith", - "author_inst": "Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Javier Castillo-Olivares", - "author_inst": "Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Helen Baxendale", - "author_inst": "Royal Papworth Hospital NHS Foundation Trust, Cambridge, UK" - }, - { - "author_name": "Bryan Charleston", - "author_inst": "The Pirbright Institute, Guildford, Surrey, GU24 0NF, United Kingdom" - }, - { - "author_name": "Jonathan Heeney", - "author_inst": "Laboratory of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom" - }, - { - "author_name": "Dalan Bailey", - "author_inst": "The Pirbright Institute, Guildford, Surrey, GU24 0NF, United Kingdom" - }, - { - "author_name": "Nigel Temperton", - "author_inst": "Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent & Greenwich, Chatham, United Kingdom" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.08.16.456531", "rel_title": "The pH Dependence of Niclosamide Solubility, Dissolution and Morphology Motivates a Potentially More Bioavailable Mucin-Penetrating Nasal and Throat Spray for COVID19, it's Contagious Variants, and Other Respiratory Viral Infections", @@ -599060,6 +602152,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.08.11.21261946", + "rel_title": "A Novel Convolutional Neural Network for COVID-19 detection and classification using Chest X-Ray images", + "rel_date": "2021-08-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.11.21261946", + "rel_abs": "The early and rapid diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), the main cause of fatal pandemic coronavirus disease 2019 (COVID-19), with the analysis of patients chest X-ray (CXR) images has life-saving importance for both patients and medical professionals. In this research a very simple novel and robust deep-learning convolutional neural network (CNN) model with less number of trainable-parameters is proposed to assist the radiologists and physicians in the early detection of COVID-19 patients. It also helps to classify patients into COVID-19, pneumonia and normal on the bases of analysis of augmented X-ray images. This augmented dataset contains 4803 COVID-19 from 686 publicly available chest X-ray images along with 5000 normal and 5000 pneumonia samples. These images are divided into 80% training and 20 % validation. The proposed CNN model is trained on training dataset and then tested on validation dataset. This model has a promising performance with a mean accuracy of 92.29%, precision of 99.96%, Specificity of 99.85% along with Sensitivity value of 85.92%. The result can further be improved if more data of expert radiologist is publically available.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Muhammad Talha Nafees", + "author_inst": "University of Engineering and Technology Peshawar" + }, + { + "author_name": "Irshad ullah", + "author_inst": "University of Engineering and Technology Peshawar" + }, + { + "author_name": "Muhammad Rizwan", + "author_inst": "University of Engineering and Technology Peshawar" + }, + { + "author_name": "Maaz ullah", + "author_inst": "University of Engineering and Technology Peshawar" + }, + { + "author_name": "Muhammad Irfanullah Khan", + "author_inst": "University of Engineering and Technology Peshawar" + }, + { + "author_name": "Muhammad Farhan", + "author_inst": "University of Engineering and Technology Peshawar" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2021.08.11.21261793", "rel_title": "Development and use analysis of 'gestioemocional.cat', a web app for promoting emotional self-care and access to professional mental health resources during the covid-19 pandemic", @@ -599265,109 +602396,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.13.21261989", - "rel_title": "Infectious SARS-CoV-2 in Exhaled Aerosols and Efficacy of Masks During Early Mild Infection", - "rel_date": "2021-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.13.21261989", - "rel_abs": "BackgroundSARS-CoV-2 epidemiology implicates airborne transmission; aerosol infectiousness and impacts of masks and variants on aerosol shedding are not well understood.\n\nMethodsWe recruited COVID-19 cases to give blood, saliva, mid-turbinate and fomite (phone) swabs, and 30-minute breath samples while vocalizing into a Gesundheit-II, with and without masks at up to two visits two days apart. We quantified and sequenced viral RNA, cultured virus, and assayed sera for anti-spike and anti-receptor binding domain antibodies.\n\nResultsWe enrolled 49 seronegative cases (mean days post onset 3.8 {+/-}2.1), May 2020 through April 2021. We detected SARS-CoV-2 RNA in 45% of fine ([≤]5 {micro}m), 31% of coarse (>5 {micro}m) aerosols, and 65% of fomite samples overall and in all samples from four alpha-variant cases. Masks reduced viral RNA by 48% (95% confidence interval [CI], 3 to 72%) in fine and by 77% (95% CI, 51 to 89%) in coarse aerosols; cloth and surgical masks were not significantly different. The alpha variant was associated with a 43-fold (95% CI, 6.6 to 280-fold) increase in fine aerosol viral RNA, compared with earlier viruses, that remained a significant 18-fold (95% CI, 3.4 to 92-fold) increase adjusting for viral RNA in saliva, swabs, and other potential confounders. Two fine aerosol samples, collected while participants wore masks, were culture-positive.\n\nConclusionSARS-CoV-2 is evolving toward more efficient aerosol generation and loose-fitting masks provide significant but only modest source control. Therefore, until vaccination rates are very high, continued layered controls and tight-fitting masks and respirators will be necessary.\n\nKey PointsO_LICases exhale infectious viral aerosols\nC_LIO_LISARS-CoV-2 evolution favors more efficient aerosol generation.\nC_LIO_LILoose-fitting masks moderately reduce viral RNA aerosol.\nC_LIO_LIVentilation, filtration, UV air sanitation, and tight-fitting masks are needed to protect vulnerable people in public-facing jobs and indoor spaces.\nC_LI", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Oluwasanmi Oladapo Adenaiye", - "author_inst": "Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Ma" - }, - { - "author_name": "Jianyu Lai", - "author_inst": "Department of Epidemiology and Biostatistics, University of Maryland School of Public Health, College Park, Maryland, USA" - }, - { - "author_name": "P. Jacob Bueno de Mesquita", - "author_inst": "Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Ma" - }, - { - "author_name": "Filbert H. Hong", - "author_inst": "Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Ma" - }, - { - "author_name": "Somayeh Youssefi", - "author_inst": "Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Ma" - }, - { - "author_name": "Jennifer Rebecca German", - "author_inst": "Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Ma" - }, - { - "author_name": "S.-H. Sheldon Tai", - "author_inst": "Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Ma" - }, - { - "author_name": "Barbara Jean Albert", - "author_inst": "Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Ma" - }, - { - "author_name": "Maria Schanz", - "author_inst": "Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Ma" - }, - { - "author_name": "Stuart Weston", - "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA" - }, - { - "author_name": "Jun Hang", - "author_inst": "Viral Diseases Branch, Walter Reed Army Institute for Research, Silver Spring, Maryland, USA" - }, - { - "author_name": "Christian K. Fung", - "author_inst": "Viral Diseases Branch, Walter Reed Army Institute for Research, Silver Spring, Maryland, USA" - }, - { - "author_name": "Hye Kyung Chung", - "author_inst": "Viral Diseases Branch, Walter Reed Army Institute for Research, Silver Spring, Maryland, USA" - }, - { - "author_name": "Kristen K. Coleman", - "author_inst": "Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore" - }, - { - "author_name": "Nicolae Sapoval", - "author_inst": "Department of Computer Science, Rice University, Houston, Texas, USA" - }, - { - "author_name": "Todd Treangen", - "author_inst": "Department of Computer Science, Rice University, Houston, Texas, USA" - }, - { - "author_name": "Irina Maljkovic Berry", - "author_inst": "Viral Diseases Branch, Walter Reed Army Institute for Research, Silver Spring, Maryland, USA" - }, - { - "author_name": "Kristin E. Mullins", - "author_inst": "Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA" - }, - { - "author_name": "Matthew Frieman", - "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA" - }, - { - "author_name": "Tianzhou Ma", - "author_inst": "Department of Epidemiology and Biostatistics, University of Maryland School of Public Health, College Park, Maryland, USA" - }, - { - "author_name": "Donald K. Milton", - "author_inst": "Public Health Aerobiology and Biomarker Laboratory, Institute for Applied Environmental Health, University of Maryland School of Public Health, College Park, Ma" - }, - { - "author_name": "- University of Maryland StopCOVID Research Group", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.11.21261829", "rel_title": "The role of incentives in deciding to receive the available COVID-19 vaccine", @@ -600954,6 +603982,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.12.456168", + "rel_title": "SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact", + "rel_date": "2021-08-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.12.456168", + "rel_abs": "The trimeric spike (S) glycoprotein, which protrudes from the SARS-CoV-2 viral envelope, binds to human ACE2, initiated by at least one protomers receptor binding domain (RBD) switching from a \"down\" (closed) to an \"up\" (open) state. Here, we used large-scale molecular dynamics simulations and two-dimensional replica exchange umbrella sampling calculations with more than a thousand windows and an aggregate total of 160 {micro}s of simulation to investigate this transition with and without glycans. We find that the glycosylated spike has a higher barrier to opening and also energetically favors the down state over the up state. Analysis of the S-protein opening pathway reveals that glycans at N165 and N122 interfere with hydrogen bonds between the RBD and the N-terminal domain in the up state, while glycans at N165 and N343 can stabilize both the down and up states. Finally we estimate how epitope exposure for several known antibodies changes along the opening path. We find that the BD-368-2 antibodys epitope is continuously exposed, explaining its high efficacy.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Yui Tik Pang", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Atanu Acharya", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Diane Lynch", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Anna Pavlova", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "James Gumbart", + "author_inst": "Georgia Institute of Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.08.13.456066", "rel_title": "SARS-CoV-2 Neutralization in Commercial Lots of Plasma-derived Immunoglobulin", @@ -601107,77 +604170,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.08.13.456266", - "rel_title": "Secreted SARS-CoV-2 ORF8 modulates the cytokine expression profile of human macrophages", - "rel_date": "2021-08-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.13.456266", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still adapting to its new human host. Attention has focussed on the viral spike protein, but substantial variation has been seen in the ORF8 gene. Here, we show that SARS-CoV-2 ORF8 protein undergoes signal peptide-mediated processing through the endoplasmic reticulum and is secreted as a glycosylated, disulphide-linked dimer. The secreted protein from the prototype SARS-CoV-2 virus had no major effect on viability of a variety of cell types, or on IFN or NF-{kappa}B signalling. However, it modulated cytokine expression from primary CSF1-derived human macrophages, most notably by decreasing IL-6 and IL-8 secretion. Furthermore, a sequence polymorphism L84S that appeared early in the pandemic associated with the Clade S lineage of virus, showed a markedly different effect, of increasing IL-6 production. We conclude that ORF8 sequence polymorphisms can potentially affect SARS-CoV-2 virulence and should therefore be monitored in sequencing-based surveillance.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Nisha Kriplani", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Sara Mary Rose Clohisey", - "author_inst": "University of Edinburgh, Roslin Institute" - }, - { - "author_name": "Sonia Fonseca", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Sarah Fletcher", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Hui-Min Lee", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Jordan Ashworth", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Dominic Kurian", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Samantha J Lycett", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Christine Tait-Burkard", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "J Kenneth Baillie", - "author_inst": "Roslin Institute, University of Edinburgh" - }, - { - "author_name": "Mark E J Woolhouse", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Simon R Carding", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "James P Stewart", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Paul Digard", - "author_inst": "University of Edinburgh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.08.12.456173", "rel_title": "Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant", @@ -603240,6 +606232,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.10.21261847", + "rel_title": "Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021", + "rel_date": "2021-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.10.21261847", + "rel_abs": "BackgroundThe COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just twenty six SARS-CoV-2 genomes available for this period, nine of which were from travellers from Lebanon detected by other countries. Additional genome sequencing is thus needed to allow surveillance of variants in circulation.\n\nMethodsNine hundred and five SARS-CoV-2 genomes were sequenced using the ARTIC protocol. The genomes were derived from SARS-CoV-2-positive samples, selected retrospectively from the sentinel COVID-19 surveillance network, to capture diversity of location, sampling time, gender, nationality and age.\n\nResultsAlthough sixteen PANGO lineages were circulating in Lebanon in January 2021, by February there were just four, with the Alpha variant accounting for 97% of samples. In the following two months, all samples contained the Alpha variant. However, this had changed dramatically by June and July, when all samples belonged to the Delta variant.\n\nDiscussionThis study provides a ten-fold increase in the number of SARS-CoV-2 genomes available from Lebanon. The Alpha variant, first detected in the UK, rapidly swept through Lebanon, causing the countrys largest wave to date, which peaked in January 2021. The Alpha variant was introduced to Lebanon multiple times despite travel restrictions, but the source of these introductions remains uncertain. The Delta variant was detected in Gambia in travellers from Lebanon in mid-May, suggesting community transmission in Lebanon several weeks before this variant was detected in the country. Prospective sequencing in June/July 2021 showed that the Delta variant had completely replaced the Alpha variant in under six weeks.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Georgi Merhi", + "author_inst": "Lebanese American University, Department of Natural Sciences, School of Arts and Sciences, Byblos-Lebanon" + }, + { + "author_name": "Alexander J Trotter", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Leonardo de Oliveira Martins", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Jad Koweyes", + "author_inst": "Lebanese American University, Department of Natural Sciences, School of Arts and Sciences, Byblos-Lebanon" + }, + { + "author_name": "Thanh Le-Viet", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Hala Abou Naja", + "author_inst": "Ministry of Public Health, Epidemiologial Surveillance Program, Museum square, Beirut, Lebanon" + }, + { + "author_name": "Mona Al Buaini", + "author_inst": "National Influenza Centre Research Laboratory, Rafic Hariri University Hospital, Beirut, Lebanon" + }, + { + "author_name": "Sophie J Prosolek", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Nabil-Fareed Alikhan", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Martin Lott", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Tatiana Tohmeh", + "author_inst": "Ministry of Public Health, Epidemiologial Surveillance Program, Museum square, Beirut, Lebanon" + }, + { + "author_name": "Bassam Badran", + "author_inst": "Laboratory of Molecular Biology and Cancer Immunology, Faculty of Sciences, Lebanese University" + }, + { + "author_name": "Orla J Jupp", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Sarah Gardner", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Matthew W Felgate", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Kate A Makin", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Janine M Wilkinson", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Rachael Stanley", + "author_inst": "Norfolk and Norwich University Hospital, Norwich, Norfolk, UK" + }, + { + "author_name": "Abdul K Sesay", + "author_inst": "MRC Unit The Gambia at LHSTM, Fajara, Gambia" + }, + { + "author_name": "Mark A Webber", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Rose K Davidson", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Nada Ghosn", + "author_inst": "Ministry of Public Health, Epidemiologial Surveillance Program, Museum square, Beirut, Lebanon" + }, + { + "author_name": "Mark Pallen", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Hamad Hasan", + "author_inst": "Ministry of Public Health, Beirut, Lebanon" + }, + { + "author_name": "Andrew J Page", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Sima Tokajian", + "author_inst": "Lebanese American University, Department of Natural Sciences, School of Arts and Sciences, Byblos-Lebanon" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.10.21261860", "rel_title": "Heterogeneity in COVID-19 Pandemic-Induced Lifestyle Stressors Predicts Mental Health in Adults and Children in the US and UK", @@ -603489,61 +606600,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.10.455874", - "rel_title": "CytokineLink: a cytokine communication map to analyse immune responses in inflammatory and infectious diseases", - "rel_date": "2021-08-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.10.455874", - "rel_abs": "Intercellular communication mediated by cytokines is critical to the development of immune responses, particularly in the context of infectious and inflammatory diseases. By releasing these small molecular weight peptides, the source cells can influence numerous intracellular processes in the target cells, including the secretion of other cytokines downstream. However, there are no readily available bioinformatic resources that can model cytokine - cytokine interactions. In this effort, we built a communication map between major tissues and blood cells that reveals how cytokine-mediated intercellular networks form during homeostatic conditions. We collated the most prevalent cytokines from literature, and assigned the proteins and their corresponding receptors to source tissue and blood cell types based on enriched consensus RNA-Seq data from the Human Protein Atlas database. To assign more confidence to the interactions, we integrated literature information on cell - cytokine interactions from two systems immunology databases, immuneXpresso and ImmunoGlobe. From the collated information, we defined two metanetworks: a cell-cell communication network connected by cytokines; and a cytokine-cytokine interaction network depicting the potential ways in which cytokines can affect the activity of each other. Using expression data from disease states, we then applied this resource to reveal perturbations in cytokine-mediated intercellular signalling in inflammatory and infectious diseases (ulcerative colitis and COVID-19, respectively). For ulcerative colitis, with CytokineLink we demonstrated a significant rewiring of cytokine-mediated intercellular communication between non-inflamed and inflamed colonic tissues. For COVID-19, we were able to identify inactive cell types and cytokine interactions that may be important following SARS-CoV-2 infection when comparing the cytokine response with other viruses capable of initiating a cytokine storm. Such findings have potential to inform the development of novel, cytokine-targeted therapeutic strategies. CytokineLink is freely available for the scientific community through the NDEx platform and the project github repository (https://github.com/korcsmarosgroup/CytokineLink).", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Marton L Olbei", - "author_inst": "Earlham Institute, Quadram Institute Bioscience" - }, - { - "author_name": "John Thomas", - "author_inst": "Norfolk & Norwich University Hospital" - }, - { - "author_name": "Isabelle Hautefort", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Agatha Treveil", - "author_inst": "Earlham Institute, Quadram Institute Bioscience" - }, - { - "author_name": "Balazs Bohar", - "author_inst": "Earlham Institute, Eotvos Lorand University" - }, - { - "author_name": "Matthew Madgwick", - "author_inst": "Earlham Institute, Quadram Institute Bioscience" - }, - { - "author_name": "Lejla Potari-Gul", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Luca Csabai", - "author_inst": "Earlham Institute, Eotvos Lorand University" - }, - { - "author_name": "Dezso Modos", - "author_inst": "Earlham Institute, Quadram Institute Bioscience" - }, - { - "author_name": "Tamas Korcsmaros", - "author_inst": "Earlham Institute, Quadram Institute Bioscience" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.08.11.455942", "rel_title": "A single shot of a hybrid hAdV5-based anti-COVID-19 vaccine induces a long-lasting immune response and broad coverage against VOC", @@ -605081,6 +608137,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.09.21261555", + "rel_title": "Mixed invasive molds among COVID-19 patients", + "rel_date": "2021-08-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.09.21261555", + "rel_abs": "PurposeDue to surge in COVID cases during the second wave of the COVID pandemic, the healthcare system collapsed in India with shortage of hospital beds, injudicious use of steroids and other immunomodulators, and poor glycaemic monitoring among a population with pre-existing risk of diabetes. Fungal epidemic was announced amid COVID pandemic with several cases of COVID-associated mucormycosis and aspergillosis being reported. But, there is no data regarding mixed fungal infections in COVID patients.\n\nMaterials and MethodsThe study presented a series of ten consecutive cases with dual invasive molds in patients infected with SARS-CoV-2. Among patients hospitalized with the diagnosis of COVID in May 2021 at a tertiary care center in North India, ten microbiologically confirmed dual/mixed COVID-associated mucor-aspergillosis (CAMA) were evaluated.\n\nResultsAll patients were diabetics with the majority having severe COVID pneumonia (6/10, 60%) either on admission or in the past one month, whilst two were each of moderate (20%) and mild (20%) categories of COVID. The patients were managed with amphotericin-B along with surgical intervention. In this case series, 70% of all CAMA (Rhizopus arrhizus with Aspergillus flavus in seven and Aspergillus fumigatus in three patients) patients survived, connoting the critical importance of a high index of clinical suspicion and accurate microbiological diagnosis for managing invasive molds.\n\nConclusionsMixed fungal infections i.e. CAMA during COVID and post-COVID periods may be an emerging disease. This outbreak is seen particularly in such patients with uncontrolled diabetes, on steroids, or cocktail therapy, or living in unhygienic environments.We believe that our findings would help gain a better insight into the risk and progression of invasive fungal mixed infections among COVID patients and thus play a pivotal role in diagnosing, classifying, and implementing an effective management strategy for treating similar cases in the future.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Vanya Singh", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Amber Prasad", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Prasan Kumar Panda", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Manjunath Totaganti", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Amit Tyagi", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Abhinav Thaduri", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Shalini Rao", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Mukesh Bairwa", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Ashok K Singh", + "author_inst": "AIIMS Rishikesh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.05.21261562", "rel_title": "Cryptic Transmission of the Delta Variant AY.3 Sublineage of SARS-CoV-2 among Fully Vaccinated Patients on an Inpatient Ward", @@ -605178,69 +608285,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.09.21261729", - "rel_title": "Symptoms that predict positive COVID-19 testing and hospitalization: an analysis of 9,000 patients", - "rel_date": "2021-08-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.09.21261729", - "rel_abs": "PurposeTo develop a reliable tool that predicts which patients are most likely to be COVID-19 positive and which ones have an increased risk of hospitalization.\n\nMethodsFrom February 2020 to April 2021, trained nurses recorded age, gender, and symptoms in an outpatient COVID-19 testing center. All positive patients were followed up by phone for 14 days or until symptom-free. We calculated the symptoms odds ratio for positive results and hospitalization and proposed a \"random forest\" machine-learning model to predict positive testing.\n\nResultsA total of 8,998 patients over 16 years old underwent COVID-19 RT-PCR, with 1,914 (21.3%) positives. Fifty patients needed hospitalization (2.6% of positives), and three died (0.15%). Most common symptoms were: cough, headache, sore throat, coryza, fever, myalgia (57%, 51%, 44%, 36%, 35%, 27%, respectively). Cough, fever, and myalgia predicted positive COVID-19 test, while others behaved as protective factors. The best predictors of positivity were fever plus anosmia/ageusia (OR=6.31), and cough plus anosmia/ageusia (OR=5.82), both p<0.0001. Our random forest model had an ROC-AUC of 0.72 (specificity=0.70, sensitivity=0.61, PPV=0.38, NPV=0.86). Having steady fever during the first days of infection and persistent dyspnea increased the risk of hospitalization (OR=6.66, p<0.0001 and OR=3.13, p=0.003, respectively), while anosmia-ageusia (OR=0.36, p=0.009) and coryza (OR=0.31, p=0.014) were protective.\n\nConclusionPresent study and algorithm may help identify patients at higher risk of having SARS-COV-2 (online calculator http://wdchealth.covid-map.com/shiny/calculator/), and also disease severity and hospitalization based on symptoms presence, pattern, and duration, which can help physicians and health care providers.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Mehrsa Jalalizadeh", - "author_inst": "University of Campinas, Unicamp" - }, - { - "author_name": "Patricia A. F. Leme", - "author_inst": "University of Campinas, Unicamp" - }, - { - "author_name": "Keini Buosi", - "author_inst": "University of Campinas, Unicamp" - }, - { - "author_name": "Franciele A. V. Dionato", - "author_inst": "University of Campinas, Unicamp" - }, - { - "author_name": "Cristiane F. Giacomelli", - "author_inst": "University of Campinas, Unicamp" - }, - { - "author_name": "Luciana S.B. Dal Col", - "author_inst": "University of Campinas, Unicamp" - }, - { - "author_name": "Karen L. Ferrari", - "author_inst": "University of Campinas, Unicamp" - }, - { - "author_name": "Ana Carolina Pagliarone", - "author_inst": "University of Campinas< Unicamp" - }, - { - "author_name": "Lucas M. Gon", - "author_inst": "University of Campinas, Unicamp" - }, - { - "author_name": "Douglas F.O. Cezar", - "author_inst": "University of Campinas, Unicamp" - }, - { - "author_name": "Akbar A. Esfahani", - "author_inst": "University of Campinas, Unicamp" - }, - { - "author_name": "Leonardo Oliveira Reis", - "author_inst": "UroScience, School of Medical Sciences, University of Campinas, UNICAMP and Pontifical Catholic University of Campinas, PUC-Campinas, Brazil." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.09.21261723", "rel_title": "In-House, Rapid, and Low-Cost SARS-CoV-2 Spike Gene Sequencing Protocol to Identify Variants of Concern Using Sanger Sequencing", @@ -606951,6 +609995,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.08.09.455656", + "rel_title": "Reprogramming of the intestinal epithelial-immune cell interactome during SARS-CoV-2 infection", + "rel_date": "2021-08-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.09.455656", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents an unprecedented worldwide health problem. Although the primary site of infection is the lung, growing evidence points towards a crucial role of the intestinal epithelium. Yet, the exact effects of viral infection and the role of intestinal epithelial-immune cell interactions in mediating the inflammatory response are not known. In this work, we apply network biology approaches to single-cell RNA-seq data from SARS-CoV-2 infected human ileal and colonic organoids to investigate how altered intracellular pathways upon infection in intestinal enterocytes leads to modified epithelial-immune crosstalk. We point out specific epithelial-immune interactions which could help SARS-CoV-2 evade the immune response. By integrating our data with existing experimental data, we provide a set of epithelial ligands likely to drive the inflammatory response upon infection. Our integrated analysis of intra- and inter-cellular molecular networks contribute to finding potential drug targets, and suggest using existing anti-inflammatory therapies in the gut as promising drug repurposing strategies against COVID-19.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Martina Poletti", + "author_inst": "Earlham Institute / Quadram Institute" + }, + { + "author_name": "Agatha Treveil", + "author_inst": "Earlham Institute, Norwich, UK" + }, + { + "author_name": "Leila Gul", + "author_inst": "Earlham Institute, Norwich UK" + }, + { + "author_name": "Dezso Modos", + "author_inst": "Quadram Institute, Norwich, UK" + }, + { + "author_name": "Matthew Madgwick", + "author_inst": "Earlham Institute" + }, + { + "author_name": "Marton Olbei", + "author_inst": "Earlham Institute, Norwich, UK" + }, + { + "author_name": "Balazs Bohar", + "author_inst": "Earlham Institute, Norwich, UK" + }, + { + "author_name": "Alberto Valdeolivas", + "author_inst": "Heidelberg University, Heidelberg, Germany" + }, + { + "author_name": "Denes Turei", + "author_inst": "Heidelberg University, Heidelberg, Germany" + }, + { + "author_name": "Bram Verstockt", + "author_inst": "KU Leuven, Leuven, Belgium" + }, + { + "author_name": "Sergio Triana", + "author_inst": "European Molecular Biology Laboratory, Heidelberg, Germany" + }, + { + "author_name": "Theodore Alexandrov", + "author_inst": "University of California San Diego, La Jolla, CA, USA" + }, + { + "author_name": "Julio Saez-Rodriguez", + "author_inst": "Heidelberg University, Heidelberg, Germany" + }, + { + "author_name": "Megan L Stanifer", + "author_inst": "Heidelberg University Hospital, Heidelberg, Germany" + }, + { + "author_name": "Steeve Boulant", + "author_inst": "Heidelberg University Hospital, Heidelberg, Germany" + }, + { + "author_name": "Tamas Korcsmaros", + "author_inst": "Earlham Institute / Quadram Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.08.08.455468", "rel_title": "A Tethered Ligand Assay to Probe SARS-CoV-2:ACE2 Interactions", @@ -607140,41 +610263,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.08.08.21261770", - "rel_title": "The effect of eye protection on SARS-CoV-2 transmission: a systematic review", - "rel_date": "2021-08-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.08.21261770", - "rel_abs": "BackgroundThe effect of eye protection to prevent SARS-CoV-2 infection in the real-world remains uncertain. We aimed to synthesize all available research on the potential impact of eye protection on transmission of SARS-CoV-2.\n\nMethodsWe searched PROSPERO, PubMed, Embase, The Cochrane Library for clinical trials and comparative observational studies in CENTRAL, and Europe PMC for pre-prints. We included studies that reported sufficient data to estimate the effect of any form of eye protection including face shields and variants, goggles, and glasses, on subsequent confirmed infection with SARS-CoV-2.\n\nFindingsWe screened 898 articles and included 6 reports of 5 observational studies from 4 countries (USA, India, Columbia, and United Kingdom) that tested face shields, googles and wraparound eyewear on 7567 healthcare workers. The three before-and-after and one retrospective cohort studies showed statistically significant and substantial reductions in SARS-CoV-2 infections favouring eye protection with odds ratios ranging from 0.04 to 0.6, corresponding to relative risk reductions of 96% to 40%. These reductions were not explained by changes in the community rates. However, the one case-control study reported odds ratio favouring no eye protection (OR 1.7, 95% CI 0.99, 3.0). The high heterogeneity between studies precluded any meaningful meta-analysis. None of the studies adjusted for potential confounders such as other protective behaviours, thus increasing the risk of bias, and decreasing the certainty of evidence to very low.\n\nInterpretationCurrent studies suggest that eye protection may play a role in prevention of SARS-CoV-2 infection in healthcare workers. However, robust comparative trials are needed to clearly determine effectiveness of eye protections and wearability issues in both healthcare and general populations.\n\nFundingThere was no funding source for this study. All authors had full access to all data and agreed to final manuscript to be submitted for publication.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Oyungerel Byambasuren", - "author_inst": "Institute for Evidence-Based Healthcare, Bond University" - }, - { - "author_name": "Elaine Beller", - "author_inst": "Institute for Evidence-Based Healthcare, Bond university" - }, - { - "author_name": "Justin Clark", - "author_inst": "Institute for Evidence-Based Healthcare, Bond university" - }, - { - "author_name": "Peter Collignon", - "author_inst": "Australian National University" - }, - { - "author_name": "Paul Glasziou", - "author_inst": "Institute for Evidence-Based Healthcare, Bond university" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.08.06.21261727", "rel_title": "Surveillance genome sequencing reveal multiple SARS-CoV-2 variants circulating in the central Texas, USA with a predominance of Delta variant and review of vaccine breakthrough cases.", @@ -609053,6 +612141,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.08.05.21261627", + "rel_title": "Systematic review protocol exploring the impact of the COVID-19 pandemic on the wellbeing of general practitioners", + "rel_date": "2021-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.05.21261627", + "rel_abs": "BackgroundOver recent years chronic stress and burnout have been reported by doctors working in general practice in the UK NHS and internationally. The COVID-19 pandemic has changed general practitioners working lives - adding potential pressures from avoiding infection and addressing pent-up demand for care, but also changing processes such as rapidly taking up remote consultations. To date, there has been a focus on exploring the impact of the pandemic on the wellbeing of hospital clinicians. No registered systematic reviews currently focus on exploring the impact of the pandemic on the mental health and wellbeing of general practitioners.\n\nAims and objectivesTo synthesise the current international evidence base exploring the impact of COVID-19 on the mental health and wellbeing of general practitioners, and which factors are associated with their reported mental health and wellbeing during the pandemic.\n\nMethodsIn this paper we report a systematic review protocol, following PRISMA guidance. In our search strategy we will identify primary research studies or systematic reviews exploring the mental health and wellbeing of general practitioners during the COVID-19 pandemic in four databases (MEDLINE, Embase, PsychInfo and Medrxiv) and Google Scholar. We will hand-search reference lists and grey literature.\n\nTwo reviewers will undertake all stages including study selection, data extraction and quality assessment, with arbitration by a third reviewer where necessary. We will use standardised quality assessment tools to ensure transparency and reduce bias in quality assessment. Depending on the quality of included studies, we may undertake a sensitivity analysis by excluding studies from narrative synthesis that are rated as low quality using the checklists.\n\nWe will describe the findings across studies using narrative thematic data synthesis, and if sufficiently homogenous data are identified, we will pool quantitative findings through meta-analysis.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Laura Jefferson", + "author_inst": "University of York" + }, + { + "author_name": "Su Golder", + "author_inst": "University of York" + }, + { + "author_name": "Veronica Dale", + "author_inst": "University of York" + }, + { + "author_name": "Holly Essex", + "author_inst": "University of York" + }, + { + "author_name": "Elizabeth McHugh", + "author_inst": "University of York" + }, + { + "author_name": "Karen Bloor", + "author_inst": "University of York" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.08.04.21261576", "rel_title": "When do elementary students need masks in school? Model-estimated risk of in-school SARS-CoV-2 transmission and related infections among household members before and after student vaccination", @@ -609182,29 +612309,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.04.21261600", - "rel_title": "On the persistence of mental health deterioration during the COVID-19 pandemic by sex and ethnicity in the UK: evidence from Understanding Society", - "rel_date": "2021-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.04.21261600", - "rel_abs": "We use longitudinal data from a representative sample of the UK and compare self-reported mental health, as measured by the GHQ-12 score, at three timepoints (2017-2019, April 2020 and March 2021), for the whole sample and by sex and ethnicity. Out of the 14,382 individuals interviewed in 2017-2019 and April 2020, 10,445 were interviewed again in March 2021. The mean GHQ-12 in April 2020 is 12.37 [95% CI: 12.22, 12.52] and in March 2021 is 12.36 [95% CI: 12.21, 12.51], above that in 2017-2019, 11.13 [95% CI: 10.99, 11.26]. We do not find evidence that the level of mental health goes back to pre-pandemic levels. In terms of inequalities, while the gender gap (mean difference between women and men) in mental health deterioration among White British is closing, there is no clear evidence that the ethnic gap (mean difference between ethnic minorities and White British) among men is changing.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Climent Quintana-Domeque", - "author_inst": "University of Exeter" - }, - { - "author_name": "Eugenio Proto", - "author_inst": "University of Glasgow" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.08.05.21261626", "rel_title": "Passive Detection of COVID-19 with Wearable Sensors and Explainable Machine Learning Algorithms", @@ -610963,6 +614067,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.06.455424", + "rel_title": "Small-molecule ligands can inhibit -1 programmed ribosomal frameshifting in a broad spectrum of coronaviruses", + "rel_date": "2021-08-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.06.455424", + "rel_abs": "Recurrent outbreaks of novel zoonotic coronavirus (CoV) diseases since 2000 have high-lighted the importance of developing therapeutics with broad-spectrum activity against CoVs. Because all CoVs use -1 programmed ribosomal frameshifting (-1 PRF) to control expression of key viral proteins, the frameshift signal in viral mRNA that stimulates -1 PRF provides a promising potential target for such therapeutics. To test the viability of this strategy, we explored a group of 6 small-molecule ligands, evaluating their activity against the frameshift signals from a panel of representative bat CoVs--the most likely source of future zoonoses--as well as SARS-CoV-2 and MERS-CoV. We found that whereas some ligands had notable activity against only a few of the frameshift signals, the serine protease inhibitor nafamostat suppressed -1 PRF significantly in several of them, while having limited to no effect on -1 PRF caused by frameshift signals from other viruses used as negative controls. These results suggest it is possible to find small-molecule ligands that inhibit -1 PRF specifically in a broad spectrum of CoVs, establishing the frameshift signal as a viable target for developing pan-coronaviral therapeutics.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Sneha Munshi", + "author_inst": "University of Alberta" + }, + { + "author_name": "Krishna Neupane", + "author_inst": "University of Alberta" + }, + { + "author_name": "Sandaru M Ileperuma", + "author_inst": "University of Alberta" + }, + { + "author_name": "Matthew TJ Halma", + "author_inst": "University of Alberta" + }, + { + "author_name": "Jamie A Kelly", + "author_inst": "University of Maryland" + }, + { + "author_name": "Clarissa F Halpern", + "author_inst": "University of Maryland" + }, + { + "author_name": "Jonathan D. Dinman", + "author_inst": "University of Maryland" + }, + { + "author_name": "Sarah Loerch", + "author_inst": "University of California Santa Cruz" + }, + { + "author_name": "Michael T Woodside", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.08.06.455384", "rel_title": "The Inherent Flexibility of Receptor Binding Domains in SARS-CoV-2 Spike Protein", @@ -611080,105 +614235,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.08.06.455382", - "rel_title": "Controlled administration of aerosolized SARS-CoV-2 to K18-hACE2 transgenic mice uncouples respiratory infection and anosmia from fatal neuroinvasion", - "rel_date": "2021-08-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.06.455382", - "rel_abs": "The development of a tractable small animal model faithfully reproducing human COVID-19 pathogenesis would arguably meet a pressing need in biomedical research. Thus far, most investigators have used transgenic mice expressing the human ACE2 in epithelial cells (K18-hACE2 transgenic mice) that are intranasally instilled with a liquid SARS-CoV-2 suspension under deep anesthesia. Unfortunately, this experimental approach results in disproportionate high CNS infection leading to fatal encephalitis, which is rarely observed in humans and severely limits this models usefulness. Here, we describe the use of an inhalation tower system that allows exposure of unanesthetized mice to aerosolized virus under controlled conditions. Aerosol exposure of K18-hACE2 transgenic mice to SARS-CoV-2 resulted in robust viral replication in the respiratory tract, anosmia, and airway obstruction, but did not lead to fatal viral neuroinvasion. When compared to intranasal inoculation, aerosol infection resulted in a more pronounced lung pathology including increased immune infiltration, fibrin deposition and a transcriptional signature comparable to that observed in SARS-CoV-2- infected patients. This model may prove useful for studies of viral transmission, disease pathogenesis (including long-term consequences of SARS-CoV-2 infection) and therapeutic interventions.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Valeria Fumagalli", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Micol Rava", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Davide Marotta", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Pietro Di Lucia", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Chiara Laura", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Eleonora Sala", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Marta Grillo", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Elisa Bono", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Leonardo Giustini", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Chiara Perucchini", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Marta Mainetti", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Alessandro Sessa", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Jose Garcia-Manteiga", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Lorena Donnici", - "author_inst": "INGM" - }, - { - "author_name": "Lara Manganaro", - "author_inst": "INGM" - }, - { - "author_name": "Serena Delbue", - "author_inst": "UniMI" - }, - { - "author_name": "Vania Broccoli", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Raffaele De Francesco", - "author_inst": "INGM" - }, - { - "author_name": "Mirela Kuka", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Luca Guidotti", - "author_inst": "San Raffaele Scientific Institute" - }, - { - "author_name": "Matteo Iannacone", - "author_inst": "San Raffaele Scientific Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.07.30.21261400", "rel_title": "Negative impact of COVID-19 associated health system shutdown on patients diagnosed with colorectal cancer: a retrospective study from a large tertiary center in Ontario, Canada.", @@ -613157,6 +616213,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.04.21261538", + "rel_title": "Association between obesity and hospitalization in mild COVID-19 young adult outpatients in Brazil: a prospective cohort study", + "rel_date": "2021-08-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.04.21261538", + "rel_abs": "Background/ObjectivesThe aim of this study was to evaluate the association between obesity and hospitalization in mild COVID-19 adult outpatients in Brazil.\n\nSubjects/MethodsAdults with signs and symptoms suggestive of acute SARS-CoV-2 infection who sought two hospitals (one public and one private) emergency department (ED) were prospectively enrolled. Patients with confirmed COVID-19 at inclusion were followed by phone calls at day (D) D7, D14 and D28. Multivariable logistic regression models were employed to explore the association between obesity and other potential predictors for hospitalization.\n\nResultsA total of 1,050 participants were screened, 310 were diagnosed with COVID-19 by RT-PCR. Median age was 37.4 (IQR 29.8-45.0) years, and 186 (60.0%) were female. Duration of symptoms was 3.0 (IQR 2.0-5.0) days, and 10.0 (IQR 8.0-12.0) was the median number of symptoms at inclusion. A total of 98 (31.6%) were obese, and 243 (78.4%) had no previous medical conditions. Twenty three participants (23/310, 7.4%) required hospitalization during the period. After adjusting, obesity (BMI[≥]30.0 kg/m2) (OR=2.69, 95%CI 1.63-4.83, P<0.001) and older age (OR=1.05, 95%CI 1.01-1.09, P<0.001), were significantly associated with higher risks of hospitalization.\n\nConclusionsObesity, followed by aging, was the main factor associated with hospital admission for COVID-19 in a young population in a low-middle income country. Our findings highlighted the need for actions to promote additional protection for obese population, such as vaccination, and to encourage lifestyle changes.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Ivaine Tais Sauthier Sartor", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Caroline Nespolo David", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Gabriela Heiden Telo", + "author_inst": "School of Medicine, Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre, Brazil" + }, + { + "author_name": "Gabriela Oliveira Zavaglia", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Ingrid Rodrigues Fernandes", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Luciane Beatriz Kern", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Marcia Polese-Bonatto", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Thais Raupp Azevedo", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Amanda Paz Santos", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Walquiria Aparecida Ferreira Almeida", + "author_inst": "General Coordination, National Immunization Program, Brazilian Ministry of Health, Brasilia, Brazil" + }, + { + "author_name": "Victor Bertollo Gomes Porto", + "author_inst": "General Coordination, National Immunization Program, Brazilian Ministry of Health, Brasilia, Brazil" + }, + { + "author_name": "Fernanda Hammes Varela", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil; School of Medicine, Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre," + }, + { + "author_name": "Marcelo Comerlato Scotta", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil; School of Medicine, Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre," + }, + { + "author_name": "Regis Goulart Rosa", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Renato T Stein", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil; School of Medicine, Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre," + }, + { + "author_name": "- COVIDa study group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.05.455290", "rel_title": "SARS-CoV-2 variants of concern have acquired mutations associated with an increased spike cleavage", @@ -613430,49 +616565,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.08.05.455040", - "rel_title": "Virucidal activity of CPC-containing oral rinses against SARS-CoV-2 variants and are active in the presence of human saliva", - "rel_date": "2021-08-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.05.455040", - "rel_abs": "The role of human saliva in aerosol-based transmission of SARS-CoV-2 has highlighted the need to understand the potential of oral hygiene products to inactivate the virus. Here we examined the efficacy of mouthwashes containing cetylpyridinium chloride (CPC) or chlorhexidine (CHX) in inactivating SARS-CoV-2. After 30 seconds contact under standard aqueous conditions CPC mouthwashes achieved a [≥]4.0log10 PFU/mL reduction in SARS-CoV-2 (USA-WA1/2020) titres whereas comparable products containing CHX achieved <2.0log10 PFU/mL reduction. Further testing with CPC mouthwashes demonstrated efficacy against multiple SARS-CoV-2 variants, with inactivation below the limit of detection observed against the Alpha (B.1.1.7), Beta (B.1.351) and Gamma (P.1) variants. Virucidal efficacy of CPC mouthwash was also observed in the presence of human saliva with the product delivering [≥]4.0log10 PFU/mL reduction in SARS-CoV-2 titres after 30 seconds providing additional evidence for the virucidal efficacy of CPC mouthwashes under simulated physiological conditions. Together these data suggest CPC-based mouthwashes are effective at inactivating SARS-CoV-2 and further supports the use of mouthwash to mitigate the risk of transmission during dentistry procedures.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Enyia R Anderson", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Edward I Patterson", - "author_inst": "Brock University" - }, - { - "author_name": "Siobhan Richards", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Alison K Green", - "author_inst": "Unilever R&D" - }, - { - "author_name": "Sayandip Mukherjee", - "author_inst": "Unilever R&D" - }, - { - "author_name": "Michael Hoptroff", - "author_inst": "Unilever R&D" - }, - { - "author_name": "Grant Hughes", - "author_inst": "Liverpool School of Tropical Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.08.04.455157", "rel_title": "Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region", @@ -614787,6 +617879,177 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.08.02.21261379", + "rel_title": "An adaptive randomized controlled trial of non-invasive respiratory strategies in acute respiratory failure patients with COVID-19", + "rel_date": "2021-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.02.21261379", + "rel_abs": "BackgroundBoth continuous positive airway pressure (CPAP) and high-flow nasal oxygenation (HFNO) have been recommended for acute respiratory failure in COVID-19. However, uncertainty exists regarding effectiveness and safety.\n\nMethodsIn the Recovery-Respiratory Support multi-center, three-arm, open-label, adaptive, randomized controlled trial, adult hospitalized patients with acute respiratory failure due to COVID-19, deemed suitable for treatment escalation, were randomly assigned to receive CPAP, HFNO, or conventional oxygen therapy. Comparisons were made between each intervention and conventional oxygen therapy. The primary outcome was a composite of tracheal intubation or mortality within 30-days.\n\nResultsOver 13-months, 1272 participants were randomized and included in the analysis (380 (29.9%) CPAP; 417 (32.8%) HFNO; 475 (37.3%) conventional oxygen therapy). The need for tracheal intubation or mortality within 30-days was lower in the CPAP group (CPAP 137 of 377 participants (36.3%) vs conventional oxygen therapy 158 of 356 participants (44.4%); unadjusted odds ratio 0.72; 95% CI 0.53 to 0.96, P=0.03). There was no difference between HFNO and conventional oxygen therapy (HFNO 184 of 414 participants (44.4%) vs conventional oxygen therapy 166 of 368 participants (45.1%); unadjusted odds ratio 0.97; 95% CI 0.73 to 1.29, P=0.85).\n\nConclusionsCPAP, compared with conventional oxygen therapy, reduced the composite outcome of intubation or death within 30 days of randomisation in hospitalized adults with acute respiratory failure due to COVID-19. There was no effect observed, compared with conventional oxygen therapy, with the use of HFNO.\n\n(Funded by the UK National Institute for Health Research; ISRCTN 16912075).", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Gavin D Perkins", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Chen Ji", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Bronwen A Connolly", + "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, UK; Lane Fox Cli" + }, + { + "author_name": "Keith Couper", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Ranjit Lall", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "J Kenneth Baillie", + "author_inst": "Roslin Institute, University of Edinburgh, Midlothian, UK; MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, University of Edinburgh, Edin" + }, + { + "author_name": "Judy M Bradley", + "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, UK" + }, + { + "author_name": "Paul Dark", + "author_inst": "NIHR Manchester Biomedical Research Centre, University of Manchester, Manchester, UK; Salford Royal Hospital, Northern Care Alliance NHS Group, Manchester, UK" + }, + { + "author_name": "Chirag Dave", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Anthony De Soyza", + "author_inst": "Population and Health Science Institute, NIHR Biomedical Research Centre, Newcastle, University, Newcastle Upon Tyne, UK; Newcastle-Upon-Tyne Hospitals NHS Foun" + }, + { + "author_name": "Anna V Dennis", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Anne Devrell", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK; Research Champion Team, West Midlands Clinical Research Network, Wolv" + }, + { + "author_name": "Sara Fairbairn", + "author_inst": "Grange University Hospital, Aneurin Bevan University Health Board, Cwmbran, UK" + }, + { + "author_name": "Hakim Ghani", + "author_inst": "Watford General Hospital, West Hertfordshire Hospitals NHS Trust, Watford, UK" + }, + { + "author_name": "Ellen A Gorman", + "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, UK" + }, + { + "author_name": "Christopher A Green", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Nicholas Hart", + "author_inst": "Lane Fox Clinical Respiratory Physiology Research Centre, Guys and St.Thomas NHS Foundation Trust, London, UK; Centre for Human and Applied Physiological Scienc" + }, + { + "author_name": "Siew Wan Hee", + "author_inst": "Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Zoe Kimbley", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Shyam Madathil", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Nicola McGowan", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Benjamin Messer", + "author_inst": "Newcastle-Upon-Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK" + }, + { + "author_name": "Jay Naisbitt", + "author_inst": "Fairfield General Hospital, Pennine Acute Hospitals NHS Trust, Northern Care Alliance NHS Group, Bury, UK" + }, + { + "author_name": "Chloe Norman", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Dhruv Parekh", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Institute of Inflammation and Ageing, School of Medical and Dental Sciences, University of" + }, + { + "author_name": "Emma M Parkin", + "author_inst": "Fairfield General Hospital, Pennine Acute Hospitals NHS Trust, Northern Care Alliance NHS Group, Bury, UK" + }, + { + "author_name": "Jaimin Patel", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Institute of Inflammation and Ageing, School of Medical and Dental Sciences, University of" + }, + { + "author_name": "Scott E Regan", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Clare Ross", + "author_inst": "Imperial College Healthcare NHS Trust, London, UK" + }, + { + "author_name": "Anthony J Rostron", + "author_inst": "Sunderland Royal Hospital, South Tyneside and Sunderland NHS Foundation Trust, Sunderland, UK; Translational and Clinical Research Institute, Newcastle Universi" + }, + { + "author_name": "Mohammad Saim", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Anita K Simonds", + "author_inst": "Royal Brompton and Harefield Hospital, Guys and St Thomas NHS Foundation Trust, London, UK" + }, + { + "author_name": "Emma Skilton", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Nigel Stallard", + "author_inst": "Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Michael Steiner", + "author_inst": "Institute for Lung Health, NIHR BRC Respiratory Medicine, Department of Respiratory Sciences, University of Leicester, Leicester, UK" + }, + { + "author_name": "Rama Vancheeswaran", + "author_inst": "Watford General Hospital, West Hertfordshire Hospitals NHS Trust, Watford, UK" + }, + { + "author_name": "Joyce Yeung", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Daniel F McAuley", + "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, UK; Royal Victor" + }, + { + "author_name": "- Recovery- RS collaborators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.08.02.21261504", "rel_title": "SARS-CoV-2 antibody binding and neutralization in dried blood spot eluates and paired plasma", @@ -615024,45 +618287,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.02.21261469", - "rel_title": "Association of chronic kidney disease, ethnicity and socioeconomic status with COVID-19 hospitalisation and mortality: a UK Biobank study", - "rel_date": "2021-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.02.21261469", - "rel_abs": "O_LIIn individuals with chronic kidney disease (CKD), Black and South Asian ethnic groups are twice as likely to have severe COVID-19 compared to White participants, whilst the most socially deprived groups are at a 50-60% increased risk of severe COVID-19.\nC_LIO_LIThis study is the first to highlight the association between ethnicity and socioeconomic deprivation and the risk of severe COVID-19 among those with CKD in the UK.\nC_LIO_LIInterventions to reduce morbidity and mortality amongst these groups and policy and practice improvements are needed to address the broad disparity among CKD patients.\nC_LI", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Thomas J Wilkinson", - "author_inst": "University of Leicester" - }, - { - "author_name": "Courtney J Lightfoot", - "author_inst": "Department of Health Sciences, University of Leicester, Leicester, UK" - }, - { - "author_name": "Alice C Smith", - "author_inst": "Department of Health Sciences, University of Leicester, Leicester, UK" - }, - { - "author_name": "Thomas Yates", - "author_inst": "Leicester Diabetes Research Centre, Leicester, UK" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "NIHR Applied Research Collaboration East Midlands, Leicester, UK; Leicester Real World Evidence Unit, University of Leicester, UK" - }, - { - "author_name": "Francesco Zaccardi", - "author_inst": "Leicester Real World Evidence Unit, University of Leicester, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2021.08.01.21261297", "rel_title": "A mucosal antibody response is induced by intra-muscular SARS-CoV-2 mRNA vaccination", @@ -616813,6 +620037,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.30.21261383", + "rel_title": "COVID-19 Vaccine Uptake among U.S. Child Care Providers", + "rel_date": "2021-08-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.30.21261383", + "rel_abs": "STRUCUTRED ABSTRACTO_ST_ABSObjectivesC_ST_ABSEnsuring a high COVID-19 vaccine uptake among U.S. child care providers is crucial to mitigating the public health implications of child-to-staff and staff-to-child transmission of SARS-CoV-2; however, the vaccination rate among this group is unknown.\n\nMethodsTo characterize the vaccine uptake among U.S. child care providers, we conducted a cross-sectional survey of the child care workforce. Providers were identified through various national databases and state registries. A link to the survey was sent via email between May 26 and June 23, 2021. Out of 44,771 potential respondents, 21,663 responded (48.4%).\n\nResultsOverall COVID-19 vaccine uptake among U.S. child care providers (78.1%, 95% CI [77.3% to 78.9%]) was higher than that of the U.S. adult population (65%). Vaccination rates varied from 53.5% to 89.4% between states. Vaccine uptake differed significantly (p < .01) based on respondent age (70.0% for ages 25-34, 91.5% for ages 75-84), race (70.0% for Black or African Americans, 92.5% for Asian-Americans), annual household income (70.7% for <$35,000, 85.0% for>$75,000), and childcare setting (72.9% for home-based, 79.7% for center-based).\n\nConclusionsCOVID-19 vaccine uptake among U.S. child care providers was higher than that of the general U.S. adult population. Those who were younger, lower income, Black or African American, resided in states either in the Mountain West or the South, and/or worked in home-based childcare programs reported the lowest rates of vaccination; state public health leaders and lawmakers should prioritize these subgroups for placement on the policy agenda to realize the largest gains in vaccine uptake among providers.\n\nTables of Contents SummaryThis article describes the results of a national survey of childcare providers to determine the overall COVID-19 vaccine uptake and the gaps in vaccine coverage.\n\nWhats Known on This SubjectEnsuring a high COVID-19 vaccine uptake among U.S. child care providers is crucial to mitigating the public health implications of child-to-staff and staff-to-child transmission of SARS-CoV-2; however, the vaccination rate among this group is unknown.\n\nWhat This Study AddsWhile the vaccine uptake among U.S. child care providers was higher than that of U.S. adults, certain subgroups continue to warrant focused attention for outreach and/or placement on the policy agenda.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Kavin Patel", + "author_inst": "Yale University" + }, + { + "author_name": "Amyn A. Malik", + "author_inst": "Yale University" + }, + { + "author_name": "Aiden Lee", + "author_inst": "Yale University" + }, + { + "author_name": "Madeline Klotz", + "author_inst": "Yale University" + }, + { + "author_name": "John Eric Humphries", + "author_inst": "Yale University" + }, + { + "author_name": "Thomas Murray", + "author_inst": "Yale University" + }, + { + "author_name": "David Wilkinson", + "author_inst": "Yale University" + }, + { + "author_name": "Mehr Shafiq", + "author_inst": "Yale University" + }, + { + "author_name": "Inci Yildirim", + "author_inst": "Yale University" + }, + { + "author_name": "Jad Elharake", + "author_inst": "Yale University" + }, + { + "author_name": "Rachel Diaz", + "author_inst": "Yale University" + }, + { + "author_name": "Chin Reyes", + "author_inst": "Yale University" + }, + { + "author_name": "Saad Omer", + "author_inst": "Yale University" + }, + { + "author_name": "Walter Gilliam", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.29.21261312", "rel_title": "COVID-ONE-humoral immune: The One-stop Database for COVID-19-specific Antibody Responses and Clinical Parameters", @@ -617142,45 +620437,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.30.21261378", - "rel_title": "Knowledge, Attitude, and Practice among the Healthcare Professionals regarding the myths on COVID-19 vaccination - Demystified.", - "rel_date": "2021-08-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.30.21261378", - "rel_abs": "BackgroundCOVID-19 vaccine is the mighty weapon opted by all the countries across the globe in an attempt to eradicate the fatal COVID-19 pandemic. The myths on the COVID-19 vaccine are spreading widely, causing a hindrance to this noble preventive measure. The prevalence of such myths among the healthcare professionals may be toxic and deadly.\n\nAim & ObjectivesTo assess the knowledge, attitude, and practice of the healthcare professionals regarding the myths on COVID-19 vaccination and to demystify them.\n\nMaterials and MethodsAn 18-item questionnaire evaluating knowledge, attitude, and practice based on the existing myths on COVID-19 vaccination was circulated through Google Forms(R) among the 412 healthcare professionals of six disciplines belonging to a private University. The responses obtained were subjected to statistical analysis using SPSS(R) 20 software package.\n\nResultsA total of 385 health professionals participated in this study. The majority of them had medium knowledge (165) and positive attitude (273) with the mean knowledge and attitude scores of 3.82 {+/-} 1.55 out of 6 and 4.3 {+/-} 1.58 out of 7 respectively. Even though 312 participants got vaccinated, 72 of them failed to receive it. The knowledge scores showed a high statistically significant difference among the participants of different designations (p=0.001), but not with gender, field, and staff with different years of experience (p>0.05). The attitude scores were statistically different among participants of fields and designation (p<0.05) but not among genders (p=0.31) and staff with different years of experience (p=0.87). Knowledge and attitude scores showed a positive linear correlation and a high statistically significant difference (p<0.001).\n\nConclusionThis study recommends more enhanced education programs on COVID-19 vaccination for the health professionals and demands an improved knowledge, attitude, and practice among them to achieve the goal of 100% vaccination so as to completely eradicate the COVID-19 pandemic.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "LOKESH KUMAR S", - "author_inst": "KAHER's KLE Vishwanath Katti Institute of Dental Sciences, Belagavi, Karnataka, India" - }, - { - "author_name": "ZAMEERA NAIK", - "author_inst": "KAHER's KLE Vishwanath Katti Institute of Dental Sciences, Belagavi, Karnataka, India." - }, - { - "author_name": "ARUN PANWAR", - "author_inst": "KAHER'S KLE Vishwanath Katti Institute of Dental Sciences, Belagavi, Karnataka, India" - }, - { - "author_name": "SRIDHAR M", - "author_inst": "KAHER's KLE Vishwanath Katti Institute of Dental Sciences, Belagavi, Karnataka, India" - }, - { - "author_name": "VAISHALI KELUSKAR", - "author_inst": "KAHER's KLE Vishwanath Katti Institute of Dental Sciences, Belagavi, Karnataka, India." - }, - { - "author_name": "RAM SURATH KUMAR K", - "author_inst": "KAHER's KLE Vishwanath Katti Institute of Dental Sciences, Belagavi, Karnataka, India." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.07.29.21261358", "rel_title": "COVID-19 Infection risk posed by drinking alcohol at restaurants or bars in Japan", @@ -618899,6 +622155,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.28.21261138", + "rel_title": "Estimates of Single Dose and Full Dose BNT162b2 Vaccine Effectiveness among USAF Academy cadets, 1 Mar - 1 May 2021", + "rel_date": "2021-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21261138", + "rel_abs": "Beginning in early March 2021 and continuing through May 2021, the USAF Academy began vaccinating cadets for protection against the SARS-CoV-2 virus with the BNT162b2 (Pfizer-BioNTech) mRNA vaccine. During this period, vaccination of the almost 4200 cadet population increased from 3% to 85% and prevalence of COVID-19 in the cadet population was constant at approximately 0.4% as indicated by weekly surveillance testing. In this study, vaccine effectiveness at preventing infection is estimated by comparing infection risk as a function of time since vaccination. A statistically significant four-fold reduction in infection risk was observed 14 days after the first vaccine dose and an eleven-fold reduction in infection risk was observed in fully vaccinated cadets. Overall, the Pfizer-BioNTech vaccine was 91% (95% confidence interval = 55-99%) effective at preventing infection in healthy young adults (17-26 years of age) in a university setting and military training environment.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Douglas P Wickert", + "author_inst": "USAF Academy" + }, + { + "author_name": "Erin Almand", + "author_inst": "US Air Force Academy" + }, + { + "author_name": "Christopher A Cullenbine", + "author_inst": "USAF Academy" + }, + { + "author_name": "Odaro J Huckstep", + "author_inst": "USAF Academy" + }, + { + "author_name": "Joseph Rohrer", + "author_inst": "USAF Academy" + }, + { + "author_name": "John C Sitko", + "author_inst": "USAF Academy" + }, + { + "author_name": "James Jordan Steel", + "author_inst": "USAF Academy" + }, + { + "author_name": "Steven Hasstedt", + "author_inst": "USAF Academy" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.28.21261286", "rel_title": "Variations in Non-Pharmaceutical Interventions by State Correlate with COVID-19 Disease Outcomes", @@ -619192,49 +622495,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.28.21261276", - "rel_title": "Emerging and Continuing Trends in Opioid Overdose Decedent Characteristics during COVID-19", - "rel_date": "2021-07-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21261276", - "rel_abs": "BackgroundSince COVID-19 erupted in the United States, little is known about how state-level opioid overdose trends and decedent characteristics have varied throughout the country.\n\nObjectiveInvestigate changes in annual overdose death rates, substances involved, and decedent demographics in opioid overdose deaths across nine states; assess whether 2019-2020 trends were emerging (i.e., change from 2019-2020 was non-existent from 2018-2019) or continuing (i.e., change from 2019-2020 existed from 2018-2019).\n\nDesignCross-sectional study using vital statistics data to conduct a retrospective analysis comparing 2020 to 2019 and 2019 to 2018 across nine states.\n\nSettingAlaska, Colorado, Connecticut, Indiana, Massachusetts, North Carolina, Rhode Island, Utah, and Wyoming.\n\nParticipantsOpioid-related overdose deaths in 2018, 2019, and 2020.\n\nMeasurementsAnnual overdose death rate, proportion of overdose deaths involving specific substances, and decedent demographics (age, sex, race, and ethnicity).\n\nResultsWe find emerging increases in annual opioid-related overdose death rates in Alaska (55.3% [P=0.020]), Colorado (80.2% [P<0.001]), Indiana (40.1% [P=0.038]), North Carolina (30.5% [P<0.001]), and Rhode Island (29.6% [P=0.011]). Decreased heroin-involved overdose deaths were emerging in Alaska (-49.5% [P=0.001]) and Indiana (-58.8% [P<0.001]), and continuing in Colorado (-33.3% [P<0.001]), Connecticut (-48.2% [P<0.001]), Massachusetts (39.9% [P<0.001]), and North Carolina (-34.8% [P<0.001]). Increases in synthetic opioid presence were emerging in Alaska (136.5% [P=0.019]) and Indiana (27.6% [P<0.001]), and continuing in Colorado (44.4% [P<0.001]), Connecticut (3.6% [P<0.05]), and North Carolina (14.6% [P<0.001]). We find emerging increases in the proportion of male decedents in Colorado (15.2% [P=0.008]) and Indiana (12.0% [P=0.013]).\n\nLimitationsDelays from state-specific death certification processes resulted in varying analysis periods across states.\n\nConclusionThese findings highlight emerging changes in opioid overdose dynamics across different states, which can inform state-specific public health interventions.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Gian-Gabriel P. Garcia", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Erin Stringfellow", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Catherine DiGennaro", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Nicole Poellinger", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Jaden Wood", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Sarah Wakeman", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Mohammad S. Jalali", - "author_inst": "Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "addiction medicine" - }, { "rel_doi": "10.1101/2021.07.28.21261200", "rel_title": "Assessing optimal time between doses in two-dose vaccination regimen in an ongoing epidemic of SARS-CoV-2", @@ -620785,6 +624045,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.27.21261221", + "rel_title": "Changes in household food security, access to health services, and income in northern Lao PDR during the COVID-19 pandemic", + "rel_date": "2021-07-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.27.21261221", + "rel_abs": "BackgroundThe COVID-19 pandemic is expected to exacerbate food insecurity in low- and middle-income countries, through loss of income and disrupted food supply chains. Lao PDR has among the highest rates of malnutrition in Southeast Asia. We assessed the relative difficulty in meeting food needs during the COVID-19 pandemic in rural districts of Luang Prabang Province, Lao PDR compared to before; determined associations between pandemic-associated difficulties in food access and household, maternal and child food security; and identified resiliency-promoting strategies.\n\nMethodsIn November 2020, households (N = 1,122) with children under five years were interviewed. Respondents reported the relative ease of access of food and health care as well as changes in income and expenditures compared to before March 2020. We used generalized linear models with cluster robust standard errors to assess univariate and multivariate associations.\n\nResultsNearly four-fifths (78.5%) found it harder to meet household food needs during the pandemic. The most common reasons were increased food prices (51.2%), loss of income (45.3%), and decreased food availability (36.6%). Adjusting for demographics, households with increased difficulty meeting food needs had lower food consumption scores and child dietary diversity. Over 85% of households lost income during the pandemic. Decreased expenditures was associated with reliance on more extreme coping strategies to meet food needs. The households who experienced no change in meeting food needs produced a greater percentage of their food from homegrown methods (4.22% more, 95% CI: 1.28, 7.15), than households who found it more difficult. We estimated that decreases in child bodyweight by 0.5 - 1% would increase wasting in this population by 1.7 - 2.1 percentage points.\n\nConclusionsPandemic-associated shocks may have large effects on malnutrition prevalence. Action is needed to mitigate consequences of the pandemic on nutrition. Local food production and safety net programs that offset income losses may help.\n\nSummary BoxO_ST_ABSWhat is already known?C_ST_ABSThe COVID-19 pandemic has disrupted food supply chains and livelihoods, causing concerns that a global nutrition crisis is imminent and prompting leaders from United Nations agencies to issue an immediate call to action to direct funds towards prevention of child malnutrition. While documented COVID-19 transmission in Lao PDR was lower than that of surrounding counties, malnutrition rates are high, particularly in the northern province of Luang Prabang, which is heavily reliant on tourism for livelihoods.\n\nWhat are the new findings?Nearly four-fifths of those interviewed in Luang Prabang Province, Lao PDR reported that it was harder to meet their households food needs, compared to before the pandemic, with 51% attributing the reason to increased food prices. Over 85% of households reported losing income. Lower expenditures and increased difficulty obtaining food were both associated with lower household food consumption scores and higher household coping strategies, in adjusted analyses. Households who obtained a greater proportion of their foods through home production appeared more resilient than households who obtained a greater proportion of their foods through purchasing.\n\nWhat do the new findings imply?The pandemic may deeply exacerbate food insecurity in Lao PDR, potentially leading to increases in child wasting. Increased local food production and establishment of safety net programs that offset income losses may be two strategies that address this problem among this population.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jennifer R Head", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Phetsavanh Chanthavilay", + "author_inst": "University of Health Sciences, Vientiane, Lao PDR" + }, + { + "author_name": "Helen Catton", + "author_inst": "Save the Children International, Lao PDR" + }, + { + "author_name": "Ammaline Vongsitthi", + "author_inst": "Save the Children International, Lao PDR" + }, + { + "author_name": "Kelley Khamphouxay", + "author_inst": "Save the Children International, Lao PDR" + }, + { + "author_name": "Niphone Simphaly", + "author_inst": "Luang Prabang Provincial Health Department, Lao PDR" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.28.21261212", "rel_title": "An investigation of spatial-temporal patterns and predictions of the COVID-19 pandemic in Colombia, 2020-2021", @@ -620954,109 +624253,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.27.21261237", - "rel_title": "Correlates of Neutralizing/SARS-CoV-2-S1-binding Antibody Response with Adverse Effects and Immune Kinetics in BNT162b2-Vaccinated Individuals", - "rel_date": "2021-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.27.21261237", - "rel_abs": "BackgroundWhile mRNA vaccines against SARS-CoV-2 have been exceedingly effective in preventing symptomatic viral infection, the features of immune response remain to be clarified.\n\nMethodsIn the present prospective observational study, 225 healthy individuals in Kumamoto General Hospital, Japan, who received two BNT162b2 doses in February 2021, were enrolled. Correlates of BNT162b2-elicited SARS-CoV-2-neutralizing activity (50% neutralization titer: NT50; assessed using infectious virions and live target cells) with SARS-CoV-2-S1-binding-IgG and -IgM levels, adverse effects (AEs), ages, and genders were examined. The average half-life of neutralizing activity and the average time length for the loss of detectable neutralizing activity were determined and the potency of serums against variants of concerns was also determined.\n\nFindingsSignificant rise in NT50s was seen in serums on day 28 post-1st dose. A moderate inverse correlation was seen between NT50s and ages, but no correlation was seen between NT50s and AEs. NT50s and IgG levels on day 28 post-1st dose and pain scores following the 2nd shot were greater in women than in men. The average half-life of neutralizing activity in the vaccinees was approximately 67.8 days and the average time length for their serums to lose the detectable neutralizing activity was 198.3 days. While serums from elite-responders (NT50s>1,500-fold: the top 4% among all participants NT50s) potently to moderately blocked the infectivity of variants of concerns, some serums with moderate NT50s failed to block the infectivity of a beta strain.\n\nInterpretationBNT162b2-elicited immune response has no significant association with AEs. BNT162b2-efficacy is likely diminished to under detection limit by 6-7 months post-1st shot. High-level neutralizing antibody-containing serums potently to moderately block the infection of SARS-CoV-2 variants; however, a few moderate-level neutralizing antibody-containing serums failed to do so. If BNT162b2-elicited immunity memory is short, an additional vaccine or other protective measures would be needed.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWhile mRNA vaccines against SARS-CoV-2 have been exceedingly effective in preventing symptomatic viral infection, the salient features of immune response including the persistence of protection remain to be clarified. There is a report that anti-SARS-CoV-2 antibodies persist through 6 months after the second dose of mRNA-1273 vaccine (Doria-Rose et al. N Engl J Med. 2021;384:2259-2261); however, more definite immune kinetics following mRNA-vaccine-elicited protection have to be clarified. The mRNA-vaccine-elicited protection against SARS-CoV-2 variants are also to be determined.\n\nAdded value of this studyIn the present prospective study, 225 twice-BNT162b2-dose-receiving individuals in Japan were enrolled. No significant correlation was seen between 50% neutralizing titers (NT50s), determined by using infectious SARS-CoV-2 virions and live target cells, and adverse effects. Largely, NT50s and IgG levels were greater in women than in men. Following 28 days post-2nd shot, significant reduction was seen in NT50s, IgG, and IgM levels. The average half-life of NT50s was [~]68 days and the average time-length for participants serums to lose the detectable activity was [~]198 days. Although serums from elite-responders potently to moderately blocked the infectivity of variants of concerns, some serums with moderate NT50s failed to block the infectivity of a beta strain.\n\nImplications of all the available evidenceBNT162b2 efficacy is likely to be diminished to under detection limit by 6-7 months post-1st shot on average. Individuals with moderate NT50s may fail to block beta variants. If BNT162b2-elicited immune memory is lost soon, additional vaccine(s) or other protective means would be needed.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Kenji Maeda", - "author_inst": "National Center For Global Health and Medicine" - }, - { - "author_name": "Masayuki Amano", - "author_inst": "Kumamoto University Hospital" - }, - { - "author_name": "Yukari Uemura", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Kiyoto Tsuchiya", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Tomoko Matsushima", - "author_inst": "Sysmex Corporation" - }, - { - "author_name": "Kenta Noda", - "author_inst": "Sysmex Corporation" - }, - { - "author_name": "Yosuke Shimizu", - "author_inst": "National Center For Global Health and Medicine" - }, - { - "author_name": "Asuka Fujiwara", - "author_inst": "National Center For Global Health and Medicine" - }, - { - "author_name": "Yuki Takamatsu", - "author_inst": "National Center For Global Health and Medicine" - }, - { - "author_name": "Yasuko Ichikawa", - "author_inst": "JCHO Kumamoto General Hospital" - }, - { - "author_name": "Hidehiro Nishimura", - "author_inst": "JCHO Kumamoto General Hospital" - }, - { - "author_name": "Mari Kinoshita", - "author_inst": "JCHO Kumamoto General Hospital" - }, - { - "author_name": "Shota Matsumoto", - "author_inst": "JCHO Kumamoto General Hospital" - }, - { - "author_name": "Hiroyuki Gatanaga", - "author_inst": "National Center For Global Health and Medicine" - }, - { - "author_name": "Kazuhisa Yoshimura", - "author_inst": "Tokyo Metropolitan Institute for Public Health" - }, - { - "author_name": "Shinichi Oka", - "author_inst": "National Center For Global Health and Medicine" - }, - { - "author_name": "Ayako Mikami", - "author_inst": "National Center For Global Health and Medicine" - }, - { - "author_name": "Wataru Sugiura", - "author_inst": "National Center For Global Health and Medicine" - }, - { - "author_name": "Toshiyuki Sato", - "author_inst": "Sysmex Corporation" - }, - { - "author_name": "Tomokazu Yoshida", - "author_inst": "Sysmex Corporation" - }, - { - "author_name": "Shinya Shimada", - "author_inst": "JCHO Kumamoto General Hospital" - }, - { - "author_name": "Hiroaki Mitsuya", - "author_inst": "National Center For Global Health and Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.28.21261241", "rel_title": "Estimation of the onset rate and the number of asymptomatic patients of COVID-19 from the proportion of untraceable patients", @@ -622567,6 +625763,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.07.25.21260838", + "rel_title": "Doxycycline is a safe alternative to Hydroxychloroquine + Azithromycin to prevent clinical worsening and hospitalization in mild COVID-19 patients: An open label randomized clinical trial (DOXYCOV)", + "rel_date": "2021-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.25.21260838", + "rel_abs": "ObjectiveWe aimed to compare the safety and efficacy of a doxycycline-based regimen against the national standard guidelines (Hydroxychloroquine plus Azithromycin) for the treatment of mild symptomatic COVID-19.\n\nMethodsWe conducted an open-label, randomized, non-inferiority trial, in Cameroon comparing Doxycycline 100mg, twice daily for 7 days versus Hydroxychloroquine, 400 mg daily for 5 days and Azithromycin 500mg at day 1 and 250mg from day 2 through 5, in mild COVID-19 patients. Clinical improvement, biological parameters and adverse events were assessed. The primary outcome was the proportion of clinical cure at day 3, 10 and 30. Non-inferiority was determined by the clinical cure rate between protocols with a 20 percentage points margin.\n\nResults194 participants underwent randomization and were treated with Doxycycline (n=97) or Hydroxychloroquine-Azithromycin (n=97). At day 3, 74/92 (80.4%) participants on Doxycycline versus 77/95 (81.1%) on Hydroxychloroquine-Azithromycin -based protocols were asymptomatic (p=0.91). At day 10, 88/92 (95.7%) participants on Doxycycline versus 93/95 (97.9%) on Hydroxychloroquine-Azithromycin were asymptomatic (p=0.44). At day 30 all participants were asymptomatic. SARS-CoV2 PCR was negative at Day 10 in 60/92 (65.2%) participants allocated to Doxycycline and 63/95 (66.3%) participants allocated to Hydroxychloroquine-Azithromycin. None of the participants were admitted for worsening of the disease after treatment initiation.\n\nConclusionDoxycycline 100 mg twice daily for 7 days is as effective and safe as Hydroxychloroquine-Azithromycin, for preventing clinical worsening of mild symptomatic or asymptomatic COVID-19, and achieving virological suppression.\n\nStrengths and Limitations[tpltrtarr] This study is one of the first randomized trial, assessing the efficacy and tolerance of Doxycycline to treat COVID-19\n[tpltrtarr]It is one of the first to evaluate disease progression and need to hospitalization in mild or asymptomatic COVID-19\n[tpltrtarr]Patients will not receive identical treatments\n[tpltrtarr]Doxycycline has advantages in terms of availability, safety and cost compared to Hydroxychloroquine and Azytromycin\n[tpltrtarr]Though this study has encounter 7 lost to follow-up, this does not have a major influence on our results\n[tpltrtarr]These data will assist clinicians in their daily practice, and provide a new tool for the fight against COVID-19", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Eugene Sobngwi", + "author_inst": "University of Yaounde 1" + }, + { + "author_name": "Sylvain Zemsi", + "author_inst": "RSD Institute" + }, + { + "author_name": "Magellan Guewo-Fokeng", + "author_inst": "RSD Institute" + }, + { + "author_name": "Jean Claude Katte", + "author_inst": "RSD Institute" + }, + { + "author_name": "Charles Kouanfack", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Liliane Mfeukeu-Kuate", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Armel Zemsi", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Yves Wasnyo", + "author_inst": "RSD Institute" + }, + { + "author_name": "Antoinette Assiga-Ntsama", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Jean Arnaud Ndi-Manga", + "author_inst": "RSD Institute" + }, + { + "author_name": "Joelle S Tambekou", + "author_inst": "RSD Institute" + }, + { + "author_name": "William Ngatchou", + "author_inst": "University of Douala, Faculty of Medicine and Pharmaceutical Sciences" + }, + { + "author_name": "Charlotte Moussi-Omgba", + "author_inst": "Ministry of Public Health Cameroon" + }, + { + "author_name": "Jean-Claude Mbanya", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Pierre Ongolo-Zogo", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Pierre-Joseph Fouda", + "author_inst": "Yaounde Central Hospital" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pharmacology and therapeutics" + }, { "rel_doi": "10.1101/2021.07.25.21260967", "rel_title": "Influence of Novel Coronavirus COVID-19 and HIV: A Scoping Review of Hospital Course and Symptomatology", @@ -622764,89 +626039,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.25.21261066", - "rel_title": "SARS-CoV-2 Antibody Response in Patients Undergoing Kidney Transplantation", - "rel_date": "2021-07-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.25.21261066", - "rel_abs": "The response of the immune system to COVID-19 in end stage kidney disease patients who undergo kidney transplantation has yet to be described. We report data on 72 patients who underwent SARS-CoV-2 antibody testing both before and after kidney transplantation and were followed for a median of 186 days (range 83, 277). Of the 25 patients with a positive antibody test at the time of transplant, 17 (68%) remained positive after transplantation. Patients were significantly more likely to have a persistently positive test if they reported a symptomatic COVID-19 infection prior to transplant (p=0.01). SARS-CoV-2 IgG index values were measured in a subset of kidney transplant recipients and compared to wait -listed dialysis patients. These assays demonstrated a more significant decline in IgG (58% versus 14% p = 0.008) in transplant recipients when compared to dialysis patients tested during the same time period. Additional analysis of the quality of the immune response measuring the binding of SARS-CoV-2 antibodies to the receptor-binding domain (RBD binding), the antibody neutralizing capability, and the antibody avidity demonstrated a more pronounced effect when comparing pre-transplant values to post-induction therapy/post transplant values. The attenuated IgG response seen in transplant patients compared to dialysis patients after induction therapy requires further study. These data have important implications for post-transplant management of vaccinated dialysis patients.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Michelle Lubetzky", - "author_inst": "New York Presbyterian-Weill Cornell" - }, - { - "author_name": "Ashely Sukhu", - "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell" - }, - { - "author_name": "Zhen Zhao", - "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell" - }, - { - "author_name": "Sophie Rand", - "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell" - }, - { - "author_name": "Vijay Sharma", - "author_inst": "Weill Cornell Medicine, Division of Nephrology" - }, - { - "author_name": "Samuel Sultan", - "author_inst": "NewYork Presbyterian Hospital, Department of Transplantation" - }, - { - "author_name": "Zoe Kapur", - "author_inst": "Weill Cornell Medicine, Division of Nephrology" - }, - { - "author_name": "Shady Albakry", - "author_inst": "Weill Cornell Medicine, Division of Nephrology" - }, - { - "author_name": "Nataliya Hauser", - "author_inst": "Weill Cornell Medicine, Division of Nephrology" - }, - { - "author_name": "Jehona Marku-Podvorica", - "author_inst": "Weill Cornell Medicine, Department of Surgery" - }, - { - "author_name": "Rebecca Craig-Schapiro", - "author_inst": "Weill Cornell Medicine, Department of Surgery" - }, - { - "author_name": "John R Lee", - "author_inst": "Weill Cornell Medicine, Division of Nephrology" - }, - { - "author_name": "Thalia Salinas", - "author_inst": "Weill Cornell Medicine, Division of Nephrology" - }, - { - "author_name": "Meredith Aull", - "author_inst": "Weill Cornell Medicine, Department of Surgery" - }, - { - "author_name": "Sandip Kapur", - "author_inst": "Weill Cornell Medicine, Department of Surgery" - }, - { - "author_name": "Melissa Cushing", - "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine" - }, - { - "author_name": "Darshana M Dadhania", - "author_inst": "Weill Cornell Medicine, Division of Nephrology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2021.07.25.21261105", "rel_title": "Development of a federated learning approach to predict acute kidney injury in adult hospitalized patients with COVID-19 in New York City", @@ -624645,6 +627837,121 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.07.27.453843", + "rel_title": "Molecular Pathophysiology of Cardiac Injury and Cardiac Microthrombi in Fatal COVID-19: Insights from Clinico-histopathologic and Single Nuclei RNA Sequencing Analyses", + "rel_date": "2021-07-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.27.453843", + "rel_abs": "Cardiac injury is associated with critical COVID-19, yet its etiology remains debated. To elucidate the pathogenic mechanisms of COVID-19-associated cardiac injury, we conducted a single-center prospective cohort study of 69 COVID-19 decedents. Of six cardiac histopathologic features, microthrombi was the most commonly detected (n=48, 70%). We tested associations of cardiac microthrombi with biomarkers of inflammation, cardiac injury, and fibrinolysis and with in-hospital antiplatelet therapy, therapeutic anticoagulation, and corticosteroid treatment, while adjusting for multiple clinical factors, including COVID-19 therapies. Higher peak ESR and CRP during hospitalization were independently associated with higher odds of microthrombi. Using single nuclei RNA-sequence analysis, we discovered an enrichment of pro-thrombotic/anti-fibrinolytic, extracellular matrix remodeling, and immune-potentiating signaling amongst cardiac fibroblasts in microthrombi-positive COVID-19 hearts relative to microthrombi-negative COVID-19. Non-COVID-19 non-failing hearts were used as reference controls. Our cumulative findings identify the specific transcriptomic changes in cardiac fibroblasts as salient features of COVID-19-associated cardiac microthrombi.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Nobuaki Fukuma", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Michelle L Hulke", + "author_inst": "Masonic Medical Research Institute" + }, + { + "author_name": "Michael I Brener", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Stephanie Golob", + "author_inst": "Department of Medicine, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Robert Zilinyi", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Zhipeng Zhou", + "author_inst": "Cardiovascular Research Foundation" + }, + { + "author_name": "Christos Tzimas", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Ilaria Russo", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Claire McGroder", + "author_inst": "Division of Pulmonary, Allergy & Critical Care Medicine, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Ryan Pfeiffer", + "author_inst": "Masonic Medical Research Institute" + }, + { + "author_name": "Alexander Chong", + "author_inst": "Division of Infectious Diseases, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Geping Zhang", + "author_inst": "Department of Pathology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Daniel Burkhoff", + "author_inst": "Cardiovascular Research Foundation" + }, + { + "author_name": "Martin B Leon", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Mathew Maurer", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Jeffrey W Moses", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Anne-Catrin Uhlemann", + "author_inst": "Division of Infectious Diseases, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Hanina Hibshoosh", + "author_inst": "Department of Pathology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Nil Uriel", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Matthias J Szabolcs", + "author_inst": "Department of Pathology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Bj\u00f6rn Redfors", + "author_inst": "Cardiovascular Research Foundation" + }, + { + "author_name": "Charles C Marboe", + "author_inst": "Department of Pathology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Matthew R Baldwin", + "author_inst": "Division of Pulmonary, Allergy & Critical Care Medicine, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Nathan R Tucker", + "author_inst": "Masonic Medical Research Institute" + }, + { + "author_name": "Emily J Tsai", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2021.07.27.453973", "rel_title": "Executable Network of SARS-CoV-2-Host Interaction Predicts Drug Combination Treatments", @@ -624774,97 +628081,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.23.21261042", - "rel_title": "Robust antibody levels in both diabetic and non-diabetic individuals after BNT162b2 mRNA COVID-19 vaccination", - "rel_date": "2021-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.23.21261042", - "rel_abs": "The emergence of effective vaccines for COVID-19 has been welcomed by the world with great optimism. Given their increased susceptibility to COVID-19, the question arises whether individuals with type-2 diabetes mellitus (T2DM) and other metabolic conditions can respond effectively to the mRNA-based vaccine. We aimed to evaluate the levels of anti-SARS-CoV-2 IgG and neutralizing antibodies in people with T2DM and/or other metabolic risk factors (hypertension and obesity) compared to those without. This study included 262 people that took two doses of BNT162b2 (Pfizer-BioNTech) mRNA vaccine. Both T2DM and non-diabetic individuals had a robust response to vaccination as demonstrated by their high antibody titers. However, both SARS-CoV-2 IgG and neutralizing antibodies titers were lower in people with T2DM. Their levels were 154{+/-}49.1 vs. 138{+/-}59.4BAU/mL for IgG and 87.1{+/-}11.6 vs. 79.7{+/-}19.5% for neutralizing antibodies in individuals without diabetes compared to those with T2DM, respectively. In a multiple linear regression adjusted for individual characteristics, comorbidities, previous COVID-19 infection and duration since second vaccine dose, diabetics had 13.86 BAU/ml (95%CI: -27.08 to -0.64BAU/ml, p=0.041) less IgG antibodies and 4.42% (95%CI: -8.53 to -0.32%, p=0.036) less neutralizing antibodies than non-diabetics. Hypertension and obesity did not show significant changes in antibody titers. Taken together, both type-2 diabetic and non-diabetic individuals elicited strong immune responses to SARS-CoV-2 BNT162b2 mRNA vaccine; nonetheless, lower levels were seen in people with diabetes. Continuous monitoring of the antibody levels might be a good indicator to guide personalized needs for further booster shots to maintain adaptive immunity.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Hamad Ali", - "author_inst": "Kuwait University" - }, - { - "author_name": "Abdulmohsen Al-Terki", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Sardar Sindhu", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Barrak Alahmad", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Maha Hammad", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Salman Al-Sabah", - "author_inst": "Kuwait University" - }, - { - "author_name": "Mohammad Alghounaim", - "author_inst": "Ministry of Health" - }, - { - "author_name": "Mohammad H. Jamal", - "author_inst": "Kuwait University" - }, - { - "author_name": "Ali Aldei", - "author_inst": "Ministry of Health" - }, - { - "author_name": "Mohammad J. Mairza", - "author_inst": "Ministry of Health" - }, - { - "author_name": "Maitham Husain", - "author_inst": "Ministry of Health" - }, - { - "author_name": "Sriraman Devarajan", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Rasheed Ahmad", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Preethi Cherian", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Irina Alkhairi", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Abdullah Alkandari", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Jehad Abubaker", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Mohamed Abu-farha", - "author_inst": "Dasman Diabetes Institute" - }, - { - "author_name": "Fahd Al-Mulla", - "author_inst": "Dasman Diabetes Institute" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.23.21261025", "rel_title": "Clinical echocardiography does not indicate cardiac dysfunction in critically ill Covid-19 patients", @@ -626659,6 +629875,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2021.07.22.21260878", + "rel_title": "Mental Health of HBCU College Students during the COVID-19 Pandemic", + "rel_date": "2021-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.22.21260878", + "rel_abs": "ObjectiveThis study investigated rates and predictors of mental health issues (e.g., depression and anxiety) in a sample of college students currently attending a historically Black college/university (HBCU) during the COVID-19 pandemic.\n\nParticipants/Methods98 undergraduate students (81 female and 17 male) completed an online survey containing questions about demographics, socioeconomic status, academic characteristics, and pandemic-related concerns. The survey also included PHQ-9 and GAD-7 questionnaires to evaluate depression and anxiety, respectively.\n\nResults49% of students met the clinical cutoff for depression, 39% for anxiety, and 52% for depression and/or anxiety. Significant predictors of meeting the cutoffs included parental job loss/hour reduction, being a senior, and feeling that the pandemic negatively impacted daily life, among other factors. Demographic variables (age, gender, etc.) had no effect.\n\nConclusionHBCU students show high rates of depression and anxiety during the COVID-19 pandemic, which may be predicted based on the students academic, socioeconomic, and pandemic-related concerns.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sharron Xuanren Wang", + "author_inst": "Delaware State University" + }, + { + "author_name": "Jarid Goodman", + "author_inst": "Delaware State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.07.22.21260793", "rel_title": "A spatio-temporal study of state-wide case-fatality risks during the first wave of the COVID-19 pandemic in Mexico", @@ -626764,93 +630003,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.23.21260740", - "rel_title": "Antiviral metabolite 3'-Deoxy-3',4'-didehydro-cytidine is detectable in serum and identifies acute viral infections including COVID-19", - "rel_date": "2021-07-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.23.21260740", - "rel_abs": "There is a critical need for improved infectious disease diagnostics to enable rapid case identification in a viral pandemic and support targeted antimicrobial prescribing. Here we use high-resolution liquid chromatography coupled with mass spectrometry to compare the admission serum metabolome of patients attending hospital with a range of viral infections, including SARS-CoV-2, to those with bacterial infections, non-infected inflammatory conditions and healthy controls. We demonstrate for the first time that 3-Deoxy-3,4-didehydro-cytidine (ddhC), a free base of the only known human antiviral small molecule ddhC-triphosphate (ddhCTP), is detectable in serum. ddhC acts as an accurate biomarker for viral infections, generating an area under the receiver operating characteristic curve of 0.954 (95% confidence interval 0.923-0.986) when comparing viral to non-viral cases. Gene expression of viperin, the enzyme responsible for ddhCTP synthesis, is highly correlated with ddhC, providing a biological mechanism for its increase during viral infection. These findings underline a key future diagnostic role of ddhC in the context of pandemic preparedness and antimicrobial stewardship.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Ravi Mehta", - "author_inst": "Imperial College London" - }, - { - "author_name": "Elena Chekmeneva", - "author_inst": "The National Phenome Centre" - }, - { - "author_name": "Heather Jackson", - "author_inst": "Imperial College London" - }, - { - "author_name": "Caroline Sands", - "author_inst": "The National Phenome Centre" - }, - { - "author_name": "Ewurabena Mills", - "author_inst": "Imperial College London" - }, - { - "author_name": "Dominique Arancon", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Ho Kwong Li", - "author_inst": "Imperial College London" - }, - { - "author_name": "Paul Arkell", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Timothy Miles Rawson", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Robert Hammond", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Maisarah Amran", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Anna Haber", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Graham Cooke", - "author_inst": "Imperial College London" - }, - { - "author_name": "Mahdad Noursadeghi", - "author_inst": "University College London" - }, - { - "author_name": "Myrsini Kaforou", - "author_inst": "Imperial College London" - }, - { - "author_name": "Matthew Lewis", - "author_inst": "The National Phenome Centre" - }, - { - "author_name": "Zoltan Takats", - "author_inst": "The National Phenome Centre" - }, - { - "author_name": "Shiranee Sriskandan", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.25.21261094", "rel_title": "Shocked-relaxed-tired: Mental health during the three waves of the Covid-19", @@ -628641,6 +631793,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.19.21260721", + "rel_title": "Present knowledge, attitude, practice, and fear level of Bangladeshi people towards covid-19 after one year of the pandemic situation: a web-based cross-sectional study.", + "rel_date": "2021-07-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260721", + "rel_abs": "In the earlier phase of the pandemic situation, the governments of Bangladesh badly suffered to adhere their people to preventive measures probably due to less knowledge and attitude towards covid-19. To tackle the second wave of coronavirus, the governments again enforced an array of preventive measures, but still encountering the same problem after a year of the pandemic situation. In an attempt to find out the reasons behind this, our study aimed to assess the present knowledge, attitude, practice, and fear level of the people. A cross-sectional study was conducted from 15th to 25th April 2021. A total of 402 participants met all the inclusion criteria and were considered for performing all statistical analyses (Descriptive statistics, Mann-Whitney U test, Kruskal-Wallis H test, Multiple logistic regression, Spearman rank-order correlation). Out of 402 participants, more than 90% participants were students and all were adults aged 16 to 30. 84.6%, 65.7%, 54%, and 21.6% participants had more adequate knowledge, more positive attitude, more frequent practice, and moderate to high fear towards covid-19, respectively. Knowledge, attitude, practice, and fear were interrelated directly or indirectly. It was found knowledgeable participants were more likely to have more positive attitude (OR = 2.12, 95% CI = 1.14-3.95, P < 0.05) and very less fear (OR = 1.98, 95% CI = 1.02-3.82, P < 0.05). More positive attitude was found as a good predictor of more frequent practice (OR = 4.33, 95% CI = 2.66-7.04, P < 0.001), and very less fear had same negative impact on both attitude (OR = 0.48, 95% CI = 0.25-0.91, P < 0.05) and practice (OR = 0.48, 95% CI = 0.27-0.85, P < 0.05). Our findings reflect that knowledge level has elevated but attitude level subsided, and practice level stayed same as was in the earlier phase of pandemic and people are no longer panicked.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Tahsin Ahmed Rupok", + "author_inst": "Department of Pharmacy, University of Rajshahi, Rajshahi-6205, Bangladesh." + }, + { + "author_name": "Sunandan Dey", + "author_inst": "Department of Pharmacy, University of Rajshahi, Rajshahi-6205, Bangladesh." + }, + { + "author_name": "Rashni Agarwala", + "author_inst": "Department of Pharmacy, Islamic University, Kushtia-7003, Bangladesh." + }, + { + "author_name": "Md. Nurnobi Islam", + "author_inst": "Department of Chemistry, Shahjalal University of Science & Technology, Sylhet-3114, Bangladesh." + }, + { + "author_name": "Bayezid Bostami", + "author_inst": "Department of Pharmacy, University of Rajshahi, Rajshahi-6205, Bangladesh." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.21.21260624", "rel_title": "New susceptibility loci for severe COVID-19 by detailed GWAS analysis in European populations", @@ -630142,37 +633329,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.18.21260711", - "rel_title": "On dynamics of fractional incommensurate model of Covid-19 with nonlinear saturated incidence rate", - "rel_date": "2021-07-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.18.21260711", - "rel_abs": "In December 2019, a new virus belonging to the coronavirus strain has been discovered in Wuhan, China, this virus has attracted world-wide attention and it spread rapidly in the world, reaching nearly 216 countries in the world in November 2020. In this chapter, we study the fractional incommensurate SIQR (susceptible, infections,quarantined and removed) COVID-19 model with nonlinear saturated incidence rate using Atangana-Baleanu fractional derivatives. The existence and uniqueness of the solutions for the fractional model is proved using fixed point theorem, the model are shown to have two equilibrium point (disease-free and an endemic equilibrium). Some numerical simulations using Euler method are also carried out to support our theoretical results. We estimated the value of the fractional orders and the parameters of the proposed model using the least squares method.. Further, the sensitivity analysis of the parameter is performed as a result, our incommensurate model gives a good approximation to real data of COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Abdelouahed ALLA HAMOU Sr.", - "author_inst": "Sidi Mohamed Ben Abdellah University" - }, - { - "author_name": "ELHOUSSINE AZROUL", - "author_inst": "Sidi Moahamed ben abdellah university" - }, - { - "author_name": "Zakia Hammouch", - "author_inst": "Ton Duc Thang University, Ho Chi Minh City, Vietnam" - }, - { - "author_name": "Abdelilah Lamrani alaoui", - "author_inst": "Regional Center of Education and Professional Training,B.P. 49, 30000 Fez, Morocco" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.21.21260971", "rel_title": "Trait Mindful Nonreactivity and Nonjudgment Prospectively Predict of COVID-19 Health Protective Behaviors Across a Two-Month Interval in a USA Sample", @@ -631515,6 +634671,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.07.20.21260558", + "rel_title": "Intentions to participate in cervical and colorectal cancer screening during the COVID-19 pandemic: a mixed-methods study", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260558", + "rel_abs": "Worldwide, cancer screening faced significant disruption in 2020 due to the COVID-19 pandemic. If this has led to changes in public attitudes towards screening and reduced intention to participate, there is a risk of long-term adverse impact on cancer outcomes. In this study, we examined previous participation and future intentions to take part in cervical and colorectal cancer (CRC) screening following the first national lockdown in the UK.\n\nOverall, 7543 adults were recruited to a cross-sectional online survey in August-September 2020. Logistic regression analyses were used to identify correlates of strong screening intentions among 2,319 participants eligible for cervical screening and 2,502 eligible for home-based CRC screening. Qualitative interviews were conducted with a sub-sample of 30 participants. Verbatim transcripts were analysed thematically.\n\nOf those eligible, 74% of survey participants intended to attend cervical screening and 84% intended to complete home-based CRC screening when next invited. Thirty percent and 19% of the cervical and CRC samples respectively said they were less likely to attend a cancer screening appointment now than before the pandemic. Previous non-participation was the strongest predictor of low intentions for cervical (aOR 26.31, 95% CI: 17.61-39.30) and CRC (aOR 67.68, 95% CI: 33.91-135.06) screening. Interview participants expressed concerns about visiting healthcare settings but were keen to participate when screening programmes resumed.\n\nIntentions to participate in future screening were high and strongly associated with previous engagement in both programmes. As screening services recover, it will be important to monitor participation and to ensure people feel safe to attend.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Rebecca Wilson", + "author_inst": "Cardiff University" + }, + { + "author_name": "Harriet Quinn-Scoggins", + "author_inst": "Cardiff University" + }, + { + "author_name": "Yvonne Moriarty", + "author_inst": "Cardiff University" + }, + { + "author_name": "Jacqueline Hughes", + "author_inst": "Cardiff University" + }, + { + "author_name": "Mark Goddard", + "author_inst": "Cardiff University" + }, + { + "author_name": "Rebecca Cannings-John", + "author_inst": "Cardiff University" + }, + { + "author_name": "Victoria Whitelock", + "author_inst": "Cancer Research UK" + }, + { + "author_name": "Katriina L Whitaker", + "author_inst": "University of Surrey" + }, + { + "author_name": "Detelina Grozeva", + "author_inst": "Cardiff University" + }, + { + "author_name": "Julia Townson", + "author_inst": "Cardiff University" + }, + { + "author_name": "Kirstie Osborne", + "author_inst": "Cancer Research UK" + }, + { + "author_name": "Stephanie Smits", + "author_inst": "Cardiff University" + }, + { + "author_name": "Michael Robling", + "author_inst": "Cardiff University" + }, + { + "author_name": "Julie Hepburn", + "author_inst": "Public Involvement Community, Health and Care Research Wales" + }, + { + "author_name": "Graham Moore", + "author_inst": "Cardiff University" + }, + { + "author_name": "Ardiana Gjini", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Kate Brain", + "author_inst": "Cardiff University" + }, + { + "author_name": "Jo Waller", + "author_inst": "Kings College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2021.07.19.21260139", "rel_title": "Plasma cell-free DNA promise disease monitoring and tissue injury assessment of COVID-19", @@ -631808,113 +635051,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.19.21260776", - "rel_title": "Integrative Metabolomic and Proteomic Signatures Define Clinical Outcomes in Severe COVID-19", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260776", - "rel_abs": "The novel coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2 has ravaged global healthcare with previously unseen levels of morbidity and mortality. To date, methods to predict the clinical course, which ranges from the asymptomatic carrier to the critically ill patient in devastating multi-system organ failure, have yet to be identified. In this study, we performed large-scale integrative multi-omics analyses of serum obtained from COVID-19 patients with the goal of uncovering novel pathogenic complexities of this disease and identifying molecular signatures that predict clinical outcomes. We assembled a novel network of protein-metabolite interactions in COVID-19 patients through targeted metabolomic and proteomic profiling of serum samples in 330 COVID-19 patients compared to 97 non-COVID, hospitalized controls. Our network identified distinct protein-metabolite cross talk related to immune modulation, energy and nucleotide metabolism, vascular homeostasis, and collagen catabolism. Additionally, our data linked multiple proteins and metabolites to clinical indices associated with long-term mortality and morbidity, such as acute kidney injury. Finally, we developed a novel composite outcome measure for COVID-19 disease severity and created a clinical prediction model based on the metabolomics data. The model predicts severe disease with a concordance index of around 0.69, and furthermore shows high predictive power of 0.83-0.93 in two previously published, independent datasets.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Mustafa Buyukozkan", - "author_inst": "Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; Meyer Cancer Center and Caryl and Israel Englander Institute for Precision M" - }, - { - "author_name": "Sergio Alvarez-Mulett", - "author_inst": "Department of Medicine, Division of Pulmonary and Critical Care Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Alexandra C. Racanelli", - "author_inst": "Department of Medicine, Division of Pulmonary and Critical Care Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Frank Schmidt", - "author_inst": "Department of Biochemistry, Weill Cornell Medicine - Qatar, Qatar Foundation, Doha, Qatar" - }, - { - "author_name": "Richa Batra", - "author_inst": "Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; Meyer Cancer Center and Caryl and Israel Englander Institute for Precision M" - }, - { - "author_name": "Katherine L. Hoffman", - "author_inst": "Department of Population Health Sciences, Division of Biostatistics, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Hina Sarwath", - "author_inst": "Department of Biochemistry, Weill Cornell Medicine - Qatar, Qatar Foundation, Doha, Qatar" - }, - { - "author_name": "Rudolf Engelke", - "author_inst": "Department of Biochemistry, Weill Cornell Medicine - Qatar, Qatar Foundation, Doha, Qatar" - }, - { - "author_name": "Luis Gomez-Escobar", - "author_inst": "Department of Medicine, Division of Pulmonary and Critical Care Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Will Simmons", - "author_inst": "Department of Population Health Sciences, Division of Biostatistics, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Elisa Benedetti", - "author_inst": "Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; Meyer Cancer Center and Caryl and Israel Englander Institute for Precision M" - }, - { - "author_name": "Kelsey Chetnik", - "author_inst": "Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; Meyer Cancer Center and Caryl and Israel Englander Institute for Precision M" - }, - { - "author_name": "Guoan Zhang", - "author_inst": "Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Edward Schenck", - "author_inst": "Department of Medicine, Division of Pulmonary and Critical Care Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Karsten Suhre", - "author_inst": "Department of Biochemistry, Weill Cornell Medicine - Qatar, Qatar Foundation, Doha, Qatar" - }, - { - "author_name": "Justin J. Choi", - "author_inst": "Department of Medicine, Division of General Internal Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Zhen Zhao", - "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Sabrina Racine-Brzostek", - "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "He S. Yang", - "author_inst": "Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Mary E. Choi", - "author_inst": "Division of Nephrology and Hypertension, Joan and Sanford I. Weill Department of Medicine, New York, NY, USA" - }, - { - "author_name": "Augustine M.K. Choi", - "author_inst": "Department of Medicine, Division of Pulmonary and Critical Care Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Soo Jung Cho", - "author_inst": "Department of Medicine, Division of Pulmonary and Critical Care Medicine, Weill Cornell Medicine, New York, NY, USA" - }, - { - "author_name": "Jan Krumsiek", - "author_inst": "Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; Meyer Cancer Center and Caryl and Israel Englander Institute for Precision M" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.17.21260316", "rel_title": "Validation and performance evaluation of a novel interferon-\u03b3 release assay for the detection of SARS-CoV-2 specific T-cell response", @@ -633541,6 +636677,425 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.19.21260779", + "rel_title": "Surveillance of SARS-CoV-2 variants in Argentina: detection of Alpha, Gamma, Lambda, Epsilon and Zeta in locally transmitted and imported cases", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260779", + "rel_abs": "Molecular surveillance of SARS-CoV-2 variants was performed on a total of 2,406 samples from the capital city and nine provinces of Argentina, during 30 epidemiological weeks (EW) that covered the end of the first wave and the beginning of the ongoing second wave of the COVID-19 pandemic in the country (EW 44/2020 to EW 20/2021). The surveillance strategy was mainly based on Sanger sequencing of a Spike coding region that allows the simultaneous identification of signature mutations associated with worldwide circulating variants. In addition, whole SARS-CoV-2 genome sequences were obtained from 456 samples. The main variants found were Gamma, Lambda and Alpha, and to a lesser extent, Zeta and Epsilon. Whereas Gamma dominated in different regions of the country, both Gamma and Lambda prevailed in the most populated area, the metropolitan region of Buenos Aires (MABA), although showing a heterogeneous distribution along this region. This cost-effective surveillance protocol allowed for a rapid response in a limited access to resources scenario, added information on the expansion of the Lambda variant in South America and contributed to the implementation of public health measures to control the disease spread in Argentina.", + "rel_num_authors": 101, + "rel_authors": [ + { + "author_name": "Carolina Torres", + "author_inst": "Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Instituto de Investigaciones en Bacteriologia y Virologia Molecular (IBaViM), Buenos Aires, Arge" + }, + { + "author_name": "Laura Mojsiejczuk", + "author_inst": "Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Instituto de Investigaciones en Bacteriologia y Virologia Molecular (IBaViM), Buenos Aires, Arge" + }, + { + "author_name": "Dolores Acuna", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina; Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos" + }, + { + "author_name": "Sofia Alexay", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Ariel Amadio", + "author_inst": "Instituto de Investigacion de la Cadena Lactea (IDICAL) INTA-CONICET. Ruta 34 km 227, Rafaela (2300), Santa Fe, Argentina; Consejo Nacional de Investigaciones C" + }, + { + "author_name": "Paula Aulicino", + "author_inst": "Laboratorio de Biologia Celular y Retrovirus. Hospital de Pediatria Prof. Juan P. Garrahan, CABA, Argentina; Consejo Nacional de Investigaciones Cientificas y T" + }, + { + "author_name": "Humberto Debat", + "author_inst": "Instituto de Patologia Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnologia Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5" + }, + { + "author_name": "Franco Fernandez", + "author_inst": "Instituto de Patologia Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnologia Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5" + }, + { + "author_name": "Stephanie Goya", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Guido Konig", + "author_inst": "Instituto de Biotecnologia/Instituto de Agrobiotecnologia y Biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina." + }, + { + "author_name": "Mercedes Nabaes Jodar", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina; Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos" + }, + { + "author_name": "Luis Pianciola", + "author_inst": "Laboratorio Central ciudad de Neuquen, Ministerio de Salud, Neuquen, Argentina" + }, + { + "author_name": "Sofia Bengoa", + "author_inst": "Instituto de Biotecnologia/Instituto de Agrobiotecnologia y Biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina." + }, + { + "author_name": "Marco Cacciahue", + "author_inst": "Instituto de Biotecnologia/Instituto de Agrobiotecnologia y Biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina." + }, + { + "author_name": "Cecilia Camussone", + "author_inst": "Instituto de Investigacion de la Cadena Lactea (IDICAL) INTA-CONICET. Ruta 34 km 227, Rafaela (2300), Santa Fe, Argentina" + }, + { + "author_name": "Maria Jose Dus Santos", + "author_inst": "Instituto de Virologia e Innovaciones Tecnologicas (INTA-CONICET), Hurlingham, Buenos Aires, Argentina; Laboratorio de Diagnostico-UNIDAD COVID- Universidad Nac" + }, + { + "author_name": "Maria Florencia Eberhardt", + "author_inst": "Instituto de Investigacion de la Cadena Lactea (IDICAL) INTA-CONICET. Ruta 34 km 227, Rafaela (2300), Santa Fe, Argentina; Consejo Nacional de Investigaciones C" + }, + { + "author_name": "Ailen Fernandez", + "author_inst": "Laboratorio Central ciudad de Neuquen, Ministerio de Salud, Neuquen, Argentina" + }, + { + "author_name": "Maria Ines Gismondi", + "author_inst": "Instituto de Biotecnologia/Instituto de Agrobiotecnologia y Biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina; Universidad Nacional de Luja" + }, + { + "author_name": "Matias Irazoqui", + "author_inst": "Instituto de Investigacion de la Cadena Lactea (IDICAL) INTA-CONICET. Ruta 34 km 227, Rafaela (2300), Santa Fe, Argentina; Consejo Nacional de Investigaciones " + }, + { + "author_name": "Silvina Lusso", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Nathalie Marquez", + "author_inst": "Instituto de Patologia Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnologia Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5" + }, + { + "author_name": "Marianne Munoz", + "author_inst": "Unidad de Genomica del Instituto de Biotecnologia/Instituto de Agrobiotecnologia y biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina." + }, + { + "author_name": "Monica Natale", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Belen Pisano", + "author_inst": "Instituto de Virologia Dr. J. M. Vanella, Facultad de Ciencias Medicas, Universidad Nacional de Cordoba; Consejo Nacional de Investigaciones Cientificas y Tecni" + }, + { + "author_name": "Andrea Puebla", + "author_inst": "Instituto de Biotecnologia/Instituto de Agrobiotecnologia y Biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina." + }, + { + "author_name": "Viviana Re", + "author_inst": "Instituto de Virologia Dr. J. M. Vanella, Facultad de Ciencias Medicas, Universidad Nacional de Cordoba; Consejo Nacional de Investigaciones Cientificas y Tecni" + }, + { + "author_name": "Ezequiel Sosa", + "author_inst": "Instituto de Quimica Biologica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina" + }, + { + "author_name": "Jonathan Zaiat", + "author_inst": "Instituto de Quimica Biologica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina" + }, + { + "author_name": "Sebastian Zunino", + "author_inst": "Laboratorio de Virologia Molecular, Hospital Blas L. Dubarry de Mercedes, provincia de Buenos Aires, Argentina; Universidad Nacional de Lujan, Departamento de C" + }, + { + "author_name": "Dario Do porto", + "author_inst": "Instituto de Quimica Biologica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina" + }, + { + "author_name": "Maria Elina Acevedo", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Cristina Alvarez Lopez", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Maria Laura Alvarez", + "author_inst": "Laboratorio del Hospital Zonal Dr. Ramon Carrillo, San Carlos De Bariloche, provincia de Rio Negro, Argentina" + }, + { + "author_name": "Patricia Angeleri", + "author_inst": "Comite Operativo de Emergencia COVID, Ministerio de Salud de la Ciudad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Andres Angelletti", + "author_inst": "Laboratorio de salud publica, Facultad de Ciencias Exactas, UNLP, La Plata, Provincia de Buenos Aires, Argentina; Laboratorio de Virologia, HIEAyC San Juan de D" + }, + { + "author_name": "Manuel Arca", + "author_inst": "Laboratorio de Virologia del Hospital JJ Urquiza, Concepcion del Uruguay, provincia de Entre Rios, Argentina" + }, + { + "author_name": "Gabriela Barbas", + "author_inst": "Secretaria de Prevencion y Promocion, Ministerio de Salud de la provincia de Cordoba, Argentina." + }, + { + "author_name": "Ana Bertone", + "author_inst": "Laboratorio de la Direccion de Epidemiologia, Santa Rosa, provincia de La Pampa, Argentina." + }, + { + "author_name": "Agustina Bonnet", + "author_inst": "Laboratorio de Virologia del Hospital JJ Urquiza, Concepcion del Uruguay, provincia de Entre Rios, Argentina" + }, + { + "author_name": "Ignacio Bourlot", + "author_inst": "Laboratorio de biologia molecular del Hospital Centenario, Gualeguaychu, provincia de Entre Rios, Argentina." + }, + { + "author_name": "Alejandro Castello", + "author_inst": "Plataforma de Servicios Biotecnologicos; UTTIPP/PSB, Bernal, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Gonzalo Castro", + "author_inst": "Laboratorio Central de la Provincia de Cordoba, Ministerio de Salud la provincia de Cordoba, Argentina." + }, + { + "author_name": "Carolina Ceriani", + "author_inst": "Laboratorio de Virologia de la Facultad de Veterinaria de la Universidad Nacional del Centro de la provincia de Buenos Aires (UNCPBA), Tandil, provincia de Buen" + }, + { + "author_name": "Carlos Cimino", + "author_inst": "Instituto Nacional de Epidemiologia Dr. Jara (Mar del Plata, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Julian Cipelli", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Maria Colmeiro", + "author_inst": "Laboratorio de Virologia, HIEAyC \"San Juan de Dios\", La Plata, provincia de Buenos Aires, Argentina" + }, + { + "author_name": "Andres Cordero", + "author_inst": "Laboratorio de salud publica, Facultad de Ciencias Exactas, UNLP, La Plata, Provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Carolina Cristina", + "author_inst": "Centro de Investigaciones Basicas y Aplicadas, UNNOBA, Junin, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Sofia Di Bella", + "author_inst": "Laboratorio de Virologia, HIEAyC San Juan de Dios, La Plata, provincia de Buenos Aires, Argentina" + }, + { + "author_name": "Regina Ercole", + "author_inst": "Laboratorio de Virologia, HIEAyC San Juan de Dios, La Plata, provincia de Buenos Aires, Argentina" + }, + { + "author_name": "Yesica Espasandin", + "author_inst": "Laboratorio del Hospital Zonal Dr. Ramon Carrillo, San Carlos De Bariloche, provincia de Rio Negro, Argentina" + }, + { + "author_name": "Carlos Espul", + "author_inst": "Direccion de epidemiologia y Red de Laboratorios del Ministerio de Salud de la provincia de Mendoza, Argentina." + }, + { + "author_name": "Andrea Falaschi", + "author_inst": "Direccion de epidemiologia y Red de Laboratorios del Ministerio de Salud de la provincia de Mendoza, Argentina." + }, + { + "author_name": "Facundo Fernandez Moll", + "author_inst": "Centro de Investigaciones Basicas y Aplicadas, UNNOBA, Junin, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Andrea Gatelli", + "author_inst": "Laboratorio de Virologia, HIEAyC San Juan de Dios, La Plata, provincia de Buenos Aires, Argentina" + }, + { + "author_name": "Sandra Goni", + "author_inst": "Plataforma de Servicios Biotecnologicos; UTTIPP/PSB, Bernal, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Maria E Jofre", + "author_inst": "Laboratorio de Biologia Molecular Bolivar, LABBO, Bolivar, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Jose Jaramillo", + "author_inst": "Laboratorio de Virologia Molecular, Hospital Blas L. Dubarry de Mercedes, provincia de Buenos Aires, Argentina" + }, + { + "author_name": "Natalia Labarta", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Maria A Lacaze", + "author_inst": "Programa Laboratorio de Salud Publica Dr Dalmiro Perez Laborda, Ministerio de Salud de la provincia de San Luis, Argentina." + }, + { + "author_name": "Rocio Larreche", + "author_inst": "Laboratorio de Biologia Molecular Bolivar, LABBO, Bolivar, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Viviana Leiva", + "author_inst": "Laboratorio de Biologia Molecular Bolivar, LABBO, Bolivar, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Gustavo Levin", + "author_inst": "Laboratorio de biologia molecular del Hospital Centenario, Gualeguaychu, provincia de Entre Rios, Argentina." + }, + { + "author_name": "Erica Luczak", + "author_inst": "Laboratorio del Hospital Interzonal General de Agudos Evita, Lanus, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Marcelo Mandile", + "author_inst": "Plataforma de Servicios Biotecnologicos; UTTIPP/PSB, Bernal, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Carla Massone", + "author_inst": "Laboratorio de Virologia Molecular, Hospital Blas L. Dubarry de Mercedes, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Melina Mazzeo", + "author_inst": "Laboratorio Central ciudad de Neuquen, Ministerio de Salud, Neuquen, Argentina" + }, + { + "author_name": "Carla Medina", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina." + }, + { + "author_name": "Belen Monaco", + "author_inst": "Laboratorio de Virologia Molecular, Hospital Blas L. Dubarry de Mercedes, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Luciana Montoto", + "author_inst": "Laboratorio de Biologia Molecular Hospital Pedro de Elizalde, Cuidad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Viviana Mugna", + "author_inst": "Laboratorio Central, ciudad de Santa Fe, provincia de Santa Fe. Argentina." + }, + { + "author_name": "Alejandra Musto", + "author_inst": "Laboratorio del Hospital Interzonal General de Agudos Evita, Lanus, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Guillermo Ojeda", + "author_inst": "Laboratorio Central, ciudad de Santa Fe, provincia de Santa Fe. Argentina." + }, + { + "author_name": "Carolina Pintos", + "author_inst": "Laboratorio Central ciudad de Neuquen, Ministerio de Salud, Neuquen, Argentina." + }, + { + "author_name": "Marcia Pozzati", + "author_inst": "Laboratorio de Biologia Molecular, Hospital Cosme Argerich, Cuidad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Marilina Rahhal", + "author_inst": "Laboratorio de Hospital El Cruce Dr. Nestor C. Kirchner, CEMET, Florencio Varela, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Claudia Rechimont", + "author_inst": "Laboratorio de la Direccion de Epidemiologia, Santa Rosa, provincia de La Pampa, Argentina." + }, + { + "author_name": "Federico Remes Lenicov", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y Sida, CONICET-UBA, Cuidad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Gabriela Rompato", + "author_inst": "Laboratorio Central, ciudad de Santa Fe, provincia de Santa Fe. Argentina." + }, + { + "author_name": "Vanesa Seery", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y Sida, CONICET-UBA, Cuidad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Leticia Siri", + "author_inst": "Laboratorio de biologia molecular del Hospital Centenario, Gualeguaychu, provincia de Entre Rios, Argentina." + }, + { + "author_name": "Julieta Spina", + "author_inst": "Laboratorio de Biologia Molecular. Hospital Dr. Hector Cura, Olavarria, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Cintia Streitenberger", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina." + }, + { + "author_name": "Ariel Suarez", + "author_inst": "Departamento de Biologia y genetica molecular; IACA Laboratorios, Bahia Blanca, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Jorgelina Suarez", + "author_inst": "Centro de Investigaciones Basicas y Aplicadas, UNNOBA, Junin, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Paula Sujanski", + "author_inst": "Comite Operativo de Emergencia COVID, Ministerio de Salud de la Ciudad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Juan M Talia", + "author_inst": "Programa Laboratorio de Salud Publica Dr Dalmiro Perez Laborda, Ministerio de Salud de la provincia de San Luis, Argentina." + }, + { + "author_name": "Clara Theaux", + "author_inst": "Laboratorio de Biologia molecular del Hospital General de Agudos Dr. Carlos G. Durand, Cuidad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Guillermo Thomas", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina." + }, + { + "author_name": "Marina Ticeira", + "author_inst": "Laboratorio de Biologia Molecular Bolivar, LABBO, Bolivar, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Estefania Tittarelli", + "author_inst": "Departamento de Biologia y genetica molecular; IACA Laboratorios, Bahia Blanca, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Rosana Toro", + "author_inst": "Laboratorio de salud publica, Facultad de Ciencias Exactas, UNLP, La Plata, Provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Osvaldo Uez", + "author_inst": "Instituto Nacional de Epidemiologia Dr. Jara (Mar del Plata, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Maria B Zaffanella", + "author_inst": "Laboratorio de Biologia Molecular. Hospital Dr. Hector Cura, Olavarria, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Cecilia Ziehm", + "author_inst": "Laboratorio Central ciudad de Neuquen, Ministerio de Salud, Neuquen, Argentina." + }, + { + "author_name": "Martin Zubieta", + "author_inst": "Laboratorio de Hospital El Cruce Dr. Nestor C. Kirchner, CEMET, Florencio Varela, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "- PAIS Consortium", + "author_inst": "-" + }, + { + "author_name": "Alicia Mistchenko", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina; Comision de Investigaciones Cientificas de la provincia de Buenos Aires, Arg" + }, + { + "author_name": "Laura Valinotto", + "author_inst": "Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina; Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez" + }, + { + "author_name": "Mariana Viegas", + "author_inst": "Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina; Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.19.21260759", "rel_title": "Development and validation of a prognostic model for COVID-19: a population-based cohort study in Iceland", @@ -633734,73 +637289,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.19.21260815", - "rel_title": "RNA viromics of Southern California wastewater and detection of SARS-CoV-2 single nucleotide variants.", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260815", - "rel_abs": "Municipal wastewater provides an integrated sample of a diversity of human-associated microbes across a sewershed, including viruses. Wastewater-based epidemiology (WBE) is a promising strategy to detect pathogens and may serve as an early-warning system for disease outbreaks. Notably, WBE has garnered substantial interest during the COVID-19 pandemic to track disease burden through analyses of SARS-CoV-2 RNA. Throughout the COVID-19 outbreak, tracking SARS-CoV-2 in wastewater has been an important tool for understanding the spread of the virus. Unlike traditional sequencing of SARS-CoV-2 isolated from clinical samples, which adds testing burden to the healthcare system, in this study, metatranscriptomics was used to sequence virus directly from wastewater.\n\nHere, we present a study in which we explored RNA viral diversity through sequencing 94 wastewater influent samples across seven treatment plants (WTPs), collected August 2020 - January 2021, representing approximately 16 million people in Southern California. Enriched viral libraries identified a wide diversity of RNA viruses that differed between WTPs and over time, with detected viruses including coronaviruses, influenza A, and noroviruses. Furthermore, single nucleotide variants (SNVs) of SARS-CoV-2 were identified in wastewater and we measured proportions of overall virus and SNVs across several months. We detected several SNVs that are markers for clinically-important SARS-CoV-2 variants, along with SNVs of unknown function, prevalence, or epidemiological consequence.\n\nOur study shows the potential of WBE to detect viruses in wastewater and to track the diversity and spread of viral variants in urban and suburban locations, which may aid public health efforts to monitor disease outbreaks.\n\nImportanceWastewater based epidemiology (WBE) can detect pathogens across sewersheds, which represents the collective waste of human populations. As there is a wide diversity of RNA viruses in wastewater, monitoring the presence of these viruses is useful for public health, industry, and ecological studies. Specific to public health, WBE has proven valuable during the COVID-19 pandemic to track the spread of SARS-CoV-2 without adding burden to healthcare systems. In this study, we used metatranscriptomics and RT-ddPCR to assay RNA viruses across Southern California wastewater from August 2020 - January 2021, representing approximately 16 million people from Los Angeles, Orange, and San Diego counties. We found that SARS-CoV-2 quantification in wastewater correlates well with county-wide COVID-19 case data, and that we can detect SARS-CoV-2 single nucleotide variants through sequencing. Likewise, WTPs harbored different viromes, and we detected other human pathogens such as noroviruses and adenoviruses, furthering our understanding of wastewater viral ecology.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Jason A Rothman", - "author_inst": "University of California: Irvine" - }, - { - "author_name": "Theresa B Loveless", - "author_inst": "University of California: Irvine" - }, - { - "author_name": "Joseph Kapcia III", - "author_inst": "University of California: Irvine" - }, - { - "author_name": "Eric D Adams", - "author_inst": "University of California: Irvine" - }, - { - "author_name": "Joshua A Steele", - "author_inst": "Southern California Coastal Water Research Project" - }, - { - "author_name": "Amity G Zimmer-Faust", - "author_inst": "Southern California Coastal Water Research Project" - }, - { - "author_name": "Kylie Langlois", - "author_inst": "Southern California Coastal Water Research Project" - }, - { - "author_name": "David Wanless", - "author_inst": "Southern California Coastal Water Research Project" - }, - { - "author_name": "Madison Griffith", - "author_inst": "Southern California Coastal Water Research Project" - }, - { - "author_name": "Lucy Mao", - "author_inst": "Southern California Coastal Water Research Project" - }, - { - "author_name": "Jeffrey Chokry", - "author_inst": "Southern California Coastal Water Research Project" - }, - { - "author_name": "John F Griffith", - "author_inst": "Southern California Coastal Water Research Project" - }, - { - "author_name": "Katrine L Whiteson", - "author_inst": "University of California, Irvine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.19.21260802", "rel_title": "Effectiveness of the ChAdOx1 vaccine in the elderly during SARS-CoV-2 Gamma variant transmission in Brazil", @@ -635363,6 +638851,65 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.07.22.453287", + "rel_title": "Competent immune responses to SARS-CoV-2 variants in older adults following mRNA vaccination", + "rel_date": "2021-07-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.22.453287", + "rel_abs": "Aging is associated with a reduced magnitude of primary immune responses to vaccination and constriction of immune receptor repertoire diversity. Clinical trials demonstrated high efficacy of mRNA based SARS-CoV-2 vaccines in older adults but concerns about virus variant escape have not been well addressed. We have conducted an in-depth analysis of humoral and cellular immunity against an early-pandemic viral isolate and compared that to the P.1. (Gamma) and B.1.617.2 (Delta) variants in <50 and >55 age cohorts of mRNA vaccine recipients. We have further measured neutralizing antibody titers for B.1.617.1 (Kappa) and B.1.595; a SARS-CoV-2 isolate bearing Spike mutation E484Q. As reported, robust immunity required the second dose of vaccine. Older vaccinees manifested robust cellular immunity against early-pandemic SARS-CoV-2 and more recent variants, which remained statistically comparable to the adult group. The older cohort had lower neutralizing capacity at the first time point following the second dose, but at later time points immunity was indistinguishable between them. While the duration of these immune responses remains to be determined over longer periods of time, these results provide reasons for optimism regarding vaccine protection of older adults against SARS-CoV-2 variants and inform thinking about boost vaccination with variant vaccines.\n\neTOC summaryVaccine responses are often diminished with aging, but we found strong responses to SARS-CoV-2 in older adults following mRNA vaccination. T cell responses were not diminished when confronted by SARS-CoV-2 variants. Neutralizing Ab were reduced but not more than those in adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC=\"FIGDIR/small/453287v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (16K):\norg.highwire.dtl.DTLVardef@1091655org.highwire.dtl.DTLVardef@1996173org.highwire.dtl.DTLVardef@ccf2f9org.highwire.dtl.DTLVardef@163ed22_HPS_FORMAT_FIGEXP M_FIG C_FIG Created with BioRender.com", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Mladen Jergovi\u0107", + "author_inst": "University of Arizona" + }, + { + "author_name": "Jennifer L. Uhrlaub", + "author_inst": "University of Arizona" + }, + { + "author_name": "Makiko Watanabe", + "author_inst": "University of Arizona" + }, + { + "author_name": "Christine M. Bradshaw", + "author_inst": "University of Arizona" + }, + { + "author_name": "Lisa M. White", + "author_inst": "University of Arizona" + }, + { + "author_name": "Bonnie J. LaFleur", + "author_inst": "University of Arizona" + }, + { + "author_name": "Taylor Edwards", + "author_inst": "University of Arizona" + }, + { + "author_name": "Ryan Sprissler", + "author_inst": "University of Arizona" + }, + { + "author_name": "Michael Worobey", + "author_inst": "University of Arizona" + }, + { + "author_name": "Deepta Bhattacharya", + "author_inst": "University of Arizona" + }, + { + "author_name": "Janko Nikolich-\u017dugich", + "author_inst": "University of Arizona" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.07.20.21260892", "rel_title": "Variation in SARS-CoV-2 bioaerosol production in exhaled breath", @@ -635480,25 +639027,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.20.21260840", - "rel_title": "Will a natural collective immunity of Ukrainians restrain new COVID-19 waves?", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260840", - "rel_abs": "The visible and real sizes the COVID-19 epidemic in Ukraine were estimated with the use of the number of laboratory-confirmed cases (accumulated in May and June 2021), the generalized SIR-model and the parameter identification procedure taking into account the difference between registered and real number of cases. The calculated optimal value of the visibility coefficient shows that most Ukrainians have already been infected with the coronavirus, and some more than once, i.e., Ukrainians have probably achieved a natural collective immunity. Nevertheless, a large number of new strains and short-lived antibodies can cause new pandemic waves. In particular, the beginning of such a wave, we probably see in Ukraine in mid-July 2021. The further dynamics of the epidemic and its comparison with the results of mathematical modeling will be able to answer many important questions about the natural immunity and effectiveness of vaccines.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Igor Nesteruk", - "author_inst": "Institute of Hydromechanics National Academy of sciences of Ukraine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.19.21260661", "rel_title": "Characterization of SARS CoV-2 Antibodies in Breast Milk from 21 Women with Confirmed COVID-19 Infection", @@ -637049,6 +640577,49 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.07.20.453118", + "rel_title": "Integrin activation is an essential component of SARS-CoV-2 infection", + "rel_date": "2021-07-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.20.453118", + "rel_abs": "Cellular entry of coronaviruses depends on binding of the viral spike (S) protein to a specific cellular receptor, the angiotensin-converting enzyme 2 (ACE2). Furthermore, the viral spike protein expresses an RGD motif, suggesting that cell surface integrins may be attachment co-receptors. However, using infectious SARS-CoV-2 requires a biosafety level 3 laboratory (BSL-3), which limits the techniques that can be used to study the mechanism of cell entry. Here, we UV-inactivated SARS-CoV-2 and fluorescently labeled the envelope membrane with octadecyl rhodamine B (R18) to explore the role of integrin activation in mediating both cell entry and productive infection. We used flow cytometry and confocal fluorescence microscopy to show that fluorescently labeled SARS-CoV-2R18 particles engage basal-state integrins. Furthermore, we demonstrate that Mn2+, which activates integrins and induces integrin extension, enhances cell binding and entry of SARS-CoV-2R18 in proportion to the fraction of integrins activated. We also show that one class of integrin antagonist, which binds to the I MIDAS site and stabilizes the inactive, closed conformation, selectively inhibits the engagement of SARS-CoV-2R18 with basal state integrins, but is ineffective against Mn2+-activated integrins. At the same time, RGD-integrin antagonists inhibited SARS-CoV-2R18 binding regardless of integrin activity state. Integrins transmit signals bidirectionally: inside-out signaling primes the ligand binding function of integrins via a talin dependent mechanism and outside-in signaling occurs downstream of integrin binding to macromolecular ligands. Outside-in signaling is mediated by G13 and induces cell spreading, retraction, migration, and proliferation. Using cell-permeable peptide inhibitors of talin, and G13 binding to the cytoplasmic tail of an integrins {beta} subunit, we further demonstrate that talin-mediated signaling is essential for productive infection by SARS-CoV-2.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Peter Simons", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Derek Rinaldi", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Virginie Bondu", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Alison Kell", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Steven Bradfute", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Diane Lidke", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Tione Buranda", + "author_inst": "University of New Mexico School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2021.07.20.453054", "rel_title": "Discovery of nanobodies against SARS-CoV-2 and an uncommon neutralizing mechanism", @@ -637234,109 +640805,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.07.20.452858", - "rel_title": "Cornering an Ever-Evolving Coronavirus: TATX-03, a fully human synergistic multi-antibody cocktail targeting the SARS-CoV-2 Spike Protein with in vivo efficacy", - "rel_date": "2021-07-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.20.452858", - "rel_abs": "The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created an ongoing global human health crisis and will likely become endemic, requiring novel sustainable therapeutic strategies. We report on the discovery of a fully human multi-antibody cocktail (TATX-03) targeting diversified non-overlapping epitopes on the SARS-CoV-2 spike protein that suppressed replication-competent viral titers to undetectable levels in the lungs of SARS-CoV-2 challenged hamsters upon both prophylactic and therapeutic administration. While monotherapy with two of the individual cocktail components also showed clear in vivo protection, neither recapitulated the efficacy of TATX-03. This synergistic effect was further supported by examining in vivo efficacy of these individual antibodies and corresponding combination therapy at a lower dose. Furthermore, in vitro screenings using VSV-particles pseudo-typed with spike proteins representing the SARS-CoV-2 variants of concern Alpha, Beta, and Delta showed that TATX-03 maintained its neutralization potency. These results merit further development of TATX-03 as a potential therapy for SARS-CoV-2 infection with resistance to mutagenic escape.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Ilse Roodink", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Maartje van Erp", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Andra Li", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Sheila Potter", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Sander Martinus Johannes van Duijnhoven", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Arthur J Kuipers", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Bert Kazemier", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Ellen van Geffen", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Wieger Hemrika", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Bob Berkeveld", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Glenn Sonnemans", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Britte S de Vries", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Bianca Boers", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Milou Smits", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Sanne Meurs", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Maaike de Pooter", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Alexandra Thom", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Barry Neil Duplantis", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Roland A Romijn", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Jeremy S Houser", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Jennifer Bath", - "author_inst": "ImmunoPrecise Antibodies Ltd." - }, - { - "author_name": "Yasmina N Abdiche", - "author_inst": "ImmunoPrecise Antibodies Ltd." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.07.20.453042", "rel_title": "An untargeted metabolomic approach to identify antiviral defense mechanisms in memory leukocytes secreting in vitro IgG anti-SARS-Cov-2", @@ -638899,6 +642367,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2021.07.15.21260543", + "rel_title": "Understanding Adverse Population Sentiment Towards the Spread of COVID-19 in the United States", + "rel_date": "2021-07-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260543", + "rel_abs": "BackgroundDuring the ongoing COVID-19 pandemic, the immediate threat of illness and mortality is not the only concern. In the United States, COVID-19 is not only causing physical suffering to patients, but also great levels of adverse sentiment (e.g., fear, panic, anxiety) among the public. Such secondary threats can be anticipated and explained through sentiment analysis of social media, such as Twitter.\n\nMethodsWe obtained a dataset of geotagged tweets on the topic of COVID-19 in the contiguous United States during the period of 11/1/2019 - 9/15/2020. We classified each tweet into \"adverse\" and \"non-adverse\" using the NRC Emotion Lexicon and tallied up the counts for each category per county per day. We utilized the space-time scan statistic to find clusters and a three-stage regression approach to identify socioeconomic and demographic correlates of adverse sentiment.\n\nResultsWe identified substantial spatiotemporal variation in adverse sentiment in our study area/period. After an initial period of low-level adverse sentiment (11/1/2019 - 1/15/2020), we observed a steep increase and subsequent fluctuation at a higher level (1/16/2020 - 9/15/2020). The number of daily tweets was low initially (11/1/2019 - 1/22/2020), followed by spikes and subsequent decreases until the end of the study period. The space-time scan statistic identified 12 clusters of adverse sentiment of varying size, location, and strength. Clusters were generally active during the time period of late March to May/June 2020. Increased adverse sentiment was associated with decreased racial/ethnic heterogeneity, decreased rurality, higher vulnerability in terms of minority status and language, and housing type and transportation.\n\nConclusionsWe utilized a dataset of geotagged tweets to identify the spatiotemporal patterns and the spatial correlates of adverse population sentiment during the first two waves of the COVID-19 pandemic in the United States. The characteristics of areas with high adverse sentiment may be relevant for communication of containment measures. The combination of spatial clustering and regression can be beneficial for understanding of the ramifications of COVID-19, as well as disease outbreaks in general.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Alexander Hohl", + "author_inst": "Department of Geography, University of Utah" + }, + { + "author_name": "Moongi Choi", + "author_inst": "Department of Geography, University of Utah" + }, + { + "author_name": "Richard Medina", + "author_inst": "Department of Geography, University of Utah" + }, + { + "author_name": "Neng Wan", + "author_inst": "Department of Geography, University of Utah" + }, + { + "author_name": "Ming Wen", + "author_inst": "Department of Sociology, University of Utah" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.15.21260346", "rel_title": "Elderly acceptance of telemedicine use in Hong Kong during and after the COVID-19 pandemic: a cross-sectional cohort survey", @@ -639036,37 +642539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.15.21260595", - "rel_title": "Identifying and alleviating bias due to differential depletion of susceptible people in post-marketing evaluations of COVID-19 vaccines", - "rel_date": "2021-07-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260595", - "rel_abs": "Recent studies have provided key information about SARS-CoV-2 vaccines efficacy and effectiveness (VE). One important question that remains is whether the protection conferred by vaccines wanes over time. However, estimates over time are subject to bias from differential depletion of susceptibles between vaccinated and unvaccinated groups. Here we examine the extent to which biases occur under different scenarios and assess whether serologic testing has the potential to correct this bias. By identifying non-vaccine antibodies, these tests could identify individuals with prior infection. We find in scenarios with high baseline VE, differential depletion of susceptibles creates minimal bias in VE estimates, suggesting that any observed declines are likely not due to spurious waning alone. However, if baseline VE is lower, the bias for leaky vaccines (that reduce individual probability of infection given contact) is larger and should be corrected by excluding individuals with past infection if the mechanism is known to be leaky. Conducting analyses both unadjusted and adjusted for past infection could give lower and upper bounds for the true VE. Studies of VE should therefore enroll individuals regardless of prior infection history but also collect information, ideally through serologic testing, on this critical variable.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Rebecca Kahn", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Stephanie J Schrag", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jennifer R Verani", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Marc Lipsitch", - "author_inst": "Harvard T.H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.15.21260597", "rel_title": "The CT Scan Lung Severity Score and Vaccination Status in COVID-19 patients during the Second Wave in India: Perspective of an Independent Radiology Practice", @@ -640905,6 +644377,49 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.07.17.452576", + "rel_title": "Mutation-induced Changes in the Receptor-binding Interface of the SARS-CoV-2 Delta Variant B.1.617.2 and Implications for Immune Evasion", + "rel_date": "2021-07-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.17.452576", + "rel_abs": "While the vaccination efforts against SARS-CoV-2 infections are ongoing worldwide, new genetic variants of the virus are emerging and spreading. Following the initial surges of the Alpha (B.1.1.7) and the Beta (B.1.351) variants, a more infectious Delta variant (B.1.617.2) is now surging, further deepening the health crises caused by the pandemic. The sharp rise in cases attributed to the Delta variant has made it especially disturbing and is a variant of concern. Fortunately, current vaccines offer protection against known variants of concern, including the Delta variant. However, the Delta variant has exhibited some ability to dodge the immune system as it is found that neutralizing antibodies from prior infections or vaccines are less receptive to binding with the Delta spike protein. Here, we investigated the structural changes caused by the mutations in the Delta variants receptor-binding interface and explored the effects on binding with the ACE2 receptor as well as with neutralizing antibodies. We find that the receptor-binding {beta}-loop-{beta} motif adopts an altered but stable conformation causing separation in some of the antibody binding epitopes. Our study shows reduced binding of neutralizing antibodies and provides a possible mechanism for the immune evasion exhibited by the Delta variant.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Prabin Baral", + "author_inst": "Florida International University" + }, + { + "author_name": "Nisha Bhattarai", + "author_inst": "Florida International University" + }, + { + "author_name": "Md Lokman Hossen", + "author_inst": "Florida International University" + }, + { + "author_name": "Vitalii Stebliankin", + "author_inst": "Florida International University" + }, + { + "author_name": "Bernard Gerstman", + "author_inst": "Florida International University" + }, + { + "author_name": "Giri Narasimhan", + "author_inst": "Florida International University" + }, + { + "author_name": "Prem P Chapagain", + "author_inst": "Florida International University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.07.16.452733", "rel_title": "One mucosal administration of a live attenuated recombinant COVID-19 vaccine protects non-human primates from SARS-CoV-2", @@ -641130,33 +644645,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.07.19.452910", - "rel_title": "Integrative multi-omics landscape of non-structural protein 3 of severe acute respiratory syndrome coronaviruses", - "rel_date": "2021-07-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.19.452910", - "rel_abs": "The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is currently a global pandemic. Extensive investigations have been performed to study the clinical and cellular effects of SARS-CoV-2 infection. Mass spectrometry-based proteomics studies have revealed the cellular changes due to the infection and identified a plethora of interactors for all SARS-CoV-2 components, except for the longest non-structural protein 3 (NSP3). Here, we expressed the full-length NSP3 proteins of SARS-CoV and SARS-CoV-2 to investigate their unique and shared functions using multi-omics methods. We conducted interactome, phosphoproteome, ubiquitylome, transcriptome, and proteome analyses of NSP3-expressing cells. We found that NSP3 plays essential roles in cellular functions such as RNA metabolism and immune response such as NF-{kappa}B signal transduction. Interestingly, we showed that SARS-CoV-2 NSP3 has both endoplasmic reticulum and mitochondrial localizations. In addition, SARS-CoV-2 NSP3 is more closely related to mitochondrial ribosomal proteins, whereas SARS-CoV NSP3 is related to the cytosolic ribosomal proteins. In summary, our multi-omics studies of NSP3 enhance our understanding of the functions of NSP3 and offer valuable insights for the development of anti-SARS strategies.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ruona Shi", - "author_inst": "Guangzhou Institutes of Biomedicine and Health" - }, - { - "author_name": "Zhenhuan Feng", - "author_inst": "Guangzhou Institutes of Biomedicine and Health" - }, - { - "author_name": "Xiaofei Zhang", - "author_inst": "Guangzhou Institutes of Biomedicine and Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.07.17.452787", "rel_title": "Unveiling Mutation Effects on the Structural Dynamics of the Main Protease from SARS-CoV-2 with Hybrid Simulation Methods", @@ -642931,6 +646419,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.11.21260318", + "rel_title": "Harnessing the Wisdom of the Crowd to Forecast Incident and Cumulative COVID-19 Mortality in the United States", + "rel_date": "2021-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.11.21260318", + "rel_abs": "BackgroundForecasting models have played a pivotal role in health policy decision making during the coronavirus disease-2019 (COVID-19) pandemic. A combined forecast from multiple models will be typically more accurate than an individual forecast, but there are few examples of studies of combined forecasts of COVID-19 data, focusing mainly on simple mean and median ensembles and involving short forecast evaluation periods. We aimed to investigate the accuracy of different ways of combining probabilistic forecasts of weekly COVID-19 mortality data, including two weighted methods that we developed previously, on an extended dataset and new dataset, and evaluate over a period of 52 weeks.\n\nMethodsWe considered 95% interval and point forecasts of weekly incident and cumulative COVID-19 mortalities between 16 May 2020 and 8 May 2021 in multiple locations in the United States. We compared the accuracy of simple and more complex combining methods, as well as individual models.\n\nResultsThe average of the forecasts from the individual models was consistently more accurate than the average performance of these models (the mean combination), which provides a fundamental motivation for combining. Weighted combining performed well for both incident and cumulative mortalities, and for both interval and point forecasting. Our inverse score with tuning method was the most accurate overall. The median combination was a leading method in the last quarter for both mortalities, and it was consistently more accurate than the mean combination for point forecasting. For interval forecasts of cumulative mortality, the mean performed better than the median. The best performance of the leading individual model was in point forecasting.\n\nConclusionsCombining forecasts can improve the contribution of probabilistic forecasting to health policy decision making during epidemics, and, when there are sufficient historical data on forecast accuracy, weighted combining provides the most accurate method.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Kathryn S Taylor", + "author_inst": "University of Oxford" + }, + { + "author_name": "James W Taylor", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.12.21258827", "rel_title": "Olfactory detection of human odorant signatures in Covid patients by trained dogs", @@ -643084,61 +646595,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.07.13.21260428", - "rel_title": "Epidemiology and Clinical Characteristics in Individuals with Confirmed SARS-CoV-2 Infection During the Early COVID-19 Pandemic in Saudi Arabia", - "rel_date": "2021-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.13.21260428", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the catastrophic coronavirus disease 2019 (COVID-19) global pandemic. This study aimed to provide epidemiologic and clinical characteristics of patients with confirmed COVID-19 in Saudi Arabia and to determine whether characteristic profiles differ between patients who are symptomatic vs. asymptomatic for the disease. The first 492 consecutive patients diagnosed with SARS-CoV-2 infection at King Faisal Specialist Hospital and Research Centre in Saudi Arabia between March and September 2020 were included in this study. An electronic case report form developed using REDCap was used to collect data for each patient, including demographic characteristics, virus exposure (travel history, and human and animal contact), vaccination history, comorbidities, signs and symptoms, laboratory and radiographic reports, cardiac workup, medications, treatment regimens, and patient outcome. This patient cohort was 54% male, with 20.4% aged more than 60 years, 19.9% aged 31 to 40 years, and 17% aged 41 to 50 years. Most patients (79.2%) were symptomatic. Variables that significantly differed between symptomatic and asymptomatic patients were age, blood oxygen saturation percentage, hemoglobin level, lymphocyte count, neutrophil to lymphocyte (NTL) ratio, alanine aminotransferase (ALT) level, and aspartate aminotransferase (AST) level. Asymptomatic patients were mostly younger, with lower body mass index and ALT and AST levels but higher lymphocyte counts, NTL ratio, and CD4, CD8, natural killer cell, IgG, and IgM levels. The median incubation period reported for this cohort was 16 day, with upper and lower 95% quartiles of 27 and 10 days, respectively. Factors associated with increased risk of mortality were age (older than 42 years) and comorbidities, including specifically diabetes mellitus and hypertension. Patients who were not given an antiviral regimen were associated with better prognosis than patients who received an antiviral regimen (HR, 0.07; 95% CI, 0.011-0.25). Similar to countries worldwide, Saudi Arabia has explored treatment options to save the lives of patients during the COVID-19 pandemic. Our analyses will inform clinicians as well as policy makers to adopt the best strategies for SARS-CoV-2 infection management and treatment options.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Fatimah S. Alhamlan", - "author_inst": "King Faisal Specialist Hospital and Research Centre, Riyadh" - }, - { - "author_name": "Reem S. Almaghrabi", - "author_inst": "King Faisal Specialist Hospital and Research Centre, Riyadh" - }, - { - "author_name": "Edward B. Devol", - "author_inst": "King Faisal Specialist Hospital and Research Centre, Riyadh" - }, - { - "author_name": "Anwar B. Alotaibi", - "author_inst": "King Faisal Specilaist Hospital and Research Centre, Riyadh" - }, - { - "author_name": "Saleh M. Alageel", - "author_inst": "King Faisal Specilaist Hospital and Research Centre, Riaydh" - }, - { - "author_name": "Dalia A. Obeid", - "author_inst": "National Health laboratory, Saudi Center for Disease Prevention and Control" - }, - { - "author_name": "Basem M. Alraddadi", - "author_inst": "King Faisal Specialist Hospital and Research Center, Jeddah" - }, - { - "author_name": "Sahar I. Althawadi", - "author_inst": "King Faisal Specialist Hospital and Research Centre, Riyadh" - }, - { - "author_name": "Maysoon S. Mutabagani", - "author_inst": "King Faisal Specialist Hospital and Research Centre, Riyadh" - }, - { - "author_name": "Ahmed A. Al-Qahtani", - "author_inst": "King Faisal Specialist Hospital and Research Centre, Riyadh" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.13.21259739", "rel_title": "Results from Canton Grisons of Switzerland Suggest Repetitive Testing Reduces SARS-CoV-2 Incidence (February-March 2021)", @@ -644521,6 +647977,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.07.12.21260345", + "rel_title": "Factors associated with transmission in COVID-19 outbreaks in long-term care facilities", + "rel_date": "2021-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.12.21260345", + "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a disproportionate impact on residents in long-term care facilities (LTCFs). Through our experience and data from managing COVID-19 exposures and outbreaks in LTCFs in the Fraser Health region in British Columbia, Canada, we identified risk factors associated with outbreak severity to inform current outbreak management strategies and future pandemic preparedness planning efforts.\n\nMethodsWe used a retrospective cohort study design to evaluate the association between non-modifiable factors (facility building, organization level, and resident population characteristics), modifiable factors (assessments for infection prevention and control (IPC) and public health measures), and severity of COVID-19 outbreaks (attack rate) in LTCFs. We modelled the COVID-19 attack rates in LTCF outbreaks using negative binomial regression models.\n\nResultsFrom March 1, 2020 to January 10, 2021, a total of 145 exposures to at least one confirmed case of COVID-19 in 82 LTCFs occurred. For every item not met in the assessment tool, a 22% increase in the attack rate was observed (rate ratio 1.2 [95% CI 1.1 - 1.4]) after adjusting for other risk factors such as age of the facility, index case type (resident vs. staff) and proportion of single bed rooms.\n\nConclusionOur findings highlight the importance of assessing IPC and public health measures for outbreak management. They also demonstrate the important modifiable and non-modifiable risk factors associated with COVID-19 outbreaks in our jurisdiction. We hope these findings will inform ongoing outbreak management and future pandemic planning efforts.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Rohit Vijh", + "author_inst": "School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada" + }, + { + "author_name": "Carmen H Ng", + "author_inst": "Office of the Medical Health Officer, Fraser Health" + }, + { + "author_name": "Mehdi Shirmaleki", + "author_inst": "Office of the Medical Health Officer, Fraser Health" + }, + { + "author_name": "Aamir Bharmal", + "author_inst": "Office of the Medical Health Officer, Fraser Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.12.21260358", "rel_title": "Increase in SARS-CoV-2 seroprevalence in healthy blood donors after the second wave of COVID-19 pandemic in South-Eastern Italy: evidence for asymptomatic young individuals as potential virus spreaders", @@ -644650,45 +648137,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.12.21260216", - "rel_title": "Quantifying social contact patterns in Minnesota during Stay-at-Home social distancing order", - "rel_date": "2021-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.12.21260216", - "rel_abs": "SARS-CoV-2 is primarily transmitted through person-to-person contacts. It is important to collect information on age-specific contact patterns because SARS-CoV-2 susceptibility, transmission, and morbidity vary by age. To reduce risk of infection, social distancing measures have been implemented. Social contact data, which identify who has contact with whom especially by age and place are needed to identify high-risk groups and serve to inform the design of non-pharmaceutical interventions.\n\nWe estimated and used negative binomial regression to compare the number of daily contacts during the first wave (April-May 2020) of the Minnesota Social Contact Study, based on respondents age, gender, race/ethnicity, region, and other demographic characteristics. We used information on age and location of contacts to generate age-structured contact matrices. Finally, we compared the age-structured contact matrices during the stay-at-home order to pre-pandemic matrices.\n\nDuring the state-wide stay-home order, the mean daily number of contacts was 5.6. We found significant variation in contacts by age, gender, race, and region. Adults between 40 and 50 years had the highest number of contacts. Respondents in Black households had 2.1 more contacts than respondent in White households, while respondents in Asian or Pacific Islander households had approximately the same number of contacts as respondent in White households. Respondents in Hispanic households had approximately two fewer contacts compared to White households. Most contacts were with other individuals in the same age group. Compared to the pre-pandemic period, the biggest declines occurred in contacts between children, and contacts between those over 60 with those below 60.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Audrey M Dorelien", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Narmada Venkateswaran", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Jiuchen Deng", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Kelly Searle", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Eva Enns", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Shalini Kulasingam", - "author_inst": "University of Minnesota" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.12.21260379", "rel_title": "Absence of SARS-CoV-2 antibodies in pre-pandemic plasma from children and adults in Vietnam", @@ -646602,6 +650050,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.10.21260293", + "rel_title": "Plasma P-selectin is an early marker of thromboembolism in COVID-19", + "rel_date": "2021-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.10.21260293", + "rel_abs": "Coagulopathy and thromboembolism are known complications of SARS-CoV-2 infection. The mechanisms of COVID-19-associated hematologic complications involve endothelial cell and platelet dysfunction and have been intensively studied. We leveraged a prospectively collected acute COVID-19 biorepository to study the association of plasma levels of a comprehensive list of coagulation proteins with the occurrence of venous thromboembolic events (VTE). We included in our analysis 305 subjects with confirmed SARS-CoV-2 infection who presented to an urban Emergency Department with acute respiratory distress during the first COVID-19 surge in 2020; 13 (4.2%) were subsequently diagnosed with venous thromboembolism during hospitalization. Serial samples were obtained and assays were performed on two highly-multiplexed proteomic platforms. Nine coagulation proteins were differentially expressed in patients with thromboembolic events. P-selectin, a cell adhesion molecule on the surface of activated endothelial cells, displayed the strongest association with the diagnosis of VTE, independent of disease severity (p=0.0025). This supports the importance of endothelial activation in the mechanistic pathway of venous thromboembolism in COVID-19. P-selectin together with D-dimer upon hospital presentation provided better discriminative ability for VTE diagnosis than D-dimer alone.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Bank Gabor Fenyves", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA, Department of Emergency Medicine, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Arnav Mehta", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "- MGH COVID-19 Collection & Processing Team", + "author_inst": "-" + }, + { + "author_name": "Kyle Kays", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Marcia Goldberg", + "author_inst": "Department of Medicine, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "Nir Hacohen", + "author_inst": "Broad Institute and Massachusetts General Hospital" + }, + { + "author_name": "Michael Filbin", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2021.07.11.21260148", "rel_title": "ONLINE QUERIES AS A CRITERION FOR EVALUATION OF THE EPIDEMIOLOGICAL STATUS AND EFFECTIVENESS OF COVID-19 EPIDEMIC CONTROL MEASURES", @@ -646695,53 +650186,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.12.21258824", - "rel_title": "STUDY OF BLOOD GROUP ANALYSIS AND ITS CORRELATION WITH LYMPHOPENIA IN COVID 19 INFECTED CASES OUR EXPERIENCE IN TERITARY CARE HOSPITAL.", - "rel_date": "2021-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.12.21258824", - "rel_abs": "AIMS AND OBJECTIVESTo study the distribution and frequencies of ABO and Rhesus (Rh) blood groups among confirmed cases of Covid-19 infection. We also studied the relation between ABO blood group system and lymphopenia and studied the gender association in COVID-19 patients.\n\nMETHODESA hospital based retrospective study was conducted at Government Medical College Suryapet from 01 Aug 2020 to 30 Sep 2020. A total of 200 Covid cases were included in the study who came to the hospital with the complaints of Fever, Sore throat, Body Pains, Cough, Breathlessness, Diarrhoea etc. Patients confirmed Covid infection was tested for blood grouping and RH typing by using forward blood grouping with the help of commercially available standard monoclonal antisera. CBP was processed in sysmax 5 part Haematology analyser. Blood group frequency was tested also assed the gender association, Covid patients presents with lymphopenia the relation between the ABO blood group and lymphocyte count was determined.\n\nRESULTSMales were more compared to the females .Middle aged group male patients were more commonly involved. Most predominant blood group was group B 79(39.5%), group O 78(39%),group A 37(18.5%), group AB 6(3%),most of them were 190 (95%)Rh positive, only 10 Rh negative (5%).To assess the Lymphopenia in our study we divided the absolute lymphocyte count into 5 groups. Group 1 cases are more 58 (29%), Group 2 91(45.5%), Group 3 30 (15%), Group 4 16(8%), Group 5 5(2.5%).\n\nCONCLUSIONMale patients with blood group B were more compared to other blood groups however more number of studies are necessary to confirm these findings in a larger sample and among individuals of different ethnicities.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Swarupa G Ravuri Sr.", - "author_inst": "Government Medical College" - }, - { - "author_name": "Swarupa Ravuri Sr.", - "author_inst": "Government Medical College." - }, - { - "author_name": "Saritha Cigiri Jr.", - "author_inst": "Government Medical College" - }, - { - "author_name": "Harika Kalangi Jr.", - "author_inst": "Government Hospital" - }, - { - "author_name": "Anunayi Jeshtadi Sr.", - "author_inst": "Government Medical College" - }, - { - "author_name": "Nithesh.K Kumar Sr.", - "author_inst": "Mamata Medical Collage" - }, - { - "author_name": "Srilatha. Bacchu Jr.", - "author_inst": "CAS, Area hospital" - }, - { - "author_name": "Vamshi Krishna Nampally Jr.", - "author_inst": "Government Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2021.07.09.21260206", "rel_title": "COVID-19 vaccine hesitancy in the UK: A longitudinal household cross-sectional study", @@ -648380,6 +651824,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.09.21260247", + "rel_title": "Spatiotemporal droplet dispersion measurements demonstrate face masks reduce risks from singing: results from the COvid aNd FacEmaSkS Study (CONFESS)", + "rel_date": "2021-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.09.21260247", + "rel_abs": "BackgroundCOVID-19 has restricted singing in communal worship. We sought to understand variations in droplet transmission and the impact of wearing face masks.\n\nMethodsUsing rapid laser planar imaging, we measured droplets while participants exhaled, said hello or snake, sang a note or Happy Birthday, with and without surgical face masks. We measured mean velocity magnitude (MVM), time averaged droplet number (TADN) and maximum droplet number (MDN). Multilevel regression models were used.\n\nResultsIn 20 participants, sound intensity was 71 Decibels (dB) for speaking and 85 dB for singing (p<0.001). MVM was similar for all tasks with no clear hierarchy between vocal tasks or people and >85% reduction wearing face masks. Droplet transmission varied widely, particularly for singing. Masks decreased TADN by 99% (p<0.001) and MDN by 98% (p<0.001) for singing and 86-97% for other tasks. Masks reduced variance by up to 48%. When wearing a mask, neither singing task transmitted more droplets than exhaling.\n\nConclusionsWide variation exists for droplet production. This significantly reduced when wearing face masks. Singing during religious worship wearing a face mask appears as safe as exhaling or talking. This has implications for UK public health guidance during the COVID-19 pandemic.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Kai Man Alexander Ho", + "author_inst": "University College London" + }, + { + "author_name": "Hywel Davies", + "author_inst": "University College London" + }, + { + "author_name": "Ruth Epstein", + "author_inst": "University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Paul Bassett", + "author_inst": "Statsconsultancy Ltd" + }, + { + "author_name": "Aine Hogan", + "author_inst": "University College London" + }, + { + "author_name": "Yusuf Kabir", + "author_inst": "University College London" + }, + { + "author_name": "John Rubin", + "author_inst": "University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Gee Yen Shin", + "author_inst": "University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Jonathan Reid", + "author_inst": "University of Bristol" + }, + { + "author_name": "Ryo Torii", + "author_inst": "University College London" + }, + { + "author_name": "Manish Tiwari", + "author_inst": "University College London" + }, + { + "author_name": "Ramanarayanan Balachandran", + "author_inst": "University College London" + }, + { + "author_name": "Laurence Lovat", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.12.21259864", "rel_title": "Evidence of SARS-Cov-2-specific memory B cells six months after vaccination with BNT162b2 mRNA vaccine", @@ -648521,29 +652032,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.11.21260317", - "rel_title": "COVID-19 vaccine uptake, predictors of vaccination, and self-reported barriers to vaccination among primary school teachers in Poland", - "rel_date": "2021-07-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.11.21260317", - "rel_abs": "It has been proposed that teachers, like healthcare workers, constitute a strategic target for COVID-19 vaccine programs as immunization is a key element in protecting both them and their pupils. The present study examined vaccine uptake among primary-school teachers and sought to identify factors associated with it. A sample was recruited from 553 Polish primary schools, and data were collected at two time points: December 2020 and March 2021. Associations between vaccine uptake among teachers and their attitudes toward COVID-19 vaccination were assessed through multivariate logistic regression. 6152 participants completed both baseline and follow-up surveys. Of these, 4502 (73.2%) reported their intention at baseline to receive a COVID-19 vaccination, if available; at follow-up, 3894 (86.5%) of the same 4502 reported having received the vaccination. A significant association was revealed between vaccine uptake and perceived severity, self-efficacy, and social norms. The principal driver for vaccine acceptance was the wish to avoid contracting the disease. Conversely, the principal driver for vaccine refusal was concern about side effects and safety. A strong association exists between intention to receive the COVID-19 vaccine and actual uptake. Future COVID-19 immunization programs may benefit from a stronger understanding of the factors associated with vaccine uptake among this cohort.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Marta Malesza", - "author_inst": "University of Economics and Human Sciences in Warsaw" - }, - { - "author_name": "Karolina Sobolewska", - "author_inst": "University of Economics and Human Sciences in Warsaw" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.07.09.21260221", "rel_title": "Genetic regulation of OAS1 nonsense-mediated decay underlies association with risk of severe COVID-19", @@ -650254,6 +653742,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.11.451855", + "rel_title": "The SARS-CoV-2 spike reversibly samples an open-trimer conformation exposing novel epitopes", + "rel_date": "2021-07-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.11.451855", + "rel_abs": "Current COVID-19 vaccines and many clinical diagnostics are based on the structure and function of the SARS-CoV-2 spike ectodomain. Using hydrogen deuterium exchange mass spectrometry, we have uncovered that, in addition to the prefusion structure determined by cryo-EM, this protein adopts an alternative conformation that interconverts slowly with the canonical prefusion structure. This new conformation--an open trimer-- contains easily accessible RBDs. It exposes the conserved trimer interface buried in the prefusion conformation, thus exposing potential epitopes for pan-coronavirus antibody and ligand recognition. The population of this state and kinetics of interconversion are modulated by temperature, receptor binding, antibody binding, and sequence variants observed in the natural population. Knowledge of the structure and populations of this conformation will help improve existing diagnostics, therapeutics, and vaccines.\n\nOne Sentence SummaryAn alternative conformation of SARS-CoV-2 spike ectodomain modulated by temperature, binding, and sequence variants.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Shawn M Costello", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Sophie R Shoemaker", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Helen T Hobbs", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Annalee W Nguyen", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Ching-Lin Hsieh", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Jennifer A Maynard", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Jason S McLellan", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "John E Pak", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Susan Marqusee", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.07.08.21259912", "rel_title": "Efficacy and safety of Andrographis paniculata extract in patients with mild COVID-19: A randomized controlled trial", @@ -650423,33 +653962,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.08.21260188", - "rel_title": "COVID-19 and Black Fungus: Analysis of the Public Perception through Machine Learning", - "rel_date": "2021-07-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.08.21260188", - "rel_abs": "While COVID-19 is ravaging the lives of millions of people across the globe, a second pandemic black fungus has surfaced robbing people of their lives especially people who are recovering from coronavirus. Again, the public perceptions regarding such pandemics can be investigated through sentiment analysis of social media data. Thus the objective of this study is to analyze public perceptions through sentiment analysis regarding black fungus during the time of the COVID-19 pandemic. To attain the objective, first, a Support Vector Machine model, with an average AUC of 82.75%, was developed to classify user sentiments in terms of anger, fear, joy, and sad. Next, this Support Vector Machine is used to supervise the class labels of the public tweets (n = 6477) related to COVID-19 and black fungus. As outcome, this study found that public perceptions belong to sad (n = 2370, 36.59 %), followed by joy (n = 2095, 32.34%), fear (n = 1914, 29.55 %) and anger (n = 98, 1.51%) towards black fungus during COVID-19 pandemic. This study also investigated public perceptions of some critical concerns (e.g., education, lockdown, hospital, oxygen, quarantine, and vaccine) and it was found that public perceptions of these issues varied. For example, for the most part, people exhibited fear in social media about education, hospital, vaccine while some people expressed joy about education, hospital, vaccine, and oxygen.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Muhammad Nazrul Islam", - "author_inst": "Military Institute of Science and Technology (MIST)" - }, - { - "author_name": "Nafiz Imtiaz Khan", - "author_inst": "Military Institute of Science and Technology (MIST)" - }, - { - "author_name": "Tahasin Mahmud", - "author_inst": "Military Institute of Science and Technology (MIST)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.07.08.21260169", "rel_title": "Endothelial dysfunction determines severe COVID-19 in combination with dysregulated lymphocyte responses and cytokine networks", @@ -651940,6 +655452,33 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2021.07.06.21260112", + "rel_title": "COVID-19 Due to Wild-Type SARS-CoV-2 More Prevalent in Adolescents and Youth than in Older Adults Based on 19 US States in Fall 2020 Prior to Vaccine Availability", + "rel_date": "2021-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21260112", + "rel_abs": "PURPOSEIn a prior study, we examined data from six US states during Summer 2020, and found that prevalence of COVID-19 for adolescents and youth was significantly greater than for older adults (p<.00001) as was a prevalence-related measure: Number of cases observed / Number of cases expected (p<.005). We now extended our study to more states in Fall 2020 to confirm the prevalence relationships we found previously. Vaccines were still not available as of Fall 2020. Presumably, the SARS-CoV-2 strain circulating at the time was the wild-type lineage since no variants were reported in the US until the end of December 2020.\n\nMETHODSWe examined data from 19 U.S. states experiencing surges in cases to determine prevalence of COVID-19, and a prevalence-related measure: [Number of cases observed in a given age group] / [Number of cases expected in the age group based on population demographics].\n\nRESULTSIn 16 of the 19 states, we found that: (1) prevalence of COVID-19 for adolescents and youth was significantly greater than for older adults (p-values ranged from p<0.00001 to p = 0.0175; (2) the ratio of cases observed to cases expected was significantly greater in adolescents and youth than in older adults (p-values ranging from p< 0.00001 to p = 0.004).\n\nCONCLUSIONSOur results are consistent with our previous study in Summer 2020. The finding of lower prevalence in older adults cannot be attributed to access to vaccination since our data are from Fall 2020 when vaccinations were not yet available. Our findings with the SARS-CoV-2 wild-type strain are consistent with the findings currently being reported in the UK for the delta variant. In both studies, prevalence in adolescents and youth exceeded that in older adults. The UK findings are more pronounced perhaps because that study transpired following months of vaccinations of older adults whereas ours occurred before vaccinations were available.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Barbara T Rumain", + "author_inst": "New York Medical College" + }, + { + "author_name": "Moshe Schneiderman", + "author_inst": "SUNY Downstate College of Medicine" + }, + { + "author_name": "Allan Geliebter", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.30.21259763", "rel_title": "Which children and young people are at higher risk of severe disease and death after SARS-CoV-2 infection: a systematic review and individual patient meta-analysis", @@ -652117,189 +655656,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.07.21253295", - "rel_title": "Mortality among Care Home Residents in England during the first and second waves of the COVID-19 pandemic: an analysis of 4.3 million adults over the age of 65", - "rel_date": "2021-07-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.07.21253295", - "rel_abs": "BackgroundResidents in care homes have been severely impacted by the COVID-19 pandemic. We describe trends in risk of mortality among care home residents compared to residents in private homes in England.\n\nMethodsOn behalf of NHS England, we used OpenSAFELY-TPP, an analytics platform running across the linked electronic health records of approximately a third of the English population, to calculate monthly age-standardised risks of death due to all causes and COVID-19 among adults aged >=65 years between 1/2/2019 and 31/03/2021. Care home residents were identified using linkage to the Care and Quality Commission.\n\nFindingsWe included 4,329,078 people aged 65 years or older on the 1st of February 2019, 2.2% of whom were classified as residing in a care or nursing home. Age-standardised mortality risks were approximately 10 times higher among care home residents compared to non-residents in February 2019 residents (CMF = 10.59, 95%CI = 9.51, 11.81 among women, CMF = 10.82, 95%CI = 9.89, 11.84 among men). This increased to more than 17 times in April 2020 (CMF = 17.52, 95%CI = 16.38, 18.74 among women, CMF = 18.12, 95%CI = 17.17 - 19.12 among men) before returning to pre-pandemic levels in June 2020. CMFs did not increase during the second wave, despite a rise in the absolute age-standardised COVID-19 mortality risks.\n\nInterpretationThe first COVID-19 wave had a disproportionate impact on care home residents in England compared to older private home residents. A degree of immunity, improved protective measures or changes in the underlying frailty of the populations may explain the lack of an increase in the relative mortality risks during the second wave. The care home population should be prioritised for measures aimed at controlling the spread of COVID-19.\n\nFundingMedical Research Council MR/V015737/1", - "rel_num_authors": 42, - "rel_authors": [ - { - "author_name": "Anna Schultze", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "Emily Nightingale", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "David Evans", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "William J Hulme", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Alicia Rosello", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Chris Bates", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" - }, - { - "author_name": "Jonathan Cockburn", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Helen J Curtis", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Richard Croker", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Seb Bacon", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Helen I McDonald", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "Christopher T. Rentsch", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "Krishnan Bhaskaran", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "Rohini Mathur", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "Laurie A Tomlinson", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "Elizabeth J Williamson", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "Harriet Forbes", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "John Tazare", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "Daniel J Grint", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "Alex J Walker", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Nicholas J DeVito", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "George Hickman", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Simon Davy", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Tom Ward", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Louis Fisher", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Amelia CA Green", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Kevin Wing", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "Angel YS Wong", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "Robert McManus", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" - }, - { - "author_name": "John Parry", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" - }, - { - "author_name": "Frank Hester", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" - }, - { - "author_name": "Sam Harper", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" - }, - { - "author_name": "Stephen JW Evans", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "Ian J Douglas", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "Liam Smeeth", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "David A Leon", - "author_inst": "London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.07.21260137", "rel_title": "Anxiety and depression symptoms after COVID-19 infection: results from the COVID Symptom Study app", @@ -653830,6 +657186,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.07.06.21259473", + "rel_title": "Cross-sectional cycle threshold values reflect epidemic dynamics of COVID-19 in Madagascar", + "rel_date": "2021-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21259473", + "rel_abs": "As the national reference laboratory for febrile illness in Madagascar, we processed samples from the first epidemic wave of COVID-19, between March and September 2020. We fit generalized additive models to cycle threshold (Ct) value data from our RT-qPCR platform, demonstrating a peak in high viral load, low-Ct value infections temporally coincident with peak epidemic growth rates estimated in real time from publicly-reported incidence data and retrospectively from our own laboratory testing data across three administrative regions. We additionally demonstrate a statistically significant effect of duration of time since infection onset on Ct value, suggesting that Ct value can be used as a biomarker of the stage at which an individual is sampled in the course of an infection trajectory. As an extension, the population-level Ct distribution at a given timepoint can be used to estimate population-level epidemiological dynamics. We illustrate this concept by adopting a recently-developed, nested modeling approach, embedding a within-host viral kinetics model within a population-level Susceptible-Exposed-Infectious-Recovered (SEIR) framework, to mechanistically estimate epidemic growth rates from cross-sectional Ct distributions across three regions in Madagascar. We find that Ct-derived epidemic growth estimates slightly precede those derived from incidence data across the first epidemic wave, suggesting delays in surveillance and case reporting. Our findings indicate that public reporting of Ct values could offer an important resource for epidemiological inference in low surveillance settings, enabling forecasts of impending incidence peaks in regions with limited case reporting.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Soa Fy Andriamandimby", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Cara E. Brook", + "author_inst": "Cara Brook" + }, + { + "author_name": "Norosoa H Razanajatovo", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Jean-Marius Rakotondramanga", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Fidisoa Rasambainarivo", + "author_inst": "Princeton University" + }, + { + "author_name": "Vaomalala Raharimanga", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Iony M. Razanajatovo", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Reziky Mangahasimbola", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Richter L Razafindratsimandresy", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Santatra Randrianarisoa", + "author_inst": "University of Antananarivo" + }, + { + "author_name": "Barivola Bernardson", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Joelinotahina H Rabarison", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Mirella Randrianarisoa", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Frederick S Nasolo", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Roger M Rabetombosoa", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Rindra V Randremanana", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Jean-Michel Heraud", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Philippe G Dussart", + "author_inst": "Institut Pasteur de Madagascar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.08.21259776", "rel_title": "Effectiveness of SARS-CoV-2 mRNA Vaccines for Preventing Covid-19 Hospitalizations in the United States", @@ -654183,25 +657626,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.06.21260105", - "rel_title": "Excess mortality analysis for Germany for all three COVID-19 waves in 2020 - 2021", - "rel_date": "2021-07-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21260105", - "rel_abs": "Background and AimsThe excess mortality has been used as a metric to estimate the impact of COVID-19 across countries. For Germany, we observe that during the second half of the first and second COVID-19 waves, the COVID-19 deaths are significantly higher than the excess mortality. We attribute the difference to the pre-dying effect. We then compare the excess mortality to the official COVID-19 death numbers and calculate the infection fatality rates (IFRs) and the percentage of infected individuals from excess mortality for different age bands. We also compare the impact of COVID-19 to past influenza waves and analyze the vaccination effect on excess mortality.\n\nMethodsWe forecast the baseline mortality from official data on deaths in Germany. Distributing a part of excess mortality into the near future, we lower the baseline simulating the pre-dying effect. From the observed mortality deficit, we estimate the percentage of infected individuals and then estimate the age-dependent IFRs.\n\nResultsIn the first wave, we find an overall excess mortality of ca. 8 000. For the second wave, the overall excess mortality adds up to ca. 56 000. We find, that the pre-dying effect explains the difference between the official COVID-19 deaths and excess mortality in the second half of the waves to a high degree. Attributing the whole excess mortality to COVID-19, we find that the IFRs are significantly higher in the second wave. In the third wave, the overall excess mortality is ca. 5 000. We find an excess mortality in mid-age bands which cannot be explained by the official COVID-19 deaths. For the senior band 80+, we find results in favor of a strong and positive vaccination effect for the third COVID-19 wave.\n\nConclusionsWe conclude that in the first and second COVID-19 waves, the COVID-19 deaths explain almost all excess mortality when the pre-dying effect is taken into account. In the third wave in 2021, the excess mortality is not very pronounced for the 80+ age band, probably due to vaccination. The partially unvaccinated 40-80 age group experiences a pronounced excess mortality in the third wave while there are too few official COVID-19 deaths to explain the excess. The no-vaccination scenario for the 80+ age band results in a similarly high excess mortality as for the more younger age bands, suggesting a very positive vaccination effect on reduction of COVID-19 deaths.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Alexej Weber", - "author_inst": "Independent researcher" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.07.21260092", "rel_title": "POST-COVID-19 SYNDROME, INFLAMMATORY MARKERS AND SEX DIFFERENCES", @@ -655844,6 +659268,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.03.21259953", + "rel_title": "High resolution linear epitope mapping of the receptor binding domain of SARS-CoV-2 spike protein in COVID-19 mRNA vaccine recipients.", + "rel_date": "2021-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.03.21259953", + "rel_abs": "The prompt rollout of the coronavirus disease (COVID-19) messenger RNA (mRNA) vaccine is facilitating population immunity, which shall become more dominant than natural infection-induced immunity. At the beginning of the vaccine era, understanding the epitope profiles of vaccine-elicited antibodies will be the first step in assessing functionality of vaccine-induced immunity. In this study, the high-resolution linear epitope profiles of Pfizer-BioNTech COVID-19 mRNA vaccine recipients and COVID-19 patients were delineated by using microarrays mapped with overlapping peptides of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. The vaccine-induced antibodies targeting RBD had broader distribution across the RBD than that induced by the natural infection. Thus, relatively lower neutralizability was observed when a half-maximal neutralization titer measured in vitro by live virus neutralization assays was normalized to a total anti-RBD IgG titer. However, mutation panel assays targeting the SARS-CoV-2 variants of concern have shown that the vaccine-induced epitope variety, rich in breadth, may grant resistance against future viral evolutionary escapes, serving as an advantage of vaccine-induced immunity.\n\nImportanceEstablishing vaccine-based population immunity has been the key factor in attaining herd protection. Thanks to expedited worldwide research efforts, the potency of messenger RNA vaccines against the coronavirus disease 2019 (COVID-19) is now incontestable. The next debate is regarding the coverage of SARS-CoV-2 variants. At the beginning of this vaccine era, it is of importance to describe the similarities and differences between the immune responses of COVID-19 vaccine recipients and naturally infected individuals. In this study, we demonstrated that the antibody profiles of vaccine recipients are richer in variety, targeting a key protein of the invading virus, than those of naturally infected individuals. Yet vaccine-elicited antibodies included more non-neutralizing antibodies than infection-elicited, their breadth in antibody variations suggested possible resilience against future SARS-CoV-2 variants. The antibody profile achieved by vaccinations in naive individuals pose important insight into the first step towards vaccine-based population immunity.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Yuko Nitahara", + "author_inst": "Osaka City University" + }, + { + "author_name": "Yu Nakagama", + "author_inst": "Osaka City University" + }, + { + "author_name": "Natsuko Kaku", + "author_inst": "Osaka City University" + }, + { + "author_name": "Katherine Candray", + "author_inst": "Osaka City University" + }, + { + "author_name": "Yu Michimuko", + "author_inst": "Osaka City University" + }, + { + "author_name": "Evariste Tshibangu-Kabamba", + "author_inst": "Osaka City University" + }, + { + "author_name": "Akira Kaneko", + "author_inst": "Osaka City University" + }, + { + "author_name": "Hiromasa Yamamoto", + "author_inst": "Osaka City University" + }, + { + "author_name": "Yasumitsu Mizobata", + "author_inst": "Osaka City University" + }, + { + "author_name": "Hiroshi Kakeya", + "author_inst": "Osaka City University" + }, + { + "author_name": "Mayo Yasugi", + "author_inst": "Osaka Prefecture University" + }, + { + "author_name": "Yasutoshi Kido", + "author_inst": "Osaka City University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.03.21254541", "rel_title": "Anticoagulants and Antiplatelets in COVID-19: Impact on Survival and Thromboembolism Development", @@ -656033,25 +659520,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "anesthesia" }, - { - "rel_doi": "10.1101/2021.07.03.21259973", - "rel_title": "Critical Role of the Subways in the Initial Spread of SARS-CoV-2 in New York City", - "rel_date": "2021-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.03.21259973", - "rel_abs": "We studied the possible role of the subways in the spread of SARS-CoV-2 in New York City during late February and March 2020. Data on cases and hospitalizations, along with phylogenetic analyses of viral isolates, demonstrate rapid community transmission throughout all five boroughs within days. The near collapse of subway ridership during the second week of March was followed within 1-2 weeks by the flattening of COVID-19 incidence curve. We observed persistently high entry into stations located along the subway line serving a principal hotspot of infection in Queens. We used smartphone tracking data to estimate the volume of subway visits originating from each zip code tabulation area (ZCTA). Across ZCTAs, the estimated volume of subway visits on March 16 was strongly predictive of subsequent COVID-19 incidence during April 1-8. In a spatial analysis, we distinguished between the conventional notion of geographic contiguity and a novel notion of contiguity along subway lines. We found that the March 16 subway-visit volume in subway-contiguous ZCTAs had an increasing effect on COVID-19 incidence during April 1-8 as we enlarged the radius of influence up to 5 connected subway stops. By contrast, the March 31 cumulative incidence of COVID-19 in geographically-contiguous ZCTAs had an increasing effect on subsequent COVID-19 incidence as we expanded the radius up to 3 connected ZCTAs. The combined evidence points to the initial citywide dissemination of SARS-CoV-2 via a subway-based network, followed by percolation of new infections within local hotspots.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Jeffrey E Harris", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.05.21259918", "rel_title": "Durable Humoral and Cellular Immune Responses Following Ad26.COV2.S Vaccination for COVID-19", @@ -657534,6 +661002,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.07.05.21260050", + "rel_title": "Progressive Increase in Virulence of Novel SARS-CoV-2 Variants in Ontario, Canada, February to June, 2021", + "rel_date": "2021-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21260050", + "rel_abs": "BackgroundThe period from February to June 2021 was one during which initial wild-type SARS-CoV-2 strains were supplanted in Ontario, Canada, first by variants of concern (VOC) with the N501Y mutation (Alpha/B1.1.17, Beta/B.1.351 and Gamma/P.1 variants), and then by the Delta/B.1.617 variant. The increased transmissibility of these VOCs has been documented but data for increased virulence is limited. We used Ontarios COVID-19 case data to evaluate the virulence of these VOCs compared to non-VOC SARS-CoV-2 infections, as measured by risk of hospitalization, intensive care unit (ICU) admission, and death.\n\nMethodsWe created a retrospective cohort of people in Ontario testing positive for SARS-CoV-2 and screened for VOCs, with dates of test report between February 7 and June 27, 2021 (n=212,332). We constructed mixed effects logistic regression models with hospitalization, ICU admission, and death as outcome variables. Models were adjusted for age, sex, time, vaccination status, comorbidities, and pregnancy status. Health units were included as random intercepts.\n\nResultsCompared to non-VOC SARS-CoV-2 strains, the adjusted elevation in risk associated with N501Y-positive variants was 52% (43-62%) for hospitalization; 89% (67-116%) for ICU admission; and 51% (30-74%) for death. Increases with Delta variant were more pronounced: 108% (80-138%) for hospitalization; 234% (164-331%) for ICU admission; and 132% (47-230%) for death.\n\nInterpretationThe progressive increase in transmissibility and virulence of SARS-CoV-2 VOCs will result in a significantly larger, and more deadly, pandemic than would have occurred in the absence of VOC emergence.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "David Fisman", + "author_inst": "University of Toronto" + }, + { + "author_name": "Ashleigh Tuite", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.06.21260055", "rel_title": "Critical timing for triggering public health interventions to prevent COVID-19 resurgence: a mathematical modelling study", @@ -657751,81 +661242,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.07.06.21260080", - "rel_title": "Untargeted saliva metabolomics reveals COVID-19 severity: Saliva Metabolomics for SARS-COV-2 Prognosis", - "rel_date": "2021-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21260080", - "rel_abs": "BackgroundThe COVID-19 pandemic is likely to represent an ongoing global health issue given the potential for vaccine escape and the low likelihood of eliminating all reservoirs of the disease. Whilst diagnostic testing has progressed at pace, there is an unmet clinical need to develop tests that are prognostic, to triage the high volumes of patients arriving in hospital settings. Recent research has shown that serum metabolomics has potential for prognosis of disease progression. 1 In a hospital setting, collection of saliva samples is more convenient for both staff and patients, and therefore offers an alternative sampling matrix to serum. We demonstrate here for the first time that saliva metabolomics can reveal COVID-19 severity.\n\nMethods88 saliva samples were collected from hospitalised patients with clinical suspicion of COVID-19, alongside clinical metadata. COVID-19 diagnosis was confirmed using RT-PCR testing. COVID severity was classified using clinical descriptors first proposed by SR Knight et al. Metabolites were extracted from saliva samples and analysed using liquid chromatography mass spectrometry.\n\nResultsIn this work, positive percent agreement of 1.00 between a PLS-DA metabolomics model and the clinical diagnosis of COVID severity was achieved. The negative percent agreement with the clinical severity diagnosis was also 1.00, for overall percent agreement of 1.00.\n\nConclusionsThis research demonstrates that liquid chromatography-mass spectrometry can identify salivary biomarkers capable of separating high severity COVID-19 patients from low severity COVID-19 patients in a small cohort study.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Cecile Frampas", - "author_inst": "University of Surrey" - }, - { - "author_name": "Katie Longman", - "author_inst": "University of Surrey" - }, - { - "author_name": "Matt P Spick", - "author_inst": "University of Surrey" - }, - { - "author_name": "Holly M Lewis", - "author_inst": "University of Surrey" - }, - { - "author_name": "Catia D Costa", - "author_inst": "University of Surrey" - }, - { - "author_name": "Alexander Stewart", - "author_inst": "University of Surrey" - }, - { - "author_name": "Deborah Dunn-Walters", - "author_inst": "University of Surrey" - }, - { - "author_name": "Debra Skene", - "author_inst": "University of Surrey" - }, - { - "author_name": "Danni Greener", - "author_inst": "Frimley Health NHS Trust" - }, - { - "author_name": "George E Evetts", - "author_inst": "Frimley Health NHS Trust" - }, - { - "author_name": "Drupad K Trivedi", - "author_inst": "University of Manchester" - }, - { - "author_name": "Perdita Barran", - "author_inst": "The University of Manchester" - }, - { - "author_name": "Andrew Pitt", - "author_inst": "University of Manchester" - }, - { - "author_name": "Katherine Hollywood", - "author_inst": "University of Manchester" - }, - { - "author_name": "Melanie Bailey", - "author_inst": "University of Surrey" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.06.21260038", "rel_title": "Prevalence of SARS-CoV-2 Antibodies from a one-year National Serosurveillance of Kenyan Blood Transfusion Donors", @@ -659628,6 +663044,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.05.21260021", + "rel_title": "Knowledge, attitude, and practice related to the COVID-19 pandemic among undergraduate medical students in Indonesia: a nationwide cross-sectional study", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21260021", + "rel_abs": "IntroductionThe potential role of medical students in raising awareness during public health emergencies has been acknowledged. To further explore their potentials as public educators and role models for the communities during the coronavirus disease 2019 (COVID-19) pandemic, a study is conducted to assess the knowledge, attitude, and practice of these students toward COVID-19.\n\nMethodsAn online cross-sectional survey was conducted among undergraduate medical students in Indonesia. Socio-demographical characteristics, social interaction history, information-seeking behavior, as well as knowledge, attitude, and practice toward COVID-19 were collected through a self-reported questionnaire. A p-value of <0.05 indicated statistical significance.\n\nResultsOut of 4870 respondents, 64.9% and 51.5% had positive attitude and practice toward COVID-19 while only 29.8% had adequate knowledge. Knowledge was slightly positively correlated with attitude and practice ({rho}=0.074 and {rho}=0.054, respectively; both p<0.001), while attitude was weakly correlated with practice ({rho}=0.234, p<0.001). Several factors including age, sex, place of residence, institution type, academic level, family income, history of chronic illness, prior volunteering experience, and perceptual awareness on COVID-19 were significantly associated with either knowledge, attitude, and/or practice toward COVID-19. Furthermore, health institutions and the governments press releases, as well as health expert opinions were deemed as the most reliable sources of COVID-19-related information - yet trivially none of these sources were associated with knowledge, attitude, and practice in the study population.\n\nConclusionMany undergraduate medical students in Indonesia had positive attitude and practice against COVID-19, yet only a few had adequate knowledge. This warrants further interventions to keep them updated with COVID-19 evidence to maximize their potentials in raising public awareness on COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Imam Adli", + "author_inst": "Facullty of Medicine Universitas Indonesia" + }, + { + "author_name": "Indah Suci Widyahening", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "Gilbert Lazarus", + "author_inst": "Faculty of Medicine, Universitas Indonesia" + }, + { + "author_name": "Jason Phowira", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "Lyanna Azzahra", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "Bagas Ariffandi", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "Aziz Muhammad Putera", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "David Nugraha", + "author_inst": "Faculty of Medicine Universitas Airlangga" + }, + { + "author_name": "Nico Gamalliel", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "Ardi Findyartini", + "author_inst": "Faculty of Medicine Universitas Indonesia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "medical education" + }, { "rel_doi": "10.1101/2021.07.04.21259985", "rel_title": "Covid-19 Vaccination in Pregnancy: A Systematic Review", @@ -659741,61 +663212,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.07.05.21260014", - "rel_title": "Mild SARS-CoV-2 infection modifies DNA methylation of peripheral blood mononuclear cells from COVID-19 convalescents", - "rel_date": "2021-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21260014", - "rel_abs": "BackgroundEpigenetic alterations upon microbial challenge have been described as both a defence strategy and a result of pathogenic manipulation. While most COVID-19 studies focus on inflammatory and immune-mediated responses, little is known about epigenetic modifications in response to SARS-CoV-2 infection.\n\nMethodsEpigenome-wide DNA methylation patterns from COVID-19 convalescents were compared to uninfected controls from before and after the pandemic. Peripheral blood mononuclear cell (PBMC) DNA was extracted from uninfected controls, COVID-19 convalescents and symptom-free individuals with SARS-CoV-2-specific T cell-responses, as well as from PBMCs stimulated in vitro with SARS-CoV-2. Subsequently, the Illumina MethylationEPIC 850K array was performed, and statistical/bioinformatic analyses comprised differential DNA methylation, pathway over-representation and module identification analyses.\n\nResultsDifferential DNA methylation patterns distinguished COVID-19 convalescents from uninfected controls, with similar results in an experimental SARS-CoV-2 infection model. A SARS-CoV-2-induced module was identified in vivo, comprising 66 genes of which six (TP53, INS, HSPA4, SP1, ESR1 and FAS) were present in corresponding in vitro analyses. Over-representation analyses revealed involvement in Wnt, muscarinic acetylcholine receptor signalling and gonadotropin-releasing hormone receptor pathways. Furthermore, numerous differentially methylated and network genes from both settings interacted with the SARS-CoV-2 interactome.\n\nConclusionsAltered DNA methylation patterns of COVID-19 convalescents suggest recovery from mild-to-moderate SARS-CoV-2 infection leaves longstanding epigenetic traces. As in vitro SARS-CoV-2 infection corroborated in vivo exposure results, this indicates DNA methylation is involved in immune cell responses to challenge with this virus. Future studies should determine whether this reflects host-induced protective antiviral defence or targeted viral hijacking to evade host defence.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Johanna Huoman", - "author_inst": "Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linkoeping University, Linkoeping, Sweden" - }, - { - "author_name": "Shumaila Sayyab", - "author_inst": "Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linkoeping University, Linkoeping, Sweden" - }, - { - "author_name": "Eirini Apostolou", - "author_inst": "Division of Cell Biology, Department of Biomedical and Clinical Sciences, Linkoeping University, Linkoeping, Sweden" - }, - { - "author_name": "Lovisa Karlsson", - "author_inst": "Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linkoeping University, Linkoeping, Sweden" - }, - { - "author_name": "Lucas Porcile", - "author_inst": "Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linkoeping University, Linkoeping, Sweden" - }, - { - "author_name": "Muhammad Rizwan", - "author_inst": "Division of Cell Biology, Department of Biomedical and Clinical Sciences, Linkoeping University, Linkoeping, Sweden" - }, - { - "author_name": "Sumit Sharma", - "author_inst": "Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linkoeping University, Linkoeping, Sweden" - }, - { - "author_name": "Jyotirmoy Das", - "author_inst": "Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linkoeping University, Linkoeping, Sweden" - }, - { - "author_name": "Anders Rosen", - "author_inst": "Division of Cell Biology, Department of Biomedical and Clinical Sciences, Linkoeping University, Linkoeping, Sweden" - }, - { - "author_name": "Maria Lerm", - "author_inst": "Division of Inflammation and Infection, Department of Biomedical and Clinical Sciences, Linkoeping University, Linkoeping, Sweden" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.04.21259979", "rel_title": "Death profiling of hospitalized patients with COVID-19: Experience from a specialized hospital in Bangladesh", @@ -661262,6 +664678,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.06.21259749", + "rel_title": "Application of nasal spray containing dimethyl sulfoxide (DSMO) and ethanol during the COVID-19 pandemic may protect healthcare workers: A randomized controlled trials", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21259749", + "rel_abs": "BackgroundCoronavirus pandemic has affected a large population worldwide. Currently, the standard care for individuals who are exposed is supportive care, symptomatic management, and isolation. The aim of our study was to evaluate effects of combined use of ethanol and DMSO as a nasal spray in preventing COVID-19.\n\nMethodsWe conducted a randomized controlled trial on volunteer healthcare workers of medical centers that were at the forefront of the fight against COVID-19 in Shahroud, Iran. Two hundred and thirty-two participants were randomly assigned to intervention and control groups to receive DMSO/ethanol or routine care, respectively. The subjects were followed for 4 weeks to determine the incidence of COVID-19 infection in each group based on the RT-qPCR test. Finally, absolute risk difference and relative risk were calculated to evaluate the effect of DMSO in prevent COVID-19.\n\nResultsThe results showed that the incidence of COVID-19 in the control group and intervention group were 0.07 and 0.008, respectively. The relative risk (RR) was 0.12 (0.9-0.02) according to the incidence rate in the two groups.\n\nConclusioncombined application of DMSO and ethanol in healthcare providers can considerably prevent COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Ali Hosseinzadeh", + "author_inst": "Shahroud University of medical sciences" + }, + { + "author_name": "Abbas Tavakkolian", + "author_inst": "Islamic Azad University, Shahroud Branch, Shahroud, Iran." + }, + { + "author_name": "Vahid Kia", + "author_inst": "Shahroud University of Medical Sciences" + }, + { + "author_name": "Hossein Ebrahimi", + "author_inst": "Shahroud University School of Medical Sciences" + }, + { + "author_name": "Hossein Sheibani", + "author_inst": "Shahroud University School of Medical Sciences" + }, + { + "author_name": "Ehsan Binesh", + "author_inst": "Shahroud University School of Medical Sciences" + }, + { + "author_name": "Reza Jafari", + "author_inst": "Shahroud University of Medical Sciences" + }, + { + "author_name": "Seyed Mohammad Mirrezaie", + "author_inst": "Shahroud University School of Medical Sciences" + }, + { + "author_name": "Moslem Jafarisani", + "author_inst": "Shahroud University of medical Sciences" + }, + { + "author_name": "Mohammad Hassan Emamian", + "author_inst": "Shahroud University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.05.451222", "rel_title": "Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques", @@ -661563,49 +665034,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.07.02.21259929", - "rel_title": "Analysis of Feature Influence on Covid-19 Death Rate Per Country Using a Novel Orthogonalization Technique", - "rel_date": "2021-07-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.02.21259929", - "rel_abs": "We have developed a new technique of Feature Importance, a topic of machine learning, to analyze the possible causes of the Covid-19 pandemic based on country data. This new approach works well even when there are many more features than countries and is not affected by high correlation of features. It is inspired by the Gram-Schmidt orthogonalization procedure from linear algebra. We study the number of deaths, which is more reliable than the number of cases at the onset of the pandemic, during Apr/May 2020. This is while countries started taking measures, so more light will be shed on the root causes of the pandemic rather than on its handling.\n\nThe analysis is done against a comprehensive list of roughly 3,200 features. We find that globalization is the main contributing cause, followed by calcium intake, economic factors, environmental factors, preventative measures, and others. This analysis was done for 20 different dates and shows that some factors, like calcium, phase in or out over time. We also compute row explainability, i.e. for every country, how much each feature explains the death rate. Finally we also study a series of conditions, e.g. comorbidities, immunization, etc. which have been proposed to explain the pandemic and place them in their proper context. While there are many caveats to this analysis, we believe it sheds light on the possible causes of the Covid-19 pandemic.\n\nOne-Sentence SummaryWe use a novel feature importance technique to find that globalization, followed by calcium intake, economic factors, environmental factors, and some aspects of societal quality are the main country-level data that explain early Covid-19 death rates.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Gaston Gonnet", - "author_inst": "ETH Zurich" - }, - { - "author_name": "John Stewart", - "author_inst": "Polyalgorithm Machine Learning" - }, - { - "author_name": "Joseph Lafleur", - "author_inst": "Polyalgorithm Machine Learning" - }, - { - "author_name": "Stephen Keith", - "author_inst": "Polyalgorith Machine Learning" - }, - { - "author_name": "Mark McLellan", - "author_inst": "Rowbot.io" - }, - { - "author_name": "David Jiang-Gorsline", - "author_inst": "Polyalgorithm Machine Learning" - }, - { - "author_name": "Tim Snider", - "author_inst": "Polyalgorithm Machine Learning" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.06.30.21259782", "rel_title": "Will Vaccine-derived Protective Immunity Curtail COVID-19 Variants in the US?", @@ -662908,6 +666336,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.03.21259959", + "rel_title": "Efficacy and safety of cyclosporine in the management of coronavirus disease 2019: A protocol for systematic review and meta-analysis", + "rel_date": "2021-07-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.03.21259959", + "rel_abs": "IntroductionCyclosporine may improve the clinical course and outcomes of Coronavirus disease 2019 (COVID-19) due to its antiviral and anti-cytokine effects as shown in vitro. A few ongoing trials are exploring the benefit of adding it to the standard of care (SOC) of COVID-19 patients.\n\nObjectivesThe primary objective is to evaluate the severity of COVID-19, determined by oxygen saturation, intensive care unit (ICU) admission, or the World Health Organization COVID-19 clinical severity scale in patients treated with oral or intravenous cyclosporine added to SOC compared SOC alone or placebo. Secondary objectives include mortality, length of hospitalization, length of ICU stay, and laboratory measurements as well as the safety outcomes of cyclosporine.\n\nMethodologyA systematic review and meta-analysis of randomized clinical trials and observational studies that compared cyclosporine to placebo or SOC in COVID-19 patients will be conducted. PubMed, EMBASE, Web of Science, Cochrane Central Register of Controlled Trials, Google Scholar, and ClinicalTrials.gov will be explored for studies that satisfy pre-specified inclusion criteria. Quality assessment of all included studies will be performed. Meta-analyses will be done utilizing random effect models to estimate the effect of cyclosporine on the severity of COVID-19. Heterogeneity will be assessed utilizing Q statistics. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines will be followed.\n\nResultsThe result of this synthesis will inform potential changes in the management of COVID-19 patients, especially regarding the role of calcineurin inhibitors. Additionally, it will serve as hypothesis generating for potential future prospective studies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ibtihal Abdallah", + "author_inst": "Clinical Pharmacy Department, Hamad General Hospital, Hamad Medical Corporation" + }, + { + "author_name": "Mohamed Aabdien", + "author_inst": "Community Medicine Training Program, Medical Education, Hamad Medical Corporation" + }, + { + "author_name": "Mohammed Danjuma", + "author_inst": "Division of General Internal Medicine, Weill Cornell affliated-Hamad General Hospital, Hamad Medical Corporation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.02.21259665", "rel_title": "Assessment and Modeling of COVID-19 Outcomes in a Longitudinal Cohort of Hospitalized Adults", @@ -663113,113 +666568,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.06.30.21259761", - "rel_title": "Post-vaccination SARS-COV-2 among healthcare workers in New Jersey: a genomic epidemiological study", - "rel_date": "2021-07-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.30.21259761", - "rel_abs": "Emergence of SARS-CoV-2 with high transmission and immune evasion potential, the so-called Variants of Concern (VOC), is a major concern. We describe the early genomic epidemiology of SARS-CoV-2 recovered from vaccinated healthcare professionals (HCP). Our post-vaccination COVID-19 symptoms-based surveillance program among HCPs in a 17-hospital network, identified all vaccinated HCP who tested positive for COVID-19 after routine screening or after self-reporting. From 01/01/2021 to 04/30/2021, 23,687 HCP received either mRNA-1273 or BNT162b2 mRNA vaccine. All available post-vaccination SARS-CoV-2 samples and a random collection from non-vaccinated patients during the similar timeframe were subjected to VOC screening and whole genome sequencing (WGS). 62% (23,697/37,500) of HCPs received at least one vaccine dose, with 95% (22,458) fully vaccinated. We detected 138 (0.58%, 138/23,697) COVID-19 cases, 105 among partially vaccinated and 33 (0.15%, 33/22,458) among fully vaccinated. Five partially vaccinated required hospitalization, four with supplemental oxygen. VOC screening from 16 fully vaccinated HCPs identified 6 (38%) harboring N501Y and 1 (6%) with E484K polymorphisms; concurrent non-vaccinated samples was 37% (523/1404) and 20% (284/1394), respectively. There was an upward trend from January to April for E484K/Q (3% to 26%) and N501Y (1% to 49%). WGS analysis from vaccinated and non-vaccinated individuals indicated highly congruent phylogenies. We did not detect an increased frequency of any RBD/NTD polymorphism between groups (P>0.05). Our results support robust protection by vaccination, particularly among recipients of both doses. Despite VOCs accounting for over 40% of SARS-CoV-2 from fully vaccinated individuals, the genomic diversity appears to proportionally represent those among non-vaccinated populations.\n\nIMPORTANCEA number of highly effective vaccines have been developed and deployed to combat the COVID-19 pandemic. The emergence and epidemiological dominance of SARS-CoV-2 mutants, with high transmission potential and immune evasion properties, the so-called Variants of Concern (VOC), continues to be a major concern. Whether these VOCs alter the efficacy of the administered vaccines is of great concern, and a critical question to study. We describe the initial genomic epidemiology of SARS-CoV-2 recovered from vaccinated healthcare professionals and probe specifically for VOC enrichment. Our findings support the high-level of protection provided by full vaccination despite a steep increase in the prevalence of polymorphisms associated with increased transmission potential (N501Y) and immune evasion (E484K) in the non-vaccinated population. Thus, we do not find evidence of VOC enrichment among vaccinated groups. Overall, the genomic diversity of SARS-CoV-2 recovered post-vaccination appears to proportionally represent the observed viral diversity within the community.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Barun Mathema", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Liang Chen", - "author_inst": "Hackensack Meridian Health Center for Discovery and Innovation" - }, - { - "author_name": "Kar Fai Chow", - "author_inst": "Hackensack Meridian Health Biorepository" - }, - { - "author_name": "Yanan Zhao", - "author_inst": "CDI, hackensack meridian health" - }, - { - "author_name": "Michael C Zody", - "author_inst": "New York Genome Center" - }, - { - "author_name": "Jose R Mediavilla", - "author_inst": "Hackensack Meridian Health Center for Discovery and Innovation" - }, - { - "author_name": "Marcus H Cunningham", - "author_inst": "Hackensack Meridian Health Center for Discovery and Innovation" - }, - { - "author_name": "Kaelea Composto", - "author_inst": "Hackensack Meridian Health Center for Discovery and Innovation" - }, - { - "author_name": "Annie Lee", - "author_inst": "Hackensack Meridian Health Center for Discovery and Innovation" - }, - { - "author_name": "Dayna M Oschwald", - "author_inst": "New York Genome Center" - }, - { - "author_name": "Soren Germer", - "author_inst": "New York Genome Center" - }, - { - "author_name": "Samantha Fennessey", - "author_inst": "New York Genome Center" - }, - { - "author_name": "Kishan Patel", - "author_inst": "Hackensack Meridian Health Biorepository" - }, - { - "author_name": "David Wilson", - "author_inst": "Hackensack Meridian Health BI Analytics" - }, - { - "author_name": "Ann Cassell", - "author_inst": "Hackensack Meridian Health BI Analytics" - }, - { - "author_name": "Lauren Pascual", - "author_inst": "John Theurer Cancer Center" - }, - { - "author_name": "Andrew Ip", - "author_inst": "John Theurer Cancer Center" - }, - { - "author_name": "Andre Corvelo", - "author_inst": "New York Genome Center" - }, - { - "author_name": "Sophia Dar", - "author_inst": "Hackensack Meridian Health Biorepository" - }, - { - "author_name": "Yael Kramer", - "author_inst": "Hackensack Meridian Health Biorepository" - }, - { - "author_name": "Tom Maniatis", - "author_inst": "5.\tNew York Genome Center" - }, - { - "author_name": "David S Perlin", - "author_inst": "Hackensack Meridian Health Center for Discovery and Innovation" - }, - { - "author_name": "Barry N Kreiswirth", - "author_inst": "Center for Discovery and Innovation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.05.21260003", "rel_title": "Soft drinks can be misused to give false false positive SARS-CoV-2 lateral flow device results", @@ -664638,6 +667986,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.29.21259605", + "rel_title": "The SARS-CoV-2 receptor-binding domain expressed in Pichia pastoris as a candidate vaccine antigen", + "rel_date": "2021-07-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.29.21259605", + "rel_abs": "1.The effort to develop vaccines based on economically accessible technological platforms available by developing countries vaccine manufacturers is essential to extend the immunization to the whole world population and to achieve the desired herd immunity, necessary to end the COVID-19 pandemic. Here we report on the development of a SARS-CoV-2 receptor-binding domain (RBD) protein, expressed in yeast Pichia pastoris. The RBD was modified with addition of flexible N- and C-terminal amino acid extensions aimed to modulate the protein/protein interactions and facilitate protein purification. Fermentation with yeast extract culture medium yielded 30-40 mg/L. After purification by immobilized metal ion affinity chromatography and hydrophobic interaction chromatography, the RBD protein was characterized by mass-spectrometry, circular dichroism, and binding affinity to angiotensin-converting enzyme 2 (ACE2) receptor. The recombinant protein shows high antigenicity with convalescent human sera and also with sera from individuals vaccinated with the Pfizer-BioNTech mRNA or Sputnik V adenoviral-based vaccines. The RBD protein stimulates IFN{gamma}, IL-2, IL-6, IL-4, and TNF in mice secreting splenocytes from PBMC and lung CD3+ enriched cells. Immunogenicity studies with 50 {micro}g of the recombinant RBD formulated with alum, induce high levels of binding antibodies in mice and non-human primates, assessed by ELISA plates covered with RBD protein expressed in HEK293T cells. The mouse sera inhibited the RBD binding to ACE2 receptor in an in-vitro test and show neutralization of SARS-CoV-2 infection of Vero E6 cells. These data suggest that the RBD recombinant protein expressed in yeast P. pastoris is suitable as a vaccine candidate against COVID-19.\n\nHighlightsO_LIThe RBD protein (C-RBD-H6 PP) is expressed with high purity in P. pastoris.\nC_LIO_LIPhysico-chemical characterization confirms the right folding of the protein.\nC_LIO_LIThe recombinant protein shows high antigenicity with sera from convalescents.\nC_LIO_LIThe sera from animals inhibit the RBD-ACE2 binding and neutralize the virus.\nC_LIO_LIThe C-RBD-H6 protein stimulates IFN{gamma}, IL-2, IL-6, IL-4, and TNF in mice.\nC_LI", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Miladys Limonta-Fernandez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba" + }, + { + "author_name": "Glay Chinea-Santiago", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Alejandro Miguel Martin-Dunn", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Diamile Gonzalez-Roche", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Monica Bequet-Romero", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Gabriel Marquez-Perera", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Isabel Gonzalez-Moya", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Camila Canaan-Haden-Ayala", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Ania Cabrales-Rico", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Luis Ariel Espinosa-Rodriguez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Yassel Ramos-Gomez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Ivan Andujar-Martinez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Luis Javier Gonzalez-Lopez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Mariela Perez de la Iglesia", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Jesus Zamora-Sanchez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Otto Cruz-Sui", + "author_inst": "Civilian Defense Scientific Research Center, Carretera de Jamaica y Autopista Nacional, San Jose de las Lajas, Mayabeque, Cuba" + }, + { + "author_name": "Gilda Lemos-Perez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Gleysin Cabrera-Herrera", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Jorge Valdes-Hernandez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Eduardo Martinez-Diaz", + "author_inst": "Biotechnology and Pharmaceutical Industries Group, BioCubaFarma, Ave. Independencia 8126, esq. a Calle 100. Boyeros. La Habana, Cuba." + }, + { + "author_name": "Eulogio Pimentel-Vazquez", + "author_inst": "Biotechnology and Pharmaceutical Industries Group, BioCubaFarma, Ave. Independencia 8126, esq. a Calle 100. Boyeros. La Habana, Cuba." + }, + { + "author_name": "Marta Ayala-Avila", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Gerardo Guillen-Nieto", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.28.21259452", "rel_title": "Persistent symptoms following SARS-CoV-2 infection in a random community sample of 508,707 people", @@ -664819,45 +668274,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.28.21259657", - "rel_title": "PERFORMANCE AND UTILITY OF AN ORAL FLUID-BASED RAPID POINT-OF-CARE TEST FOR SARS-COV-2 ANTIBODY RESPONSE FOLLOWING COVID-19 INFECTION OR VACCINATION", - "rel_date": "2021-07-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259657", - "rel_abs": "Analysis of anti-SARS-CoV-2 antibodies can identify recent-onset or prior COVID-19 infection or vaccine-induced humoral immunity. We have developed a rapid point-of-care test for IgG, M, or A-class immunoglobulins that recognize the S1 domain of the SARS-CoV-2 spike protein (CovAb). The test employs a lateral-flow strip design with a recombinant SARS-CoV-2 spike protein S1 domain capture antigen to detect anti-SARS-CoV-2 antibodies in oral fluid samples. Oral fluid samples are collected with a swab that captures the gingival crevicular fluid component of oral fluid that represents a plasma transudate and that is the primary source of oral fluid monomeric antibodies. The sensitivity of the CovAb test is 97.29% and the specificity is 98.13%, and the results obtained are similar to those obtained using matched fingerstick whole blood samples and in an EUA-approved commercial serology test. Oral fluid SARS-CoV-2 antibodies could be detected in subjects more than 7 months post-symptom onset. We also demonstrate the utility of the CovAb test in characterizing adaptive immune responses to vaccination in COVID-19-naive and exposed populations after first and second vaccine doses and show that significant heterogeneity in magnitude of antibody titers achieved is seen after both doses and that prior COVID-19 exposure increases the adaptive immune response to vaccination.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Paturi V Rao", - "author_inst": "Diabetomics, Inc." - }, - { - "author_name": "Dhanalakshmi Nair-Schaef", - "author_inst": "Diabetomics, Inc." - }, - { - "author_name": "Siting Chen", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Steven C Kazmierczak", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Charles T Roberts Jr.", - "author_inst": "Diabetomics, Inc." - }, - { - "author_name": "Srinivasa R Nagalla", - "author_inst": "Diabetomics.com" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.28.21259398", "rel_title": "RT-LAMP has high accuracy for detecting SARS-CoV-2 in saliva and naso/oropharyngeal swabs from asymptomatic and symptomatic individuals", @@ -666684,6 +670100,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.28.21259384", + "rel_title": "Comparison of Mental Health Symptom Changes from pre-COVID-19 to COVID-19 by Sex or Gender: A Systematic Review and Meta-analysis", + "rel_date": "2021-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259384", + "rel_abs": "ImportanceWomen and gender-diverse individuals have faced disproportionate socioeconomic burden during COVID-19. There have been reports that this has translated into greater negative changes in mental health, but this has been based on cross-sectional research that has not accounted for pre-COVID-19 differences.\n\nObjectiveTo compare mental health symptom changes since pre-COVID-19 by sex or gender.\n\nData SourcesMEDLINE, PsycINFO, CINAHL, EMBASE, Web of Science, China National Knowledge Infrastructure, Wanfang, medRxiv, and Open Science Framework (December 31, 2019 to August 30, 2021).\n\nStudy SelectionEligible studies compared mental health symptom changes from pre-COVID-19 to COVID-19 by sex or gender.\n\nData Extraction and SynthesisData was extracted by a single reviewer with validation by a second reviewer. Adequacy of study methods and reporting was assessed using an adapted version of the Joanna Briggs Institute Checklist for Prevalence Studies. A restricted maximum-likelihood random-effects meta-analyses was conducted.\n\nMain Outcomes and MeasuresAnxiety symptoms, depression symptoms, general mental health, and stress measured continuously or dichotomously.\n\nResults12 studies (10 unique cohorts) were included. All compared females or women to males or men; none included gender-diverse individuals. Continuous symptom change differences were not statistically significant for depression (standardized mean difference [SMD]= 0.12, 95% CI -0.09 to 0.33; 4 studies, 4,475 participants; I2=69.0%) and stress (SMD= - 0.10, 95% CI -0.21 to 0.01; 4 studies, 1,533 participants; I2=0.0%), but anxiety (SMD= 0.15, 95% CI 0.07 to 0.22; 4 studies, 4,344 participants; I2=3.0%) and general mental health (SMD= 0.15, 95% CI 0.12 to 0.18; 3 studies, 15,692 participants; I2=0.0%) worsened more among females or women than males or men during COVID-19. There were no significant differences in changes in proportion above a cut-off: anxiety (difference= -0.05, 95% CI -0.20 to 0.11; 1 study, 217 participants), depression (difference= 0.12, 95% CI -0.03 to 0.28; 1 study, 217 participants), general mental health (difference= -0.03, 95% CI -0.09 to 0.04; 3 studies, 18,985 participants; I2=94.0%), stress (difference= 0.04, 95% CI -0.10 to 0.17; 1 study, 217 participants).\n\nConclusion and RelevanceMental health outcomes did not differ or were worse by amounts below thresholds for clinical significance for women compared to men.\n\nRegistrationPROSPERO (CRD42020179703).\n\nKEY MESSAGESO_ST_ABSQuestionC_ST_ABSDid mental health symptoms worsen more for females or women than males or men in COVID-19?\n\nFindingsWe reviewed almost 65,000 citations and identified 12 studies that provided data to directly compare mental health symptom changes from pre-COVID-19 to during COVID-19 for females or women versus males or men. Statistically significant, but small, sex- or gender-based differences were found in 2 of 8 mental health outcomes.\n\nMeaningMental health changes among females or women were not significantly different from males or men for most outcomes, and differences that were identified were small and less than minimally important difference thresholds.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Tiffany Dal Santo", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Ying Sun", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Yin Wu", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Chen He", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Yutong Wang", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Xiaowen Jiang", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Kexin Li", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Olivia Bonardi", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Ankur Krishnan", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Jill T. Boruff", + "author_inst": "Schulich Library of Physical Sciences, Life Sciences, and Engineering, McGill University" + }, + { + "author_name": "Danielle B. Rice", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Sarah Markham", + "author_inst": "Department of Biostatistics and Health Informatics, King's College London" + }, + { + "author_name": "Brooke Levis", + "author_inst": "Centre for Prognosis Research, School of Medicine, Keele University" + }, + { + "author_name": "Marleine Azar", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Dipika Neupane", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Amina Tasleem", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Anneke Yao", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Ian Thombs-Vite", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Branka Agic", + "author_inst": "Centre for Addiction and Mental Health" + }, + { + "author_name": "Christine Fahim", + "author_inst": "Li Ka Shing Knowledge Institute, Unity Health Toronto" + }, + { + "author_name": "Michael S. Martin", + "author_inst": "School of Epidemiology and Public Health, University of Ottawa" + }, + { + "author_name": "Sanjeev Sockalingam", + "author_inst": "Centre for Addiction and Mental Health" + }, + { + "author_name": "Gustavo Turecki", + "author_inst": "Department of Psychology, McGill University" + }, + { + "author_name": "Andrea Benedetti", + "author_inst": "Department of Epidemiology, Biostatistics and Occupational Health, McGill University" + }, + { + "author_name": "Brett B Thombs", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.06.27.21259131", "rel_title": "Face mask use and associated factors among students in rural Eastern Uganda amidst the COVID-19 pandemic", @@ -666857,49 +670388,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.06.29.21255526", - "rel_title": "Transmissibility of COVID-19 among Vaccinated Individuals: A Rapid Literature Review", - "rel_date": "2021-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.29.21255526", - "rel_abs": "ObjectivesThis is an update of a previous report that examined literature published up to March 11th, 2021. Sixteen additional studies have been included in this update. The objective of this report is to identify comparative observational studies and randomized controlled trials (RCTs) evaluating the efficacy and effectiveness of COVID-19 vaccination in reducing forward transmission from vaccinated people, and studies examining the biological plausibility of vaccination-induced transmission reduction.\n\nMethodA search of databases, MEDLINE, Embase, L-OVE and the Cochrane Central Register of Controlled Trials was conducted to identify RCTs or comparative observational studies evaluating the efficacy and effectiveness of COVID-19 vaccination in the prevention of transmission, asymptomatic infections and transmissibility of COVID-19 among vaccinated persons. An additional search of grey literature was conducted. This search is current to May 4th, 2021.\n\nResultsIn this update, 16 additional studies, including 9 human and 7 animal studies, were included. Therefore, this review examines a total of 33 included studies: 21 human studies and 12 preclinical animal studies. Evidence from two large household surveillance studies from the UK suggests that a single or full dose of AstraZeneca (AZ) and Pfizer-BioNtech (PfBnT) vaccines may prevent household transmission of COVID-19 after 14 days of vaccination by up to 54%. The AZ vaccine trials in the general population suggest that an initial low dose followed by a standard dose may provide up to 59% protection against asymptomatic or unknown infection, although efficacy against these outcomes was not demonstrated following two standard doses. PfBnT vaccine observational studies in the general population suggest up to 90% effectiveness against asymptomatic infection after seven or more days of full dose vaccination. Up to 75% effectiveness against asymptomatic infection was reported after full- dose in healthcare workers. Across RCTs examining asymptomatic infection in the general population, one dose of Moderna was shown to provide an efficacy of 61.4% against asymptomatic infection 21 days after the first dose; in another trial, the J&J vaccine had an efficacy of 74% 28 days after the first dose. Lastly, seven of eight studies found significantly increased cycle threshold, suggestive of lower viral load, in PfBnT or AZ vaccinated individuals compared with those who were unvaccinated.\n\nConclusionThe AZ and PfBnT vaccines may prevent household transmission of COVID-19 after 14 days of vaccination. More studies have found the vaccines to significantly reduce the risk of asymptomatic infection and significantly increase cycle threshold, suggestive of lower viral load. Further research is needed to evaluate post-vaccination infectivity and transmission of both the wild type COVID-19 virus and the variants of concern from other jurisdictions.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Oluwaseun Egunsola", - "author_inst": "University of Calgary, Health Technology Assessment Unit" - }, - { - "author_name": "Liza Mastikhina", - "author_inst": "University of Calgary, Health Technology Assessment Unit" - }, - { - "author_name": "Laura Dowsett", - "author_inst": "University of Calgary, Health Technology Assessment Unit" - }, - { - "author_name": "Brenlea Farkas", - "author_inst": "University of Calgary, Health Technology Assessment Unit" - }, - { - "author_name": "Mark Hofmeister", - "author_inst": "University of Calgary, Health Technology Assessment Unit" - }, - { - "author_name": "Lynora Saxinger", - "author_inst": "University of Alberta, Division of Infectious Diseases" - }, - { - "author_name": "Fiona Clement", - "author_inst": "University of Calgary, Health Technology Assessment Unit" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.28.21259338", "rel_title": "Evolution of Anti-SARS-CoV-2 IgG Antibody and IgG Avidity Post Pfizer and Moderna mRNA Vaccinations", @@ -668882,6 +672370,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.28.21259628", + "rel_title": "Rotation-based schedules in elementary schools to prevent COVID-19 spread: A simulation study", + "rel_date": "2021-07-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259628", + "rel_abs": "BackgroundRotations of schoolchildren on a weekly basis is one of the nonpharmaceutical interventions often considered in the covid-19 pandemic. This study aims to investigate the impact of different types of rotations in various testing contexts.\n\nMethodsWe built an agent-based model of interactions among pupils and teachers based on an online survey in an elementary school in Prague, Czechia. This model contains 624 schoolchildren and 55 teachers (679 nodes) and about 27 thousands social contacts (edges) in 10 layers. The layers reflect different types of contacts (in classroom, cafeteria etc.) as described in the survey. On this multi-graph structure we run a modified SEIR model of the covid-19 dynamics. The parameters of the model are calibrated on data from the outbreak in the Czech Republic in the period March to June 2020.\n\nFindingsThere are three main findings in our paper.\n\nO_LIWeekly rotations of in-class and distance learning reduce the spread of covid-19 by 75-81% and thus represent an effective preventative measure in school setting.\nC_LIO_LIRegular antigen testing twice a week, or weekly PCR testing, significantly reduces infections even when using tests with a lower sensitivity: tests with a 40% sensitivity reduce infections by more than 50 percent.\nC_LIO_LIThe density of revealed contact graphs for older pupils is 1.5 times higher than the younger pupils graph, the teachers network is yet an order of magnitude denser. Consequently, the infection transmission between teachers is highly overproportional in our school. Moreover, teachers act as bridges connecting clusters of classes, especially in the secondary grade where they are responsible for 14-18% of infections, in comparison to 8-11% in primary grade.\nC_LI\n\nInterpretationWeekly rotations with regular testing are a highly effective non-pharmaceutical intervention for the prevention of covid-19 spread in schools and a way to keep schools open during an epidemic or to reopen them as the epidemiological situation improves.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Cyril Brom", + "author_inst": "Faculty of Mathematics and Physics, Charles University" + }, + { + "author_name": "Tomas Diviak", + "author_inst": "School of Social Sciences, University of Manchester" + }, + { + "author_name": "Jakub Drbohlav", + "author_inst": "Ministry of Education, Youth and Sports of the Czech Republic" + }, + { + "author_name": "Vaclav Korbel", + "author_inst": "CERGE-EI" + }, + { + "author_name": "Rene Levinsky", + "author_inst": "CERGE-EI" + }, + { + "author_name": "Roman Neruda", + "author_inst": "The Czech Academy of Sciences, Institute of Computer Science" + }, + { + "author_name": "Gabriela Suchoparova", + "author_inst": "The Czech Academy of Sciences, Institute of Computer Science" + }, + { + "author_name": "Josef Slerka", + "author_inst": "Faculty of Arts, Charles University" + }, + { + "author_name": "Martin Smid", + "author_inst": "The Czech Academy of Sciences, Institute of Information Theory and Automation" + }, + { + "author_name": "Jan Trnka", + "author_inst": "Third Faculty of Medicine, Charles University" + }, + { + "author_name": "Petra Vidnerova", + "author_inst": "The Czech Academy of Sciences, Institute of Computer Science" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.28.21259620", "rel_title": "The Evolution of Young People's Mental Health during COVID-19: Evidence from four Low-and-Middle-Income-Countries", @@ -669099,29 +672646,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.06.28.21259631", - "rel_title": "Correlation between the environmental parameters with outbreak pattern of COVID-19: A district level investigation based on yearlong period in India", - "rel_date": "2021-07-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259631", - "rel_abs": "The present study has investigated the role of regional meteorology and air quality parameters in the outbreak pattern of COVID-19 pandemic in India. Using the remote sensing based dataset of 12 environmental variables we correlated infective case counts at a district level in India. Our investigation carried out on the circumstantial data from more than 300 major affected districts in India and found that air quality parameters are playing very crucial role in this outbreak. Among the air pollutants, O3 was better correlating with infection counts followed by AOD, CO, NO2, BC and SO2. We also observed that among the weather parameters air temperature, incoming shortwave radiation, wind speed are positively and significantly associate with outbreak pattern and precipitation and humidity are negatively correlated with confirmed cases; only cloud cover has no significant relation. We noted that coastal districts in the both coast of India and districts located in the plain and low-lying areas have experienced bitter situation during this pandemic. Our study suggests that improving air quality with proper strict regulations and complete lockdown during the peak of pandemic could reduce the misfortune in all over India.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Amitesh Gupta", - "author_inst": "Indian Institution of Remote Sensing" - }, - { - "author_name": "Labani Saha", - "author_inst": "Savitribai Phule Pune University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.01.450707", "rel_title": "Ad26.COV2.S elicited neutralizing activity against Delta and other SARS-CoV-2 variants of concern", @@ -670592,6 +674116,81 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2021.06.30.450617", + "rel_title": "Detection of potential new SARS-CoV-2 Gamma-related lineage in Tocantins shows the spread and ongoing evolution of P.1 in Brazil", + "rel_date": "2021-06-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.30.450617", + "rel_abs": "After more than a year of the pandemic situation of COVID-19, the United Kingdom (UK), South Africa, and Brazil became the epicenter of new lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Variants of Concern (VOCs) were identified through a continuous genomic surveillance global effort, the B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and P.1 (Gamma) harboring a constellation set of mutations. This research aims to: (i) report the predominance of the Gamma (P.1) lineage presenting the epidemiological situation of the SARS-CoV-2 genomic surveillance at the state of Tocantins, and (ii) describe the emergence of possible new mutations and viral variants with the potential new lineage (P1-related) represented by 8 genomes from the Tocantins harboring the mutation L106F in ORF3a. At the moment, 6,687 SARS-CoV-2 genomes from GISAID carry this mutation. The whole-genome sequencing has an important role in understanding the evolution and genomic diversity of SARS-CoV-2, thus, the continuous monitoring will help in the control measures and restrictions imposed by the secretary of health of the state to prevent the spread of variants.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Ueric Jose Borges de Souza", + "author_inst": "Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi, Tocantins, 77410-570, Brazil." + }, + { + "author_name": "Raissa Nunes dos Santos", + "author_inst": "Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi, Tocantins, 77410-570, Brazil." + }, + { + "author_name": "Fernando Lucas Melo", + "author_inst": "Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Distrito Federal, 70910-900, Brazil." + }, + { + "author_name": "Aline Belmok", + "author_inst": "Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Distrito Federal, 70910-900, Brazil." + }, + { + "author_name": "Jucimaria Dantas Galvao", + "author_inst": "Central Public Health Laboratory of the State of Tocantins, Palmas, Tocantins, 77054-970, Brazil" + }, + { + "author_name": "Sirlene Borges Damasceno", + "author_inst": "Central Public Health Laboratory of the State of Tocantins, Palmas, Tocantins, 77054-970, Brazil" + }, + { + "author_name": "Tereza Cristina Vieira de Rezende", + "author_inst": "Central Public Health Laboratory of the State of Tocantins, Palmas, Tocantins, 77054-970, Brazil" + }, + { + "author_name": "Miguel de Souza Andrade", + "author_inst": "Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Distrito Federal, 70910-900, Brazil" + }, + { + "author_name": "Bergmann Morais Ribeiro", + "author_inst": "Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Distrito Federal, 70910-900, Brazil" + }, + { + "author_name": "Jose Carlos Ribeiro Junior", + "author_inst": "Postgraduate Program in Animal Health and Public Health in the Tropics, Federal University of Tocantins, Araguaina, Tocantins, 77804-970, Brazil" + }, + { + "author_name": "Rogerio Fernandes Carvalho", + "author_inst": "Postgraduate Program in Animal Health and Public Health in the Tropics, Federal University of Tocantins, Araguaina, Tocantins, 77804-970, Brazil" + }, + { + "author_name": "Monike da Silva Oliveira", + "author_inst": "Postgraduate Program in Tropical Medicine and Public Health, Federal University of Goias, Goiania, Goias, 74690-900, Brazil." + }, + { + "author_name": "Isac Gabriel Cunha dos Santos", + "author_inst": "Postgraduate Program in Animal Health and Public Health in the Tropics, Federal University of Tocantins, Araguaina, Tocantins, 77804-970, Brazil" + }, + { + "author_name": "Fernando Rosado Spilki", + "author_inst": "One Health Laboratory, Feevale Techpark, Feevale University, Campo Bom, Rio Grande do Sul, 93700-000, Brazil and Molecular Microbiology Laboratory, Feevale Univ" + }, + { + "author_name": "Fabricio Souza Campos", + "author_inst": "Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi, Tocantins, 77410-570, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.06.30.450547", "rel_title": "Computational saturation mutagenesis of SARS-CoV-1 spike glycoprotein: stability, binding affinity, and comparison with SARS-CoV-2", @@ -670709,229 +674308,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.23.21259416", - "rel_title": "Characterizing Long COVID: Deep Phenotype of a Complex Condition", - "rel_date": "2021-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.23.21259416", - "rel_abs": "ImportanceSince late 2019, the novel coronavirus SARS-CoV-2 has given rise to a global pandemic and introduced many health challenges with economic, social, and political consequences. In addition to a complex acute presentation that can affect multiple organ systems, there is mounting evidence of various persistent long-term sequelae. The worldwide scientific community is characterizing a diverse range of seemingly common long-term outcomes associated with SARS-CoV-2 infection, but the underlying assumptions in these studies vary widely making comparisons difficult. Numerous publications describe the clinical manifestations of post-acute sequelae of SARS-CoV-2 infection (PASC or \"long COVID\"), but they are difficult to integrate because of heterogeneous methods and the lack of a standard for denoting the many phenotypic manifestations of long COVID.\n\nObservationsWe identified 303 articles published before April 29, 2021, curated 59 relevant manuscripts that described clinical manifestations in 81 cohorts of individuals three weeks or more following acute COVID-19, and mapped 287 unique clinical findings to Human Phenotype Ontology (HPO) terms.\n\nConclusions and RelevancePatients and clinicians often use different terms to describe the same symptom or condition. Addressing the heterogeneous and inconsistent language used to describe the clinical manifestations of long COVID combined with the lack of standardized terminologies for long COVID will provide a necessary foundation for comparison and meta-analysis of different studies. Translating long COVID manifestations into computable HPO terms will improve the analysis, data capture, and classification of long COVID patients. If researchers, clinicians, and patients share a common language, then studies can be compared or pooled more effectively. Furthermore, mapping lay terminology to HPO for long COVID manifestations will help patients assist clinicians and researchers in creating phenotypic characterizations that are computationally accessible, which may improve the stratification and thereby diagnosis and treatment of long COVID.", - "rel_num_authors": 52, - "rel_authors": [ - { - "author_name": "Rachel R Deer", - "author_inst": "University of Texas Medical Branch, Galveston, TX, USA" - }, - { - "author_name": "Madeline A Rock", - "author_inst": "University of Texas Medical Branch, Galveston, TX, USA" - }, - { - "author_name": "Nicole Vasilevsky", - "author_inst": "Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, CO, USA" - }, - { - "author_name": "Leigh C Carmody", - "author_inst": "The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA." - }, - { - "author_name": "Halie M Rando", - "author_inst": "Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, CO, USA" - }, - { - "author_name": "Alfred J Anzalone", - "author_inst": "Department of Neurological Sciences, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA" - }, - { - "author_name": "Tiffany J Callahan", - "author_inst": "Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, CO, USA" - }, - { - "author_name": "Carolyn T Bramante", - "author_inst": "Departments of Internal Medicine and Pediatrics, University of Minnesota Medical School, Minneapolis, MN 55455" - }, - { - "author_name": "Christopher G Chute", - "author_inst": "Johns Hopkins University, Schools of Medicine, Public Health, and Nursing, Baltimore, MD, USA" - }, - { - "author_name": "Casey S Greene", - "author_inst": "Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, CO, USA" - }, - { - "author_name": "Joel J Gagnier", - "author_inst": "Departments of Orthopaedic Surgery & Epidemiology, University of Michigan, Ann Arbor, MI, USA" - }, - { - "author_name": "Haitao Chu", - "author_inst": "Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN USA" - }, - { - "author_name": "Farrukh M Koraishy", - "author_inst": "Division of Nephrology, Department of Medicine, Stony Brook University" - }, - { - "author_name": "Chen Liang", - "author_inst": "Arnold School of Public Health, University of South Carolina, Columbia, SC, USA" - }, - { - "author_name": "Feifan Liu", - "author_inst": "Department of Population and Quantitative Health Sciences, University of Massachusetts Medical School, Worcester, MA, USA" - }, - { - "author_name": "Charisse R Madlock-Brown", - "author_inst": "Department of Diagnostic and Health Sciences, University of Tennessee Health Science Center, 920 Madison Ave. Suite 518N, Memphis TN 38613" - }, - { - "author_name": "Diego R Mazzotti", - "author_inst": "Division of Medical Informatics, Department of Internal Medicine, University of Kansas Medical Center" - }, - { - "author_name": "Douglas S McNair", - "author_inst": "Quantitative Sciences, Global Health Div., Gates Foundation, Seattle, WA 98109, USA" - }, - { - "author_name": "Ann M Parker", - "author_inst": "Pulmonary and Critical Care Medicine, Johns Hopkins University, Schools of Medicine, Baltimore, MD, USA" - }, - { - "author_name": "Ben D Coleman", - "author_inst": "The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA." - }, - { - "author_name": "Hannah E Davis", - "author_inst": "Patient-Led Research Collaborative" - }, - { - "author_name": "Mallory A Perry", - "author_inst": "Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA (current)" - }, - { - "author_name": "Justin T Reese", - "author_inst": "Lawrence Berkeley National Laboratory" - }, - { - "author_name": "Joel H Saltz", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Anthony E Solomonides", - "author_inst": "Outcomes Research Network, Research Institute, NorthShore University HealthSystem, Evanston, IL 60201, USA" - }, - { - "author_name": "Anupam A Sule", - "author_inst": "St Joseph Mercy Oakland, Pontiac, MI, USA" - }, - { - "author_name": "Gary S Stein", - "author_inst": "University of Vermont Larner College of Medicine, Departments of Biochemistry and Surgery, Burlington, Vermont 05405" - }, - { - "author_name": "Sebastian Kohler", - "author_inst": "Ada Health GmbH, Berlin, Germany" - }, - { - "author_name": "Teshamae S Monteith", - "author_inst": "University of Miami, Miller School of Medicine, Miami, Fl 331336" - }, - { - "author_name": "Vithal Madhira", - "author_inst": "Palila Software LLC , Reno , NV, USA" - }, - { - "author_name": "Wesley D Kimble", - "author_inst": "West Virginia Clinical and Translational Science Institute, West Virginia University, Morgantown, WV, USA" - }, - { - "author_name": "Ramakanth Kavuluru", - "author_inst": "Institute for Biomedical Informatics, University of Kentucky" - }, - { - "author_name": "William B Hillegass", - "author_inst": "University of Mississippi Medical Center, University of Mississippi Medical Center, Jackson, MS, USA" - }, - { - "author_name": "Lauren E Chan", - "author_inst": "College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA" - }, - { - "author_name": "James Brian Byrd", - "author_inst": "Department of Internal Medicine, Division of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109" - }, - { - "author_name": "Eilis A Boudreau", - "author_inst": "Department of Neurology; Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239" - }, - { - "author_name": "Hongfang Liu", - "author_inst": "Department of Artificial Intelligence and Informatics, Mayo Clinic, MN, USA" - }, - { - "author_name": "Julie A McMurry", - "author_inst": "Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, CO, USA" - }, - { - "author_name": "Emily R Pfaff", - "author_inst": "UNC Chapel Hill" - }, - { - "author_name": "Nicolas Matentzoglu", - "author_inst": "Semanticly Ltd" - }, - { - "author_name": "Rose Relevo", - "author_inst": "Oregon Health & Science University, Portland, OR, USA" - }, - { - "author_name": "Richard A Moffitt", - "author_inst": "Stony Brook University, Stony Brook, NY 11794, USA" - }, - { - "author_name": "Robert A Schuff", - "author_inst": "OCHIN, Inc Portland, OR, USA" - }, - { - "author_name": "Julian Solway", - "author_inst": "Institute for Translational Medicine, University of Chicago, Chicago, IL, USA" - }, - { - "author_name": "Heidi Spratt", - "author_inst": "University of Texas Medical Branch, Galveston, TX, USA" - }, - { - "author_name": "Timothy Bergquist", - "author_inst": "Sage Bionetworks, Seattle, WA" - }, - { - "author_name": "Tellen D Bennett", - "author_inst": "Section of Informatics and Data Science, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA" - }, - { - "author_name": "Marc D Basson", - "author_inst": "Department of Surgery, University of North Dakota School of Medicine and Health Sciences" - }, - { - "author_name": "Umit Topaloglu", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "Liwei Wang", - "author_inst": "Department of Artificial Intelligence and Informatics, Mayo Clinic, MN, USA" - }, - { - "author_name": "Melissa A Haendel", - "author_inst": "Center for Health AI, University of Colorado Anschutz Medical Campus, Aurora, CO, USA" - }, - { - "author_name": "Peter N Robinson", - "author_inst": "The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.23.21259392", "rel_title": "DEVELOPMENT AND VALIDATION OF AN ENZYME-LINKED IMMUNOASSAY KIT FOR DIAGNOSIS AND SURVEILLANCE OF COVID-19", @@ -672810,6 +676186,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.06.24.21259087", + "rel_title": "Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children", + "rel_date": "2021-06-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259087", + "rel_abs": "Children are consistently reported to have reduced SARS-CoV-2 infection rates and a substantially lower risk for developing severe COVID-19. However, the molecular mechanisms underlying protection against COVID-19 in younger age groups remain widely unknown. Here, we systematically characterized the single-cell transcriptional landscape in the upper airways in SARS-CoV-2 negative and age-matched SARS-CoV-2 positive children (n=42) and corresponding samples from adults (n=44), covering an age range of four weeks to 77 years. Children displayed higher basal expression of the relevant pattern recognition receptor (PRR) pathways in upper airway epithelial cells, macrophages, and dendritic cells, resulting in stronger innate antiviral responses upon SARS-CoV-2 infection compared to adults. We further detected distinct immune cell subpopulations with an overall dominance of neutrophils and a population of cytotoxic T cells occurring predominantly in children. Our study provides evidence that the airway epithelial and mucosal immune cells of children are pre-activated and primed for virus sensing, resulting in a stronger early innate antiviral responses to SARS-CoV-2 infection compared to adults.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Jennifer Loske", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Jobst R\u00f6hmel", + "author_inst": "Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Soeren Lukassen", + "author_inst": "Center for Digital Health, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Sebastian Stricker", + "author_inst": "Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Vladimir Gon\u00e7alves Magalh\u00e3es", + "author_inst": "Research group Dynamics of Early Viral Infection and the Innate Antiviral Response, division F170, German Cancer Research Center (DKFZ)" + }, + { + "author_name": "Johannes Liebig", + "author_inst": "Center for Digital Health, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Robert Lorenz Chua", + "author_inst": "Center for Digital Health, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Loreen Th\u00fcrmann", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Marey Messingschlager", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Anke Seegebarth", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Bernd Timmermann", + "author_inst": "Max Planck Institute for Molecular Genetics, Berlin" + }, + { + "author_name": "Sven Klages", + "author_inst": "Max Planck Institute for Molecular Genetics, Berlin" + }, + { + "author_name": "Markus Ralser", + "author_inst": "Institute of Biochemistry, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Birgit Sawitzki", + "author_inst": "Institute of Medical Immunology, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Leif Erik Sander", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Victor M Corman", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Christian Conrad", + "author_inst": "Center for Digital Health, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Sven Laudi", + "author_inst": "Department of Anesthesiology and Intensive Care, University Hospital Leipzig" + }, + { + "author_name": "Marco Binder", + "author_inst": "Research group Dynamics of Early Viral Infection and the Innate Antiviral Response, division F170, German Cancer Research Center (DKFZ)," + }, + { + "author_name": "Saskia Trump", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin Center for Digital Health, Berlin Institute of Health at Charite" + }, + { + "author_name": "Roland Eils", + "author_inst": "Center for Digital Health, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Marcus Mall", + "author_inst": "Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Irina Lehmann", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin Center for Digital Health, Berlin Institute of Health at Charite" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.23.21259394", "rel_title": "Macro-Level Drivers of SARS-CoV-2 Transmission: A Data-Driven Analysis of Factors Contributing to Epidemic Growth During the First Wave of outbreaks in the United States", @@ -673475,29 +676958,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.23.21259422", - "rel_title": "Overcoming COVID-19 vaccine preferential bias in Europe: Is the end of the pandemic still foreseeable?", - "rel_date": "2021-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.23.21259422", - "rel_abs": "The availability of safe and effective vaccine alone does not save lives; it is the inoculation plus other public health measures that do. Recent reports suggest the growing trend in vaccine preferential bias in parts of the world but not much in Europe. The present paper aims to investigate the occurrence of COVID-19 vaccine preferential bias in Europe for effective vaccination planning and pandemic control.\n\nMethodData on vaccine delivered and vaccination campaigns of the EU member states was collected from Eu center for disease control (EUCDC) on COVID-19 vaccination radar. The data was processed for analysis on MS excel and both descriptive and statistical analysis was done with IBMs SPSS version 21. Analysis was performed at 95% confidence interval and statistically significant difference was considered at p < 0.05.\n\nResultsWe observed statistically significantly lower vaccine uptake compared to the vaccine delivered doses in the present study (average at 62.678 +/-3.928%) (p< 0.05, CI = 95%). Great variances in uptake for Oxford-AstraZeneca vaccines (50.927 +/-4.626 %) compared to Pfizer-Biontech vaccine (86.285 +/- 2.1052 %) was observed compared to previous prospective study on the wiliness to receive COVID-19 vaccine in the region (75%).\n\nConclusionPublic health practitioners and policy makers need to factor the existence of COVID-19 preferential bias based on vaccine type or manufacturer. This will enable them introduce policies including public educational campaigns to overcome biasness on the wiliness to inoculate thereby enhancing vaccine uptake for smooth and effective control of the pandemic.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Frank Adusei-Mensah", - "author_inst": "Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Finland." - }, - { - "author_name": "Ivy Eyiah Inkum", - "author_inst": "City of Kuopio Care Home, Kuopio, Finland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.28.450181", "rel_title": "A bacterial extracellular vesicle-based intranasal vaccine against SARS-CoV-2", @@ -675576,6 +679036,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.24.21259444", + "rel_title": "Early warning signals predict emergence of COVID-19 waves", + "rel_date": "2021-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259444", + "rel_abs": "Early warning signals (EWSs) aim to predict changes in complex systems from phenomenological signals in time series data. These signals have recently been shown to precede the initial emergence of disease outbreaks, offering hope that policy makers can make predictive rather than reactive management decisions. Here, using daily COVID-19 case data in combination with a novel, sequential analysis, we show that composite EWSs consisting of variance, autocorrelation, and return rate not only pre-empt the initial emergence of COVID-19 in the UK by 14 to 29 days, but also the following wave six months later. We also predict there is a high likelihood of a third wave as of the data available on 9th June 2021. Our work suggests that in highly monitored disease time series such as COVID-19, EWSs offer the opportunity for policy makers to improve the accuracy of time critical decisions based solely upon surveillance data.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Duncan A O'Brien", + "author_inst": "University of Bristol" + }, + { + "author_name": "Christopher F Clements", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.24.21259469", "rel_title": "Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner", @@ -675769,53 +679252,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.08.21258599", - "rel_title": "Susceptibility of zero community transmission regimes to new variants of SARS-CoV-2: a modelling study of Queensland", - "rel_date": "2021-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258599", - "rel_abs": "We used an agent-based model Covasim to assess the risk of sustained community transmission of SARS-CoV-2/COVID-19 in Queensland (Australia) in the presence of high-transmission variants of the virus. The model was calibrated using the demographics, policies, and interventions implemented in the state. Then, using the calibrated model, we simulated possible epidemic trajectories that could eventuate due to leakage of infected cases with high-transmission variants, during a period without recorded cases of locally acquired infections, known in Australian settings as \"zero community transmission\". We also examined how the threat of new variants reduces given a range of vaccination levels. Specifically, the model calibration covered the first-wave period from early March 2020 to May 2020. Predicted epidemic trajectories were simulated from early February 2021 to late March 2021. Our simulations showed that one infected agent with the ancestral (A.2.2) variant has a 14% chance of crossing a threshold of sustained community transmission (SCT) (i.e., > 5 infections per day, more than 3 days in a row), assuming no change in the prevailing preventative and counteracting policies. However, one agent carrying the alpha (B.1.1.7) variant has a 43% chance of crossing the same threshold; a threefold increase with respect to the ancestral strain; while, one agent carrying the delta (B.1.617.2) variant has a 60% chance of the same threshold, a fourfold increase with respect to the ancestral strain. The delta variant is 50% more likely to trigger SCT than the alpha variant. Doubling the average number of daily tests from [~] 6,000 to 12,000 results in a decrease of this SCT probability from 43% to 33% for the alpha variant. However, if the delta variant is circulating we would need an average of 100,000 daily tests to achieve a similar decrease in SCT risk. Further, achieving a full-vaccination coverage of 70% of the adult population, with a vaccine with 70% effectiveness against infection, would decrease the probability of SCT from a single seed of alpha from 43% to 20%, on par with the ancestral strain in a naive population. In contrast, for the same vaccine coverage and same effectiveness, the probability of SCT from a single seed of delta would decrease from 62% to 48%, a risk slightly above the alpha variant in a naive population. Our results demonstrate that the introduction of even a small number of people infected with high-transmission variants dramatically increases the probability of sustained community transmission in Queensland. Until very high vaccine coverage is achieved, a swift implementation of policies and interventions, together with high quarantine adherence rates, will be required to minimise the probability of sustained community transmission.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Paula Sanz-Leon", - "author_inst": "QIMR Berghofer" - }, - { - "author_name": "Nathan J Stevenson", - "author_inst": "QIMR Berghofer" - }, - { - "author_name": "Robyn Margaret Stuart", - "author_inst": "University of Copenhagen" - }, - { - "author_name": "Romesh G Abeysuriya", - "author_inst": "Burnet Institute" - }, - { - "author_name": "James C Pang", - "author_inst": "QIMR Berghofer" - }, - { - "author_name": "Stephen B Lambert", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Cliff C Kerr", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "James A Roberts", - "author_inst": "QIMR Berghofer" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.20.21259212", "rel_title": "Potential environmental transmission routes of SARS-CoV-2 inside a large meat processing plant experiencing COVID-19 clusters", @@ -677234,6 +680670,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.24.21259218", + "rel_title": "Long-term course of humoral and cellular immune responses in outpatients after SARS-CoV-2 infection", + "rel_date": "2021-06-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259218", + "rel_abs": "Characterisation of the naturally acquired B and T cell immune responses to SARS-CoV-2 is important for the development of public health and vaccination strategies to manage the burden of COVID-19 disease. We conducted a prospective, longitudinal analysis in COVID-19 recovered patients at various time points over a 10-month period in order to determine how circulating antibody levels and interferon-gamma (IFN-{gamma}) release by peripheral blood cells change over time following natural infection.\n\nFrom March 2020 till January 2021, we enrolled 412 adults mostly with mild or moderate disease course. At each study visit, subjects donated peripheral blood for testing of anti-SARS-CoV-2 IgG antibodies and IFN-{gamma} release after SARS-CoV-2 S-protein stimulation. Anti-SARS-CoV-2 IgG antibodies were identified in 316/412 (76.7%) of the patients and 215/412 (52.2%) had positive neutralizing antibody levels. Likewise, in 274/412 (66.5 %) positive IFN-{gamma} release and IgG antibodies were detected. With respect to time after infection, both IgG antibody levels and IFN-{gamma} concentrations decreased by about half within three hundred days. Statistically, IgG and IFN-{gamma} production were closely associated, but on an individual basis we observed patients with high antibody titres but low IFN-{gamma} levels and vice versa.\n\nOur data suggest that immunological reaction is acquired in most individuals after infection with SARS-CoV-2 and is sustained in the majority of patients for at least 10 months after infection. Since no robust marker for protection against COVID-19 exists so far, we recommend utilizing both, IgG and IFN-{gamma} release for an individual assessment of immunity status.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Julia Schiffner", + "author_inst": "University of Luebeck, Center for Infection and Inflammation Research, Luebeck, Germany" + }, + { + "author_name": "Insa Backhaus", + "author_inst": "Institute of Medical Sociology, Centre for Health and Society, Medical Faculty and University Hospital, Heinrich-Heine-University, Duesseldorf, Germany" + }, + { + "author_name": "Jens Rimmele", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Soeren Schulz", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Till Moehlenkamp", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Julia Maria Klemens", + "author_inst": "Institute for Experimental Immunology, affiliated to EUROIMMUN Medizinische Labordiagnostika AG, Luebeck, Germany" + }, + { + "author_name": "Dorinja Zapf", + "author_inst": "Institute for Experimental Immunology, affiliated to EUROIMMUN Medizinische Labordiagnostika AG, Luebeck, Germany" + }, + { + "author_name": "Werner Solbach", + "author_inst": "University of Luebeck, Center for Infection and Inflammation Research, Luebeck, Germany" + }, + { + "author_name": "Alexander Mischnik", + "author_inst": "Health Protection Authority, Luebeck, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.22.21259316", "rel_title": "Investigating phenotypes of pulmonary COVID-19 recovery: a longitudinal observational prospective multicenter trial", @@ -677423,57 +680910,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.21.21257586", - "rel_title": "Data-Driven Prediction of COVID-19 Cases in Germany for Decision Making", - "rel_date": "2021-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.21.21257586", - "rel_abs": "BackgroundThe COVID-19 pandemic has led to a high interest in mathematical models describing and predicting the diverse aspects and implications of the virus outbreak. Model results represent an important part of the information base for the decision process on different administrative levels. The Robert-Koch-Institute (RKI) initiated a project whose main goal is to predict COVID-19-specific occupation of beds in intensive care units: Steuerungs-Prognose von Intensivmedizinischen COVID-19 Kapazitaten (SPoCK). The incidence of COVID-19 cases is a crucial predictor for this occupation.\n\nMethodsWe developed a model based on ordinary differential equations for the COVID-19 spread with a time-dependent infection rate described by a spline. Furthermore, the model explicitly accounts for weekday-specific reporting and adjusts for reporting delay. The model is calibrated in a purely data-driven manner by a maximum likelihood approach. Uncertainties are evaluated using the profile likelihood method. The uncertainty about the appropriate modeling assumptions can be accounted for by including and merging results of different modelling approaches.\n\nResultsThe model is calibrated based on incident cases on a daily basis and provides daily predictions of incident COVID-19 cases for the upcoming three weeks including uncertainty estimates for Germany and its subregions. Derived quantities such as cumulative counts and 7-day incidences with corresponding uncertainties can be computed. The estimation of the time-dependent infection rate leads to an estimated reproduction factor that is oscillating around one. Data-driven estimation of the dark figure purely from incident cases is not feasible.\n\nConclusionsWe successfully implemented a procedure to forecast near future COVID-19 incidences for diverse subregions in Germany which are made available to various decision makers via an interactive web application. Results of the incidence modeling are also used as a predictor for forecasting the need of intensive care units.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Lukas Refisch", - "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg" - }, - { - "author_name": "Fabian Lorenz", - "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg" - }, - { - "author_name": "Torsten Riedlinger", - "author_inst": "German Aerospace Center, Earth Observation Center" - }, - { - "author_name": "Hannes Taubenb\u00f6ck", - "author_inst": "German Aerospace Center, Earth Observation Center" - }, - { - "author_name": "Martina Fischer", - "author_inst": "Robert-Koch-Institute, Department for Methodology and Research Infrastructure" - }, - { - "author_name": "Linus Grabenhenrich", - "author_inst": "Robert-Koch-Institute, Department for Methodology and Research Infrastructure" - }, - { - "author_name": "Martin Wolkewitz", - "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg" - }, - { - "author_name": "Harald Binder", - "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg" - }, - { - "author_name": "Clemens Kreutz", - "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center, University of Freiburg" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.21.21259001", "rel_title": "Socioeconomic position and SARS-CoV-2 infections: seroepidemiological findings from a German nationwide dynamic cohort", @@ -679028,6 +682464,25 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.06.23.449627", + "rel_title": "E484K and N501Y SARS-CoV 2 Spike Mutants Increase ACE2 Recognition but Reduce Affinity for Neutralizing Antibody", + "rel_date": "2021-06-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.23.449627", + "rel_abs": "SARS-CoV2 mutants emerge as variants of concern (VOC) due to altered selection pressure and rapid replication kinetics. Among them, lineages B.1.1.7, B.1.351, and P.1 contain a key mutation N501Y. B.1.135 and P.1 lineages have another mutation, E484K. Here, we decode the effect of these two mutations on the host receptor, ACE2, and neutralizing antibody (B38) recognition. The gain in binding affinity for the N501Y RBD mutant to the ACE2 is attributed to improved {pi}-{pi} stacking and {pi}-cation interactions. The enhanced receptor affinity of the E484K mutant is caused due to the formation of a specific hydrogen bond and salt-bridge interaction with Glu75 of ACE2. Notably, both the mutations reduce the binding affinity for B38 due to the loss of several hydrogen-bonding interactions. The insights obtained from the study are crucial to interpret the increased transmissibility and reduction in the neutralization efficacy of rapidly emerging SARS-CoV2 VOCs.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Sandipan Chakraborty", + "author_inst": "Amity University, Kolkata" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.06.23.449535", "rel_title": "Integrative COVID-19 Biological Network Inference with Probabilistic Core Decomposition", @@ -679193,61 +682648,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.06.22.21259354", - "rel_title": "Selective tweeting of COVID-19 articles: Does title or abstract positivity influence dissemination?", - "rel_date": "2021-06-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.22.21259354", - "rel_abs": "BackgroundPrevious research has shown that articles may be cited more frequently on the basis of title or abstract positivity. Whether a similar selective sharing practice exists on Twitter is not well understood. The objective of this study was to assess if COVID-19 articles with positive titles or abstracts were tweeted more frequently than those with non-positive titles or abstracts.\n\nMethodsCOVID-19 related articles published between January 1st and April 14th, 2020 were extracted from the LitCovid database and all articles were screened for eligibility. Titles and abstracts were classified using a list of positive and negative words from a previous study. A negative binomial regression analysis controlling for confounding variables (2018 impact factor, open access status, continent of the corresponding author, and topic) was performed to obtain regression coefficients, with the p values obtained by likelihood ratio testing.\n\nResultsA total of 3752 COVID-19 articles were included. Of the included studies, 44 titles and 112 abstracts were positive; 1 title and 7 abstracts were negative; and 3707 titles and 627 abstracts were neutral. Articles with positive titles had a lower tweet rate relative to articles with non-positive titles, with a regression coefficient of -1.10 (P < .001), while the positivity of the abstract did not impact tweet rate (P = .2218).\n\nConclusionCOVID-19 articles with non-positive titles are preferentially tweeted, while abstract positivity does not influence tweet rate.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Nicholas Fabiano", - "author_inst": "Department of Radiology, Faculty of Medicine, University of Ottawa" - }, - { - "author_name": "Zachary Hallgrimson", - "author_inst": "Department of Radiology, Faculty of Medicine, University of Ottawa" - }, - { - "author_name": "Stanley Wong", - "author_inst": "Department of Radiology, Faculty of Medicine, University of Ottawa" - }, - { - "author_name": "Jean-Paul Salameh", - "author_inst": "Clinical Epidemiology Program, Ottawa Hospital Research Institute" - }, - { - "author_name": "Sakib Kazi", - "author_inst": "Department of Radiology, Faculty of Medicine, University of Ottawa" - }, - { - "author_name": "Rudy R Unni", - "author_inst": "Department of Medicine, Faculty of Medicine, University of Ottawa" - }, - { - "author_name": "Lee Treanor", - "author_inst": "Department of Radiology, Faculty of Medicine, University of Ottawa" - }, - { - "author_name": "Robert Frank", - "author_inst": "Department of Radiology, Faculty of Medicine, University of Ottawa" - }, - { - "author_name": "Ross Prager", - "author_inst": "Department of Medicine, Faculty of Medicine, University of Ottawa" - }, - { - "author_name": "Matthew DF McInnes", - "author_inst": "University of Ottawa Department of Radiology. Clinical Epidemiology Program, Ottawa Hospital Research Institute." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.06.23.21259376", "rel_title": "Trends in COVID-19 vaccination intent, determinants and reasons for vaccine hesitancy: results from repeated cross-sectional surveys in the adult general population of Greece during November 2020-June 2021", @@ -680734,6 +684134,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.23.449583", + "rel_title": "The Influence of Public Health Faculty on College and University Plans during the COVID-19 Pandemic", + "rel_date": "2021-06-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.23.449583", + "rel_abs": "The purpose of this study was to determine whether the institutional presence of public health faculty within colleges and universities influenced operational plans for the fall semester of 2020. Using cross-sectional data collected by the College Crisis Initiative of Davidson College, six levels of instructional modalities (ranked from least to most restrictive) were compared between Council on Education of Public Health (CEPH)-accredited and non-CEPH-accredited 4-year institutions. Institutions with CEPH-accredited schools and programs were more likely to select some restrictive teaching modalities: 63.8% more likely to use hybrid/hyflex or more restrictive and 66.9% more likely to be primarily online (with some in person) or more restrictive. However, having CEPH-accredited programs did not push institutions to the most restrictive modalities. COVID-19 cases in county, enrollment, and political affiliation of the state governor were also found to influence instructional modality selection. While any ecological study has certain limitations, this study demonstrates that college and university fall plans appear to have been influenced by the presence of CEPH-accredited schools and programs of public health, and/or the input of their faculty. The influence of relevant faculty expertise on institutional decision-making can help inform college and university responses to future crises.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "David A Johnson", + "author_inst": "University of Louisville, School of Public Heath and Information Sciences" + }, + { + "author_name": "Meredith Cahill", + "author_inst": "University of Louisville, School of Public Health and Information Sciences" + }, + { + "author_name": "Sara Choate", + "author_inst": "University of Louisville, School of Public Health and Information Sciences" + }, + { + "author_name": "Dave Roelfs", + "author_inst": "University of Louisville, College of Arts and Sciences, Department of Sociology" + }, + { + "author_name": "Sarah E Walsh", + "author_inst": "Eastern Michigan University, School of Health Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2021.06.18.21258477", "rel_title": "The polarity and specificity of SARS-CoV2 -specific T lymphocyte responses determine disease susceptibility", @@ -681019,141 +684454,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.06.22.21259318", - "rel_title": "Efficacy of Proxalutamide in Hospitalized COVID-19 Patients: A Randomized, Double-Blind, Placebo-Controlled, Parallel-Design Clinical Trial", - "rel_date": "2021-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.22.21259318", - "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infectivity is mediated by the androgen-promoted protease, transmembrane protease, serine 2 (TMPRSS2). Previously, we have shown that treatment with proxalutamide, a non-steroidal androgen receptor antagonist, accelerates viral clearance and clinical remission in outpatients with coronavirus disease 2019 (COVID-19) compared to placebo. The effects in hospitalized COVID-19 patients were unknown.\n\nMethodsMen and women hospitalized but not requiring mechanical ventilation were randomized (1:1 ratio) to receive 300 mg of proxalutamide per day or placebo for 14 days. The study was conducted at eight sites in the state of Amazonas, Brazil. The primary outcome measure was the clinical status (8-point ordinal scale) at 14-days post-randomization. The primary efficacy endpoint was the 14-day recovery ratio (alive hospital discharge [scores 1, 2]).\n\nFindingsA total of 645 patients were randomized (317 received proxalutamide, 328 placebo) and underwent intention-to-treat analysis. The 14-day median ordinal scale score in the proxalutamide group was 1 (interquartile range [IQR]=1-2) versus 7 (IQR=2-8) for placebo, P<0.001. The 14-day recovery rate was 81.4% for proxalutamide and 35.7% for placebo (recovery ratio, 2.28; 95% CI 1.95-2.66 [P<0.001]). The 28-day all-cause mortality rate was 11.0% for proxalutamide versus 49.4% for placebo (hazard ratio, 0.16; 95% CI 0.11-0.24). The median post-randomization time to recovery was 5 days (IQR=3- 8) for proxalutamide versus 10 days (IQR=6-15) for placebo.\n\nInterpretationHospitalized COVID-19 patients not requiring mechanical ventilation receiving proxalutamide had a 128% higher recovery rate than those treated with placebo. All-cause mortality was reduced by 77.7% over 28 days. (ClinicalTrials.gov number, NCT04728802).", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Flavio A Cadegiani", - "author_inst": "Applied Biology Inc. Irvine, CA, USA, and Corpometria Institute, Brasilia, Brazil" - }, - { - "author_name": "Daniel N Fonseca", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "John McCoy", - "author_inst": "Applied Biology Inc., Irvine, CA, USA" - }, - { - "author_name": "Ricardo A. Zimerman", - "author_inst": "Hospital da Brigada Militar, Porto Alegre, Brazil" - }, - { - "author_name": "Fatima N Mirza", - "author_inst": "Department of Dermatology, Alpert Medical School of Brown University, Providence, RI, USA." - }, - { - "author_name": "Michael N Correia", - "author_inst": "Hospital Regional Jose Mendes, Itacoatiara, Amazonas, Brazil" - }, - { - "author_name": "Renan N Barros", - "author_inst": "Hospital Municipal Jofre Cohen, Parintins, Amazonas, Brazil" - }, - { - "author_name": "Dirce C Onety", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Karla Cristina P Israel", - "author_inst": "Centro de Doencas Renais do Amazonas, Manaus, Brazil and Programa de Pos-Graduacao em Medicina Tropical, FMT/UEA, Manaus, Brazil" - }, - { - "author_name": "Brenda G Almeida", - "author_inst": "Hospital Raimunda Francisca Dinelli da Silva, Maues, Amazonas, Brazil" - }, - { - "author_name": "Emilyn O Guerreiro", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Jose Enrique M Medeiros", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Raquel N Nicolau", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Luiza FM Nicolau", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Rafael X Cunha", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Maria Fernanda R Barroco", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Patricia S da Silva", - "author_inst": "Samel & Oscar Nicolau Hospitals, Manaus, Brazil" - }, - { - "author_name": "Gabriel S Ferreira", - "author_inst": "Hospital Municipal Jofre Cohen, Parintins, Amazonas, Brazil" - }, - { - "author_name": "Flavio Renan PC Alcantara", - "author_inst": "Hospital de Campanha de Manacapuru, Manacapuru, Amazonas, Brazil" - }, - { - "author_name": "Angelo M Ribeiro", - "author_inst": "Hospital de Campanha de Manacapuru, Manacapuru, Amazonas, Brazil" - }, - { - "author_name": "Felipe O de Almeida", - "author_inst": "Hospital de Campanha de Manacapuru, Manacapuru, Amazonas, Brazil" - }, - { - "author_name": "Adailson A de Souza", - "author_inst": "Hospital de Campanha de Manacapuru, Manacapuru, Amazonas, Brazil" - }, - { - "author_name": "Suzyane S do Rosario", - "author_inst": "Hospital Regional Dr. Hamilton Maia Cidae, Manicore, Amazonas, Brazil" - }, - { - "author_name": "Raysa WS Paulain", - "author_inst": "Hospital Municipal Jofre Cohen, Parintins, Amazonas, Brazil" - }, - { - "author_name": "Alessandra Reis", - "author_inst": "Department of Restorative Dentistry, State University of Ponta Grossa, Ponta Grossa, Parana, Brazil" - }, - { - "author_name": "Marissa Li", - "author_inst": "Applied Biology, Inc. Irvine, CA, USA." - }, - { - "author_name": "Claudia E Thompson", - "author_inst": "Department of Pharmacosciences, Universidade Federal de Ciencias da Saude de Porto Alegre." - }, - { - "author_name": "Gerald J Nau", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA." - }, - { - "author_name": "Carlos Gustavo Wambier", - "author_inst": "Department of Dermatology, Alpert Medical School of Brown University, Providence, RI, USA." - }, - { - "author_name": "Andy Goren", - "author_inst": "Applied Biology, Inc. Irvine, CA, USA." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.21.21259286", "rel_title": "Predicting the mutational drivers of future SARS-CoV-2 variants of concern", @@ -682072,6 +685372,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.19.21258892", + "rel_title": "Breastfeeding mother-child clinical outcomes after COVID-19 vaccination", + "rel_date": "2021-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.19.21258892", + "rel_abs": "This is a prospective cohort study of 88 lactating women in Singapore who received two doses of BNT162b2 vaccination (Pfizer/BioNTech), whereby outcomes of mother-child dyads within 28 days after the second vaccine dose were determined through a structured questionnaire. Minimal effects related to breastfeeding were reported in this cohort; 3 of 88 (3.4%) women had mastitis with 1 of 88 (1.1%) women experiencing breast engorgement. We report an incidence of lymphadenopathy in our cohort at 5 of 88 (5.7%). Reassuringly, there was no change in reported breastmilk supply after vaccination. The most common side effect was pain/redness/swelling at the injection site, which was experienced by 57 of 88 (64.8%) women. There were no serious adverse events of anaphylaxis and hospital admissions. No adverse symptoms were reported in 67 of 88 (76.1%) breastfed children.\n\nWhats known on this subjectTwo studies reported no serious adverse effects in both mother-child dyads after mRNA COVID-19 vaccination in mothers. Up to 61.9-67% lactating women experienced minor side effects.\n\nWhat this study addsWe report an incidence of lymphadenopathy in our cohort at 5.7% as opposed to 0.3% from the Pfizer-BioNTech COVID-19 trial. Reassuringly, there was no change in reported milk supply after vaccination. Minimal effects related to breastfeeding were reported in this cohort; 3 (3.4%) women had mastitis with 1 person experiencing breast engorgement. The most common side effect was pain/redness/swelling at the injection site at 64.8%, which was experienced by 57 of 88 (65%) women. No adverse symptoms were reported in the breastfed children.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jia Ming Low", + "author_inst": "National University Hospital of Singapore" + }, + { + "author_name": "Le Ye Lee", + "author_inst": "National University Hospital of Singapore" + }, + { + "author_name": "Yvonne Peng Mei Ng", + "author_inst": "National University Hospital of Singapore" + }, + { + "author_name": "Youjia Zhong", + "author_inst": "National University Hospital of Singapore" + }, + { + "author_name": "Zubair Amin", + "author_inst": "National University Hospital of Singapore" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.06.21.449352", "rel_title": "Cytoplasmic tail truncation of SARS-CoV-2 Spike protein enhances titer of pseudotyped vectors but masks the effect of the D614G mutation", @@ -682265,49 +685600,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.21.449058", - "rel_title": "I will teach you here or there, I will try to teach you anywhere: perceived supports and barriers for emergency remote teaching during COVID-19 pandemic", - "rel_date": "2021-06-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.21.449058", - "rel_abs": "BackgroundDue to the COVID-19 pandemic, many universities moved to emergency remote teaching (ERT). This allowed institutions to continue their instruction despite not being in person. However, ERT is not without consequences. For example, students may have inadequate technological supports, such as reliable internet and computers. Students may also have poor learning environments at home and may need to find added employment to support their families. Additionally, there were consequences to faculty. It has been shown that female instructors are more disproportionately impacted in terms of mental health issues and increased domestic labor.\n\nThis research aims to investigate instructors and students perceptions of their transition to ERT. Specifically, we wanted to: O_LIIdentify supports and barriers during the transition to ERT\nC_LIO_LICompare instructors experiences with the student experiences\nC_LIO_LIExplore these supports and barriers within the context of social presence, teaching presence, and/or cognitive presence during ERT as well as how these supports and barriers relate to scaffolding in emergency remote courses\nC_LI\n\nDesignUsing grounded theory techniques, we applied two-cycle, qualitative analyses to assess the instructor transcripts. In first-cycle analysis, we used open coding to develop initial ideas from the data. We then used second cycle coding to generate categories with definitions and criteria agreed upon during discussion-based consensus building. Finally, these categories and descriptions were used to code student survey data.\n\nAnalyses/InterpretationsInstructors identified twice as many barriers as supports in their teaching during the transition to ERT and identified casual and formal conversations with colleagues as valuable supports. Emerging categories for barriers consisted of academic integrity concerns as well as technological difficulties. Similarly, students identified more barriers than supports in their learning during the transition to ERT. More specifically, students described pre-existing course structure, classroom technology, and community as best supporting their learning. Barriers that challenged student learning included classroom environment, student availability, and student emotion and comfort.\n\nContributionTogether, this research will help us understand supports and barriers to teaching and learning during the transition to ERT. This understanding can help us better plan and prepare for future emergencies, particularly at MSIs, where improved communication and increased access to resources for both students and instructors are key.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Cristie Donham", - "author_inst": "University of California Merced" - }, - { - "author_name": "Hillary A Barron", - "author_inst": "Bemidji State University" - }, - { - "author_name": "Jourjina Alkhouri", - "author_inst": "University of California Merced" - }, - { - "author_name": "Maya Changaran Kumarath", - "author_inst": "University of California Merced" - }, - { - "author_name": "Wesley Alejandro", - "author_inst": "University of California Merced" - }, - { - "author_name": "Erik Menke", - "author_inst": "University of California Merced" - }, - { - "author_name": "Petra Kranzfelder", - "author_inst": "University of California Merced" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2021.06.16.21259063", "rel_title": "Sources of variability in methods for processing, storing, and concentrating SARS-CoV-2 in influent from urban wastewater treatment plants", @@ -683822,6 +687114,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.15.21258529", + "rel_title": "The impact of temperature on the transmission potential and virulence of COVID-19 in Tokyo, Japan", + "rel_date": "2021-06-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258529", + "rel_abs": "BackgroundAssessing the impact of temperature on COVID-19 epidemiology is critical for implementing non-pharmaceutical interventions. However, few studies have accounted for the nature of contagious diseases, i.e., their dependent happenings.\n\nAimWe aimed to quantify the impact of temperature on the transmissibility and virulence of COVID-19 in Tokyo, Japan. We employed two epidemiological measurements of transmissibility and severity: the effective reproduction number (Rt) and case fatality risk (CFR).\n\nMethodsWe used empirical surveillance data and meteorological data in Tokyo to estimate the Rt and time-delay adjusted CFR and to subsequently assess the nonlinear and delay effect of temperature on Rt and time-delay adjusted CFR.\n\nResultsFor Rt at low temperatures, the cumulative relative risk (RR) at first temperature percentile (3.3{degrees}C) was 1.3 (95% confidence interval (CI): 1.1-1.7). As for the virulence to humans, moderate cold temperatures were associated with higher CFR, and CFR also increased as the temperature rose. The cumulative RR at the 10th and 99th percentiles of temperature (5.8{degrees}C and 30.8{degrees}C) for CFR were 3.5 (95%CI: 1.3-10) and 6.4 (95%CI: 4.1-10.1).\n\nConclusionsThis study provided information on the effects of temperature on the COVID-19 epidemiology using Rt and time-delay adjusted CFR. Our results suggest the importance to take precautions to avoid infection in both cold and warm seasons to avoid severe cases of COVID-19. The results and proposed framework will also help in assessing possible seasonal course of COVID-19 in the future.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Lisa Yamasaki", + "author_inst": "Department of Global Health Policy, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Hiroaki Murayama", + "author_inst": "International University of Health and Welfare" + }, + { + "author_name": "Masahiro Hashizume", + "author_inst": "Department of Global Health Policy, Graduate School of Medicine, The University of Tokyo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.18.21258649", "rel_title": "Large-scale screening of asymptomatic for SARS-CoV-2 variants of concern and rapid P.1 takeover, Curitiba, Brazil", @@ -684031,45 +687350,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.18.21258699", - "rel_title": "Screening for the alpha variant of SARS-CoV-2 (B.1.1.7) and the impact of this variant on circulating biomarkers in hospitalised patients", - "rel_date": "2021-06-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.18.21258699", - "rel_abs": "Control of SARS-CoV-2 transmission is complicated by the emergence of variants, especially those containing mutations in the spike protein. By enhancing infectivity and evading immunity, infection with these variants might result in more severe clinical outcomes as well as being more resistant to vaccines developed on the basis of the original prototypic virus variant. One such example is the alpha variant (B.1.1.7), which has been detected in more than 100 countries and rapidly become the dominant strain in the UK in late 2020 and early 2021. There is an urgent need to develop appropriate surveillance programmes to rapidly monitor the spread of variants and to better understand the role of variants in disease outcomes and immune evasion. The nucleotide sequencing method, the gold standard of variant detection, is unsuitable as a fast-response surveillance tool by frontline diagnostic services which require detection methods with short turnaround times. We developed a screening protocol based of sequential allele-specific qPCR for detection of the N501Y mutation and H69/V70 deletion present in the alpha/B.1.1.7 variant. We tested this protocol in previously confirmed positive samples from the Pathology Dept, University Hospital Coventry and Warwickshire during the second wave period in the UK (December 2020-March 2021). In these samples variant identity was confirmed by NGS sequencing via COG-UK. Our results identified increased incidence of variants containing both N501Y and {Delta}69/70 HV mutations, especially in patients admitted during January and early February 2021. This approach, which yields results within 3 hours, can be used as an initial rapid screening step with NGS as confirmatory follow-up. We also report that the increased prevalence of alpha/B.1.1.7 variant in admitted patients since mid-January 2021, a period that characterised peaked mortality rates, was associated with a sharp 2.5-fold rise in the mean circulating IL-6 level and to a lesser extent Troponin-T. More detailed biomarker analysis of a small cohort of patients (n=83), where variant status and clinical outcomes were available, demonstrated that deceased patients infected with the alpha/B.1.1.7 variant had significantly higher levels of inflammation and cell injury markers, especially IL-6 and LDH, compared to deceased patients infected with a non-alpha/B.1.1.7 variant, pointing towards a more severe inflammatory disease phenotype. In contrast, both groups survivors most biomarker exhibited levels below the group average, with distinct patterns of modified z-scores present.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "emma braybrook", - "author_inst": "Institute of Precision Diagnostics and Translational Medicine, Pathology, UHCW NHS Trust, and Warwick Medical School, Coventry, UK" - }, - { - "author_name": "Sarojini Pandey", - "author_inst": "Institute of Precision Diagnostics and Translational Medicine, Pathology, UHCW NHS Trust, Coventry," - }, - { - "author_name": "Evangelos Vryonis", - "author_inst": "Infectious Diseases, UHCW NHS Trust, Coventry, UK" - }, - { - "author_name": "Neil R Anderson", - "author_inst": "Institute of Precision Diagnostics and Translational Medicine, Pathology, UHCW NHS Trust, Coventry, UK" - }, - { - "author_name": "Lawrence Young", - "author_inst": "Warwick Medical School, University of Warwick, Coventry, UK" - }, - { - "author_name": "dimitris grammatopoulos", - "author_inst": "Institute of Precision Diagnostics and Translational Medicine, Pathology, UHCW NHS Trust and Warwick Medical School, University of Warwick, Coventry, UK" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.19.21257191", "rel_title": "Poliovirus Vaccination Induces a Humoral Immune Response that Cross Reacts with SARS-CoV-2", @@ -686103,6 +689383,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.06.17.448816", + "rel_title": "Structural basis for the interaction of SARS-CoV-2 virulence factor nsp1 with Pol \u03b1 - Primase", + "rel_date": "2021-06-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.17.448816", + "rel_abs": "The molecular mechanisms that drive the infection by the SARS-CoV-2 coronavirus - the causative agent of the COVID-19 (Coronavirus disease-2019) pandemic - are under intense current scrutiny, to understand how the virus operates and to uncover ways in which the disease can be prevented or alleviated.\n\nRecent cell-based analyses of SARS-CoV-2 protein - protein interactions have mapped the human proteins targeted by the virus. The DNA polymerase - primase complex or primosome - responsible for initiating DNA synthesis in genomic duplication - was identified as a target of nsp1 (non structural protein 1), a major virulence factor in the SARS-CoV-2 infection.\n\nHere, we report the biochemical characterisation of the interaction between nsp1 and the primosome and the cryoEM structure of the primosome - nsp1 complex. Our data provide a structural basis for the reported interaction between the primosome and nsp1. They suggest that Pol - primase plays a part in the immune response to the viral infection, and that its targeting by SARS-CoV-2 aims to interfere with such function.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Mairi L Kilkenny", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Charlotte E Veale", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Amir Guppy", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Steven W Hardwick", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Dimitri Y Chirgadze", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Neil J Rzechorzek", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Joseph D Maman", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Luca Pellegrini", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.06.18.449086", "rel_title": "Differences in IgG antibody responses following BNT162b2 and mRNA-1273 Vaccines", @@ -686304,57 +689631,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.06.10.21258611", - "rel_title": "Working in a care home during the COVID-19 pandemic: How has the pandemic changed working practices?", - "rel_date": "2021-06-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.10.21258611", - "rel_abs": "The aim of this research was to explore the impact of COVID-19 on the working practices of care home staff, caring for people living with dementia. Remote qualitative, semi-structured interviews were conducted with care home staff caring for people living with dementia (PLWD) in the UK. Participants were recruited to the larger programme of research via convenience sampling. Interviews were conducted via telephone or online platforms. This research employed inductive thematic analysis. Sixteen care home staff were included in this study. Three overarching themes were developed from the analysis that conveyed changes to the everyday working practices of the care home workforce and the impact such changes posed to staff wellbeing: (1) Practical implications of working in a care home during the COVID-19 pandemic; (2); Staff values and changes to the staff roles (3): Impact to the care home staff and concerns for the care sector. The COVID-19 pandemic has significantly disrupted the daily working practices of care home staff, with staff forced to adopt additional roles on top of increased workloads to compensate for the loss of external agencies and support. Support and guidance must be offered urgently to inform care home staff on how to best adapt to their new working practices, ensuring that they are adequately trained.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Kerry L Hanna", - "author_inst": "Department of Primary Care & Mental Health, University of Liverpool" - }, - { - "author_name": "Clarissa Giebel", - "author_inst": "Department of Primary Care & Mental Health, University of Liverpool" - }, - { - "author_name": "Jacqueline Cannon", - "author_inst": "Lewy Body Society" - }, - { - "author_name": "Justine Shenton", - "author_inst": "Sefton Advocacy" - }, - { - "author_name": "Stephen Mason", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Hilary Tetlow", - "author_inst": "SURF Liverpool" - }, - { - "author_name": "Paul Marlow", - "author_inst": "NIHR Applied Research and Care North West Coast" - }, - { - "author_name": "Manoj Rajagopal", - "author_inst": "Lancashire and South Cumbria NHS Foundation Trust" - }, - { - "author_name": "Mark Gabbay", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "geriatric medicine" - }, { "rel_doi": "10.1101/2021.06.14.21258917", "rel_title": "Gender Balance and Readability of COVID-19 Scientific Publishing: A Quantitative Analysis of 90,000 Preprint Manuscripts", @@ -687881,6 +691157,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.15.21258928", + "rel_title": "Benefits of Surveillance Testing and Quarantine in a SARS-CoV-2 Vaccinated Population of Students on a University Campus", + "rel_date": "2021-06-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258928", + "rel_abs": "Surveillance testing and quarantine have been effective measures for limiting SARS-CoV-2 transmission on university campuses. However, the importance of these measures needs to be re-evaluated in the context of a complex and rapidly changing environment that includes vaccines, variants, and waning immunity. Also, recent guidelines from the CDC suggest that vaccinated students do not need to participate in surveillance testing. We used an agent-based SEIR model to evaluate the utility of surveillance testing and quarantine in a fully vaccinated student population where vaccine effectiveness may be impacted by the type of vaccination, the presence of variants, and the loss of vaccine-induced or natural immunity over time. We found that weekly surveillance testing at 90% vaccine effectiveness only marginally reduces viral transmission as compared to no testing. However, at 50%-75% effectiveness, surveillance testing can provide over 10-fold reduction in the number of infections on campus over the course of the semester. We also show that a 10-day quarantine protocol for exposures has limited effect on infections until vaccine effectiveness drops to 50%, and that increased surveillance testing for exposures is at least as effective as quarantine at limiting infections. Together these findings provide a foundation for universities to design appropriate mitigation protocols for the 2021-2022 academic year.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Francis C. Motta", + "author_inst": "Department of Mathematical Sciences, Florida Atlantic University" + }, + { + "author_name": "Kevin A. McGoff", + "author_inst": "Department of Mathematics and Statistics, University of North Carolina, Charlotte" + }, + { + "author_name": "Anastasia Deckard", + "author_inst": "Office of Information Technology, Duke University" + }, + { + "author_name": "Cameron R. Wolfe", + "author_inst": "Department of Medicine, Duke University School of Medicine" + }, + { + "author_name": "M. Anthony Moody", + "author_inst": "Department of Pediatrics, Duke University School of Medicine" + }, + { + "author_name": "Kyle Cavanaugh", + "author_inst": "Department of Family Medicine, Duke University School of Medicine" + }, + { + "author_name": "Thomas N. Denny", + "author_inst": "Duke Human Vaccine Institute & Department of Medicine, Duke University School of Medicine" + }, + { + "author_name": "John Harer", + "author_inst": "Department of Mathematics, Duke University" + }, + { + "author_name": "Steven B. Haase", + "author_inst": "Department of Biology, Duke University & Department of Medicine, Duke University School of Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.16.21258981", "rel_title": "Remdesivir to treat COVID-19: can dosing be optimized?", @@ -687950,89 +691277,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.12.21258345", - "rel_title": "Coadministration of AYUSH 64 as an adjunct to Standard of Care in mild and moderate COVID-19: A randomised, controlled, multicentric clinical trial", - "rel_date": "2021-06-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.12.21258345", - "rel_abs": "ObjectivesTo compare the co-administration of an Ayurvedic drug AYUSH 64 as an adjunct to standard of care (SOC) and SOC for efficacy and safety in the management of COVID-19.\n\nDesignMulticentre, parallel efficacy, randomized, controlled, open label, assessor blind, exploratory trial with a convenience sample. Patients followed to complete 12 weeks of study duration.\n\nSettingCOVID-19 dedicated non-intensive care wards at 1 government hospital, 1 medical college teaching hospital and 1 medical university teaching hospital\n\nParticipants140 consenting, eligible, hospitalized adult patients suffering from mild and moderate symptomatic COVID-19 and confirmed by a diagnostic (SARS-CoV-2) RT-PCR assay on nasal and throat swab were randomized to SOC or SOC plus AYUSH 64. To be withdrawn if disease becomes severe.\n\nInterventionsTwo tablets of AYUSH 64, 500 mg each, twice daily after meals, and continued till study completion. SOC (symptomatic and supportive) as per national guidelines of India for mild and moderate disease.\n\nMain outcome measuresTime period to clinical recovery (CR) from randomization baseline and proportion with CR within 28 days time frame; CR defined in the protocol\n\nResults140 patients randomized (70 in each arm); 138 patients with CR qualified for analysis. Both groups were matched at baseline. The mean time to CR from randomization was significantly superior in AYUSH 64 group (95% CI -3.03 to 0.59 days); a higher proportion (69.7%) in the first week (p=0.046, Chi-square). No significant differences observed for COVID-19 related blood assays (such as D-Dimer). AYUSH 64 arm showed significant (p<0.05) superior persistent improvement in general health, quality of life, fatigue, anxiety, stress, sleep and other psychosocial metrics. 1 patient on SOC required critical care. 48 adverse events (AE) reported in each group. Barring three SAE (in SOC), AE were mild and none were drug related. 22 participants (8 on AYUSH) were withdrawn. No deaths were reported.\n\nConclusionsAYUSH 64 hastened recovery, reduced hospitalization and improved overall health in mild and moderate COVID-19 when co-administered with SOC under medical supervision. It was safe and well tolerated. Further studies are warranted.\n\nTrial registrationThe Clinical Trials Registry India Number CTRI/2020/06/025557\n\nFundingCCRAS, Ministry of AYUSH, Government of India", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Arvind Chopra", - "author_inst": "Centre for Rheumatic Diseases, Pune, India" - }, - { - "author_name": "Girish Tillu", - "author_inst": "Interdisciplinary School of Health Sciences, Savitribai Phule Pune University, Pune, India" - }, - { - "author_name": "Kuldeep Chaudhary", - "author_inst": "Central Ayurveda Research Institute, Mumbai, India" - }, - { - "author_name": "Govind Reddy", - "author_inst": "Regional Ayurveda Research Institute, Nagpur, India" - }, - { - "author_name": "Alok Srivastava", - "author_inst": "Regional Ayurveda Research Institute, Lucknow, India" - }, - { - "author_name": "Muffazal Lakdawala", - "author_inst": "H.N. Reliance Foundation Hospital and Research Centre, Mumbai, India" - }, - { - "author_name": "Dilip Gode", - "author_inst": "Datta Meghe Institute of Medical Sciences, Nagpur, India" - }, - { - "author_name": "Himanshu Reddy", - "author_inst": "King George's Medical University, Lucknow, India" - }, - { - "author_name": "Sanjay Tamboli", - "author_inst": "Target Institute of Medical Education & Research, Mumbai, India" - }, - { - "author_name": "Manjit Saluja", - "author_inst": "Centre for Rheumatic Diseases, Pune, India" - }, - { - "author_name": "Sanjeev Sarmukkaddam", - "author_inst": "Centre for Rheumatic Diseases, Pune, India" - }, - { - "author_name": "Manohar Gundeti", - "author_inst": "Central Ayurveda Research Institute, Mumbai, India" - }, - { - "author_name": "Ashwinikumar Raut", - "author_inst": "Medical Research Centre, Kasturba Health Society, Mumbai, India" - }, - { - "author_name": "BCS Rao", - "author_inst": "Central Council for Research in Ayurvedic Sciences, New Delhi, India" - }, - { - "author_name": "Babita Yadav", - "author_inst": "Central Council for Research in Ayurvedic Sciences, New Delhi, India" - }, - { - "author_name": "Narayanam Srikanth", - "author_inst": "Central Council for Research in Ayurvedic Sciences, New Delhi, India" - }, - { - "author_name": "Bhushan Patwardhan", - "author_inst": "Interdisciplinary School of Health Sciences, Savitribai Phule Pune University, Pune, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2021.06.16.448772", "rel_title": "Designing a Novel Multi-Epitope Vaccine against SARS-CoV-2; Implication for Viral Binds and Fusion Inhibition through Inducing Neutralizing Antibodies", @@ -690251,6 +693495,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.15.448611", + "rel_title": "SARS-CoV-2 Viral Replication in a High Throughput Human Primary Epithelial Airway Organ Model", + "rel_date": "2021-06-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.15.448611", + "rel_abs": "COVID-19 emerged as a worldwide pandemic early in 2020, and at this writing has caused over 170 million cases and 3.7 million deaths worldwide, and almost 600,000 deaths in the United States. The rapid development of several safe and highly efficacious vaccines stands as one of the most extraordinary achievements in modern medicine, but the identification and administration of efficacious therapeutics to treat patients suffering from COVID-19 has been far less successful. A major factor limiting progress in the development of effective treatments has been a lack of suitable preclinical models for the disease, currently reliant upon various animal models and in vitro culture of immortalized cell lines. Here we report the first successful demonstration of SARS-CoV-2 infection and viral replication in a human primary cell-based organ-on-chip, leveraging a recently developed tissue culture platform known as PREDICT96. This successful demonstration of SARS-CoV-2 infection in human primary airway epithelial cells derived from a living donor represents a powerful new pathway for disease modeling and an avenue for screening therapeutic candidates in a high throughput platform.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Christine R Fisher", + "author_inst": "Draper" + }, + { + "author_name": "Felix Mba Medie", + "author_inst": "Draper" + }, + { + "author_name": "Rebeccah J Luu", + "author_inst": "Draper" + }, + { + "author_name": "Rob Gaibler", + "author_inst": "Draper" + }, + { + "author_name": "Caitlin R Miller", + "author_inst": "Draper" + }, + { + "author_name": "Thomas J Mulhern", + "author_inst": "Draper" + }, + { + "author_name": "Vidhya Vijayakumar", + "author_inst": "Draper" + }, + { + "author_name": "Elizabeth Marr", + "author_inst": "Draper" + }, + { + "author_name": "Jehan Alladina", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Benjamin Medoff", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Jeffrey T Borenstein", + "author_inst": "Draper" + }, + { + "author_name": "Ashley L Gard", + "author_inst": "Draper" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2021.06.12.21258829", "rel_title": "The Spectre of SARS-CoV-2 in the Ambient Urban Natural Water in Ahmedabad and Guwahati: A Tale of Two Cities", @@ -690604,61 +693911,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.06.16.448653", - "rel_title": "Nafamostat-interferon-alpha combination suppresses SARS-CoV-2 infection in vitro and in vivo", - "rel_date": "2021-06-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.16.448653", - "rel_abs": "SARS-CoV-2 and its vaccine/immune-escaping variants continue to pose a serious threat to public health due to a paucity of effective, rapidly deployable, and widely available treatments. Here, we address these challenges by combining Pegasys (IFNa) and nafamostat to effectively suppress SARS-CoV-2 infection in cell culture and hamsters. Our results indicate that Serpin E1 is an important mediator of the antiviral activity of IFNa and that both Serpin E1 and camostat can target the same cellular factor TMPRSS2, which plays a critical role in viral replication. The low doses of the drugs in combination may have several clinical advantages, including fewer adverse events and improved patient outcome. Thus, our study may provide a proactive solution for the ongoing pandemic and potential future coronavirus outbreaks, which is still urgently required in many parts of the world.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Aleksandr Ianevski", - "author_inst": "NTNU" - }, - { - "author_name": "Rouan Yo", - "author_inst": "NTNU" - }, - { - "author_name": "Hilde Lysvand", - "author_inst": "NTNU" - }, - { - "author_name": "Gunnveig Grodeland", - "author_inst": "UiO" - }, - { - "author_name": "Nicolas Legrand", - "author_inst": "Oncodesign" - }, - { - "author_name": "Valentyn Oksenych", - "author_inst": "NTNU" - }, - { - "author_name": "Eva Zusinaite", - "author_inst": "University of Tartu" - }, - { - "author_name": "Tanel Tenson", - "author_inst": "University of Tartu" - }, - { - "author_name": "Magnar Bjoras", - "author_inst": "NTNU" - }, - { - "author_name": "Denis E Kainov", - "author_inst": "NTNU" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.06.16.448642", "rel_title": "Ceylon cinnamon and its major compound Cinnamaldehyde can limit overshooting inflammatory signaling and angiogenesis in vitro: implications for COVID-19 treatment", @@ -692108,6 +695360,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.15.21258346", + "rel_title": "Antibody response after a single dose of ChAdOx1-nCOV (Covishield) vaccine in subjects with prior SARS-CoV2 infection: Is a single dose sufficient?", + "rel_date": "2021-06-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258346", + "rel_abs": "It is crucial to know whether a single dose of vaccine against SARS-CoV-2 is sufficient to elicit immune response in previously infected people in India. A total of 121 participants (baseline seropositive 46 and seronegative 75) were included to study the immune response to ChAdOx1-nCOV (Covishield) vaccine in previously infected or uninfected people. IgG antibodies were estimated at three different time intervals, i.e. pre-vaccination, 25-35 days post 1st vaccination and 25-35 days post 2nd vaccination. The IgG antibody titre was significantly high among previous seropositive subjects with single dose of vaccine compared to seronegative group with both doses of vaccine respectively (4.59{+/-}1.04 vs 3.08{+/-}1.22, p-value: <0.0001).\n\nIn conclusion, a single dose of Covishield(R) vaccine might be sufficient to induce an effective immune responsein subjects with prior SARS-CoV2 infection. Stratifying vacinees based on their SARS-CoV2 IgG antibody titre before vaccination would help in meeting the increasing vaccine demand and could be effective to circumvent further wave of the pandemic in India.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Biswajyoti Borkakoty", + "author_inst": "ICMR Regional Medical Research Centre NE Region" + }, + { + "author_name": "Mandakini Das Sarmah", + "author_inst": "ICMR Regional Medical Research Centre NE Region" + }, + { + "author_name": "Chandra Kanta Bhattacharjee", + "author_inst": "ICMR Regional Medical Research Centre NE Region" + }, + { + "author_name": "Nargis Bali", + "author_inst": "Sher-i- Kasmir Institute of Medical Science, Jammu and Kasmir, India" + }, + { + "author_name": "Gayatri Gogoi", + "author_inst": "Assam Medical College and Hospital, Dibrugarh, Assam, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.14.21258871", "rel_title": "SARS-CoV-2 Spike protein binding of glycated serum albumin - its potential role in the pathogenesis of the COVID-19 clinical syndromes and bias towards individuals with pre-diabetes/type 2 diabetes & metabolic diseases.", @@ -692241,45 +695528,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.06.13.21258857", - "rel_title": "Estimating decay curves of neutralising antibodies to SARS-CoV-2 infection", - "rel_date": "2021-06-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.13.21258857", - "rel_abs": "Estimating the longevity of an individual's immune response to the Sars-Cov-2 virus is vital for future planning, particularly of vaccine requirements. Neutralising antibodies (Nabs) are increasingly being recognised as a correlate of protection and whilst there are many studies which follow the response of a cohort of people, each study alone is not enough to predict the long term response. Studies use different assays to measure Nabs making them hard to combine. We present a modelling method which can combine multiple datasets and can be updated as more detailed data becomes available. Combining data from six published datasets we predict that after a short period of rapid decay the half-life of the NAb response is approximately one year giving optimism that the response will be long-lived.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Megan Poehler", - "author_inst": "School of Mathematics and Statistics, University of Canterbury, New Zealand." - }, - { - "author_name": "Liam Gibson", - "author_inst": "School of Mathematics and Statistics, University of Canterbury, New Zealand." - }, - { - "author_name": "Audrey Lustig", - "author_inst": "Manaaki Whenua, Lincoln, New Zealand." - }, - { - "author_name": "Nicole Jane Moreland", - "author_inst": "The University of Auckland" - }, - { - "author_name": "Reuben McGregor", - "author_inst": "University of Auckland" - }, - { - "author_name": "Alex James", - "author_inst": "University of Canterbury, NZ" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.06.15.21256661", "rel_title": "Study on the mucosal and serological immune response to the Novel Coronavirus (SARS-CoV-2) vaccine", @@ -693363,6 +696611,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.11.21258564", + "rel_title": "Chronic fatigue and post-exertional malaise in people living with long COVID", + "rel_date": "2021-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258564", + "rel_abs": "PurposePeople living with long COVID describe a high symptom burden, and a more detailed assessment of chronic fatigue and post-exertional malaise (PEM) may inform the development of rehabilitation recommendations. The aims of this study were to use validated questionnaires to measure the severity of fatigue and compare this with normative data and thresholds for clinical relevance in other diseases; measure and describe the impact of PEM; and assess symptoms of dysfunctional breathing, self-reported physical activity/sitting time, and health-related quality of life.\n\nMethodsThis was an observational study involving an online survey for adults living with long COVID (data collection from February-April, 2021) following a confirmed or suspected SARS-CoV-2 infection. Questionnaires included the Functional Assessment of Chronic Illness Therapy-Fatigue Scale (FACIT-F) and DePaul Symptom Questionnaire-Post-Exertional Malaise.\n\nResultsAfter data cleaning, n=213 participants were included in the analysis. Participants primarily identified as women (85.5%), aged 40-59 (78.4%), who had been experiencing long COVID symptoms for [≥]6 months (72.3%). The total FACIT-F score was 18{+/-}10 (where the score can range from 0-52, and a lower score indicates more severe fatigue), and 71.4% were experiencing chronic fatigue. Post-exertional symptom exacerbation affected most participants, and 58.7% met the scoring thresholds used in people living with myalgic encephalomyelitis/chronic fatigue syndrome. PEM occurred alongside a reduced capacity to work, be physically active, and function both physically and socially.\n\nConclusionLong COVID is characterized by chronic fatigue that is clinically relevant and is at least as severe as fatigue in several other clinical conditions, including cancer. PEM appears to be a common and significant challenge for the majority of this patient group. Patients, researchers, and allied health professionals are seeking information on safe rehabilitation for people living with long COVID, particularly regarding exercise. Fatigue and post-exertional symptom exacerbation must be monitored and reported in studies involving interventions for people with long COVID.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Rosie Twomey", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jessica DeMars", + "author_inst": "Breath Well Physio" + }, + { + "author_name": "Kelli Franklin", + "author_inst": "Patient Partner" + }, + { + "author_name": "S. Nicole Culos-Reed", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jason Weatherald", + "author_inst": "University of Calgary" + }, + { + "author_name": "James G Wrightson", + "author_inst": "University of Calgary" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.11.21258445", "rel_title": "Estimating the Burden of SARS-CoV-2 among the Rohingya Refugees", @@ -693532,57 +696819,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2021.06.11.21258735", - "rel_title": "Quarantine and testing strategies to reduce transmission risk from imported SARS-CoV-2 infections: a global modelling study", - "rel_date": "2021-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258735", - "rel_abs": "BackgroundMany countries require incoming air travellers to quarantine on arrival and/or undergo testing to limit importation of SARS-CoV-2.\n\nMethodsWe developed mathematical models of SARS-CoV-2 viral load trajectories over the course of infection to assess the effectiveness of quarantine and testing strategies. We consider the utility of pre and post-flight Polymerase Chain Reaction (PCR) and lateral flow testing (LFT) to reduce transmission risk from infected arrivals and to reduce the duration of, or replace, quarantine. We also estimate the effect of each strategy relative to domestic incidence, and limits of achievable risk reduction, for 99 countries where flight data and case numbers are estimated.\n\nResultsWe find that LFTs immediately pre-flight are more effective than PCR tests 3 days before departure in decreasing the number of departing infectious travellers. Pre-flight LFTs and post-flight quarantines, with tests to release, may prevent the majority of transmission from infectious arrivals while reducing the required duration of quarantine; a pre-flight LFT followed by 5 days in quarantine with a test to release would reduce the expected number of secondary cases generated by an infected traveller compared to symptomatic self-isolation alone, Rs, by 85% (95% UI: 74%, 96%) for PCR and 85% (95% UI: 70%, 96%) for LFT, even assuming imperfect adherence to quarantine (28% of individuals) and self-isolation following a positive test (86%). Under the same adherence assumptions, 5 days of daily LFT testing would reduce Rs by 91% (95% UI: 75%, 98%).\n\nConclusionsStrategies aimed at reducing the risk of imported cases should be considered with respect to: domestic incidence, transmission, and susceptibility; measures in place to support quarantining travellers; and incidence of new variants of concern in travellers origin countries. Daily testing with LFTs for 5 days is comparable to 5 days of quarantine with a test on exit or 14 days with no test.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Billy J Quilty", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Timothy W Russell", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Samuel Clifford", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Stefan Flasche", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Suzanne Pickering", - "author_inst": "King's College London" - }, - { - "author_name": "Stuart JD Neil", - "author_inst": "King's College London" - }, - { - "author_name": "Rui Pedro Gal\u00e3o", - "author_inst": "King's College London" - }, - { - "author_name": "W John Edmunds", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "- CMMID COVID-19 Working Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.11.21258797", "rel_title": "Coupling freedom from disease principles and early warning from wastewater surveillance to improve health security", @@ -695185,6 +698421,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.06.08.21258533", + "rel_title": "The impact of co-circulating pathogens on SARS-CoV-2/COVID-19 surveillance. How concurrent epidemics may decrease true SARS-CoV-2 percent positivity.", + "rel_date": "2021-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258533", + "rel_abs": "BackgroundCirculation of non-SARS-CoV-2 respiratory viruses during the COVID-19 pandemic may alter quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures. Here, we assess the impact of an increased circulation of other respiratory viruses on the monitoring of positivity rates of SARS-CoV-2 and interpretation of surveillance data.\n\nMethodsUsing a multi-pathogen Susceptible-Exposed-Infectious-Recovered (SEIR) transmission model formalizing co-circulation of SARS-CoV-2 and another respiratory we assess how an outbreak of secondary virus may inflate the number of SARS-CoV-2 tests and affect the interpretation of COVID-19 surveillance data. Using simulation, we assess to what extent the use of multiplex PCR tests on a subsample of symptomatic individuals can support correction of the observed SARS-CoV-2 percent positive during other virus outbreaks and improve surveillance quality.\n\nResultsModel simulations demonstrated that a non-SARS-CoV-2 epidemic creates an artificial decrease in the observed percent positivity of SARS-CoV-2, with stronger effect during the growth phase, until the peak is reached. We estimate that performing one multiplex test for every 1,000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percent positive.\n\nConclusionsThis study highlights that co-circulating respiratory viruses can disrupt SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex PCR, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.\n\nSummaryCOVID-19 surveillance indicators may be impacted by increased co-circulation of other respiratory viruses delaying control measure implementation. Continued surveillance through multiplex PCR testing in a subsample of the symptomatic population may play a role in fixing this problem.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Aleksandra Kovacevic", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Rosalind M Eggo", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Marc Baguelin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Matthieu Domenech de Cell\u00e8s", + "author_inst": "Max Planck Institute for Infection Biology" + }, + { + "author_name": "Lulla Opatowski", + "author_inst": "Univ Versailles Saint Quentin / Institut Pasteur / Inserm" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.10.21254528", "rel_title": "NEWS-2 score assessment of inpatient referral during the COVID 19 epidemic", @@ -695338,105 +698609,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.09.21258422", - "rel_title": "Impact of baseline SARS-CoV-2 antibody status on syndromic surveillance and the risk of subsequent Covid-19 -- a prospective multicentre cohort study", - "rel_date": "2021-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.09.21258422", - "rel_abs": "ObjectivesIn a prospective healthcare worker (HCW) cohort, we assessed the risk of SARS-CoV-2 infection according to baseline serostatus.\n\nMethodsBaseline serologies were performed among HCW from 23 Swiss healthcare institutions between June and September 2020, before the second COVID-19 wave. Participants answered weekly electronic questionnaires covering information about nasopharyngeal swabs (PCR/rapid antigen tests) and symptoms compatible with Coronavirus Disease 2019 (COVID-19). Screening of symptomatic staff by nasopharyngeal swabs was routinely performed in participating facilities. We compared numbers of positive nasopharyngeal tests and occurrence of COVID-19 symptoms between HCW with and without anti-nucleocapsid antibodies.\n\nResultsA total of 4818 HCW participated, whereof 144 (3%) were seropositive at baseline. We analysed 107820 questionnaires with a median follow-up of 7.9 months. Median number of answered questionnaires was similar (24 vs. 23 per person, P=0.83) between those with and without positive baseline serology. Among 2713 HCW with [≥]1 SARS-CoV-2 test during follow-up, 3/67 (4.5%) seropositive individuals reported a positive result (one of whom asymptomatic), compared to 547/2646 (20.7%) seronegative participants, 12 of whom asymptomatic (risk ratio [RR] 0.22; 95% confidence interval [CI] 0.07 to 0.66). Seropositive HCWs less frequently reported impaired olfaction/taste (6/144, 4.2% vs. 588/4674, 12.6%, RR 0.33, 95%-CI: 0.15-0.73), chills (19/144, 13.2% vs. 1040/4674, 22.3%, RR 0.59, 95%-CI: 0.39-0.90), and limb/muscle pain (28/144, 19.4% vs. 1335/4674, 28.6%, RR 0.68 95%-CI: 0.49-0.95). Impaired olfaction/taste and limb/muscle pain also discriminated best between positive and negative SARS-CoV-2 results.\n\nConclusionsHaving SARS-CoV-2 anti-nucleocapsid antibodies provides almost 80% protection against SARS-CoV-2 re-infection for a period of at least eight months.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Philipp Kohler", - "author_inst": "Kantonsspital St. Gallen" - }, - { - "author_name": "Sabine Guesewell", - "author_inst": "Kantonsspital St. Gallen" - }, - { - "author_name": "Marco Seneghini", - "author_inst": "Kantonsspital St. Gallen" - }, - { - "author_name": "Thomas Egger", - "author_inst": "Kantonsspital St. Gallen" - }, - { - "author_name": "Onicio Leal-Neto", - "author_inst": "University of Zurich, Economics" - }, - { - "author_name": "Angela Brucher", - "author_inst": "St. Gallische Psychiatrie-Dienste Sued" - }, - { - "author_name": "Eva Lemmenmaier", - "author_inst": "Clienia Littenheid AG" - }, - { - "author_name": "Carsten Moeller", - "author_inst": "Rehabilitation Hospital Zihlschlacht" - }, - { - "author_name": "Philip Rieder", - "author_inst": "Hirslanden AG" - }, - { - "author_name": "Markus Ruetti", - "author_inst": "Spitalregion Fuerstenland Toggenburg Spital Wattwil" - }, - { - "author_name": "Reto Stocker", - "author_inst": "Hirslanden AG" - }, - { - "author_name": "Danelle Vuichard-Gysin", - "author_inst": "Kantonsspital Muensterlingen" - }, - { - "author_name": "Benedikt Wiggli", - "author_inst": "Kantonspital Baden" - }, - { - "author_name": "Ulrike Besold", - "author_inst": "Buergerspital St. Gallen" - }, - { - "author_name": "Andree Friedl", - "author_inst": "Kantonspital Baden" - }, - { - "author_name": "Stefan Kuster", - "author_inst": "Kantonsspital St. Gallen" - }, - { - "author_name": "Allison McGeer", - "author_inst": "Mount Sinai Hospita" - }, - { - "author_name": "Lorenz Risch", - "author_inst": "Labormedizinisches Zentrum Dr Risch" - }, - { - "author_name": "Matthias Schlegel", - "author_inst": "Kantonsspital St. Gallen" - }, - { - "author_name": "Pietro Vernazza", - "author_inst": "Kantonsspital St. Gallen" - }, - { - "author_name": "Christian R. Kahlert", - "author_inst": "Kantonsspital St. Gallen" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.09.21258479", "rel_title": "A clinical observational analysis of aerosol emissions from dental procedures.", @@ -696959,6 +700131,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.06.11.448011", + "rel_title": "B.1.1.7 and B.1.351 SARS-CoV-2 variants display enhanced Spike-mediated fusion", + "rel_date": "2021-06-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.11.448011", + "rel_abs": "Severe COVID-19 is characterized by lung abnormalities, including the presence of syncytial pneumocytes. Syncytia form when SARS-CoV-2 spike protein expressed on the surface of infected cells interacts with the ACE2 receptor on neighbouring cells. The syncytia forming potential of spike variant proteins remain poorly characterized. Here, we first assessed Alpha and Beta spread and fusion in cell cultures. Alpha and Beta replicated similarly to D614G reference strain in Vero, Caco-2, Calu-3 and primary airway cells. However, Alpha and Beta formed larger and more numerous syncytia. Alpha, Beta and D614G fusion was similarly inhibited by interferon induced transmembrane proteins (IFITMs). Individual mutations present in Alpha and Beta spikes differentially modified fusogenicity, binding to ACE2 and recognition by monoclonal antibodies. We further show that Delta spike also triggers faster fusion relative to D614G. Thus, SARS-CoV-2 emerging variants display enhanced syncytia formation.\n\nSynopsisThe Spike protein of the novel SARS-CoV-2 variants are comparative more fusogenic than the earlier strains. The mutations in the variant spike protein differential modulate syncytia formation, ACE2 binding, and antibody escape.\n\nO_LIThe spike protein of Alpha, Beta and Delta, in the absence of other viral proteins, induce more syncytia than D614G\nC_LIO_LIThe ACE2 affinity of the variant spike proteins correlates to their fusogenicity\nC_LIO_LIVariant associated mutations P681H, D1118H, and D215G augment cell-cell fusion, while antibody escape mutation E484K, K417N and {Delta}242-244 hamper it.\nC_LIO_LIVariant spike-mediated syncytia formation is effectively restricted by IFITMs\nC_LI", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Maaran Michael Rajah", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Mathieu Hubert", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Elodie Bishop", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Nell Saunders", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "R\u00e9my Robinot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Ludivine Grzelak", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Delphine Planas", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Jeremy Dufloo", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Stacy Gellenoncourt", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Alice Bongers", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Marija Zivaljic", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Cyril Planchais", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Florence Guivel-Benhassine", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Fran\u00e7oise Porrot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Hugo Mouquet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Lisa Chakrabarti", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Julian Buchrieser", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Olivier Schwartz", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.10.447999", "rel_title": "A combination of RBD and NTD neutralizing antibodies limits the generation of SARS-CoV-2 spike neutralization-escape mutants", @@ -697232,41 +700491,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.06.08.21258471", - "rel_title": "BNT162b2 mRNA vaccinations in Israel: understanding the impact and improving the vaccination policies by redefining the immunized population", - "rel_date": "2021-06-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258471", - "rel_abs": "By the end of February 2021, when 48% of the Israeli population was immune, the number of new positive COVID-19 cases significantly dropped across all ages. Understanding which parameters influenced this drop and how to minimize the number of hospitalizations and overall positive cases is urgently needed.\n\nIn this study we conducted an observational analysis which included COVID-19 data with over 12,000,000 PCR tests from 250 cities in Israel. In addition, we performed a simulation of different vaccination campaigns to find the optimal policy.\n\nOur analysis revealed that cities with younger populations reached a decrease in new cases when a lower percentage of their residents were immunized, showing that median age is a crucial parameter effecting overall immunity, while other parameters appeared to be insignificant. This variance between cities is explained by recalculating the immunized population and multiplying each individual by a factor symbolizing the impact of their age on the spread on the virus. This factor is easily calculated from historical data of positive cases per age.\n\nThe simulation proves that prioritizing different age groups or changing the rate of vaccinations drastically effects the overall hospitalizations and positive cases.\n\nOne-Sentence Summaryunderstanding what influences reaching covid-19 overall immunity and how to maximize the effect of the vaccination campaign.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "chana ross", - "author_inst": "Robert Bosch Technologies Israel Ltd" - }, - { - "author_name": "oren spector", - "author_inst": "Robert Bosch Technologies Israel Ltd." - }, - { - "author_name": "Meytal Avgil Tsadok", - "author_inst": "TIMNA Big Data Platform, Israel Ministry of Health, Jerusalem, Israel" - }, - { - "author_name": "Yossi Weiss", - "author_inst": "Assuta Heath Services Research Institute, Assuta Medical Center, Tel Aviv, Israel" - }, - { - "author_name": "Royi Barnea", - "author_inst": "Assuta Heath Services Research Institute, Assuta Medical Center, Tel Aviv, Israel" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.06.07.21258465", "rel_title": "The potential of SARS-CoV-2 antigen-detection tests in the screening of asymptomatic persons", @@ -698889,6 +702113,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.06.21258425", + "rel_title": "Functional dependence of COVID-19 growth rate on lockdown conditions and rate of vaccination.", + "rel_date": "2021-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.06.21258425", + "rel_abs": "It is shown that derived from the solution of differential equations analytical model adequately describes development epidemics with changes in both lockdown conditions and the effective rate of mass vaccination of the population. As in previous studies, the control calculations are in good agreement with observations at all stages of epidemic growth. One of the two model coefficients is uniquely related to the lockdown efficiency parameter. We obtained an approximate correlation between this parameter and the main conditions of lockdown, in particular, physical distancing, reduction in social contacts and strictness of the mask regime.\n\nThe calculation of the incident over a seven-day period using the proposed model is in good agreement with the observational data. Analysis of both curves shows that a better agreement can be obtained by taking into account the lag time of the epidemic response of about 10 days.\n\nFrom the reverse calculation a time-varying curve of the infection rate associated with the \"new\" virus strain under mutation conditions is obtained, which is qualitatively confirmed by the sequencing data.\n\nBased on these studies, it is possible to conclude that the ASILV analytical model developed here can be used to reliably and promptly predict epidemic development under conditions of lockdown and mass vaccination without the use of numerical methods.\n\nThe functional relationships identified allow us to conduct a rapid analysis of the impact of each of the model parameters on the overall process of the epidemic.\n\nIn contrast to previous studies, the calculations of the proposed model were performed using EXCEL, rather than a standard calculator. This is due to the need to account for multiple changes in lockdown conditions and vaccination rates.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Felix Mairanowski", + "author_inst": "Husmann Rus" + }, + { + "author_name": "Denis Below", + "author_inst": "Potsdam Universitet" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.09.21258609", "rel_title": "Depressive and anxiety symptoms and COVID-19-related factors among men and women in Nigeria", @@ -699042,41 +702289,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.07.21258447", - "rel_title": "Breakthrough infection with SARS-CoV-2 and its predictors among healthcare workers in a medical college and hospital complex in Delhi, India", - "rel_date": "2021-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.07.21258447", - "rel_abs": "IntroductionThe study objective was to determine the breakthrough infection rate of Covid-19 (SARS-CoV-2) infection in those vaccinated with either BBV152 or AZD1222 (ChAdOx1-S) vaccine among healthcare workers (HCWs).\n\nMethodsA cross-sectional analysis was conducted a medical college and hospital complex in Delhi, India through telephonic interviews among HCWs who had received at-least one dose of a Covid-19 vaccine during January to March 2021. Breakthrough infections were operationally defined as occurrence of Covid-19 infection [≥]14 days after administration of two doses of either Covid-19 vaccine.\n\nResultsWe enrolled 325 HCWs with mean (SD) age of 29.1 (9.9) years including 211 (64.9%) males. Two seventy nine (85.8%) HCWs were fully vaccinated while 46 (14.2%) were partially vaccinated. There were 168 (51.7%) BBV152 and 157 (48.3%) AZD1222 (ChAdOx1-S) recipients.\n\nA total of 37 (11.3%, 95% C.I. 8.3, 15.3) breakthrough infections were observed in the HCWs. The median (IQR) time until incidence of Covid-19 breakthrough infection since receiving second dose of either Covid-19 vaccine was 47 (28.5, 55) days. Additionally, 20 (6.1%) non-breakthrough Covid-19 infections were recorded in the HCWs post vaccination with either a single dose of a Covid-19 vaccine or both doses but prior to a period of 14 days since administration of the second dose.\n\nMost breakthrough infection cases (94.4%) were mild and did not require supplemental oxygen therapy. HCWs without a history of natural Covid-19 infection and recovery prior to vaccination were 3.8 times more at risk to contract a Covid-19 infection or reinfection in spite of vaccination with at-least one dose of either Covid-19 vaccine.\n\nConclusionNearly one in nine HCWs experienced a Covid-19 breakthrough infection in the present study.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Pragya Sharma", - "author_inst": "Department of Community Medicine, Maulana Azad Medical College, New Delhi" - }, - { - "author_name": "Suruchi Mishra", - "author_inst": "Department of Community Medicine, Maulana Azad Medical College, New Delhi" - }, - { - "author_name": "Saurav Basu", - "author_inst": "Department of Community Medicine, Maulana Azad Medical College, New Delhi" - }, - { - "author_name": "Neha Tanwar", - "author_inst": "Department of Community Medicine, Maulana Azad Medical College, New Delhi" - }, - { - "author_name": "Rajesh Kumar", - "author_inst": "Department of Community Medicine, Maulana Azad Medical College, New Delhi" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.07.21258318", "rel_title": "Testing for SARS-CoV-2 among cruise ship travelers repatriated to the United States, February to March 2020", @@ -700943,6 +704155,153 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.06.09.447527", + "rel_title": "Second Generation Antibodies Neutralize Emerging SARS-CoV-2 Variants of Concern", + "rel_date": "2021-06-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.09.447527", + "rel_abs": "Recently emerged SARS-CoV-2 variants show resistance to some antibodies that were authorized for emergency use. We employed hybridoma technology combined with authentic virus assays to develop second-generation antibodies, which were specifically selected for their ability to neutralize new variants of SARS-CoV-2. AX290 and AX677, two monoclonal antibodies with non-overlapping epitopes, exhibit subnanomolar or nanomolar affinities to the receptor binding domain of the viral Spike protein carrying amino acid substitutions N501Y, N439K, E484K, K417N, and a combination N501Y/E484K/K417N found in the circulating virus variants. The antibodies showed excellent neutralization of an authentic SARS-CoV-2 virus representing strains circulating in Europe in spring 2020 and also the variants of concern B.1.1.7 and B.1.351. Finally, the combination of the two antibodies prevented the appearance of escape mutations of the authentic SARS-CoV-2 virus. The neutralizing properties were fully reproduced in chimeric mouse-human versions, which may represent a promising tool for COVID-19 therapy.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Branislav Kovacech", + "author_inst": "AXON COVIDAX a. s., Slovakia" + }, + { + "author_name": "Lubica Fialova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Peter Filipcik", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Monika Zilkova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Rostislav Skrabana", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Natalia Paulenka-Ivanovova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Andrej Kovac", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Denisa Palova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Gabriela Paulikova Rolkova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Katarina Tomkova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Natalia Turic Csokova", + "author_inst": "Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Karina Markova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Michaela Skrabanova", + "author_inst": "Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Kristina Sinska", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Neha Basheer", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Petra Majerova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Jozef Hanes", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Vojtech Parrak", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Michal Prcina", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Ondrej Cehlar", + "author_inst": "Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Martin Cente", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Juraj Piestansky", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Michal Fresser", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Michal Novak", + "author_inst": "Axon Neuroscience SE, Cyprus" + }, + { + "author_name": "Monika Slavikova", + "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Kristina Borsova", + "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia; Department of Microbiology and Virology, Faculty of Natural" + }, + { + "author_name": "Viktoria Cabanova", + "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Bronislava Brejova", + "author_inst": "Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Slovakia" + }, + { + "author_name": "Tomas Vinar", + "author_inst": "Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Slovakia" + }, + { + "author_name": "Jozef Nosek", + "author_inst": "Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Slovakia" + }, + { + "author_name": "Boris Klempa", + "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Norbert Zilka", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Eva Kontsekova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.09.21258553", "rel_title": "Analysis of cell-mediated immunity in people with long Covid.", @@ -701036,149 +704395,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.07.21258351", - "rel_title": "Antibody longevity and cross-neutralizing activity following SARS-CoV-2 wave 1 and B.1.1.7 infections", - "rel_date": "2021-06-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.07.21258351", - "rel_abs": "As SARS-CoV-2 variants continue to emerge globally, a major challenge for COVID-19 vaccination is the generation of a durable antibody response with cross-neutralizing activity against both current and newly emerging viral variants. Cross-neutralizing activity against major variants of concern (B.1.1.7, P.1 and B.1.351) has been observed following vaccination, albeit at a reduced potency, but whether vaccines based on the Spike glycoprotein of these viral variants will produce a superior cross-neutralizing antibody response has not been fully investigated. Here, we used sera from individuals infected in wave 1 in the UK to study the long-term cross-neutralization up to 10 months post onset of symptoms (POS), as well as sera from individuals infected with the B.1.1.7 variant to compare cross-neutralizing activity profiles. We show that neutralizing antibodies with cross-neutralizing activity can be detected from wave 1 up to 10 months POS. Although neutralization of B.1.1.7 and B.1.351 is lower, the difference in neutralization potency decreases at later timepoints suggesting continued antibody maturation and improved tolerance to Spike mutations. Interestingly, we found that B.1.1.7 infection also generates a cross-neutralizing antibody response, which, although still less potent against B.1.351, can neutralize parental wave 1 virus to a similar degree as B.1.1.7. These findings have implications for the optimization of vaccines that protect against newly emerging viral variants.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Liane Dupont", - "author_inst": "King's College London" - }, - { - "author_name": "Luke B Snell", - "author_inst": "Guy's and St Thomas' NHS Trust" - }, - { - "author_name": "Carl Graham", - "author_inst": "King's College London" - }, - { - "author_name": "Jeffrey Seow", - "author_inst": "King's College London" - }, - { - "author_name": "Blair Merrick", - "author_inst": "Guy's and St Thomas' NHS Trust" - }, - { - "author_name": "Thomas Lechmere", - "author_inst": "King's College London" - }, - { - "author_name": "Sadie R. Hallett", - "author_inst": "King's College London" - }, - { - "author_name": "Themoula Charalampous", - "author_inst": "Guy's and St Thomas' NHS Trust" - }, - { - "author_name": "Adela Alcolea-Medina", - "author_inst": "Guy's and St Thomas' NHS Trust" - }, - { - "author_name": "Isabella Huettner", - "author_inst": "King's College London" - }, - { - "author_name": "Thomas J.A. Maguire", - "author_inst": "King's College London" - }, - { - "author_name": "Sam Acors", - "author_inst": "King's College London" - }, - { - "author_name": "Nathalia Almeida", - "author_inst": "King's College London" - }, - { - "author_name": "Daniel Cox", - "author_inst": "King's College London" - }, - { - "author_name": "Ruth E Dickenson", - "author_inst": "King's College London" - }, - { - "author_name": "Rui Pedro Galao", - "author_inst": "King's College London" - }, - { - "author_name": "Jose M Jimenez-Guarde\u00f1o", - "author_inst": "King's College London" - }, - { - "author_name": "Neophytos Kouphou", - "author_inst": "King's College London" - }, - { - "author_name": "Marie Jose Lista", - "author_inst": "King's College London" - }, - { - "author_name": "Suzanne Pickering", - "author_inst": "King's College London" - }, - { - "author_name": "Ana Maria Ortega-Prieto", - "author_inst": "King's College London" - }, - { - "author_name": "Harry Wilson", - "author_inst": "King's College London" - }, - { - "author_name": "Helena Winstone", - "author_inst": "King's College London" - }, - { - "author_name": "Cassandra Fairhead", - "author_inst": "Guy's and St Thomas' NHS Trust" - }, - { - "author_name": "Jia Su", - "author_inst": "Guy's and St Thomas' NHS Trust" - }, - { - "author_name": "Gaia Nebbia", - "author_inst": "Guy's and St Thomas' NHS Trust" - }, - { - "author_name": "Rahul Batra", - "author_inst": "Guy's and St Thomas' NHS Trust" - }, - { - "author_name": "Stuart Neil", - "author_inst": "King's College London" - }, - { - "author_name": "Manu Shankar-Hari", - "author_inst": "King's College London" - }, - { - "author_name": "Jonathan D Edgeworth", - "author_inst": "Guy's and St Thomas' NHS Trust" - }, - { - "author_name": "Michael H Malim", - "author_inst": "King's College London" - }, - { - "author_name": "Katie Doores", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.08.21258535", "rel_title": "Altered neutrophil phenotype and function in non-ICU COVID-19 patients correlated with disease severity", @@ -702889,6 +706105,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.06.05.21258407", + "rel_title": "Prediction of severe COVID-19 cases requiring intensive care in Osaka, Japan", + "rel_date": "2021-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.05.21258407", + "rel_abs": "BackgroundTo avoid exhaustion of medical resources by COVID-19 care, policy-makers must predict care needs, specifically estimating the proportion of severe cases likely to require intensive care. In Osaka prefecture, Japan, the number of these severe cases exceeded the capacity of ICU units prepared for COVID-19 from mid-April, 2021.\n\nObjectiveThis study used a statistical model to elucidate dynamics of severe cases in Osaka and validated the model through prospective testing.\n\nMethodsThe study extended from April 3, 2020 through April 26, 2021 in Osaka prefecture, Japan prefecture. We regressed the number of severe cases on the number of severe cases the day prior and the newly onset patients of more than 21 days prior.\n\nResultsWe selected the number of severe cases the day prior and the number of newly onset patients on 21 and 28 days prior as explanatory variables for explaining the number of severe cases based on the adjusted determinant coefficient. The adjusted coefficient of determination was greater than 0.995 and indicated good fit. Prospective out of sample three-week prediction forecast the peak date precisely, but the level was not t.\n\nDiscussion and ConclusionA reason for the gap in the prospective prediction might be the emergence of variant strains.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Junko Kurita", + "author_inst": "Tokiwa University, Ibaraki, Japan" + }, + { + "author_name": "Tamie Sugawara", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + }, + { + "author_name": "Yasushi Ohkusa", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.04.21257951", "rel_title": "Early Epidemiological Evidence of Public Health Value of WA Notify, a Smartphone-based Exposure Notification Tool: Modeling COVID-19 Cases Averted in Washington State", @@ -703018,85 +706261,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2021.06.06.21258414", - "rel_title": "Effects of immunosuppressive therapy reduction and early post-infection graft function in kidney transplant recipients with COVID-19", - "rel_date": "2021-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.06.21258414", - "rel_abs": "BackgroundKidney transplant recipients with COVID-19 are at high risk of poor outcome because of comorbidities and immunosuppression. The effects of immunosuppressive therapy reduction are unclear in patients with COVID-19.\n\nMethodsWe conducted a retrospective study on 45 consecutive kidney transplant recipients followed at the University Hospital of Modena who tested positive for COVID-19 by RT-PCR analysis.\n\nResultsThe median age of patients was 56.1 (interquartile range, [IQR] 47.3-61.1) years with a predominance of male (64.4%). Kidney transplantation vintage was 10.1 (2.7-16) years, and more than half of patients (55.6%) was on triple immunosuppressive therapy. Early reduction of immunosuppression occurred in 62.8% of patients and included antimetabolite (88.8%) and calcineurin inhibitor withdrawal (22.2%).\n\nOf the 45 patients, 88.9% became symptomatic and 40% required hospitalization. Overall mortality was 17.8%. There were no differences in outcomes between full- and reduced-dose immunosuppressive therapy at the end of follow-up. One hospitalized patient experienced irreversible graft failure. There were no differences in serum creatinine level and proteinuria in non-hospitalized patients with COVID-19. Admitted patients had better kidney function after dismission (P=0.019). Risk factors for death were age (odds ratio [OR]: 1.19; 95%CI: 1.01-1.39), and duration of kidney transplant (OR: 1.17; 95%CI: 1.01-1.35). One kidney transplant recipient experienced symptomatic COVID-19 reinfection after primary infection and anti-SARS-CoV-2 mRNA vaccine.\n\nConclusionsDespite the reduction of immunosuppression, COVID-19 affected survival of kidney transplant recipients with COVID-19. Age and duration of kidney transplant were independent predictors of death in COVID-19. Early kidney function was favorable in most survivors after COVID-19.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Gaetano Alfano", - "author_inst": "Policlinico of Modena" - }, - { - "author_name": "Francesca Damiano", - "author_inst": "Policlinico of Modena" - }, - { - "author_name": "Francesco Fontana", - "author_inst": "Azienda Ospedaliera Universitaria di Modena" - }, - { - "author_name": "Camilla Ferri", - "author_inst": "Policlinico of Modena" - }, - { - "author_name": "Francesco Giaroni", - "author_inst": "Policlinico of Modena" - }, - { - "author_name": "Andrea Melluso", - "author_inst": "Policlinico of Modena" - }, - { - "author_name": "Martina Montani", - "author_inst": "Policlinico of Modena" - }, - { - "author_name": "Niccolo' Morisi", - "author_inst": "Policlinico of Modena" - }, - { - "author_name": "Jessica Plessi", - "author_inst": "Policlinico of Modena" - }, - { - "author_name": "Lorenzo Tei", - "author_inst": "Policlinico of Modena" - }, - { - "author_name": "Silvia Giovanella", - "author_inst": "Policlinico of Modena" - }, - { - "author_name": "Giulia Ligabue", - "author_inst": "Policlinico of Modena" - }, - { - "author_name": "Giacomo Mori", - "author_inst": "Policlinico of Modena" - }, - { - "author_name": "Giovanni Guaraldi", - "author_inst": "Policlinico of Modena" - }, - { - "author_name": "Riccardo Magistroni", - "author_inst": "Policlinico of Modena" - }, - { - "author_name": "Gianni Cappelli", - "author_inst": "Policlinico of Modena" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2021.06.04.21258376", "rel_title": "Ambient air pollution and COVID-19 in National Capital Territory of Delhi, India: a time-series evidence", @@ -704499,6 +707663,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.03.21258307", + "rel_title": "Loss of recognition of SARS-CoV-2 B.1.351 variant spike epitopes but overall preservation of T cell immunity", + "rel_date": "2021-06-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258307", + "rel_abs": "SARS-CoV-2 variants have emerged that escape neutralization and potentially impact vaccine efficacy. T cell responses play a role in protection from reinfection and severe disease, but the potential for spike mutations to affect T cell immunity is poorly studied. We assessed both neutralizing antibody and T cell responses in 44 South African COVID-19 patients infected either with B.1.351, now dominant in South Africa, or infected prior to its emergence ( first wave), to provide an overall measure of immune evasion. We show for the first time that robust spike-specific CD4 and CD8 T cell responses were detectable in B.1.351-infected patients, similar to first wave patients. Using peptides spanning only the B.1.351 mutated regions, we identified CD4 T cell responses targeting the wild type peptides in 12/22 (54.5%) first wave patients, all of whom failed to recognize corresponding B.1.351-mutated peptides (p=0.0005). However, responses to the mutated regions formed only a small proportion (15.7%) of the overall CD4 response, and few patients (3/44) mounted CD8 responses that targeted the mutated regions. First wave patients showed a 12.7 fold reduction in plasma neutralization of B.1.351. This study shows that despite loss of recognition of immunodominant CD4 epitope(s), overall CD4 and CD8 T cell responses to B.1.351 are preserved. These observations may explain why, despite substantial loss of neutralizing antibody activity against B.1.351, several vaccines have retained the ability to protect against severe COVID-19 disease.\n\nOne Sentence SummaryT cell immunity to SARS-CoV-2 B.1.351 is preserved despite some loss of variant epitope recognition by CD4 T cells.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Catherine Riou", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Roanne Keeton", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Thandeka Moyo-Gwete", + "author_inst": "National Institute for Communicable Diseases" + }, + { + "author_name": "Tandile Hermanus", + "author_inst": "National Institute for Communicable Diseases" + }, + { + "author_name": "Prudence Kgagudi", + "author_inst": "National Institute for Communicable Diseases" + }, + { + "author_name": "Richard Baguma", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Houriiyah Tegally", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP)" + }, + { + "author_name": "Deelan Doolabh", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Arash Iranzadeh", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Lynn Tyers", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Hygon Mutavhatsindi", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Marius Tincho", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Ntombi Benede", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Gert Marais", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Lionel Chinhoyi", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Mathilda Mennen", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Sango Skelem", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Elsa Bruyn", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Cari Stek", + "author_inst": "University of Cape Town" + }, + { + "author_name": "- SA-CIN", + "author_inst": "" + }, + { + "author_name": "Tulio de Oliveira", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP)" + }, + { + "author_name": "Carolyn Williamson", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Penny Moore", + "author_inst": "National Institute for Communicable Diseases" + }, + { + "author_name": "Robert Wilkinson", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Ntobeko Ntusi", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Wendy Burgers", + "author_inst": "University of Cape Town" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.04.447160", "rel_title": "Drug Repurposing for the SARS-CoV-2 Papain-Like Protease", @@ -704664,65 +707947,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.03.21258300", - "rel_title": "Field evaluation of specificity and sensitivity of a standard SARS-CoV-2 antigen rapid diagnostic test: A prospective study at a teaching hospital in Northern Ghana", - "rel_date": "2021-06-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258300", - "rel_abs": "BackgroundThe testing capacity for SARS-CoV-2 in Africa is rather limited. Antigen-detection rapid diagnostic tests (Ag-RDTs) are a cheap and rapid alternative to reverse transcriptase-polymerase chain reaction (RT-PCR) tests, but there is little data about their performance under real life conditions in tropical countries.\n\nObjectiveTo evaluate the performance of a standard Ag-RDT in a population of a major hospital in northern Ghana.\n\nMethodsProspective, cross-sectional, blinded verification of the performance of the SD Biosensor Standard Q SARS-CoV-2 Ag-RDT under real life conditions in 135 symptomatic patients and 58 contacts of RT-PCR positives at Tamale Teaching Hospital in February 2021. Nasopharyngeal samples were taken under standard conditions and tested against RT-PCR in the hospital laboratory.\n\nResults193 participants (median age 35 years, 109 male) were included into the study for which both RT-PCR test and Ag-RDT results were available. A total of 42 (22%) were RT-PCR positive. Of the 42 RT-PCR positives, 27 were Ag-RDT positive, resulting in a sensitivity of 64% (95% CI 49-79). Sensitivity among symptomatic patients was 58% (95% CI 38-78). 123 were identified Ag-RDT negatives of the 151 RT-PCR negatives, resulting in a specificity of 81% (95% CI 75-87).\n\nConclusionsSARS-CoV-2 Ag-RDTs appear to have a rather low sensitivity and particularly a low specificity under real life conditions in Africa. The role of existing Ag-RDTs in countries with high-temperature climates and limited resources still needs more data and discussion.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Alhassan Abdul-Mumin", - "author_inst": "University for Development Studies, School of Medicine, Department of Paediatrics and Child Health, Tamale, Ghana; Tamale Teaching Hospital, Tamale, Ghana" - }, - { - "author_name": "Abdulai Abubakari", - "author_inst": "University for Development Studies, School of Public Health, Department of Global Health, Tamale, Ghana" - }, - { - "author_name": "Faith Agbozo", - "author_inst": "University of Health and Allied Sciences, School of Public Health, Department of Family and Community Health, Hohoe, Ghana" - }, - { - "author_name": "Abass Abdul-Karim", - "author_inst": "Ghana Health Service, Zonal Public Health and Reference Laboratory, Tamale, Ghana" - }, - { - "author_name": "Benjamin Demah Nuertey", - "author_inst": "Tamale Teaching Hospital, Tamale, Ghana" - }, - { - "author_name": "Kareem Mumuni", - "author_inst": "Tamale Teaching Hospital, Tamale, Ghana" - }, - { - "author_name": "Anna-Katharina Heuschen", - "author_inst": "Institute for Global Health, University Hospital Heidelberg, Ruprecht-Karls-University Heidelberg" - }, - { - "author_name": "Lisa Hennig", - "author_inst": "Institute for Global Health, University Hospital Heidelberg, Ruprecht-Karls-University Heidelberg" - }, - { - "author_name": "Claudia M. Denkinger", - "author_inst": "Institute for Global Health, University Hospital Heidelberg, Ruprecht-Karls-University Heidelberg" - }, - { - "author_name": "Olaf Mueller", - "author_inst": "Institute for Global Health, University Hospital Heidelberg, Ruprecht-Karls-University Heidelberg" - }, - { - "author_name": "Albrecht Jahn", - "author_inst": "Institute for Global Health, University Hospital Heidelberg, Ruprecht-Karls-University Heidelberg" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.04.447156", "rel_title": "Combustible and electronic cigarette exposures increase ACE2 activity and SARS-CoV-2 Spike binding", @@ -706157,6 +709381,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.06.03.446942", + "rel_title": "Visualization of SARS-CoV-2 infection dynamic", + "rel_date": "2021-06-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.03.446942", + "rel_abs": "Replication-competent recombinant viruses expressing reporter genes provide valuable tools to investigate viral infection. Low levels of reporter gene expressed from previous reporter-expressing rSARS-CoV-2 have jeopardized their use to monitor the dynamics of SARS-CoV-2 infection in vitro or in vivo. Here, we report an alternative strategy where reporter genes were placed upstream of the viral nucleocapsid gene followed by a 2A cleavage peptide. The higher levels of reporter expression using this strategy resulted in efficient visualization of rSARS-CoV-2 in infected cultured cells and K18 hACE2 transgenic mice. Importantly, real-time viral infection was readily tracked using a non-invasive in vivo imaging system and allowed us to rapidly identify antibodies which are able to neutralize SARS-CoV-2 infection in vivo. Notably, these reporter-expressing rSARS-CoV-2 retained wild-type virus like pathogenicity in vivo, supporting their use to investigate viral infection, dissemination, pathogenesis and therapeutic interventions for the treatment of SARS-CoV-2 in vivo.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Chengjin Ye", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Kevin Chiem", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jun-Gyu Park", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jesus Silvas", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Desarey Morales Vasquez", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jordi B Torrelles", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "James Kobie", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Mark R Walter", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Juan C de la Torre", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.04.447114", "rel_title": "Sub-Picomolar Detection of SARS-CoV-2 RBD via Computationally-Optimized Peptide Beacons", @@ -706298,41 +709577,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.03.21258009", - "rel_title": "Comparing India's second COVID wave with the first wave, a single center experience", - "rel_date": "2021-06-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258009", - "rel_abs": "BackgroundThe COVID-19 pandemic has resurfaced in India in the form of a hard-hitting second wave. This study aims to compare the clinical profile of the first wave (April-June 2020) and the second wave (March-May 2021) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a single tertiary care center of India. This will help prioritize the target population group and management strategies in the upcoming third wave if any.\n\nMethodsIn this retrospective observational study, we examined the demographic profile, symptoms at presentation, the severity of illness, baseline investigations, treatments received, underlying comorbidities, and outcomes of the COVID-19 patients belonging to the first (W1) and the second wave (W2) of the pandemic in India.\n\nFindingsAmong 106 patients in W1 and 104 patients in W2, the age group affected most was 37{middle dot}1 (SD=16{middle dot}9) years compared with 50.5 (SD=17.7) years respectively. The baseline oxygen saturation is lower in W2, being 84{middle dot}0 (13{middle dot}4) % compared with 91{middle dot}9 (7{middle dot}4) % in W1. 70.2 % of the cases belonged to the severe category in W2 compared to 37.5% in W1. W2 patients demonstrated higher transaminase levels [SGOT, 108.3 (99.3) v/s 54.6 (69.3); SGPT, 97.6 (82.3) v/s 58.7 (69.7)] with respect to W1. Similarly, the CT severity score for W2 [29.5 (6.7)] was higher than W1 [23{middle dot}2 (11{middle dot}5)][All P<0.05]. The proportion of patients requiring oxygen (81.8% v/s 11.2%), high flow nasal cannula (11.4% v/s 5.6%), non-invasive ventilation (41.2% v/s 1.5%), invasive ventilation (24.5% v/s 0.9%), as well as ICU/HDU admissions (56.4% v/s 12.0%) was higher for W2 as compared with W1. The measured case fatality rate varies from 29% for W2 to 9.6% for W1.\n\nInterpretationHigher age, oxygen requirement, ventilator requirement, ICU admission, and organ impairment are more prevalent in the admitted COVID-19 cases during the second wave that has hit India compared to the first wave and associated with more fatalities. Strategy for another wave should be planned accordingly.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSWhat are the differences between the clinical profile of the first wave (W1) and the second wave (W2) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a single tertiary care center of India?\n\nFindingsIn this observational study among 106 patients in W1 (April-June 2020) and 104 patients in W2 (March-May 2021), there were higher proportion of increased age, oxygen requirement, ventilator requirement, ICU admission, and organ impairment in the admitted COVID-19 cases during the second wave.\n\nMeaningThe second wave hits India badly than the first wave and associated with more fatalities.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mayank Kapoor", - "author_inst": "AIIMS Rishikesh" - }, - { - "author_name": "Budha O Singh", - "author_inst": "AIIMS Rishikesh" - }, - { - "author_name": "Prasan Kumar Panda", - "author_inst": "AIIMS Rishikesh" - }, - { - "author_name": "Pathik Dhangar", - "author_inst": "AIIMS Rishikesh" - }, - { - "author_name": "Anant Kataria", - "author_inst": "AIIMS Rishikesh" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.04.21257852", "rel_title": "Definitions matter: heterogeneity of COVID-19 disease severity criteria and incomplete reporting compromise meta-analysis", @@ -708091,6 +711335,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.06.01.21258172", + "rel_title": "Humoral and cellular immune response against SARS-CoV-2 variants following heterologous and homologous ChAdOx1 nCoV-19/BNT162b2 vaccination.", + "rel_date": "2021-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.01.21258172", + "rel_abs": "Cerebral venous thrombosis was reported as a rare but serious adverse event in young and middle-aged vaccinees following immunization with AstraZenecas ChAdOx1-nCov-19 vaccine. As a consequence, several European governments recommended using this vaccine only in individuals older than 60 years leaving millions of ChAd primed individuals with the decision to either receive a second shot of ChAd or a heterologous boost with mRNA-based vaccines. However, such combinations have not been tested so far. We used Hannover Medical Schools COVID-19 Contact (CoCo) Study cohort of health care professionals (HCP) to monitor ChAd primed immune responses before and three weeks after booster with ChAd or BioNTech/Pfizers BNT162b2. Whilst both vaccines boosted prime-induced immunity, BNT induced significantly higher frequencies of Spike-specific CD4 and CD8 T cells and, in particular, high titers of neutralizing antibodies against the B.1.1.7, B.1.351 and the P.1 variants of concern of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2).", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Joana Barros-Martins", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Swantje Hammerschmidt", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Anne Cossmann", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Ivan Odak", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Metodi V Stankov", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Gema Morillas Ramos", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Alexandra Jablonka", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Annika Heidemann", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Christiane Ritter", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Michaela Friedrichsen", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Christian R Schultze-Florey", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Inga Ravens", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Willenzon Stefanie", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Anja Bubke", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Jasmin Ristenpart", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Anika Janssen", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "George Ssebyatika", + "author_inst": "University of Luebeck" + }, + { + "author_name": "Guenter Bernhardt", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Jan R Muench", + "author_inst": "Ulm University" + }, + { + "author_name": "Markus Hoffmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" + }, + { + "author_name": "Stefan Poehlmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" + }, + { + "author_name": "Thomas Krey", + "author_inst": "University of Luebeck" + }, + { + "author_name": "Berislav Bosnjak", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Reinhold Foerster", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Georg MN Behrens", + "author_inst": "Hannover Medical School" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.01.21258150", "rel_title": "Ten months of temporal variation in the clinical journey of hospitalised patients with COVID-19: an observational cohort", @@ -708248,57 +711607,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.02.21258073", - "rel_title": "Affinity tag coating enables reliable detection of antigen-specific B cells in ImmunoSpot assays", - "rel_date": "2021-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.02.21258073", - "rel_abs": "Assessment of humoral immunity to SARS-CoV-2 and other infectious agents is typically restricted to detecting antigen-specific antibody in the serum. Rarely does immune monitoring entail assessment of the memory B cell compartment itself, although it is these cells that engage in secondary antibody responses capable of mediating immune protection when pre-existing antibodies fail to prevent re-infection. There are few techniques that are capable of detecting rare antigen-specific B cells while also providing information regarding their precursory frequency, class/subclass usage and functional affinity. In theory, the ELISPOT/FluoroSpot (collectively ImmunoSpot) assay platform is ideally-suited for antigen-specific B cell assessments since it provides this information at single-cell resolution for individual antibody-secreting cells (ASC). Here, we tested the hypothesis that antigen coating efficiency could be universally improved across a diverse set of viral antigens if the standard direct (non-specific, low affinity) antigen absorption to the membrane was substituted by high affinity capture. Specifically, we report an enhancement in assay sensitivity and a reduction in required protein concentrations through the capture of recombinant proteins via their encoded hexahistidine (6XHis) affinity tag. Affinity tag antigen coating enabled detection of SARS-CoV-2 Spike receptor binding domain (RBD)-reactive ASC, and also significantly improved assay performance using additional control antigens. Collectively, establishment of a universal antigen coating approach streamlines characterization of the memory B cell compartment after SARS-CoV-2 infection or COVID-19 vaccinations, and facilitates high-throughput immune monitoring efforts of large donor cohorts in general.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sebastian Koppert", - "author_inst": "Institute of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nurnberg" - }, - { - "author_name": "Carla Wolf", - "author_inst": "Institute of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nurnberg" - }, - { - "author_name": "Noemi Becza", - "author_inst": "Research & Development Department, Cellular Technology Limited" - }, - { - "author_name": "Giuseppe A Sautto", - "author_inst": "Center for Vaccines and Immunology, University of Georgia" - }, - { - "author_name": "Fridolin Franke", - "author_inst": "Research & Development Department, Cellular Technology Limited" - }, - { - "author_name": "Stefanie Kurten", - "author_inst": "Institute of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nurnberg" - }, - { - "author_name": "Paul V Lehmann", - "author_inst": "Research & Development Department, Cellular Technology Limited" - }, - { - "author_name": "Ted M Ross", - "author_inst": "University System of Georgia" - }, - { - "author_name": "Greg A Kirchenbaum", - "author_inst": "Research & Development Department, Cellular Technology Limited" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.06.01.21258143", "rel_title": "The COVID-19 pandemic storm in India subsides, but the calm is still far away", @@ -710001,6 +713309,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.05.29.21258010", + "rel_title": "Rapid and sustained decline in CXCL-10 (IP-10) annotates clinical outcomes following TNF-\u03b1 antagonist therapy in hospitalized patients with severe and critical COVID-19 respiratory failure", + "rel_date": "2021-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.29.21258010", + "rel_abs": "BackgroundA feed-forward pathological signaling loop generated by TNF and IFN-{gamma} in inflamed lung tissue, driving CXCL-10 (IP-10) and CXCL-9 chemokine-mediated activated T-cell and monocyte/macrophage tissue recruitment, may define, sustain and amplify the inflammatory biology of lethal COVID-19 respiratory failure.\n\nMethodsTo assess TNF-antagonist therapy, 18 hospitalized adults with hypoxic respiratory failure and COVID-19 pneumonia received single-dose infliximab-abda therapy 5mg/kg intravenously between April and December 2020. The primary endpoint was time to increase in oxygen saturation to fraction of inspired oxygen ratio (SpO2/FiO2) by [≥] 50 compared to baseline and sustained for 48 hours. Secondary endpoints included 28-day mortality, dynamic cytokine profiles (Human Cytokine 48-Plex Discovery Assay, Eve Technologies), secondary infections, duration of supplemental oxygen support and hospitalization.\n\nFindingsPatients were predominantly in critical respiratory failure (15/18, 83%), male (14/18, 78%), above 60 years (median 63 yrs, range 31-80), race-ethnic minorities (13/18, 72%), lymphopenic (13/18, 72%), steroid-treated (17/18, 94%), with a median ferritin of 1953ng/ml. Sixteen patients (89%) met the primary endpoint within a median of 4 days, 15/18 (83%) recovered from respiratory failure, and 14/18 (78%) were discharged in a median of 8 days and were alive at 28-day follow-up. Deaths among three patients [≥] 65yrs age with pre-existing lung disease or multiple comorbidities were attributed to secondary lung infection. Mean plasma IP-10 levels declined sharply from 9183 pg/ml to 483 pg/ml at Day 3 and further to 146 pg/ml at Day 14/discharge. Significant declines in IFN-{gamma}, TNF, IL-27, CRP and ferritin were specifically observed at Day 3 whereas other cytokines were unmodified. IL-6 levels declined sharply among patients with baseline levels >10 pg/ml. Among 13 lymphopenic patients, six (46%) had resolution of lymphopenia by day 3, and 11 by day 14. CXCR3-ligand (IP-10 and CXCL-9) declines were strongly correlated among patients with lymphopenia reversal (Day 3, Pearson r: 0.98, p-value: 0.0006).\n\nInterpretationConsistent with a pathophysiological role of TNF, the clinical and cytokine data indicate that infliximab-abda may rapidly abrogate pathological inflammatory signaling to facilitate clinical recovery in severe and critical COVID-19. Randomized studies are required to formally assess mortality outcomes. Funding: National Center for Advancing Translational Sciences", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Hilal Hachem", + "author_inst": "Tufts Medical Center, Boston MA (current affiliation: Northern Light Cancer Institute,Bangor ME)" + }, + { + "author_name": "Amandeep Godara", + "author_inst": "Tufts Medical Center, Boston MA (current affiliation: University of Utah, Salt Lake City, UT)" + }, + { + "author_name": "Courtney Schroeder", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Daniel Fein", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Hashim Mann", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Christian Lawlor", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Jill Marshall", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Andreas Klein", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Deborah Poutsiaka", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Janis L Breeze", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Raghav Joshi", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Paul Mathew", + "author_inst": "Tufts Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.25.21257820", "rel_title": "The Female Predominant Persistent Immune Dysregulation of the Post COVID Syndrome: A Cohort Study", @@ -710178,57 +713549,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.27.21257583", - "rel_title": "Vaccine effectiveness of the BNT162b2 mRNA COVID-19 vaccine against RT-PCR confirmed SARS-CoV-2 infections, hospitalisations and mortality in prioritised risk groups", - "rel_date": "2021-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.27.21257583", - "rel_abs": "ObjectiveTo estimate in a real life setting, the vaccine effectiveness of the BNT162b2 mRNA vaccine against confirmed SARS-CoV-2 infection, hospital admission, and death among five priority groups for vaccination\n\nDesignCohort study\n\nSettingRoll-out of the BNT162b2 mRNA vaccine in Denmark\n\nParticipants864,096 individuals who were first inline to receive the BNT162b2 mRNA vaccine: 46,101 long-term care facility (LTCF) residents, 61,805 individuals 65 years and older living at home but requiring practical help and personal care (65PHC), 98,533 individuals [≥]85 years of age (+85), 425,799 health-care workers (HCWs), and 231,858 individuals with comorbidities that predispose for severe COVID-19 disease (SCD).\n\nInterventionvaccination with BNT162b2 mRNA vaccine\n\nMain outcome measuresRT-PCR confirmed SARS-CoV-2 infections, COVID-19 related admissions within 14 days after a confirmed SARS-CoV-2 infection, all-cause admission, COVID-19 related death within 30 days after confirmed SARS-CoV-2 infection, and all-cause death.\n\nResultsBeyond 7 days after the second dose, the VE against SARS-CoV-2 infection in all groups ranged from 53-86%. In 65PHC, HCW and SCD, we observed a substantial reduction in risk of infection 0-7 days after the second dose ranging from 46-71%. The VE against COVID-19 related admissions ranged from 75-87% in all groups except +85 and HCWs where no events occurred. For COVID-19 related deaths, a significant VE was observed in LTCF residents (VE of 89%) and 65PHC (VE of 97%), whereas no events were observed in the three remaining groups. VE against all-cause death ranged from 26-73% in all groups except HCW where an insignificant VE was estimated. For all-cause admission, the VE ranged from 37-50% in all groups except in SCD where a negative VE was observed.\n\nConclusionIn a real-life setting and more than 7 days after the second dose of BNT162b2 mRNA was administered to the most vulnerable individuals, the vaccine was associated with a reduction of SARS-CoV-2 infection (53-86%) and COVID-19 related admissions ([≥]75%) or deaths ([≥]89%).", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Hanne-Dorthe Emborg", - "author_inst": "Statens Serum Institut, Department of Infectious Disease Epidemiology and Prevention, Copenhagen, Denmark" - }, - { - "author_name": "Palle Valentiner-Branth", - "author_inst": "Statens Serum Institut, Department of Infectious Disease Epidemiology and Prevention, Copenhagen, Denmark" - }, - { - "author_name": "Astrid Blicher Schelde", - "author_inst": "Statens Serum Institut, Department of Infectious Disease Epidemiology and Prevention, Copenhagen, Denmark" - }, - { - "author_name": "Katrine Finderup Nielsen", - "author_inst": "Statens Serum Institut, Department of Infectious Disease Epidemiology and Prevention, Copenhagen, Denmark" - }, - { - "author_name": "Mie Agermose Gram", - "author_inst": "Statens Serum Institut, Department of Infectious Disease Epidemiology and Prevention, Copenhagen, Denmark" - }, - { - "author_name": "Ida Rask Moustsen-Helms", - "author_inst": "Statens Serum Institut, Department of Infectious Disease Epidemiology and Prevention, Copenhagen, Denmark" - }, - { - "author_name": "Manon Chaine", - "author_inst": "Statens Serum Institut, Data Integration and Analysis, Copenhagen, Denmark" - }, - { - "author_name": "Ulla Holten Seidelin", - "author_inst": "Statens Serum Institut, Data Integration and Analysis, Copenhagen, Denmark" - }, - { - "author_name": "Jens Nielsen", - "author_inst": "Statens Serum Institut, Department of Infectious Disease Epidemiology and Prevention, Copenhagen, Denmark" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.01.21258140", "rel_title": "Occupational inequalities in the prevalence of COVID-19: A longitudinal observational study of England, August 2020 to January 2021", @@ -711775,6 +715095,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.28.21258008", + "rel_title": "College Students' COVID-19 Vaccine Beliefs and Intentions: Implications for interventions", + "rel_date": "2021-06-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.28.21258008", + "rel_abs": "On college campuses, effective management of vaccine-preventable transmissible pathogens requires understanding student vaccination intentions. This is necessary for developing and tailoring health messaging to maximize uptake of health information and vaccines. The current study explored students beliefs and attitudes about vaccines in general, and the new COVID-19 vaccines specifically. This study provides insights into effective health messaging needed to rapidly increase COVID-19 vaccination on college campuses--information that will continue to be informative in future academic years across a broad scope of pathogens. Data were collected via an online cohort survey of college students aged 18 years and older residing on or near the campus of a large public university during fall 2020. Overall, we found COVID-19 vaccine hesitancy in college students correlated strongly with some concerns about vaccines in general as well as with concerns specific to COVID-19 vaccines. Taken together, these results provide further insight for message development and delivery, and can inform more effective interventions to advance critical public health outcomes on college campuses beyond the current pandemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Meg L Small", + "author_inst": "Penn State University" + }, + { + "author_name": "Robert Lennon", + "author_inst": "Penn State University" + }, + { + "author_name": "John Dziak", + "author_inst": "Penn State University" + }, + { + "author_name": "Rachel A Smith", + "author_inst": "Penn State University" + }, + { + "author_name": "Gillian Sommerville", + "author_inst": "Penn State University" + }, + { + "author_name": "Nita Bharti", + "author_inst": "Penn State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.31.21257656", "rel_title": "Acute kidney injury in hospitalized patients due to COVID-19", @@ -711964,61 +715323,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.01.21257665", - "rel_title": "Self-resetting Molecular Probes for Nucleic Acids Enabled by Fuel Dissipative Systems", - "rel_date": "2021-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.01.21257665", - "rel_abs": "Withdraw disclaimer statementThe authors have withdrawn this manuscript because lots of additional experiments which are not discussed in this version have been performed to further support the conclusion. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Na Li", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Yu Liu", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Zhe Yin", - "author_inst": "Academy of Military Medical Sciences Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Rui Liu", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Linghao Zhang", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Yuee Zhao", - "author_inst": "Academy of Military Medical Sciences Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Liang Ma", - "author_inst": "China-Japan Friendship Hospital" - }, - { - "author_name": "Xiaochuan Dai", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Dongsheng Zhou", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Xin Su", - "author_inst": "Beijing University of Chemical Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.29.21258056", "rel_title": "Covid-19: Comparisons by Country and Implications for Future Pandemics", @@ -713229,6 +716533,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2021.05.28.21257993", + "rel_title": "The UGT2A1/UGT2A2 locus is associated with COVID-19-related anosmia", + "rel_date": "2021-05-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.28.21257993", + "rel_abs": "Loss of sense of smell is a characteristic symptom of infection with SARS-CoV-2. However, specific mechanisms linking infection with loss of smell are poorly understood. Using self-reported symptom data from the 23andMe COVID-19 study, we describe the demographic patterns associated with COVID-19 related anosmia, and find the symptom is more often reported in women and younger respondents, and less often by those of East Asian and African American ancestry compared to those of European ancestry. We ran a trans-ethnic genome-wide association study (GWAS) comparing loss of smell or taste (n=47,298) with no loss of smell or taste (n=22,543) among those with a positive SARS-CoV-2 test result. We identified an association (rs7688383) in the vicinity of the UGT2A1 and UGT2A2 genes (OR=1.115, p-value=4x10-15), which have been linked to olfactory function. These results may shed light on the biological mechanisms underlying COVID-19 related anosmia.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Janie F. Shelton", + "author_inst": "23andMe" + }, + { + "author_name": "Anjali J. Shastri", + "author_inst": "23andMe" + }, + { + "author_name": "- The 23andMe COVID-19 Team", + "author_inst": "" + }, + { + "author_name": "Stella Aslibekyan", + "author_inst": "23andMe" + }, + { + "author_name": "Adam Auton", + "author_inst": "23andMe" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2021.05.28.21258007", "rel_title": "Temporal stability and detection sensitivity of the dry swab-based diagnosis of SARS-CoV-2", @@ -713358,49 +716697,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.05.29.445137", - "rel_title": "Functional characterization of SARS-CoV-2 vaccine elicited antibodies in immunologically naive and pre-immune humans", - "rel_date": "2021-05-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.29.445137", - "rel_abs": "As the COVID-19 pandemic continues, the authorization of vaccines for emergency use has been crucial in slowing down the rate of infection and transmission of the SARS-CoV-2 virus that causes COVID-19. In order to investigate the longitudinal serological responses to SARS-CoV-2 natural infection and vaccination, a large-scale, multi-year serosurveillance program entitled SPARTA (SARS SeroPrevalence and Respiratory Tract Assessment) was initiated at 4 locations in the U.S. The serological assay presented here measuring IgG binding to the SARS-CoV-2 receptor binding domain (RBD) detected antibodies elicited by SARS-CoV-2 infection or vaccination with a 95.5% sensitivity and a 95.9% specificity. We used this assay to screen more than 3100 participants and selected 20 previously infected pre-immune and 32 immunologically naive participants to analyze their antibody binding to RBD and viral neutralization (VN) responses following vaccination with two doses of either the Pfizer-BioNTech BNT162b2 or the Moderna mRNA-1273 vaccine. Vaccination not only elicited a more robust immune reaction than natural infection, but the level of neutralizing and anti-RBD antibody binding after vaccination is also significantly higher in pre-immune participants compared to immunologically naive participants (p<0.0033). Furthermore, the administration of the second vaccination did not further increase the neutralizing or binding antibody levels in pre-immune participants (p=0.69). However, ~46% of the immunologically naive participants required both vaccinations to seroconvert.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "David Forgacs", - "author_inst": "University of Georgia" - }, - { - "author_name": "Hyesun Jang", - "author_inst": "University of Georgia" - }, - { - "author_name": "Rodrigo B Abreu", - "author_inst": "University of Georgia" - }, - { - "author_name": "Hannah B Hanley", - "author_inst": "University of Georgia" - }, - { - "author_name": "Jasper L Gattiker", - "author_inst": "University of Georgia" - }, - { - "author_name": "Alexandria M Jefferson", - "author_inst": "University of Georgia" - }, - { - "author_name": "Ted M Ross", - "author_inst": "University of Georgia" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.05.30.446357", "rel_title": "Complete protection by a single dose skin patch delivered SARS-CoV-2 spike vaccine", @@ -714850,6 +718146,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.26.21257854", + "rel_title": "Corowa-kun: Impact of a COVID-19 vaccine information chatbot on vaccine hesitancy, Japan 2021", + "rel_date": "2021-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.26.21257854", + "rel_abs": "BackgroundFew studies have assessed how mobile messenger apps affect COVID-19 vaccine hesitancy. We created a COVID-19 vaccine information chatbot in a popular messenger app in Japan to answer commonly asked questions.\n\nMethodsLINE is the most popular messenger app in Japan. Corowa-kun, a free chatbot, was created in LINE on February 6, 2021. Corowa-kun provides instant, automated answers to frequently asked COVID-19 vaccine questions. In addition, a cross-sectional survey assessing COVID-19 vaccine hesitancy was conducted via Corowa-kun during April 5-12, 2021.\n\nResultsA total of 59,676 persons used Corowa-kun during February-April 2021. Of them, 10,192 users (17%) participated in the survey. Median age was 55 years (range 16-97), and most were female (74%). Intention to receive a COVID-19 vaccine increased from 59% to 80% after using Corowa-kun (p < 0.01). Overall, 20% remained hesitant: 16% (1,675) were unsure, and 4% (364) did not intend to be vaccinated. Factors associated with vaccine hesitancy were: age 16 to 34 (odds ratio [OR] = 3.7, 95% confidential interval [CI]: 3.0-4.6, compared to age [≥]65), female sex (OR = 2.4, Cl: 2.1-2.8), and history of a previous vaccine side-effect (OR = 2.5, Cl: 2.2-2.9). Being a physician (OR = 0.2, Cl: 0.1-0.4) and having received a flu vaccine the prior season (OR = 0.4, Cl: 0.3-0.4) were protective.\n\nConclusionsCorowa-kun reduced vaccine hesitancy by providing COVID-19 vaccine information in a messenger app. Mobile messenger apps could be leveraged to increase COVID-19 vaccine acceptance.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Takaaki Kobayashi", + "author_inst": "University of Iowa Hospitals and Clinics" + }, + { + "author_name": "Yuka Nishina", + "author_inst": "Juntendo University Faculty of Medicine" + }, + { + "author_name": "Hana Tomoi", + "author_inst": "MSc Public Health (Cand.), Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Ko Harada", + "author_inst": "Okayama University Graduate School of Medicine" + }, + { + "author_name": "Kyuto Tanaka", + "author_inst": "Kawasaki Municipal Hospital" + }, + { + "author_name": "Eiyu Matsumoto", + "author_inst": "University of Iowa Hospitals & Clinics" + }, + { + "author_name": "Kenta Horimukai", + "author_inst": "Jikei University Katsushika Medical Center" + }, + { + "author_name": "Jun Ishihara", + "author_inst": "Imperial College London" + }, + { + "author_name": "Shugo Sasaki", + "author_inst": "Saitama Medical University Hospital" + }, + { + "author_name": "Kanako Inaba", + "author_inst": "Kanto Central Hospital" + }, + { + "author_name": "Kyosuke Seguchi", + "author_inst": "Kameda Medical Center" + }, + { + "author_name": "Hiromizu Takahashi", + "author_inst": "Juntendo University Faculty of Medicine" + }, + { + "author_name": "Jorge Salinas", + "author_inst": "University of Iowa Hospitals & Clinics" + }, + { + "author_name": "Yuji Yamada", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.29.443900", "rel_title": "Broadening a SARS-CoV-1 neutralizing antibody for potent SARS-CoV-2 neutralization through directed evolution", @@ -715035,81 +718402,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.05.28.446065", - "rel_title": "Human genome integration of SARS-CoV-2 contradicted by long-read sequencing", - "rel_date": "2021-05-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.28.446065", - "rel_abs": "A recent study proposed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hijacks the LINE-1 (L1) retrotransposition machinery to integrate into the DNA of infected cells. If confirmed, this finding could have significant clinical implications. Here, we applied deep (>50x) long-read Oxford Nanopore Technologies (ONT) sequencing to HEK293T cells infected with SARS-CoV-2, and did not find the virus integrated into the genome. By examining ONT data from separate HEK293T cultivars, we completely resolved 78 L1 insertions arising in vitro in the absence of L1 overexpression systems. ONT sequencing applied to hepatitis B virus (HBV) positive liver cancer tissues located a single HBV insertion. These experiments demonstrate reliable resolution of retrotransposon and exogenous virus insertions via ONT sequencing. That we found no evidence of SARS-CoV-2 integration suggests such events are, at most, extremely rare in vivo, and therefore are unlikely to drive oncogenesis or explain post-recovery detection of the virus.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Nathan Smits", - "author_inst": "Mater Research Institute - University of Queensland, TRI Building, Woolloongabba QLD 4102, Australia." - }, - { - "author_name": "Jay Rasmussen", - "author_inst": "Queensland Brain Institute, University of Queensland, Brisbane QLD 4072, Australia." - }, - { - "author_name": "Gabriela O Bodea", - "author_inst": "Queensland Brain Institute, University of Queensland, Brisbane QLD 4072, Australia." - }, - { - "author_name": "Alberto A Amarilla", - "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane QLD 4072, Australia." - }, - { - "author_name": "Patricia Gerdes", - "author_inst": "Mater Research Institute - University of Queensland, TRI Building, Woolloongabba QLD 4102, Australia." - }, - { - "author_name": "Francisco J Sanchez-Luque", - "author_inst": "GENYO, Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PTS Granada 18016, Spain." - }, - { - "author_name": "Prabha Ajjikuttira", - "author_inst": "Queensland Brain Institute, University of Queensland, Brisbane QLD 4072, Australia." - }, - { - "author_name": "Naphak Modhiran", - "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane QLD 4072, Australia." - }, - { - "author_name": "Benjamin Liang", - "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane QLD 4072, Australia." - }, - { - "author_name": "Jamila Faivre", - "author_inst": "INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France." - }, - { - "author_name": "Ira W Deveson", - "author_inst": "Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney NSW 2010, Australia." - }, - { - "author_name": "Alexander A Khromykh", - "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane QLD 4072, Australia." - }, - { - "author_name": "Daniel Watterson", - "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane QLD 4072, Australia." - }, - { - "author_name": "Adam D Ewing", - "author_inst": "Mater Research Institute - University of Queensland, TRI Building, Woolloongabba QLD 4102, Australia." - }, - { - "author_name": "Geoffrey J Faulkner", - "author_inst": "Mater Research Institute - University of Queensland, TRI Building, Woolloongabba QLD 4102, Australia." - } - ], - "version": "1", - "license": "cc_no", - "type": "contradictory results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.05.29.446300", "rel_title": "Antibody Display of cell surface receptor Tetraspanin12 and SARS-CoV-2 spike protein", @@ -716584,6 +719876,101 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.28.446159", + "rel_title": "SARS-CoV-2 transmission via apical syncytia release from primary bronchial epithelia and infectivity restriction in children epithelia", + "rel_date": "2021-05-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.28.446159", + "rel_abs": "The beta-coronavirus SARS-CoV-2 is at the origin of a persistent worldwide pandemic. SARS-CoV-2 infections initiate in the bronchi of the upper respiratory tract and are able to disseminate to the lower respiratory tract eventually causing acute severe respiratory syndrome with a high degree of mortality in the elderly. Here we use reconstituted primary bronchial epithelia from adult and children donors to follow the infection dynamic following infection with SARS-CoV-2. We show that in bronchial epithelia derived from adult donors, infections initiate in multi-ciliated cells. Then, infection rapidly spread within 24-48h throughout the whole epithelia. Within 3-4 days, large apical syncytia form between multi-ciliated cells and basal cells, which dissipate into the apical lumen. We show that these syncytia are a significant source of the released infectious dose. In stark contrast to these findings, bronchial epithelia reconstituted from children donors are intrinsically more resistant to virus infection and show active restriction of virus spread. This restriction is paired with accelerated release of IFN compared to adult donors. Taken together our findings reveal apical syncytia formation as an underappreciated source of infectious virus for either local dissemination or release into the environment. Furthermore, we provide direct evidence that children bronchial epithelia are more resistant to infection with SARS-CoV-2 providing experimental support for epidemiological observations that SARS-CoV-2 cases fatality is linked to age.\n\nSignificance StatementBronchial epithelia are the primary target for SARS-CoV-2 infections. Our work uses reconstituted bronchial epithelia from adults and children. We show that infection of adult epithelia with SARS-CoV-2 is rapid and results in the synchronized release of large clusters of infected cells and syncytia into the apical lumen contributing to the released infectious virus dose. Infection of children derived bronchial epithelia revealed an intrinsic resistance to infection and virus spread, probably as a result of a faster onset of interferon secretion. Thus, our data provide direct evidence for the epidemiological observation that children are less susceptible to SARS-CoV-2.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Guillaume Beucher", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Marie-Lise Blondot", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Alexis Celle", + "author_inst": "INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, Bordeaux, 33000, France.," + }, + { + "author_name": "Noemie Pied", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France" + }, + { + "author_name": "Patricia Recordon-Pinson", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France" + }, + { + "author_name": "Pauline Esteves", + "author_inst": "INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, Bordeaux, 33000, France.," + }, + { + "author_name": "Muriel Faure", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Mathieu Metifiot", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Sabrina Lacomme", + "author_inst": "University of Bordeaux, CNRS, Institute of Neurodegenerative Diseases, IINS, UMR 5293, Bordeaux, France, University of Bordeaux, CNRS, INSERM, Bordeaux Imaging " + }, + { + "author_name": "Denis Dacheaux", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Derrick Roy Robinson", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Gernot Laengst", + "author_inst": "Universitaet Regensburg" + }, + { + "author_name": "Fabien Beaufils", + "author_inst": "INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, Bordeaux, 33000, France.," + }, + { + "author_name": "Marie-Edith Lafon", + "author_inst": "CHU de Bordeaux, Laboratoire de Virologie, 33000 Bordeaux, France" + }, + { + "author_name": "Patrick Berger", + "author_inst": "INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, Bordeaux, 33000, France." + }, + { + "author_name": "Marc Landry", + "author_inst": "University of Bordeaux, CNRS, Institute of Neurodegenerative Diseases, IINS, UMR 5293, Bordeaux, France, University of Bordeaux, CNRS, INSERM, Bordeaux Imaging " + }, + { + "author_name": "Jean-Marie Denis Malvy", + "author_inst": "Department for infectious and tropical d ideales, University Hospital center Pellegrin, Bordeaux, & Inserm 1219, University of Bordeaux, Bordeaux, France" + }, + { + "author_name": "Thomas Trian", + "author_inst": "INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, Bordeaux, 33000, France." + }, + { + "author_name": "Marie-Line Andreola", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France" + }, + { + "author_name": "Harald Wodrich", + "author_inst": "Universite de Bordeaux" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.05.28.446020", "rel_title": "Evaluating the risk of SARS-CoV-2 transmission to bats using a decision analytical framework", @@ -716713,61 +720100,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.05.28.446155", - "rel_title": "Digital PCR to quantify ChAdOx1 nCoV-19 copies in blood and tissues", - "rel_date": "2021-05-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.28.446155", - "rel_abs": "Vaccination with the adenoviral-vector based Astra Zeneca ChAdOx1 nCov-19 vaccine is efficient and safe. However, in rare cases vaccinated individuals developed life-threatening thrombotic complications, including thrombosis in cerebral sinus and splanchnic veins. Monitoring of the applied vector in vivo represents an important precondition to study the molecular mechanisms underlying vaccine-driven adverse effects now referred to as vaccine-induced immune thrombotic thrombocytopenia (VITT). We previously have shown that digital PCR is an excellent tool to quantify transgene copies in vivo. Here we present a highly sensitive digital PCR for in-situ quantification of ChAdOx1 nCoV-19 copies. Using this method, we quantified vector copies in human serum 24, 72 and 168 hours post vaccination, and in a variety of murine tissues in an experimental vaccination model 30 minutes post injection. We describe a method for high-sensitivity quantitative detection of ChAdOx1 nCoV-19 with possible implications to elucidate the mechanisms of severe ChAdOx1 nCov-19 vaccine complications.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Anita Badbaran", - "author_inst": "UMC Hamburg-Eppendorf, Dept. of Stem Cell Transplantation" - }, - { - "author_name": "Reiner Mailer", - "author_inst": "University Medical Center Hamburg-Eppendorf, Institute of Clinical Chemistry and Laboratory Medicine" - }, - { - "author_name": "Christine Dahlke", - "author_inst": "University Medical Center Hamburg-Eppendorf, Division of Infectious Diseases, 1st Department of Medicine" - }, - { - "author_name": "Jannis Woens", - "author_inst": "University Medical Center Hamburg-Eppendorf, Dept. of Stem Cell Transplantation, Research Dept. Cell and Gene Therapy" - }, - { - "author_name": "Anahita Fathi", - "author_inst": "University Medical Center Hamburg-Eppendorf, Division of Infectious Diseases, 1st Department of Medicine" - }, - { - "author_name": "Sibylle C. Mellinghoff", - "author_inst": "University Medical Center Hamburg-Eppendorf, Division of Infectious Diseases, 1st Department of Medicine" - }, - { - "author_name": "Thomas Renne", - "author_inst": "University Medical Center Hamburg-Eppendorf, Institute of Clinical Chemistry and Laboratory Medicine" - }, - { - "author_name": "Marylyn M. Addo", - "author_inst": "University Medical Center Hamburg-Eppendorf, Division of Infectious Diseases, 1st Department of Medicine" - }, - { - "author_name": "Kristoffer Riecken", - "author_inst": "University Medical Center Hamburg-Eppendorf, Dept. of Stem Cell Transplantation, Research Dept. Cell and Gene Therapy" - }, - { - "author_name": "Boris Fehse", - "author_inst": "University Medical Center Hamburg-Eppendorf, Dept. of Stem Cell Transplantation, Research Dept. Cell and Gene Therapy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.28.446163", "rel_title": "The SARS-CoV-2 variants associated with infections in India, B.1.617, show enhanced spike cleavage by furin", @@ -718093,6 +721425,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.05.25.21257811", + "rel_title": "Fast Evaluation of Viral Emerging Risks (FEVER): A computational tool for biosurveillance, diagnostics, and mutation typing of emerging viral pathogens", + "rel_date": "2021-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.25.21257811", + "rel_abs": "Viral pathogen can rapidly evolve, adapt to novel hosts and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA viruses can mutate rapidly, hampering biosurveillance and diagnostic efforts. Here, we present a novel computational approach called FEVER (Fast Evaluation of Viral Emerging Risks) to design assays that simultaneously accomplish: 1) broad-coverage biosurveillance of an entire class of viruses, 2) accurate diagnosis of an outbreak strain, and 3) mutation typing to detect variants of public health importance. We demonstrate the application of FEVER to generate assays to simultaneously 1) detect sarbecoviruses for biosurveillance; 2) diagnose infections specifically caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); and 3) perform rapid mutation typing of the D614G SARS-CoV-2 spike variant associated with increased pathogen transmissibility. These FEVER assays had a high in silico recall (predicted positive) up to 99.7% of 525,708 SARS-CoV-2 sequences analyzed and displayed sensitivities and specificities as high as 92.4% and 100% respectively when validated in 100 clinical samples. The D614G SARS-CoV-2 spike mutation PCR test was able to identify the single nucleotide identity at position 23,403 in the viral genome of 96.6% SARS-CoV-2 positive samples without the need for sequencing. This study demonstrates the utility of FEVER to design assays for biosurveillance, diagnostics, and mutation typing to rapidly detect, track, and mitigate future outbreaks and pandemics caused by emerging viruses.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Zachary R Stromberg", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "James Theiler", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Brian T Foley", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Ad\u00e1n Myers y Guti\u00e9rrez", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Attelia Hollander", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Samantha J Courtney", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Alina Deshpande", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Ebany J Martinez-Finley", + "author_inst": "Presbyterian Healthcare Services" + }, + { + "author_name": "Jason Mitchell", + "author_inst": "Presbyterian Healthcare Services" + }, + { + "author_name": "Harshini Mukundan", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Karina Yusim", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Jessica Z Kubicek-Sutherland", + "author_inst": "Los Alamos National Laboratory" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.25.21257828", "rel_title": "Correlation of the commercial anti-SARS-CoV-2 receptor binding domain antibody test with the chemiluminescent reduction neutralizing test and possible detection of antibodies to emerging variants", @@ -718414,29 +721809,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.25.21257716", - "rel_title": "Behaviour of smokers and their influencers in the UK during COVID-19 pandemic", - "rel_date": "2021-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.25.21257716", - "rel_abs": "PurposeThe COVID-19 pandemic has resulted in unprecedented circumstances and changes in behaviour. This research sought to better understand the impact of the COVID-19 pandemic, and lockdown, on smoking behaviour in the UK from the perspectives of consumers (current and former smokers) and some of their smoking-related behaviour-influencers.\n\nDesign/methodology/approachThis research project encompassed two surveys, one for current and former smokers (Consumers) and one for those individuals in professions with the potential to influence smoking behaviours (Influencers). Both surveys were conducted online and were infield for approximately two weeks during UKs first COVID-19 lockdown. Because of the unprecedented times the society was experiencing, several questions relating directly to COVID-19 were added to the survey and this paper is based only on findings only from those questions and not the whole project. The results were analysed descriptively.\n\nFindingsA total of 954 consumers and 1027 influencers participated in the surveys. Increased smoking was reported by 67% of the consumers mainly due to stress and boredom arising out of COVID-19 lockdown. Consumers under 45 years of age, those in professional and managerial occupations, and among dual users reported increased smoking in lockdown. The COVID-19 situation changed the plans to quit smoking in 36% of consumers, with only 6% deciding to quit. Only 40% of healthcare professionals (HCPs) documented patient smoking status in over half their interactions.\n\nOriginality/ valueThis research among current and former smokers and their influencers highlights important changes in behaviour during the COVID-19 times and underscores urgent measures to be taken by HCPs and policymakers for staying on course of achieving smokefree goals despite challenges posed by COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Sudhanshu Ramesh Patwardhan", - "author_inst": "Centre for Health Research and Education" - }, - { - "author_name": "Claudia Trainer", - "author_inst": "Ogilvy Consulting Behavioural Science Practice" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.24.21257732", "rel_title": "Feasibility and utility of rapid antigen testing for COVID-19 in a university residence: a cross sectional study", @@ -720267,6 +723639,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.24.21257465", + "rel_title": "Psychological factors underpinning vaccine willingness in Israel, Japan and Hungary", + "rel_date": "2021-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257465", + "rel_abs": "The rapid international spread of the SARS-CoV-2 virus 19 led to unprecedented attempts to develop and administer an effective vaccine. However, there is considerable vaccine hesitancy in some countries. We investigated willingness to vaccinate in three nations with historically different levels of vaccine willingness and attitudes: Israel, Japan and Hungary. Employing an ecological-systems approach we analysed associations between demographic factors and health status, individual cognitions, normative pressures, trust in government, belief in COVID-19 myths and willingness to be vaccinated, using data from three nationally representative samples (Israel, N=1011 (Jan 2021); Japan, N= 997 (Feb 2021); Hungary, N=1131 (Apr 2021)). In Israel 74% indicated a willingness to vaccinate, but only 51% in Japan and 31% in Hungary. Multigroup regression analyses indicated greater vaccine willingness amongst those who perceived benefits to vaccination, anticipated regret if not vaccinated and trusted the government. Multi-group latent class analysis of ten COVID-19 (mis)beliefs identified three classes of myths, with concerns about the alteration of DNA (Israel), allergies (Hungary) and catching COVID-19 from the vaccine (Japan) specific to vaccine willingness for each culture. Intervention campaigns should focus on increasing trust and addressing culturally specific myths while emphasising the individual and social group benefits of vaccination.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Robin Goodwin", + "author_inst": "University of Warwick" + }, + { + "author_name": "Menachem Ben-Ezra", + "author_inst": "Ariel University" + }, + { + "author_name": "Masahito Takahashi", + "author_inst": "Yamaguchi University Japan" + }, + { + "author_name": "Lan Anh Nguyen Luu", + "author_inst": "Eotvos Lorand University Budapest" + }, + { + "author_name": "Krisztina Borsfay", + "author_inst": "Eotvos Lorand University Budapest" + }, + { + "author_name": "Monika Kovacs", + "author_inst": "Eotvos Lorand University Budapest" + }, + { + "author_name": "Wai Kai Hou", + "author_inst": "Education University Hong Kong" + }, + { + "author_name": "Yaira Hamama-Raz", + "author_inst": "Ariel University" + }, + { + "author_name": "Yafit Levin", + "author_inst": "University of Zurich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.21.21257612", "rel_title": "COVID-19 vaccination hesitancy model: The impact of vaccine education on controlling the outbreak in the United States", @@ -720340,49 +723763,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.24.21257365", - "rel_title": "Monitoring of SARS-CoV-2 B.1.1.7 variant early-phase spreading in South-Moravian Region in the Czech Republic and evaluation of its pathogenicity", - "rel_date": "2021-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257365", - "rel_abs": "SARS-CoV-2 emerged in Wuhan, China, in December 2019. Starting in January 2020, over a period of several months, the initial virus (Wuhan-Hu-1/2019; Wu et al. 2020) diverged in a descendant strain carrying D614G amino acid mutation in spike protein. By summer 2020 this novel coronavirus (nCoV) became the most dominant form of the virus circulating worldwide and raised serious international concern. Currently (April 2021), there are 3598 subsequent PANGO branched lineages recognized that carry numerous mutations. To date, the most emerging lineages of SARS-CoV-2 worldwide include B.1.1.7 lineage with a frequency of 48% followed by several dozens of others with frequencies 7.5% or less, such as B.1.351, B.1.1.28, B.1.2, B.1.1.519, P.1, R.1, etc. (www.nextrain.org, Centers for Disease Control and Prevention; CDC 2020 www.cdc.gov).\n\nIn this study, we monitored the spreading of B.1.1.7 lineage from the early phase of its appearance until it became predominant in the South-Moravian region of the Czech Republic. We measured significantly associated clinical marker (Ct; cycle threshold) correlating with viral load in B.1.1.7 lineage. Interestingly, we found that the spreading of B.1.1.7 strain was associated with a shift in patients average age, as compared to the former predominant lineage. Finally, we calculated the impact of the B.1.1.7 lineage on hospitalization and case fatality of the patients on the intensive care unit in the central South-Moravian faculty hospital.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Daniel Diabelko", - "author_inst": "St Anne's University Hospital, CZ-65691 Brno, Czech Republic, Faculty of Medicine, Masaryk University, Brno, the Czech Republic" - }, - { - "author_name": "Milada Dvorackova", - "author_inst": "St Anne's University Hospital, CZ-65691 Brno, Czech Republic & Faculty of Medicine, Masaryk University, Brno, the Czech Republic" - }, - { - "author_name": "Monika Dvorakova Heroldova", - "author_inst": "St Anne's University Hospital, CZ-65691 Brno, Czech Republic" - }, - { - "author_name": "Giancarlo Forte", - "author_inst": "International Clinical Research Center (ICRC), St Anne's University Hospital, CZ-65691 Brno, Czech Republic" - }, - { - "author_name": "Ivan Cundrle", - "author_inst": "St Anne's University Hospital, CZ-65691 Brno, Czech Republic" - }, - { - "author_name": "Filip Ruzicka", - "author_inst": "St Anne's University Hospital, CZ-65691 Brno, Czech Republic & Faculty of Medicine, Masaryk University, Brno, the Czech Republic" - }, - { - "author_name": "Jan Vrbsky", - "author_inst": "International Clinical Research Center (ICRC), St Anne's University Hospital, CZ-65691 Brno, Czech Republic" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.21.21257603", "rel_title": "COVID-19 County Level Severity Classification with Class Imbalance: A NearMiss Under-sampling Approach", @@ -721997,6 +725377,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.05.25.445601", + "rel_title": "Genomic Surveillance of COVID-19 Variants with Language Models and Machine Learning", + "rel_date": "2021-05-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.25.445601", + "rel_abs": "The global efforts to control COVID-19 are threatened by the rapid emergence of novel SARS-CoV-2 variants that may display undesirable characteristics such as immune escape, increased transmissibility or pathogenicity. Early prediction for emergence of new strains with these features is critical for pandemic preparedness. We present Strainflow, a supervised and causally predictive model using unsupervised latent space features of SARS-CoV-2 genome sequences. Strainflow was trained and validated on 0.9 million sequences for the period December, 2019 to June, 2021 and the frozen model was prospectively validated from July, 2021 to December, 2021. Strainflow captured the rise in cases two months ahead of the Delta and Omicron surges in most countries including the prediction of a surge in India as early as beginning of November, 2021. Entropy analysis of Strainflow unsupervised embeddings clearly reveals the explore-exploit cycles in genomic feature-space, thus adding interpretability to the deep learning based model. We also conducted codon-level analysis of our model for interpretability and biological validity of our unsupervised features. Strainflow application is openly available as an interactive web-application for prospective genomic surveillance of COVID-19 across the globe.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Sargun Nagpal", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Ridam Pal", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Ashima", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Ananya Tyagi", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Sadhana Tripathi", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Aditya Nagori", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Saad Ahmad", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Hara Prasad Mishra", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Rintu Kutum", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Tavpritesh Sethi", + "author_inst": "Indraprastha Institute of Information Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.05.24.445517", "rel_title": "Evolutionary Inference Predicts Novel ACE2 Protein Interactions Relevant to COVID-19 Pathologies", @@ -722202,33 +725637,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.05.24.445534", - "rel_title": "SARS-CoV-2 convergent evolution as a guide to explore adaptive advantage", - "rel_date": "2021-05-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.24.445534", - "rel_abs": "Much can be learned from 1.2 million sequences of SARS-CoV-2 generated during the last 15 months. Out of the overwhelming number of mutations sampled so far, only few rose to prominence in the viral population. Many of these emerged recently and independently in multiple lineages. Such a textbook example of convergent evolution at the molecular level is not only curiosity but a guide to uncover the basis for adaptive advantage behind these events. Focusing on the extent of the convergent evolution in the spike (S) protein, our report confirms that the most concerning SARS-CoV-2 lineages carry the heaviest burden of convergent S-protein mutations, suggesting their fundamental adaptive advantage. The great majority (21/25) of S-protein sites under convergent evolution tightly cluster in three functional domains; N-terminal domain, receptor-binding domain, and Furin cleavage site. We further show that among the S-protein receptor-binding motif mutations, ACE2 affinity-improving substitutions are favored. While the probed mutation space in the S protein covered all amino-acids reachable by single nucleotide changes, substitutions requiring two nucleotide changes or epistatic mutations of multiple-residues have only recently started to emerge. Unfortunately, despite their convergent emergence and physical association, most of these adaptive mutations and their combinations remain understudied. We aim to promote research of current variants which are currently understudied but may become important in the future.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jiri Zahradnik", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Jaroslav Nunvar", - "author_inst": "Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague" - }, - { - "author_name": "Gideon Schreiber", - "author_inst": "Weizmann Institute of Science" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2021.05.21.21256456", "rel_title": "Low-field thoracic magnetic stimulation increases peripheral oxygen saturation levels in coronavirus disease (COVID-19) patients: a single-blind, sham-controlled, crossover study", @@ -723743,6 +727151,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.20.21257542", + "rel_title": "The maladaptive vascular response in COVID-19 acute respiratory distress syndrome and recovery", + "rel_date": "2021-05-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21257542", + "rel_abs": "Vascular injury is a menacing element of acute respiratory distress syndrome (ARDS) pathogenesis. To better understand the role of vascular injury in COVID-19 ARDS, we used lung autopsy immunohistochemistry and blood proteomics from COVID-19 subjects at distinct timepoints in disease pathogenesis, including a hospitalized cohort at risk of ARDS development (\"at risk\", N=59), an intensive care unit cohort with ARDS (\"ARDS\", N=31), and a cohort recovering from ARDS (\"recovery\", N=12). COVID-19 ARDS lung autopsy tissue revealed an association between vascular injury and platelet-rich microthrombi. This link guided the derivation of a protein signature in the at risk cohort characterized by lower expression of vascular proteins in subjects who died, an early signal of vascular limitation termed the maladaptive vascular response. These findings were replicated in COVID-19 ARDS subjects, as well as when bacterial and influenza ARDS patients (N=29) were considered, hinting at a common final pathway of vascular injury that is more disease (ARDS) then cause (COVID-19) specific, and may be related to vascular cell death. Among recovery subjects, our vascular signature identified patients with good functional recovery one year later. This vascular injury signature could be used to identify ARDS patients most likely to benefit from vascular targeted therapies.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "David R Price", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Elisa Benedetti", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Katherine Hoffman", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Luis Gomez-Escobar", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Sergio Alvarez-Mulett", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Allyson Capili", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Hina Sarwath", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Christopher N. Parkhurst", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Elyse LaFond", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Karissa Weidman", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Arjun Ravishankar", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jin Gyu Cheong", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Richa Batra", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Mustafa Buyukozkan", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Kelsey Chetnik", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Imaani Easthausen", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Edward J. Schenck", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Alexandra C. Racanelli", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Hasina Outtz Reed", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jeffrey C. Laurence", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Steven Zvi Josefowicz", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Lindsay Lief", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Mary E. Choi", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Shahin Rafii", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Frank Schmidt", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Alain C. Borczuk", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jan Krumsiek", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Augustine M. K. Choi", + "author_inst": "Weill Cornell Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.05.20.21256954", "rel_title": "Efficacy and safety of novel probiotic formulation in adult Covid19 outpatients: a randomized, placebo-controlled clinical trial", @@ -724004,69 +727539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.22.21256870", - "rel_title": "Smartwatch Facilitated Remote Health Care for Patients Undergoing Transcatheter Aortic Valve Replacement Amid COVID-19 Pandemic", - "rel_date": "2021-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.22.21256870", - "rel_abs": "BACKGROUNDThe novel coronavirus disease-2019 (COVID-19 Pandemic) has brought difficulties to the management of patients undergoing transcatheter aortic valve replacement (TAVR).\n\nOBJECTIVESThis prospective, observational cohort study sought to evaluate the feasibility of a novel, virtual, and remote health care strategy for TAVR patients with smart wearable devices.\n\nMETHODSA total of 100 consecutive severe aortic stenosis patients who underwent elective transfemoral TAVR were enrolled and each received a HUAWEI smartwatch at least one day before TAVR. Vital signs were continuously tracked and recorded. Single lead electrocardiogram (ECG) was recorded periodically after TAVR. A designated heart team member was to provide remote data-assisted health care to address the medical demand.\n\nRESULTSThirty-eight cardiac events were reported in 34 patients after discharge, with most of the events (76.0%) were detected and confirmed by the smartwatch. Six patients were advised and readmitted to the hospital for arrhythmia events, among whom, four received pacemaker implantations. The remaining 28 (82.4%) patients received telemedicine monitoring instead of face-to-face clinical visits, and three of them received new medication treatment under a doctors online guidance of doctors. New-onset LBBB was found in 48 patients with transient and recovered spontaneously in 30 patients, while new-onset atrial fibrillation in 4 patients. There were no significant differences in the average weekly heart rates, the ratio of abnormal or low oxygen saturation when compared with the baseline. The average daily steps increased over time significantly (baseline, 870{+/-}1353 steps; first week, 1986{+/-}2406 steps; second week, 2707{+/-}2716 steps; third week, 3059{+/-}3036 steps; fourth week, 3678{+/-}3485 steps, p < 0.001).\n\nCONCLUSIONSSmartwatch can facilitate remote health care for patients undergoing TAVR during COVID-19 and enables a novel remote follow-up strategy. The majority of cardiac clinical events that occurred within 30-day follow-up were detected by the smartwatch, mainly due to the record of conduction abnormality. (SMART Watch Facilitated Early Discharge in Patients undergoing Transcatheter Aortic Valve Replacement, NCT04454177).", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Xianbao Liu", - "author_inst": "Second Affiliated Hospital Zhejiang University School of Medicine" - }, - { - "author_name": "Jiaqi Fan", - "author_inst": "Second Affiliated Hospital of Zhejiang University, School of Medicine" - }, - { - "author_name": "Yuchao Guo", - "author_inst": "Second Affiliated Hospital Zhejiang University School of Medicine" - }, - { - "author_name": "Hanyi Dai", - "author_inst": "Zhejiang University School of Medicine" - }, - { - "author_name": "Jianguo Xu", - "author_inst": "Second Affiliated Hospital Zhejiang University School of Medicine" - }, - { - "author_name": "Lihan Wang", - "author_inst": "Second Affiliated Hospital Zhejiang University School of Medicine" - }, - { - "author_name": "Po Hu", - "author_inst": "Second Affiliated Hospital Zhejiang University School of Medicine" - }, - { - "author_name": "Xinping Lin", - "author_inst": "Second Affiliated Hospital Zhejiang University School of Medicine" - }, - { - "author_name": "Cheng Li", - "author_inst": "Second Affiliated Hospital Zhejiang University School of Medicine" - }, - { - "author_name": "Dao Zhou", - "author_inst": "Zhejiang University School of Medicine" - }, - { - "author_name": "Huajun Li", - "author_inst": "Second Affiliated Hospital Zhejiang University School of Medicine" - }, - { - "author_name": "Jianan Wang", - "author_inst": "Second Affiliated Hospital Zhejiang University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.05.20.21257515", "rel_title": "Modeling third waves of Covid-19 spread with piecewise differential and integral operators: Turkey, Spain and Czechia", @@ -725777,6 +729249,201 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.20.21256969", + "rel_title": "Implementation of a qPCR assay coupled with genomic surveillance for real-time monitoring of SARS-CoV-2 variants of concern.", + "rel_date": "2021-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21256969", + "rel_abs": "We developed a genomic surveillance program for real-time monitoring of SARS-CoV-2 variants of concern in Uruguay. Here, we present the first results, including the proposed qPCR-VOC method, the general workflow and the report of the introduction and community transmission of the VOC P.1 in Uruguay in multiple independent events.", + "rel_num_authors": 45, + "rel_authors": [ + { + "author_name": "Natalia Rego", + "author_inst": "Unidad de Bioinformatica, Institut Pasteur de Montevideo." + }, + { + "author_name": "Alicia Costabile", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur Montevideo; Centro de Innovacion en Vigilancia Epidemiologica, Institut Pasteur Montevideo" + }, + { + "author_name": "Mercedes Paz", + "author_inst": "Centro de Innovacion en Vigilancia Epidemiologica, Institut Pasteur Montevideo" + }, + { + "author_name": "Cecilia Salazar", + "author_inst": "Laboratorio de Genomica Microbiana, Institut Pasteur Montevideo" + }, + { + "author_name": "Paula Perbolianachis", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur Montevideo; Laboratorio de Virologia Molecular, Facultad de Ciencias, UdelaR" + }, + { + "author_name": "Lucia Spangemberg", + "author_inst": "Unidad de Bioinformatica, Institut Pasteur de Montevideo" + }, + { + "author_name": "Ignacio Ferres", + "author_inst": "Laboratorio de Genomica Microbiana, Institut Pasteur Montevideo" + }, + { + "author_name": "Rodrigo Arce", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur Montevideo; Laboratorio de Virologia Molecular, Facultad de Ciencias, UdelaR; Laboratorio Biol" + }, + { + "author_name": "Alvaro Fajardo", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur Montevideo; Laboratorio de Virologia Molecular, Facultad de Ciencias, UdelaR" + }, + { + "author_name": "Mailen Arleo", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Tania Possi", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Ines Bellini", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Lucia Bilbao", + "author_inst": "Departamento de Genomica, Instituto de Investigaciones Biologicas Clemente Estable. Laboratorio de Biologia Molecular, Sanatorio Americano" + }, + { + "author_name": "Natalia Reyes", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Maria Noel Bentancor", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Andres Lizosain", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Maria Jose Benitez", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Matias Castells", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Matias Victoria", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Leticia Maya", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Viviana Bortagaray", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Ana Moller", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Gonzalo Bello", + "author_inst": "Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz Fiocruz" + }, + { + "author_name": "Ighor Arantes", + "author_inst": "Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz Fiocruz" + }, + { + "author_name": "Mariana Brandes", + "author_inst": "Unidad de Bioinformatica, Institut Pasteur de Montevideo" + }, + { + "author_name": "Pablo Smircich", + "author_inst": "Departamento de Genomica, Instituto de Investigaciones Biologicas Clemente Estable. Laboratorio de Interacciones Moleculares, Facultad de Ciencias, UdelaR." + }, + { + "author_name": "Odhille Chappos", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Melissa Duquia", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Belen Gonzalez", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Luciana Griffero", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Mauricio Mendez", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Maria Pia Techera", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Juan Zanetti", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Bernardina Rivera", + "author_inst": "Laboratorio de Diagnostico Molecular, Institut Pasteur de Montevideo" + }, + { + "author_name": "Matias Maidana", + "author_inst": "Laboratorio de Diagnostico Molecular, Institut Pasteur de Montevideo" + }, + { + "author_name": "Martina Alonso", + "author_inst": "Laboratorio de Diagnostico Molecular, Institut Pasteur de Montevideo" + }, + { + "author_name": "Cecilia Alonso", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Julio Medina", + "author_inst": "Ministerio de Salud Publica (Uruguay) / Catedra de Enfermedades Infecciosas, Fac. de Medicina, UdelaR." + }, + { + "author_name": "Henry Albornoz", + "author_inst": "Ministerio de Salud Publica (Uruguay)" + }, + { + "author_name": "Rodney Colina", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Veronica Noya", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Gregorio Iraola", + "author_inst": "Institut Pasteur de Montevideo" + }, + { + "author_name": "Tamara Fernandez-Calero", + "author_inst": "Unidad de Bioinformatica, Institut Pasteur de Montevideo" + }, + { + "author_name": "Gonzalo Andres Moratorio", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Pilar Moreno", + "author_inst": "Universidad de la Republica. Insitut Pasteur de Montevideo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.19.21257439", "rel_title": "Rapid And high throughput RT-qPCR assay for identification and differentiation between SARS-CoV-2 variants B.1.1.7 and B.1.351", @@ -725942,41 +729609,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.05.19.21257467", - "rel_title": "COVID-19 Mitigation Practices and COVID-19 Rates in Schools: Report on Data from Florida, New York and Massachusetts", - "rel_date": "2021-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.19.21257467", - "rel_abs": "This paper reports on the correlation of mitigation practices with staff and student COVID-19 case rates in Florida, New York, and Massachusetts during the 2020-2021 school year. We analyze data collected by the COVID-19 School Response Dashboard and focus on student density, ventilation upgrades, and masking. We find higher student COVID-19 rates in schools and districts with lower in-person density but no correlations in staff rates. Ventilation upgrades are correlated with lower rates in Florida but not in New York. We do not find any correlations with mask mandates. All rates are lower in the spring, after teacher vaccination is underway.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Emily Oster", - "author_inst": "Brown University" - }, - { - "author_name": "Rebecca Jack", - "author_inst": "COVID-19 School Dashboard" - }, - { - "author_name": "Clare Halloran", - "author_inst": "COVID-19 School Dashboard" - }, - { - "author_name": "John Schoof", - "author_inst": "University of Washington" - }, - { - "author_name": "Diana McLeod", - "author_inst": "Precision Dynamics, COVID-19 School Dashboard" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.05.19.21257486", "rel_title": "Evaluating the effects of vaccine rollout policies in European countries: A simulation study", @@ -727543,6 +731175,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.05.21.445152", + "rel_title": "The Role of ATP in the RNA Translocation Mechanism of SARS-CoV-2 NSP13 Helicase", + "rel_date": "2021-05-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.21.445152", + "rel_abs": "The COVID-19 pandemic has demonstrated the need to develop potent and transferable therapeutics to treat coronavirus infections. Numerous antiviral targets are being investigated, but non-structural protein 13 (nsp13) stands out as a highly conserved and yet under studied target. Nsp13 is a superfamily 1 (SF1) helicase that translocates along and unwinds viral RNA in an ATP dependent manner. Currently, there are no available structures of nsp13 from SARS-CoV-1 or SARS-CoV-2 with either ATP or RNA bound presenting a significant hurdle to the rational design of therapeutics. To address this knowledge gap, we have built models of SARS-CoV-2 nsp13 in Apo, ATP, ssRNA and ssRNA+ATP substrate states. Using 30 s of Gaussian accelerated molecular dynamics simulation (at least 6 s per substrate state), these models were confirmed to maintain substrate binding poses that are similar to other SF1 helicases. A gaussian mixture model and linear discriminant analysis structural clustering protocol was used to identify key aspects of the ATP-dependent RNA translocation mechanism. Namely, four RNA-nsp13 structures are identified that exhibit ATP-dependent populations and support the inch-worm mechanism for translocation. These four states are characterized by different RNA-binding poses for motifs Ia, IV and V and suggest a powerstroke-like motion of domain 2A relative to domain 1A. This structural and mechanistic insight of nsp13 RNA translocation presents novel targets for the further development of antivirals.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ryan Weber", + "author_inst": "Colorado State University" + }, + { + "author_name": "Martin McCullagh", + "author_inst": "Oklahoma State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.05.21.445090", "rel_title": "Water-triggered, irreversible conformational change of SARS-CoV-2 main protease on passing from the solid state to aqueous solution", @@ -727656,61 +731311,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2021.05.21.21256124", - "rel_title": "Rapid identification of Sars-CoV-2 variants of concern using the portable peakPCR platform", - "rel_date": "2021-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.21.21256124", - "rel_abs": "The need for tools which allow rapid detection and continuous monitoring of Sars-CoV-2 variants of concern (VOC) is greater than ever, as these variants are more transmissible and therefore increase the pressure of COVID-19 on healthcare systems. To address this demand, we aimed to develop and evaluate a robust and fast diagnostic approach for identification of Sars-CoV-2 VOC-associated spike gene mutations. Our diagnostic assays detect the E484K and N501Y SNPs as well as a spike gene deletion (HV69/70) and can be run on standard laboratory equipment or on the portable rapid diagnostic technology platform peakPCR. The assays achieved excellent diagnostic performance when tested with RNA extracted from culture-derived Sars-CoV-2 VOC lineages. Simplicity of usage and the relatively low costs are advantages which make our approach well-suited for decentralized and rapid testing, especially in resource limited settings.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Salome Hosch", - "author_inst": "Swiss Tropical and Public Health Institute, Basel, Switzerland" - }, - { - "author_name": "Philippe Bechtold", - "author_inst": "Diaxxo AG, Zurich, Switzerland" - }, - { - "author_name": "Philipp Wagner", - "author_inst": "Swiss Tropical and Public Health Institute, Basel, Switzerland" - }, - { - "author_name": "Amalia Ruiz-Serrano", - "author_inst": "Diaxxo AG, Zurich, Switzerland" - }, - { - "author_name": "Michele Gregorini", - "author_inst": "Diaxxo AG, Zurich, Switzerland" - }, - { - "author_name": "Denise Siegrist", - "author_inst": "Spiez Laboratory, Spiez, Switzerland" - }, - { - "author_name": "Olivier Engler", - "author_inst": "Spiez Laboratory, Spiez, Switzerland" - }, - { - "author_name": "Wendelin J. Stark", - "author_inst": "Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland," - }, - { - "author_name": "Claudia A. Daubenberger", - "author_inst": "Swiss Tropical and Public Health Institute, Basel, Switzerland" - }, - { - "author_name": "Tobias Schindler", - "author_inst": "Swiss Tropical and Public Health Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.20.444932", "rel_title": "Topic: Hyper immune Bovine Colostrum as a Low-Cost, Large-Scale Source of Antibodies against COVID-19", @@ -729485,6 +733085,177 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.05.14.21257058", + "rel_title": "Multicenter cohort study of multisystem inflammatory syndrome in children (MIS-C)", + "rel_date": "2021-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257058", + "rel_abs": "BACKGROUNDSARS-CoV-2 infection can lead to multisystem inflammatory syndrome in children (MIS-C). We investigated risk factors for severe disease and explored changes in severity over time.\n\nMETHODSChildren up to 17 years of age admitted March 1, 2020 through March 7th, 2021 to 15 hospitals in Canada, Iran and Costa Rica with confirmed or probable MIS-C were included. Descriptive analysis and comparison by diagnostic criteria, country, and admission date was performed. Adjusted absolute average risks (AR) and risk differences (RD) were estimated for characteristics associated with ICU admission or cardiac involvement.\n\nRESULTSOf 232 cases (106 confirmed) with median age 5.8 years, 56% were male, and 22% had comorbidities. ICU admission occurred in 73 (31%) but none died. Median length of stay was 6 days (inter-quartile range 4-9). Children 6 to 12 years old had the highest AR for ICU admission (44%; 95% confidence interval [CI] 34-53). Initial ferritin greater than 500 mcg/L was associated with ICU admission. When comparing cases admitted up to October 31, 2020 to those admitted later, the AR for ICU admission increased from 25% (CI 17-33) to 37% (CI 29-46) and for cardiac involvement from 44% (CI 35-53) to 75% (CI 66-84). Risk estimates for ICU admission in the Canadian cohort demonstrated a higher risk in December 2020-March 2021 compared to March-May 2020 (RD 25%; 95%CI 7-44).\n\nINTERPRETATIONMIS-C occurred primarily in previously well children. Illness severity appeared to increase over time. Despite a high ICU admission incidence, most children were discharged within one week.", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Joanna Merckx", + "author_inst": "Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal" + }, + { + "author_name": "Suzette Cooke", + "author_inst": "Department of Pediatrics, University of Calgary, Calgary, Alberta" + }, + { + "author_name": "Tala El Tal", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Ronald M. Laxer", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Ari Bitnun", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Shaun K Morris", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "E Ann Yeh", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Carmen Yea", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Peter Gill", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Jesse Papenburg", + "author_inst": "Department of Pediatrics, McGill University, Montreal, Quebec" + }, + { + "author_name": "Marie-Astrid Lefebvre", + "author_inst": "Department of Pediatrics, McGill University, Montreal, Quebec" + }, + { + "author_name": "Rolando Ulloa-Gutierrez", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Helena Brenes-Chacon", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Adriana Yock-Corrales", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Gabriela Ivankovich-Escoto", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Alejandra Soriano-Fallas", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Marcela Hernandez-de Mezerville", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Tammie Dewan", + "author_inst": "Department of Pediatrics, University of Calgary, Calgary, Alberta" + }, + { + "author_name": "Lea Restivo", + "author_inst": "Department of Pediatrics, University of Calgary, Calgary, Alberta" + }, + { + "author_name": "Alireza Nateghian", + "author_inst": "Department of Pediatrics, Iran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Behzad Haghighi Aski", + "author_inst": "Department of Pediatrics, Iran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Ali Manafi", + "author_inst": "Department of Pediatrics, Iran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Rachel Dwilow", + "author_inst": "Department of Pediatrics, University of Manitoba, Winnipeg, Manitoba" + }, + { + "author_name": "Jared Bullard", + "author_inst": "Department of Pediatrics, University of Manitoba, Winnipeg, Manitoba" + }, + { + "author_name": "Alison Lopez", + "author_inst": "Department of Pediatrics, University of British Columbia, Vancouver, BC" + }, + { + "author_name": "Manish Sadarangani", + "author_inst": "Department of Pediatrics, University of British Columbia; Vaccine Evaluation Center, BC Childrens Hospital Research Institute, Vancouver, BC" + }, + { + "author_name": "Ashley Roberts", + "author_inst": "Department of Pediatrics, University of British Columbia, Vancouver, BC" + }, + { + "author_name": "Michelle Barton", + "author_inst": "Department of Pediatrics, Western University, London, Ontario" + }, + { + "author_name": "Dara Petel", + "author_inst": "Department of Pediatrics, Western University, London, Ontario" + }, + { + "author_name": "Nicole Le Saux", + "author_inst": "Department of Pediatrics, University of Ottawa, Ottawa, Ontario" + }, + { + "author_name": "Jennifer Bowes", + "author_inst": "Department of Pediatrics, University of Ottawa, Ottawa, Ontario" + }, + { + "author_name": "Rupeena Purewal", + "author_inst": "Department of Pediatrics, University of Saskatchewan, Saskatoon, Saskatchewan" + }, + { + "author_name": "Janell Lautermilch", + "author_inst": "Department of Pediatrics, University of Saskatchewan, Saskatoon, Saskatchewan" + }, + { + "author_name": "Sarah Tehseen", + "author_inst": "Department of Pediatrics, University of Saskatchewan, Saskatoon, Saskatchewan" + }, + { + "author_name": "Ann Bayliss", + "author_inst": "Department of Pediatrics, Trillium Health Partners, Mississauga, Ontario" + }, + { + "author_name": "Jacqueline K. Wong", + "author_inst": "Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada" + }, + { + "author_name": "Kirk Leifso", + "author_inst": "Department of Pediatrics, Queens University, Kingston, Ontario" + }, + { + "author_name": "Cheryl Foo", + "author_inst": "Department of Pediatrics, Memorial University, St Johns, Newfoundland and Labrador" + }, + { + "author_name": "Joan Robinson", + "author_inst": "Department of Pediatrics, University of Alberta, Edmonton, Alberta" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.05.13.21257067", "rel_title": "Contact tracing indicators for COVID-19: rapid scoping review and conceptual framework", @@ -729634,25 +733405,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.05.17.21257358", - "rel_title": "Economic Impact Payment, Human Mobility and the COVID-19 Mitigation in the United States", - "rel_date": "2021-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.17.21257358", - "rel_abs": "This paper studies the relationship between the individuals income and COVID-19 mitigation effort contribution. The paper suggests that in addition to the government mandatory policies, the income compensation policy is an alternative government instrument that helps increase the individual and social aggregate COVID-19 mitigation effort. I empirically test the effect of the income compensation policy by utilizing the United States economic impact payment (EIP) in April 2020 as a quasi-natural experiment, and use the cellphone GPS measured human mobility data as the outcome indicator of the COVID-19 mitigation effort. I find that by receiving EIP, individuals on average significantly increase median home dwell time by 3% - 5% (about 26-45 minutes). This paper highlights an unintended effect of EIP: in addition to providing economic assistance, EIP also helps mitigate the COVID-19 virus transmission.\n\nJEL codesD11 D12 H41 I12 I14 I18", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ruohao Zhang", - "author_inst": "Binghamton University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.05.17.21257364", "rel_title": "Socioeconomic Status and COVID-19 Related Outcomes in India: Hospital Based Study", @@ -730995,6 +734747,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.14.21257224", + "rel_title": "Surveillance of COVID-19 vaccination in US nursing homes, December 2020-April 2021", + "rel_date": "2021-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257224", + "rel_abs": "Unstructured AbstractMonitoring COVID-19 vaccination coverage among nursing home (NH) residents and staff is important to ensure high coverage and guide patient-safety policies. With the termination of the federal Pharmacy Partnership for Long-Term Care Program, another source of facility-based vaccination data is needed. We compared numbers of COVID-19 vaccinations administered to NH residents and staff reported by pharmacies participating in the temporary federal Pharmacy Partnership for Long-Term Care Program with those reported by NHs participating in new COVID-19 vaccination modules of CDCs National Healthcare Safety Network (NHSN). Pearson correlation coefficients comparing the number vaccinated between the two approaches were 0.89, 0.96, and 0.97 for residents and 0.74, 0.90, and 0.90 for staff, in the weeks ending January 3, 10, and 17, respectively. Based on subsequent NHSN reporting, vaccination coverage with [≥]1 vaccine dose reached 77% for residents and 50% for staff the week ending January 31 and plateaued through April 2021.\n\nThree-question summary boxO_LIWhat is the current understanding of the subject?\nBecause of high risk of disease, nursing home residents and staff were prioritized for COVID-19 vaccination when doses were limited.\nC_LIO_LIWhat does this report add to the literature?\nNational monitoring of nursing home residents and staff vaccination coverage through the CDC National Healthcare Safety Network (NHSN) correlated with vaccination administration reports from the federal Pharmacy Partnership for Long-Term Care Program in January 2021. NHSN-reported vaccination coverage rates plateaued from February through April 2021.\nC_LIO_LIWhat are the implications for public health practice?\nNHSN can track COVID-19 vaccination in nursing homes and help guide efforts to increase vaccine uptake in residents and staff.\nC_LI", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Andrew I Geller", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Daniel S Budnitz", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Heather Dubendris", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Radhika Gharpure", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Minn Minn Soe", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Hsiu Wu", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Elizabeth J Kalayil", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Andrea L Benin", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Suchita A Patel", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Megan C Lindley", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Ruth Link-Gelles", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.13.21257164", "rel_title": "KL-MOB Automated Covid-19 Recognition Using a Novel Approach Based on Image Enhancement and a Modified MobileNet CNN", @@ -731164,53 +734975,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.14.21257244", - "rel_title": "Controlling risk of SARS-CoV-2 infection in essential workers of enclosed food manufacturing facilities", - "rel_date": "2021-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257244", - "rel_abs": "The SARS-CoV-2 global pandemic poses significant health risks to workers who are essential to maintaining the food supply chain. Using a quantitative risk assessment model, this study characterized the impact of risk reduction strategies for controlling SARS-CoV-2 transmission (droplet, aerosol, fomite-mediated) among front-line workers in a representative enclosed food manufacturing facility. We simulated: 1) individual and cumulative SARS-CoV-2 infection risks from close contact (droplet and aerosols at 1-3m), aerosol, and fomite-mediated exposures to a susceptible worker following exposure to an infected worker during an 8h-shift; and 2) the relative reduction in SARS-CoV-2 infection risk attributed to infection control interventions (physical distancing, mask use, ventilation, surface disinfection, hand hygiene). Without mitigation measures, the SARS-CoV-2 infection risk was largest for close contact (droplet and aerosol) at 1m (0.96, 95%CI: 0.67-1.0). In comparison, risk associated with fomite (0.26, 95%CI: 0.10-0.56) or aerosol exposure alone (0.05, 95%CI: 0.01-0.13) at 1m distance was substantially lower (73-95%). At 1m, droplet transmission predominated over aerosol and fomite-mediated transmission, however, this changed by 3m, with aerosols comprising the majority of the exposure dose. Increasing physical distancing reduced risk by 84% (1 to 2m) and 91% (1 to 3m). Universal mask use reduced infection risk by 52-88%, depending on mask type. Increasing ventilation (from 0.1 to 2-8 air changes/hour) resulted in risk reductions of 14-54% (1m) and 55-85% (2m). Combining these strategies, together with handwashing and surface disinfection, resulted in <1% infection risk. Current industry SARS-CoV-2 risk reduction strategies, particularly when bundled, provide significant protection to essential food workers.\n\nSignificance StatementUsing mathematical modeling, we find that workers in enclosed food manufacturing facilities are at higher risk of SARS-CoV-2 infection from close contact transmission (exposure to large droplets and small aerosol particles) than fomite transmission. Thus, strategies protecting workers should prioritize close contact transmission pathways, such as physical distancing, universal mask use, and room air changes, with surface disinfection (reducing fomite transmission) and handwashing of secondary importance. Our work supports current international (EU-OSHA), domestic (FDA, OSHA), and food industry-standard guidance for managing COVID-19 transmission in essential workers in the food manufacturing sector. Although our model was designed for an indoor food manufacturing setting, it can be readily adapted to other indoor environments and infectious respiratory pathogens.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Julia Silva Sobolik", - "author_inst": "Emory University" - }, - { - "author_name": "Elizabeth Sajewski", - "author_inst": "Emory University" - }, - { - "author_name": "Lee-Ann Jaykus", - "author_inst": "North Carolina State University" - }, - { - "author_name": "D. Kane Cooper", - "author_inst": "Emory University" - }, - { - "author_name": "Ben A. Lopman", - "author_inst": "Emory University" - }, - { - "author_name": "Alicia Kraay", - "author_inst": "Emory University" - }, - { - "author_name": "P. Barry Ryan", - "author_inst": "Emory University" - }, - { - "author_name": "Juan S. Leon", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.05.17.21256513", "rel_title": "Japan COVID-19 Task Force: a nation-wide consortium to elucidate host genetics of COVID-19 pandemic in Japan", @@ -734229,6 +737993,161 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.18.21257267", + "rel_title": "Colchicine in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", + "rel_date": "2021-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257267", + "rel_abs": "BackgroundColchicine has been proposed as a treatment for COVID-19 on the basis of its anti-inflammatory actions.\n\nMethodsIn this randomised, controlled, open-label trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care alone or usual standard of care plus colchicine twice daily for 10 days or until discharge (or one of the other treatment arms) using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).\n\nFindingsBetween 27 November 2020 and 4 March 2021, 5610 patients were randomly allocated to receive colchicine and 5730 patients to receive usual care alone. Overall, 1173 (21%) patients allocated to colchicine and 1190 (21%) patients allocated to usual care died within 28 days (rate ratio 1.01; 95% confidence interval [CI] 0.93-1.10; p=0.77). Consistent results were seen in all pre-specified subgroups of patients. There was no significant difference in duration of hospitalisation (median 10 days vs. 10 days) or the proportion of patients discharged from hospital alive within 28 days (70% vs. 70%; rate ratio 0.98; 95% CI 0.94-1.03; p=0.44). Among those not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (25% vs. 25%; risk ratio 1.02; 95% CI 0.96-1.09; p=0.47).\n\nInterpretationIn adults hospitalised with COVID-19, colchicine was not associated with reductions in 28-day mortality, duration of hospital stay, or risk of progressing to invasive mechanical ventilation or death.\n\nFundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056). Wellcome Trust (Grant Ref: 222406/Z/20/Z) through the COVID-19 Therapeutics Accelerator.", + "rel_num_authors": 35, + "rel_authors": [ + { + "author_name": "Peter W Horby", + "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and International Severe Acute Res" + }, + { + "author_name": "Mark Campbell", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King" + }, + { + "author_name": "Enti Spata", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un" + }, + { + "author_name": "Jonathan R Emberson", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un" + }, + { + "author_name": "Natalie Staplin", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un" + }, + { + "author_name": "Guilherme Pessoa-Amorim", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Leon Peto", + "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and Nuffield Department of Populat" + }, + { + "author_name": "Martin Wiselka", + "author_inst": "Department of Infectious Diseases, University Hospital Leicester, Leicester, United Kingdom" + }, + { + "author_name": "Laura Wiffen", + "author_inst": "Portsmouth Hospitals University NHS Foundation Trust, Portsmouth, United Kingdom" + }, + { + "author_name": "Simon Tiberi", + "author_inst": "Department of Infection, Barts Health NHS Trust, London, United Kingdom" + }, + { + "author_name": "Ben Caplin", + "author_inst": "Department of Renal Medicine, University College London, London, United Kingdom and Royal Free London NHS Trust, London, United Kingdom" + }, + { + "author_name": "Caroline Wroe", + "author_inst": "James Cook University Hospital, Middlesbrough, United Kingdom" + }, + { + "author_name": "Christopher Green", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom" + }, + { + "author_name": "Paul Hine", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom" + }, + { + "author_name": "Benjamin Prudon", + "author_inst": "North Tees and Hartlepool NHS Foundation Trust, Hartlepool, United Kingdom" + }, + { + "author_name": "Tina George", + "author_inst": "Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom" + }, + { + "author_name": "Andrew Wight", + "author_inst": "Wirral University Teaching Hospital NHS Foundation Trust, Birkenhead, United Kingdom" + }, + { + "author_name": "J Kenneth Baillie", + "author_inst": "Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom" + }, + { + "author_name": "Buddha Basnyat", + "author_inst": "Oxford University Clinical Research Unit -Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal" + }, + { + "author_name": "Maya H Buch", + "author_inst": "Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom" + }, + { + "author_name": "Lucy C Chappell", + "author_inst": "School of Life Course Sciences, King?s College London, London, United Kingdom" + }, + { + "author_name": "Jeremy N Day", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer" + }, + { + "author_name": "Saul N Faust", + "author_inst": "NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, " + }, + { + "author_name": "Raph L Hamers", + "author_inst": "Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia and Faculty of Medicine, University of Indonesia, Jakarta, Indonesia and Centre for Tropical Medicine " + }, + { + "author_name": "Thomas Jaki", + "author_inst": "Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom and MRC Biostatistics Unit, University of Cambridge, Cambridge, United" + }, + { + "author_name": "Edmund Juszczak", + "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom" + }, + { + "author_name": "Katie Jeffery", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom" + }, + { + "author_name": "Wei Shen Lim", + "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom and Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Notting" + }, + { + "author_name": "Alan Montgomery", + "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom" + }, + { + "author_name": "Andrew Mumford", + "author_inst": "School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom" + }, + { + "author_name": "Kathryn Rowan", + "author_inst": "Intensive Care National Audit & Research Centre, London, United Kingdom" + }, + { + "author_name": "Guy Thwaites", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer" + }, + { + "author_name": "Marion Mafham", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Richard Haynes", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King" + }, + { + "author_name": "Martin J Landray", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.16.21257283", "rel_title": "Early Anakinra Treatment for COVID-19 Guided by Urokinase Plasminogen Receptor", @@ -734550,81 +738469,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.05.18.444622", - "rel_title": "Single-dose immunisation with a multimerised SARS-CoV-2 receptor binding domain (RBD) induces an enhanced and protective response in mice", - "rel_date": "2021-05-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.18.444622", - "rel_abs": "The COVID-19 pandemic, caused by the SARS-CoV-2 coronavirus, has triggered a worldwide health emergency. So far, several different types of vaccines have shown strong efficacy. However, both the emergence of new SARS-CoV-2 variants and the need to vaccinate a large fraction of the worlds population necessitate the development of alternative vaccines, especially those that are simple and easy to store, transport and administer. Here, we showed that ferritin-like Dps protein from hyperthermophilic Sulfolobus islandicus can be covalently coupled with different SARS-CoV-2 antigens via the SpyCatcher system, to form extremely stable and defined multivalent dodecameric vaccine nanoparticles that remain intact even after lyophilisation. Immunisation experiments in mice demonstrated that the SARS-CoV-2 receptor binding domain (RBD) coupled to Dps (RBD-S-Dps) shows particular promise as it elicited a higher antibody titre and an enhanced neutralising antibody response compared to the monomeric RBD. Furthermore, we showed that a single immunisation with the multivalent RBD-S-Dps completely protected hACE2-expressing mice from serious illness and led to efficient viral clearance from the lungs upon SARS-CoV-2 infection. Our data highlight that multimerised SARS-CoV-2 subunit vaccines are a highly efficacious modality, particularly when combined with an ultra-stable scaffold.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Ralf Salzer", - "author_inst": "MRC Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Jordan J Clark", - "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK" - }, - { - "author_name": "Marina Vaysburd", - "author_inst": "MRC Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Veronica T Chang", - "author_inst": "MRC Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Anna Albecka", - "author_inst": "MRC Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Leo Kiss", - "author_inst": "MRC Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Parul Sharma", - "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK" - }, - { - "author_name": "Andres Gonzalez Llamazares", - "author_inst": "MRC Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Anja Kipar", - "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK" - }, - { - "author_name": "Julian A Hiscox", - "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK" - }, - { - "author_name": "Andrew Owen", - "author_inst": "Department of Pharmacology and Therapeutics, Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK." - }, - { - "author_name": "A. Radu Aricescu", - "author_inst": "MRC Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "James P Stewart", - "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK" - }, - { - "author_name": "Leo C James", - "author_inst": "MRC Laboratory of Molecular Biology, Cambridge, UK" - }, - { - "author_name": "Jan Lowe", - "author_inst": "MRC Laboratory of Molecular Biology, Cambridge, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.05.17.444362", "rel_title": "SARS-like coronaviruses in horseshoe bats (Rhinolophus spp.) in Russia, 2020.", @@ -736199,6 +740043,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.15.21256976", + "rel_title": "Excess mortality during the COVID-19 pandemic: a geospatial and statistical analysis in Mogadishu, Somalia", + "rel_date": "2021-05-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.15.21256976", + "rel_abs": "BackgroundWhile the impact of the COVID-19 pandemic has been well documented in high-income countries, much less is known about its impact in Somalia where health systems are weak and vital registration is under developed.\n\nMethodsWe used remote sensing and geospatial analysis to quantify the number of burials from January 2017 to September 2020 in Mogadishu. We imputed missing grave counts using surface area data. Simple interpolation and a generalised additive mixed growth model were used to predict both actual and counterfactual burial rates by cemetery and across Mogadishu during the most likely period of COVID-19 excess mortality and to compute excess burials. We also undertook a qualitative survey of key informants to determine the drivers of COVID-19 excess mortality.\n\nResultsBurial rates increased during the pandemic period with a ratio to pre-pandemic levels averaging 1.5-fold and peaking at 2.2-fold. When scaled to plausible range of baseline Crude Death Rates (CDR), excess death toll between January and September 2020 ranged between 3,200 and 11,800. When compared to burial records of the Barakaat Cemetery Committee our estimates were found to be lower.\n\nConclusionsOur study points to considerable under estimation of COVID-19 impact in Banadir and an overburdened public health system struggling to deal with the increasing severity of the epidemic in 2020.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Abdihamid Warsame", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Farah Bashiir", + "author_inst": "Somali Disaster Resilience Institute" + }, + { + "author_name": "Terri Freemantle", + "author_inst": "Satellite Applications Catapult" + }, + { + "author_name": "Chris Williams", + "author_inst": "Satellite Applications Catapult" + }, + { + "author_name": "Yolanda Vazquez", + "author_inst": "Satellite Applications Catapult" + }, + { + "author_name": "Chris Reeve", + "author_inst": "Satellite Applications Catapult" + }, + { + "author_name": "Ahmed Aweis", + "author_inst": "Somali Disaster Resilience Institute" + }, + { + "author_name": "Mohamed Ahmed", + "author_inst": "Somali Disaster Resilience Institute" + }, + { + "author_name": "Francesco Checchi", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Abdirisak Dalmar", + "author_inst": "Somali Disaster Resilience Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.12.21257123", "rel_title": "Occupation and COVID-19 mortality in England: a national linked data study of 14.3 million adults", @@ -736392,69 +740291,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2021.05.16.444324", - "rel_title": "Verification of SARS-CoV-2-Encoded small RNAs and contribution to Infection-Associated lung inflammation", - "rel_date": "2021-05-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.16.444324", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes coronavirus disease 2019 (COVID-19), the respiratory illness responsible for the COVID-19 pandemic. SARS-CoV-2 is a positive-stranded RNA virus belongs to Coronaviridae family. The viral genome of SARS-CoV-2 contains around 29.8 kilobase with a 5'-cap structure and 3'-poly-A tail, and shows 79.2% nucleotide identity with human SARS-CoV-1, which caused the 2002-2004 SARS outbreak. As the successor to SARS-CoV-1, SARS-CoV-2 now has circulated across the globe. There is a growing understanding of SARS-CoV-2 in virology, epidemiology, and clinical management strategies. In this study, we verified the existence of two 18-22 nt small viral RNAs (svRNAs) derived from the same precursor in human specimens infected with SARS-CoV-2, including nasopharyngeal swabs and formalin-fixed paraffin-embedded (FFPE) explanted lungs from lung transplantation of COVID-19 patients. We then simulated and confirmed the formation of these two SARS-CoV-2-Encoded small RNAs in human lung epithelial cells. And the potential pro-inflammatory effects of the splicing and maturation process of these two svRNAs in human lung epithelial cells were also explored. By screening cytokine storm genes and the characteristic expression profiling of COVID-19 in the explanted lung tissues and the svRNAs precursor transfected human lung epithelial cells, we found that the maturation of these two small viral RNAs contributed significantly to the infection associated lung inflammation, mainly via the activation of the CXCL8, CXCL11 and type I interferon signaling pathway. Taken together, we discovered two SARS-CoV-2-Encoded small RNAs and investigated the pro-inflammatory effects during their maturation in human lung epithelial cells, which might provide new insight into the pathogenesis and possible treatment options for COVID-19.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Cheng Zhang", - "author_inst": "the First Affiliated Hospital of Nanjing Medical University" - }, - { - "author_name": "Cheng Liu", - "author_inst": "the First Affiliated Hospital of Nanjing Medical University" - }, - { - "author_name": "Lin Jiang", - "author_inst": "the First Affiliated Hospital of Nanjing Medical University" - }, - { - "author_name": "Biao Lun Cui", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Yu Chun Li", - "author_inst": "the First Affiliated Hospital of Nanjing Medical University" - }, - { - "author_name": "Xin Guo Song", - "author_inst": "the First Affiliated Hospital of Nanjing Medical University" - }, - { - "author_name": "Rui Xu", - "author_inst": "the First Affiliated Hospital of Nanjing Medical University" - }, - { - "author_name": "Nan Xiang Geng", - "author_inst": "the First Affiliated Hospital of Nanjing Medical University" - }, - { - "author_name": "Xing Chang Luan", - "author_inst": "Nanjing Medical University" - }, - { - "author_name": "Yan Chen", - "author_inst": "the First Affiliated Hospital of Nanjing Medical University" - }, - { - "author_name": "Li Bao Zhu", - "author_inst": "Jiangsu Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Wei Zhu", - "author_inst": "the First Affiliated Hospital of Nanjing Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.15.444301", "rel_title": "SARS-CoV-2 convergent evolution cannot be reliably inferred from phylogenetic analyses", @@ -738140,6 +741976,121 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.13.444010", + "rel_title": "Durability of mRNA-1273-induced antibodies against SARS-CoV-2 variants", + "rel_date": "2021-05-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.13.444010", + "rel_abs": "SARS-CoV-2 mutations may diminish vaccine-induced protective immune responses, and the durability of such responses has not been previously reported. Here, we present a comprehensive assessment of the impact of variants B.1.1.7, B.1.351, P.1, B.1.429, and B.1.526 on binding, neutralizing, and ACE2-blocking antibodies elicited by the vaccine mRNA-1273 over seven months. Cross-reactive neutralizing responses were rare after a single dose of mRNA-1273. At the peak of response to the second dose, all subjects had robust responses to all variants. Binding and functional antibodies against variants persisted in most subjects, albeit at low levels, for 6 months after the primary series of mRNA-1273. Across all assays, B.1.351 had the greatest impact on antibody recognition, and B.1.1.7 the least. These data complement ongoing studies of clinical protection to inform the potential need for additional boost vaccinations.\n\nOne-Sentence SummaryMost mRNA-1273 vaccinated individuals maintained binding and functional antibodies against SARS-CoV-2 variants for 6 months.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Amarendra Pegu", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Stephen D. Schmidt", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Chloe A. Talana", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Jim Albert", + "author_inst": "Emmes Company, Rockville, MD, USA." + }, + { + "author_name": "Evan Anderson", + "author_inst": "Department of Medicine, Center for Childhood Infections and Vaccines (CCIV) of Childrens Healthcare of Atlanta and Emory University Department of Pediatrics, At" + }, + { + "author_name": "Hamilton Bennett", + "author_inst": "Moderna, Inc., Cambridge, MA, USA." + }, + { + "author_name": "Kizzmekia Corbett", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Britta Flach", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Lisa Jackson", + "author_inst": "Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA." + }, + { + "author_name": "Brett Leav", + "author_inst": "Moderna, Inc., Cambridge, MA, USA." + }, + { + "author_name": "Julie E. Ledgerwood", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Catherine J. Luke", + "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA." + }, + { + "author_name": "Mat Makowski", + "author_inst": "Emmes Company, Rockville, MD, USA." + }, + { + "author_name": "Paul C. Roberts", + "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA." + }, + { + "author_name": "Mario Roederer", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Paulina Alejandra Rebolledo", + "author_inst": "Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur, GA, USA." + }, + { + "author_name": "Christina A. Rostad", + "author_inst": "Department of Medicine, Center for Childhood Infections and Vaccines (CCIV) of Childrens Healthcare of Atlanta and Emory University Department of Pediatrics, At" + }, + { + "author_name": "Nadine G. Rouphael", + "author_inst": "Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur, GA, USA." + }, + { + "author_name": "Lingshu Wang", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Eun Sung Yang", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "John H. Beigel", + "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA." + }, + { + "author_name": "Barney S. Graham", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "John R. Mascola", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Adrian McDermott", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Nicole A Doria-Rose", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.14.444076", "rel_title": "The Spike Proteins of SARS-CoV-2 B.1.617 and B.1.618 Variants Identified in India Provide Partial Resistance to Vaccine-elicited and Therapeutic Monoclonal Antibodies.", @@ -738349,113 +742300,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.15.444128", - "rel_title": "Pan-ErbB inhibition protects from SARS-CoV-2 replication, inflammation, and injury", - "rel_date": "2021-05-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.15.444128", - "rel_abs": "Targeting host factors exploited by multiple viruses could offer broad-spectrum solutions for pandemic preparedness. Seventeen candidates targeting diverse functions emerged in a screen of 4,413 compounds for SARS-CoV-2 inhibitors. We demonstrated that lapatinib and other approved inhibitors of the ErbB family receptor tyrosine kinases suppress replication of SARS-CoV-2, Venezuelan equine encephalitis virus (VEEV), and other emerging viruses with a high barrier to resistance. Lapatinib suppressed SARS-CoV-2 entry and later stages of the viral life cycle and showed synergistic effect with the direct-acting antiviral nirmatrelvir. We discovered that ErbB1, 2 and 4 bind SARS-CoV-2 S1 protein and regulate viral and ACE2 internalization, and they are required for VEEV infection. In human lung organoids, lapatinib protected from SARS-CoV-2-induced activation of ErbB-regulated pathways implicated in non-infectious lung injury, pro-inflammatory cytokine production, and epithelial barrier injury. Lapatinib suppressed VEEV replication, cytokine production and disruption of the blood-brain barrier integrity in microfluidic-based human neurovascular units, and reduced mortality in a lethal infection murine model. We validated lapatinib-mediated inhibition of ErbB activity as an important mechanism of antiviral action. These findings reveal regulation of viral replication, inflammation, and tissue injury via ErbBs and establish a proof-of-principle for a repurposed, ErbB-targeted approach to combat emerging viruses.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Sirle Saul", - "author_inst": "Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University" - }, - { - "author_name": "Marwah Karim", - "author_inst": "Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University" - }, - { - "author_name": "Pei-Tzu Huang", - "author_inst": "Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University" - }, - { - "author_name": "Luca Ghita", - "author_inst": "Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University" - }, - { - "author_name": "Winston Chiu", - "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy" - }, - { - "author_name": "Sathish Kumar", - "author_inst": "Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University" - }, - { - "author_name": "Nishank Bhalla", - "author_inst": "National Center for Biodefence and Infectious Disease, Biomedical Research Laboratory, School of Systems Biology, George Mason University" - }, - { - "author_name": "Pieter Leyssen", - "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy" - }, - { - "author_name": "Courtney A. Cohen", - "author_inst": "US Army Medical Research Institute of Infectious Diseases, Viral Immunology Branch" - }, - { - "author_name": "Kathleen E. Huie", - "author_inst": "US Army Medical Research Institute of Infectious Diseases, Viral Immunology Branch" - }, - { - "author_name": "Courtney Tindle", - "author_inst": "Department of Cellular and Molecular Medicine, and HUMANOID CoRE University of California San Diego" - }, - { - "author_name": "Mamdouh Sibai", - "author_inst": "Department of Pathology, Stanford University School of Medicine, Stanford" - }, - { - "author_name": "Benjamin A. Pinsky", - "author_inst": "Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Department of Pathology, Stanfor" - }, - { - "author_name": "Soumita Das", - "author_inst": "Department of Pathology, and HUMANOID CoRE, University of California San Diego" - }, - { - "author_name": "Pradipta Ghosh", - "author_inst": "Department of Cellular and Molecular Medicine, Department of Medicine, and HUMANOID CoRE, University of California San Diego" - }, - { - "author_name": "John Dye", - "author_inst": "US Army Medical Research Institute of Infectious Diseases, Viral Immunology Branch" - }, - { - "author_name": "David E. Solow-Cordero", - "author_inst": "High-Throughput Bioscience Center, Department of Chemical and Systems Biology, Stanford" - }, - { - "author_name": "Jing Jin", - "author_inst": "Vitalant Research Institute, San Francisco" - }, - { - "author_name": "Dirk Jochmans", - "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy" - }, - { - "author_name": "Johan Neyts", - "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy" - }, - { - "author_name": "Aarthi Narayanan", - "author_inst": "National Center for Biodefence and Infectious Disease, Biomedical Research Laboratory, School of Systems Biology, George Mason University" - }, - { - "author_name": "Steven De Jonghe", - "author_inst": "KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy" - }, - { - "author_name": "Shirit Einav", - "author_inst": "Department of Medicine, Division of Infectious Diseases and Geographic Medicine, and Department of Microbiology and Immunology, Stanford University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.13.443721", "rel_title": "Host transcriptional response to SARS-CoV-2 infection in COVID-19 patients", @@ -740294,6 +744138,201 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.13.21256639", + "rel_title": "Efficacy of the NVX-CoV2373 Covid-19 Vaccine Against the B.1.1.7 Variant", + "rel_date": "2021-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21256639", + "rel_abs": "BackgroundCovid-19 vaccines are urgently needed, especially against emerging variants. NVX-CoV2373 is a recombinant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 rS) nanoparticle vaccine containing trimeric full-length SARS-CoV-2 spike glycoprotein and Matrix-M adjuvant.\n\nMethodsA phase 3, randomized, observer-blinded, placebo-controlled trial was conducted in adults 18-84 years old who received two intramuscular 5-{micro}g doses, 21 days apart, of NVX-CoV2373 or placebo (1:1) across 33 sites in the United Kingdom. The primary efficacy endpoint was virologically confirmed symptomatic Covid-19 with onset 7 days after second vaccination in serologically negative participants.\n\nResultsA total of 15,187 participants were randomized, of whom 7569 received NVX-CoV2373 and 7570 received placebo; 27.2% were 65 years or older, 44.7% had comorbidities and 4.2% had baseline serological evidence of SARS-CoV-2. There were 10 cases of Covid-19 among NVX-CoV2373 recipients and 96 cases among placebo recipients, with symptom onset at least 7 days after second vaccination; NVX-CoV2373 was 89.7% (95% confidence interval, 80.2 to 94.6) effective in preventing Covid-19, with no hospitalizations or deaths reported. There were five cases of severe Covid-19, all in the placebo group. Post hoc analysis revealed efficacies of 96.4% (73.8 to 99.5) and 86.3% (71.3 to 93.5) against the prototype strain and B.1.1.7 variant, respectively. Vaccine efficacy was similar across subgroups, including participants with comorbidities and those [≥]65 years old. Reactogenicity was generally mild and transient. The incidence of serious adverse events was low and similar in the two groups.\n\nConclusionA two-dose regimen of NVX-CoV2373 conferred 89.7% protection against a blend of prototype and variant Covid-19, demonstrated high efficacy against the B.1.1.7 variant, and had a reassuring safety profile.\n\n(Funded by Novavax, Inc. EudraCT number, 2020-004123-16).", + "rel_num_authors": 45, + "rel_authors": [ + { + "author_name": "Seth Toback", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Paul T. Heath", + "author_inst": "Vaccine Institute, St. George's, University of London and St. Georges University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Eva P. Galiza", + "author_inst": "Vaccine Institute, St. George's, University of London and St. Georges University Hospitals NHS Foundation Trust" + }, + { + "author_name": "David Baxter", + "author_inst": "Stockport NHS Foundation Trust, Stepping Hill Hospital" + }, + { + "author_name": "Marta Boffito", + "author_inst": "Chelsea and Westminster Hospital NHS Foundation Trust and Imperial College London" + }, + { + "author_name": "Duncan Browne", + "author_inst": "Royal Cornwall Hospital NHS Trust" + }, + { + "author_name": "Fiona Burns", + "author_inst": "Institute for Global Health, University College London and Royal Free London NHS Foundation Trust" + }, + { + "author_name": "David R. Chadwick", + "author_inst": "Centre for Clinical Infection, South Tees Hospitals NHS Foundation Trust, James Cook University Hospital" + }, + { + "author_name": "Rebecca Clark", + "author_inst": "Layton Medical Centre" + }, + { + "author_name": "Catherine Cosgrove", + "author_inst": "Vaccine Institute, St. Georges, University of London and St. Georges University Hospitals NHS Foundation Trust" + }, + { + "author_name": "James Galloway", + "author_inst": "Centre for Rheumatic Disease, Kings College London" + }, + { + "author_name": "Anna L. Goodman", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust, University College London" + }, + { + "author_name": "Amardeep Heer", + "author_inst": "Lakeside Healthcare Research, Lakeside Surgeries Corby" + }, + { + "author_name": "Andrew Higham", + "author_inst": "University Hospitals of Morecambe Bay NHS Foundation Trust" + }, + { + "author_name": "Shalini Iyengar", + "author_inst": "Accelerated Enrollment Solutions, Synexus Hexham, Hexham General Hospital" + }, + { + "author_name": "Arham Jamal", + "author_inst": "Accelerated Enrollment Solutions, Synexus Thames Valley" + }, + { + "author_name": "Christopher Jeanes", + "author_inst": "Norfolk and Norwich University Hospital NHS Foundation Trust" + }, + { + "author_name": "Philip A. Kalra", + "author_inst": "Salford Royal NHS Foundation Trust, Northern Care Alliance" + }, + { + "author_name": "Christina Kyriakidou", + "author_inst": "Accelerated Enrolment Solutions, Synexus Midlands" + }, + { + "author_name": "Daniel F. McAuley", + "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, Queen's University of Belfast & Royal Victoria Hospital" + }, + { + "author_name": "Agnieszka Meyrick", + "author_inst": "Accelerated Enrolment Solutions, Synexus Merseyside" + }, + { + "author_name": "Angela M. Minassian", + "author_inst": "Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford" + }, + { + "author_name": "Jane Minton", + "author_inst": "St James's University Hospital, Leeds Teaching Hospitals NHS Trust" + }, + { + "author_name": "Patrick Moore", + "author_inst": "The Adam Practice, University Hospital Southampton NHS Foundation Trust" + }, + { + "author_name": "Imrozia Munsoor", + "author_inst": "Accelerated Enrolment Solutions, Synexus Glasgow" + }, + { + "author_name": "Helen Nicholls", + "author_inst": "Accelerated Enrolment Solutions, Synexus Wales" + }, + { + "author_name": "Orod Osanlou", + "author_inst": "Bangor University and Betsi Cadwaladr University" + }, + { + "author_name": "Jonathan Packham", + "author_inst": "University of Nottingham and Haywood Hospital, Midlands Partnership NHS Foundation Trust" + }, + { + "author_name": "Carol Pretswell", + "author_inst": "Accelerated Enrolment Solutions, Synexus Lancashire" + }, + { + "author_name": "Alberto San Francisco Ramos", + "author_inst": "Vaccine Institute, St. George's, University of London and St. Georges University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Dinesh Saralaya", + "author_inst": "National Institute for Health Research and Bradford Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Ray P. Sheridan", + "author_inst": "Royal Devon & Exeter Hospital" + }, + { + "author_name": "Richard Smith", + "author_inst": "East Suffolk and North Essex NHS Foundation Trust and University of Essex" + }, + { + "author_name": "Roy L. Soiza", + "author_inst": "Aberdeen Royal Infirmary, NHS Grampian & Ageing Clinical and Experimental Research (ACER) Group, University of Aberdeen" + }, + { + "author_name": "Pauline A. Swift", + "author_inst": "Epsom and St Helier University Hospitals NHS Trust" + }, + { + "author_name": "Emma C Thomson", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Jeremy Turner", + "author_inst": "Norfolk and Norwich University Hospital NHS Foundation Trust" + }, + { + "author_name": "Marianne Elizabeth Viljoen", + "author_inst": "Accelerated Enrolment Solutions, Synexus Manchester" + }, + { + "author_name": "Gary Albert", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Iksung Cho", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Filip Dubovsky", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Greg Glenn", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Joy Rivers", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Andreana Robertson", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Kathy Smith", + "author_inst": "Novavax, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.06.21256757", "rel_title": "COVID-19 outbreak rates and infection attack rates associated with the workplace: a descriptive epidemiological study", @@ -740407,29 +744446,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.08.21256726", - "rel_title": "Acute biliary pancreatitis management during the COVID-19 pandemic", - "rel_date": "2021-05-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.08.21256726", - "rel_abs": "ObjectiveTo analyze acute biliary pancreatitis (ABP) management during the COVID-19 pandemic.\n\nMethodsThis was a retrospective cohort study conducted with ABP patients during two discrete periods: a control period from March 16, 2019, through March 15, 2020 (period 1); and a COVID-19 era between March 16, 2020, and March 15, 2021 (period 2).\n\nResultsA total of 89 patients with ABP were identified, 58 in period 1 and 31 in period 2, which equates to a 46.6% reduction. The mean age of the patients was 62.75{+/-}16.59 years, and 51 (57.3%) of the patients were female. qSOFA and WSES scores are significantly higher in the patients in period 2 (p=0.031, p=0.032). There were no significant differences regarding hematological parameters except lactate. Lactate levels were significantly higher in period 2 (p=0.012). Twenty-two patients (37.9%) in period 1 and six (19.3%) patients in period 2 underwent cholecystectomy (p=0.072). Cholecystectomy was performed laparoscopically in 18 (81.8%) patients in period 1 and in five (83.3%) patients in period 2 (p=0.932). There were no significant differences regarding surgical intervention between the two periods. Three patients were diagnosed COVID-19 in period 2. All of these patients died. The severity of ABP was significantly worse in SARS-CoV-2-positive patients, with over 100% of patients in this group developing severe pancreatitis. Six patients (10.3%) in period 1, 10 (32.2%) patients in period 2 were admitted in ICU (p=0.010). The median length of stay was 5 (1-40) days in period 1 and 4 (2-75) days in period 2 (p= 0.641). The hospital mortality rate was 3.4% and 19.3% in period l and period 2, respectively. Mortality was significantly higher in period 2 (p=0.012).\n\nConclusionDuring the COVID-19 outbreak, a significant decrease in the number of patients with ABP and increased severity was observed. Additionally, it can be said that SARS-CoV-2 infection has a mortal course in patients with ABP. Analysis and evaluation of ABP patients during the pandemic period is important to draw conclusions that will help confront future health crises.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Elif Colak", - "author_inst": "University of Samsun, Samsun Training and Research Hospital" - }, - { - "author_name": "Ahmet Burak Ciftci", - "author_inst": "Unversity of Samsun, Samsun Training and Research Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2021.05.07.21256809", "rel_title": "Cellular immunity predominates over humoral immunity after the first dose of COVID-19 vaccines in solid organ transplant recipients", @@ -742800,6 +746816,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.06.21256738", + "rel_title": "The evaluation of a novel digital immunochromatographic assay with silver amplification to detect SARS-CoV-2", + "rel_date": "2021-05-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256738", + "rel_abs": "IntroductionRapid antigen tests are convenient for diagnosing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, they have lower sensitivities than nucleic acid amplification tests. In this study, we evaluated the diagnostic performance of Quick Chaser(R) Auto SARS-CoV-2, a novel digital immunochromatographic assay that is expected to have higher sensitivity than conventional antigen tests.\n\nMethodsA prospective observational study was conducted between February 8 and March 24, 2021. We simultaneously obtained two nasopharyngeal samples, one for evaluation with the QuickChaser(R) Auto SARS-CoV-2 antigen test and the other for assessment with reverse transcription PCR (RT-PCR), considered the gold-standard reference test. The limit of detection (LOD) of the new antigen test was compared with those of four other commercially available rapid antigen tests.\n\nResultsA total of 1401 samples were analyzed. SARS-CoV-2 was detected by reference RT-PCR in 83 (5.9%) samples, of which 36 (43.4%) were collected from symptomatic patients. The sensitivity, specificity, positive predictive value, and negative predictive value were 74.7% (95% confidence interval (CI): 64.0-83.6%), 99.8% (95% CI: 99.5-100%), 96.9% (95% CI: 89.2-99.6%), and 98.4% (95% CI: 97.6-99.0%), respectively. When limited to samples with a cycle threshold (Ct) <30 or those from symptomatic patients, the sensitivity increased to 98.3% and 88.9%, respectively. The QuickChaser(R) Auto SARS-CoV-2 detected 34-120 copies/test, which indicated greater sensitivity than the other rapid antigen tests.\n\nConclusionsQuickChaser(R) Auto SARS-CoV-2 showed sufficient sensitivity and specificity in clinical samples of symptomatic patients. The sensitivity was comparable to RT-PCR in samples with Ct<30.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Yoko Kurihara", + "author_inst": "University of Tsukuba Hospital" + }, + { + "author_name": "Yoshihiko Kiyasu", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Yusaku Akashi", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Yuto Takeuchi", + "author_inst": "University of Tsukuba Hospital" + }, + { + "author_name": "Kenji Narahara", + "author_inst": "Mizuho Medy Co., Ltd." + }, + { + "author_name": "Sunao Mori", + "author_inst": "Mizuho Medy Co., Ltd." + }, + { + "author_name": "Tomonori Takeshige", + "author_inst": "Mizuho Medy Co., Ltd." + }, + { + "author_name": "Shigeyuki Notake", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Atsuo Ueda", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Koji Nakamura", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Hiroichi Ishikawa", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Hiromichi Suzuki", + "author_inst": "University of Tsukuba" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.12.21256693", "rel_title": "Nanopore Sequencing of SARS-CoV-2: Comparison of Short and Long PCR-tiling Amplicon Protocols", @@ -743085,89 +747164,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.06.21256766", - "rel_title": "SARS-CoV-2 RNA and antibody detection in human milk from a prospective multicenter study in Spain", - "rel_date": "2021-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256766", - "rel_abs": "BackgroundDuring the COVID-19 pandemic in 2020, breastfeeding in women positive for SARS-CoV-2 was compromised due to contradictory data regarding potential viral transmission. However, growing evidence confirms the relevant role of breast milk in providing passive immunity by generating and transmitting specific antibodies against the virus. Thus, our study aimed to develop and validate a specific protocol to detect SARS-CoV-2 in breast milk matrix as well as to determine the impact of maternal SARS-CoV-2 infection on presence, concentration, and persistence of specific SARS-CoV-2 antibodies.\n\nStudy design/MethodsA prospective multicenter longitudinal study in Spain was carried out from April to December 2020. A total of 60 mothers with SARS-CoV-2 infection and/or recovered from COVID-19 were included (n=52 PCR-diagnosed and n=8 seropositive). Data from maternal-infant clinical records and symptomatology were collected. A specific protocol was validated to detect SARS-CoV-2 RNA in breast milk, targeting the N1 region of the nucleocapsid gene and the envelope (E) gene. Presence and levels of SARS-CoV-2 specific immunoglobulins (Igs) -IgA, IgG, and IgM-in breast milk samples from COVID-19 patients and from 13 women before the pandemic were also evaluated.\n\nResultsAll breast milk samples showed negative results for SARS-CoV-2 RNA presence. We observed high intra- and inter-individual variability in the antibody response to the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein for each of the three isotypes IgA, IgM and IgG. Protease domain (MPro) antibodies were also detected in milk. In general, 82.9 % of the milk samples were positive for at least one of the three antibody isotypes, being 52.86 % of those positive for all three Igs. Positivity rate for IgA was relatively stable over time (65.2 - 87.5 %), whereas it raised continuously for IgG (47.8 % the first ten days to 87.5 % from day 41 up to day 206 post-PCR confirmation).\n\nConclusionsConsidering the lack of evidence for SARS-CoV-2 transmission through breast milk, our study confirms the safety of breastfeeding practices and highlights the relevance of virus-specific SARS-CoV-2 antibody transfer, that would provide passive immunity to breastfed infants and protect them against COVID-19 disease. This study provides crucial data to support official breastfeeding recommendations based on scientific evidence.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Christine Bauerl", - "author_inst": "IATA-CSIC" - }, - { - "author_name": "Walter Randazzo", - "author_inst": "IATA-CSIC" - }, - { - "author_name": "Gloria Sanchez", - "author_inst": "IATA-CSIC" - }, - { - "author_name": "Marta Selma-Royo", - "author_inst": "IATA-CSIC" - }, - { - "author_name": "Elia Garcia-Verdevio", - "author_inst": "Department of Gynecology and Obstetrics, Hospital Universitario Doctor Peset, Valencia, Spain" - }, - { - "author_name": "Laura Martinez-Rodriguez", - "author_inst": "Department of Pediatrics, Hospital Clinico Universitario, University of Valencia, Spain. Nutrition Research Group of INCLIVA, Valencia, Spain." - }, - { - "author_name": "Anna Parra-Llorca", - "author_inst": "Health Research Institute La Fe, Neonatal Research Group, Spain and University and Polytechnic Hospital La Fe, Division of Neonatology, Valencia, Spain." - }, - { - "author_name": "Carles Lerin", - "author_inst": "Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain." - }, - { - "author_name": "Victoria Fumado", - "author_inst": "Infectious Diseases Unit Department of Pediatrics, Sant Joan de Deu University Hospital, Barcelona, Spain" - }, - { - "author_name": "Francesca Crovetto", - "author_inst": "BCNatal - Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Sant Joan de Deu and Hospital Clinic), IDIBAPS, University of Barcelona, Barcelona" - }, - { - "author_name": "Fatima Crispi", - "author_inst": "BCNatal - Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Sant Joan de Deu and Hospital Clinic), IDIBAPS, University of Barcelona, Barcelona" - }, - { - "author_name": "Francisco Jose Perez-Cano", - "author_inst": "Physiology Section, Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, University of Barcelona (UB), Barcelona, Spain." - }, - { - "author_name": "Gerardo Rodriguez", - "author_inst": "Departament of Pediatrics, University of Zaragoza, Hospital Clinico Universitario Lozano Blesa, Zaragoza. Instituto de Investigacion Sanitaria Aragon (IIS Arago" - }, - { - "author_name": "Gema Ruiz-Redondo", - "author_inst": "Department of Obstetrics and Gynaecology, University Hospital Clinic San Cecilio, Health Sciences Technological Park (PTS), Granada, Spain" - }, - { - "author_name": "Cristina Campoy", - "author_inst": "Department of Pediatrics, School of Medicine, University of Granada, Granada, Spain." - }, - { - "author_name": "Cecilia Martinez-Costa", - "author_inst": "Department of Pediatrics, Hospital Clinico Universitario, University of Valencia, Spain. Nutrition Research Group of INCLIVA, Valencia, Spain." - }, - { - "author_name": "Maria Carmen Collado", - "author_inst": "IATA-CSIC" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.05.06.21256751", "rel_title": "COVID-19 wastewater based epidemiology: long-term monitoring of 10 WWTP in France reveals the importance of the sampling context", @@ -744534,6 +748530,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.05.11.21257016", + "rel_title": "Comparative sensitivity evaluation for 122 CE-marked SARS-CoV-2 antigen rapid tests", + "rel_date": "2021-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21257016", + "rel_abs": "ObjectiveIndependent evaluation of the sensitivity of CE-marked SARS-CoV-2 antigen rapid diagnostic tests (Ag RDT) offered in Germany.\n\nMethodThe sensitivity of 122 Ag RDT was adressed using a common evaluation panel. Minimum sensitivity of 75% for panel members with CT<25 was used for differentiation of devices eligible for reimbursement in in the German healthcare system.\n\nResultsThe sensitivity of different SARS-CoV-2 Ag RDT varied over a wide range. The sensitivity limit of 75% for panel members with CT <25 was met by 96 of the 122 tests evaluated; 26 tests exhibited lower sensitivity, few of which were completely failing. Some devices exhibited high sensitivity, e.g. 100% for CT<30.\n\nConclusionThis comparative evaluation succeeded to distinguish less sensitive from better performing Ag RDT. Most of the Ag RDT evaluated appear to be suitable for fast identification of acute infections associated with high viral loads. Market access of SARS-CoV-2 Ag RDT should be based on minimal requirements for sensitivity and specificity.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Heinrich Scheiblauer", + "author_inst": "Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, D-63225 Langen" + }, + { + "author_name": "Angela Filomena", + "author_inst": "Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, D-63225 Langen" + }, + { + "author_name": "Andreas Nitsche", + "author_inst": "Robert Koch-Institute, Seestrasse 10, D-13353 Berlin" + }, + { + "author_name": "Andreas Puyskens", + "author_inst": "Robert Koch-Institute, Seestrasse 10, D-13353 Berlin" + }, + { + "author_name": "Victor Corman", + "author_inst": "Institute of Virology, Charite, Chariteplatz 1, D-10117 Berlin" + }, + { + "author_name": "Christian Drosten", + "author_inst": "Institute of Virology, Charite, Chariteplatz 1, D-10117 Berlin" + }, + { + "author_name": "Katrin Zwirglmaier", + "author_inst": "Bundeswehr Institute of Microbiology, Neuherbergstr 11, D-80937 Munich" + }, + { + "author_name": "Constanze Lange", + "author_inst": "LADR GmbH, Lauenburger Str. 67, D-21502 Geesthacht" + }, + { + "author_name": "Petra Emmerich", + "author_inst": "Bernhard-Nocht Institute, Dep.Virology, Bernhard-Nocht Str. 74, D-20359 Hamburg" + }, + { + "author_name": "Michael Mueller", + "author_inst": "MVZ Labor 28 GmbH, Mecklenburgische Str. 2, D-14197 Berlin" + }, + { + "author_name": "Olivia Knauer", + "author_inst": "Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, D-63225 Langen" + }, + { + "author_name": "Micha Nuebling", + "author_inst": "Paul-Ehrlich-Institut" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.10.21256996", "rel_title": "Quantifying the potential for dominant spread of SARS-CoV-2 variant B.1.351 in the United States", @@ -744743,125 +748802,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.11.21256917", - "rel_title": "Methotrexate Hampers Immunogenicity to BNT162b2 mRNA COVID-19 Vaccine in Immune-Mediated Inflammatory Disease", - "rel_date": "2021-05-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21256917", - "rel_abs": "ObjectiveTo investigate the humoral and cellular immune response to mRNA COVID-19 vaccines in patients with immune-mediated inflammatory diseases (IMIDs) on immunomodulatory treatment.\n\nMethodsEstablished patients at NYU Langone Health with IMID (n=51) receiving the BNT162b2 mRNA vaccination were assessed at baseline and after second immunization. Healthy subjects served as controls (n=26). IgG antibody responses to the spike protein were analyzed for humoral response. Cellular immune response to SARS-CoV-2 was further analyzed using high-parameter spectral flow cytometry. A second independent, validation cohort of controls (n=182) and patients with IMID (n=31) from Erlangen, Germany were also analyzed for humoral immune response.\n\nResultsAlthough healthy subjects (n=208) and IMID patients on biologic treatments (mostly on TNF blockers, n=37) demonstrate robust antibody responses (over 90%), those patients with IMID on background methotrexate (n=45) achieve an adequate response in only 62.2% of cases. Similarly, IMID patients do not demonstrate an increase in CD8+ T cell activation after vaccination.\n\nConclusionsIn two independent cohorts of IMID patients, methotrexate, a widely used immunomodulator for the treatment of several IMIDs, adversely affected humoral and cellular immune response to COVID-19 mRNA vaccines. Although precise cut offs for immunogenicity that correlate with vaccine efficacy are yet to be established, our findings suggest that different strategies may need to be explored in patients with IMID taking methotrexate to increase the chances of immunization efficacy against SARS-CoV-2 as has been demonstrated for augmenting immunogenicity to other viral vaccines.\n\nKEY MESSAGESO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIThe impact of COVID-19 has been felt across the globe and new hope has arisen with the approval of mRNA vaccines against the SARS-CoV-2. Studies have shown immunogenicity and efficacy rates of over 90% in the immunocompetent adult population. However, there is a lack of knowledge surrounding the response of patients with immune-mediated inflammatory diseases (IMIDs) who may also be on immunomodulatory medications.\nC_LIO_LIPatients with IMID have been shown to have attenuated immune responses to seasonal influenza vaccination.\nC_LI\n\nWhat does this study add?O_LIThis study looks at the humoral and cellular immune response to two doses of BNT162b2 mRNA COVID-19 Vaccine in participants with IMID (on immunomodulators) compared with healthy controls.\nC_LIO_LIIndividuals with IMID on methotrexate demonstrate up to a 62% reduced rate of adequate immunogenicity to the BNT162b2 mRNA vaccination. Those on anti-cytokine or non-methotrexate oral medications demonstrate similar levels of immunogenicity as healthy controls (greater than 90%).\nC_LIO_LISimilarly, vaccination did not induce an activated CD8+ T cell response in participants on background methotrexate, unlike healthy controls and patients with IMID not receiving methotrexate.\nC_LI\n\nHow might this impact of clinical practice or future developments?O_LIThese results suggest that patients on methotrexate may need alternate vaccination strategies such as additional doses of vaccine, dose modification of methotrexate, or even a temporary discontinuation of this drug. Further studies will be required to explore the effect of these approaches on mRNA vaccine immunogenicity.\nC_LI", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Rebecca H Haberman", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Ramin Herati", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "David Simon", - "author_inst": "FAU Erlangen-Nuremberg and Universitatsklinikum Erlangen, Erlangen, Germany" - }, - { - "author_name": "Marie Samanovic", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Rebecca B. Blank", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Michael Tuen", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Sergei Koralov", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Raja Atreya", - "author_inst": "FAU Erlangen-Nuremberg and Universitatsklinikum Erlangen, Erlangen, Germany" - }, - { - "author_name": "Koray Tascilar", - "author_inst": "FAU Erlangen-Nuremberg and Universitatsklinikum Erlangen, Erlangen, Germany" - }, - { - "author_name": "Joseph Allen", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Rochelle Castillo", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Amber Cornelius", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Paula Rackoff", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Gary Solomon", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Samrachana Adhikari", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Natalie Azar", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Pamela Rosenthal", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Peter Izmirly", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Jonathan Samuels", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Brian Golden", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Soumya Reddy", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Markus F. Neurath", - "author_inst": "FAU Erlangen-Nuremberg and Universitatsklinikum Erlangen, Erlangen, Germany" - }, - { - "author_name": "Steven B. Abramson", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Georg Schett", - "author_inst": "FAU Erlangen-Nuremberg and Universitatsklinikum Erlangen, Erlangen, Germany" - }, - { - "author_name": "Mark J Mulligan", - "author_inst": "New York University Grossman School of Medicine" - }, - { - "author_name": "Jose U Scher", - "author_inst": "NYU School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "rheumatology" - }, { "rel_doi": "10.1101/2021.05.11.21256992", "rel_title": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence: Navigating the absence of a gold standard", @@ -746676,6 +750616,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.11.21256479", + "rel_title": "Communicable and non-communicable co-morbidities and the presentation of COVID-19 in an African setting of high HIV-1 and tuberculosis prevalence", + "rel_date": "2021-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21256479", + "rel_abs": "ObjectivesTo describe the presentation and outcome of SARS-CoV2 infection in an African setting of high non-communicable co-morbidity and also HIV-1 and tuberculosis prevalence.\n\nDesignCase control analysis with cases stratified by HIV-1 and tuberculosis status.\n\nSettingA single-centre observational case-control study of adults admitted to a South African hospital with proven SARS-CoV-2 infection or alternative diagnosis.\n\nParticipants104 adults with RT-PCR-proven SARS-CoV2 infection of which 55 (52.9%) were male and 31 (29.8%) HIV-1 co-infected. 40 adults (35.7% male, 30.9% HIV-1 co-infected) admitted during the same period with no RT-PCR or serological evidence of SARS-CoV2 infection and assigned alternative diagnoses. Additional in vitro data from prior studies of 72 healthy controls and 118 HIV-1 uninfected and infected persons participants enrolled to a prior study with either immune evidence of tuberculosis sensitization but no symptoms or microbiologically confirmed pulmonary tuberculosis.\n\nResultsTwo or more co-morbidities were present in 57.7% of 104 RT-PCR proven COVID-19 presentations, the commonest being hypertension (48%), type 2 diabetes mellitus (39%), obesity (31%) but also HIV-1 (30%) and active tuberculosis (14%). Amongst patients dually infected by tuberculosis and SARS-CoV-2, clinical features could be dominated by either SARS-CoV-2 or tuberculosis: lymphopenia was exacerbated, and some markers of inflammation (D-dimer and ferritin) elevated in singly SARS-CoV-2 infected patients were even further elevated (p < 0.05). HIV-1 and SARS-CoV2 co-infection resulted in lower absolute number and proportion of CD4 lymphocytes, with those in the lowest peripheral CD4 percentage strata exhibiting absent or lower antibody responses against SARS-CoV2. Death occurred in 30/104 (29%) of all COVID-19 patients and in 6/15 (40%) of patients with coincident SARS-CoV-2 and tuberculosis.\n\nConclusionsIn this South African setting, HIV-1 and tuberculosis are common co-morbidities in patients presenting with COVID-19. In environments in which tuberculosis is common, SARS-CoV-2 and tuberculosis may co-exist with clinical presentation being typical of either disease. Clinical suspicion of exacerbation of co-existent tuberculosis accompanying SARS-CoV-2 should be high.\n\nWhat is already known on this topic?It has been quite widely thought that Africa has been spared the worst effects of the COVID-19 pandemic. There are very few reported case series and no case-control studies comparing COVID-19 patients admitted to hospital to those admitted for other reasons. However several studies have indicated both HIV-1 and tuberculosis co-infection that are endemic in Africa constitute risk factors for poor outcome. In addition Africa is subject to demographic transition and the prevalence of non-communicable co-morbidities such as type 2 diabetes, hypertension and cardiovascular disease is rising rapidly. No study from Africa has described the clinical impact on the presentation of COVID-19 infection.\n\nWhat this study addsTwo or more co-morbidities were present in over half COVID-19 presentations, including HIV-1 (30%) and active tuberculosis (14%). Patients dually infected by tuberculosis and SARS-CoV-2, presented as either SARS-CoV-2 or tuberculosis. HIV-1 and SARS-CoV2 co-infection resulted in lower absolute number and proportion of CD4 lymphocytes, and those with low CD4 counts had absent or lower antibody responses against SARS-CoV2. Death occurred 29% of all COVID-19 patients and in 40% of patients with coincident SARS-CoV-2 and tuberculosis. Thus in environments in which tuberculosis is common, SARS-CoV-2 and tuberculosis may co-exist with clinical presentation being typical of either disease and clinical suspicion of exacerbation of co-existent tuberculosis accompanying SARS-CoV-2 should be high.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Elsa du Bruyn", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Cari Stek", + "author_inst": "University of Cape Town and Imperial College London" + }, + { + "author_name": "Remy Daroowala", + "author_inst": "Imperial College London and University of Cape Town" + }, + { + "author_name": "Qonita Said-Hartley", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Marvin Hsiao", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Rene Tina Goliath", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Fatima Abrahams", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Amanda Jackson", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Sean Wasserman", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Brian Allwood", + "author_inst": "University of Stellenbosch" + }, + { + "author_name": "Angharad G Davis", + "author_inst": "University College London, Francis Crick Institute, and University of Cape Town" + }, + { + "author_name": "Rachel Lai", + "author_inst": "Imperial College London and Francis Crick Institute" + }, + { + "author_name": "Anna Kathleen Coussens", + "author_inst": "Walter and Eliza Hall Institute and University of Cape Town" + }, + { + "author_name": "Katalin Andrea Wilkinson", + "author_inst": "The Francis Crick Institute and University of Cape Town" + }, + { + "author_name": "Jantina De Vries", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Nicki Tiffin", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Maddalena Cerrone", + "author_inst": "Imperial College London and Francis Crick Institute" + }, + { + "author_name": "Ntobeko Ntusi", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Catherine Riou", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Robert J Wilkinson", + "author_inst": "University of Cape Town" + }, + { + "author_name": "- HIATUS investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.05.11.21256877", "rel_title": "A blood atlas of COVID-19 defines hallmarks of disease severity and specificity", @@ -747665,73 +751704,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.05.21256710", - "rel_title": "Evolution of COVID-19 symptoms during the first 9 months after illness onset", - "rel_date": "2021-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256710", - "rel_abs": "BackgroundFew longitudinal data on COVID-19 symptoms across the full spectrum of disease severity are available. We evaluated symptom onset, severity and recovery up to nine months after illness onset.\n\nMethodsThe RECoVERED Study is a prospective cohort study based in Amsterdam, the Netherlands. Participants aged>18 years were recruited following SARS-CoV-2 diagnosis via the local Public Health Service and from hospitals. Standardised symptom questionnaires were completed at recruitment, at one week and month after recruitment, and monthly thereafter. Clinical severity was defined according to WHO criteria. Kaplan-Meier methods were used to compare time from illness onset to symptom recovery, by clinical severity. We examined determinants of time to recovery using multivariable Cox proportional hazards models.\n\nResultsBetween 11 May 2020 and 31 January 2021, 301 COVID-19 patients (167[55%] male) were recruited, of whom 99/301(32.9%) had mild, 140/301(46.5%) moderate, 30/301(10.0%) severe and 32/301(10.6%) critical disease. The proportion of symptomatic participants who reported at least one persistent symptom at 12 weeks after illness onset was greater in those with severe/critical disease (81.7%[95%CI=68.7-89.7%]) compared to those with mild or moderate disease (33.0%[95%CI=23.0-43.3%] and 63.8%[95%CI=54.8-71.5%]). Even at nine months after illness onset, almost half of all participants (42.1%[95%CI=35.6-48.5]) overall continued to report [≥]1 symptom. Recovery was slower in participants with BMI[≥]30kg/m2 (HR 0.51[95%CI=0.30-0.87]) compared to those with BMI<25kg/m2, after adjusting for age, sex and number of comorbidities.\n\nConclusionsCOVID-19 symptoms persisted for nine months after illness onset, even in those with mild disease. Obesity was the most important determinant of speed of recovery from symptoms.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Elke Wynberg", - "author_inst": "Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands" - }, - { - "author_name": "Hugo van Willigen", - "author_inst": "Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, th" - }, - { - "author_name": "Maartje Dijkstra", - "author_inst": "Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands" - }, - { - "author_name": "Anders Boyd", - "author_inst": "Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands" - }, - { - "author_name": "Neeltje A. Kootstra", - "author_inst": "Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands" - }, - { - "author_name": "Joost G. van den Aardweg", - "author_inst": "Department of Pulmonology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands" - }, - { - "author_name": "Marit J. van Gils", - "author_inst": "Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, th" - }, - { - "author_name": "Amy Matser", - "author_inst": "Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands" - }, - { - "author_name": "Marije R. de Wit", - "author_inst": "Department of Infectious Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands" - }, - { - "author_name": "Tjalling Leenstra", - "author_inst": "Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands" - }, - { - "author_name": "Godelieve J. de Bree", - "author_inst": "Department of Infectious Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands" - }, - { - "author_name": "Menno D. de Jong", - "author_inst": "Department of Medical Microbiology & Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, th" - }, - { - "author_name": "Maria Prins", - "author_inst": "Department of Infectious Diseases, Public Health Service of Amsterdam, Amsterdam, the Netherlands" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.11.21257033", "rel_title": "COVID-19: A comparative study of severity of patients hospitalized during the first and the second wave in South Africa.", @@ -749338,6 +753310,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.07.21256743", + "rel_title": "Effect of using personal protective equipment during the COVID-19 pandemic on the quality indicators of screening colonoscopies.", + "rel_date": "2021-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256743", + "rel_abs": "BackgroundCoronavirus Disease 2019 (COVID-19) has affected many facets of the practice of medicine including screening colonoscopies.\n\nAimsOur study looks to observe if there has been an effect on the quality of colonoscopies, as indicated by quality measures such as cecal intubation rate (CIR), cecal intubation time (CIT), scope withdrawal time (SWT) and adenoma detection rate (ADR) with the adoption of standard COVID-19 precautions.\n\nMethodsWe conducted a retrospective chart review to analyze the effects of the COVID-19 pandemic on screening colonoscopies. The study utilized data on CIR, CIT, SWT and ADR from outpatient, non-emergent procedures conducted at 3 endoscopy suites of St Lukes University Health Network. All inpatient and emergent procedures were excluded.\n\nResultsOur study demonstrated that the total number of screening colonoscopies was decreased between 2019 to 2020 (318 in 2019 vs 157 in 2020, p= 0.005). CIT (320{+/-}105 seconds in 2019 vs 392{+/-}107 seconds in 2020, p=0.001) and SWT (706{+/-}232 seconds in 2019 vs 830{+/-}241 seconds in 2020, p=0.001) were increased while CIR (98.2% in 2019 vs 96.6% in 2020, p=0.04) was decreased between 2019 and 2020 likely due to PPE introduction. ADR was similar between the two groups (38.23 (12.50-66.66) in 2019 vs 38.18(16.66-66.00) in 2020, p=0.8).\n\nConclusionOur study showed that quality indices for screening colonoscopies like CIR, CIT, and SWT were negatively impacted during the COVID-19 time period. ADR, however, were similar. Thus, the efficiency of the procedures was affected by the use of PPE but it did not affect the colonoscopys clinical benefit.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Subin G Chirayath", + "author_inst": "St. Luke's University Hospital" + }, + { + "author_name": "Janak Bahirwani", + "author_inst": "St. Luke's University Hospital" + }, + { + "author_name": "Parampreet Kaur", + "author_inst": "St. Luke's University Hospital" + }, + { + "author_name": "Noel Martins", + "author_inst": "St. Luke's University Hospital" + }, + { + "author_name": "Ronak Modi", + "author_inst": "St. Luke's University Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "gastroenterology" + }, { "rel_doi": "10.1101/2021.05.08.21256792", "rel_title": "Yet another lockdown? A large-scale study on people's unwillingness to be confined during the first 5 months of the COVID-19 pandemic in Spain", @@ -749459,41 +753466,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.05.06.21256705", - "rel_title": "Estimated Spike Evolution and Impact of Emerging SARS-CoV-2 Variants", - "rel_date": "2021-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256705", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, has been mutating and thus variants emerged. This suggests that SARS-CoV-2 could mutate at an unsteady pace. Supportive evidence comes from the accelerated evolution which was revealed by tracking mutation rates of the genomic location of Spike protein. This process is sponsored by a small portion of the virus population but not the largest viral clades. Moreover, it generally took one to six months for current variants that caused peaks of COVID-19 cases and deaths to survive selection pressure. Based on this statistic result and the above speedy Spike evolution, another upcoming peak would come around July 2021 and disastrously attack Africa, Asia, Europe, and North America. This is the prediction generated by a mathematical model on evolutionary spread. The reliability of this model and future trends out of it comes from the comprehensive consideration of factors mainly including mutation rate, selection course, and spreading speed. Notably, if the prophecy is true, then the new wave will be the first determined by accelerated Spike evolution.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yong Lu", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "Kun Han", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "Gang Xue", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "Ningbo Zheng", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "Guangxu Jin", - "author_inst": "Wake Forest School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.06.21256788", "rel_title": "Rapid detection of neutralizing antibodies to SARS-CoV-2 variants in post-vaccination sera", @@ -751592,6 +755564,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.05.21256668", + "rel_title": "COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland", + "rel_date": "2021-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256668", + "rel_abs": "The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively.\n\nClinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sofia de la Fuente Garcia", + "author_inst": "The University of Edinburgh" + }, + { + "author_name": "Fasih Haider", + "author_inst": "The University of Edinburgh" + }, + { + "author_name": "Saturnino Luz", + "author_inst": "The University of Edinburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.05.05.21256677", "rel_title": "SARS-CoV-2 RNA in urban wastewater samples to monitor the COVID-19 epidemic in Lombardy, Italy (March - June 2020)", @@ -751753,77 +755752,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.05.21256396", - "rel_title": "A prospective diagnostic study to measure the accuracy of detection of SARS-CoV-2 Variants Of Concern (VOC) utilising a novel RT-PCR GENotyping algorithm in an In silico Evaluation (VOC-GENIE)", - "rel_date": "2021-05-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256396", - "rel_abs": "BackgroundSARS-CoV-2 variants of concern (VOCs) have been associated with higher rate of transmission, and evasion of immunisation and antibody therapeutics. Variant sequencing is widely utilized in the UK. However, only 0.5% (~650k) of the 133 million cumulative positive cases worldwide were sequenced (in GISAID) on 08 April 2021 with 97% from Europe and North America and only ~0.25% (~320k) were variant sequences. This may be due to the lack of availability, high cost, infrastructure and expert staff required for sequencing.\n\nPublic health decisions based on a non-randomised sample of 0.5% of the population may be insufficiently powered, and subject to sampling bias and systematic error. In addition, sequencing is rarely available in situ in a clinically relevant timeframe and thus, is not currently compatible with diagnosis and treatment patient care pathways. Therefore, we investigated an alternative approach using polymerase chain reaction (PCR) genotyping to detect the key single nucleotide polymorphisms (SNPs) associated with increased transmission and immune evasion in SARS-CoV-2 variants.\n\nMethodsWe investigated the utility of SARS-CoV-2 SNP detection with a panel of PCR-genotyping assays in a large data set of 640,482 SARS-CoV-2 high quality, full length sequences using a prospective in silico trial design and explored the potential impact of rapid in situ variant testing on the COVID-19 diagnosis and treatment patient pathway.\n\nResultsFive SNPs were selected by screening the published literature for a reported association with increased transmission and / or immune evasion. 344881 sequences contained one or more of the five SNPs. This algorithm of SNPs was found to be able to identify the four variants of concern (VOCs) and sequences containing the E484K and L452R escape mutations.\n\nInterpretationThe in silico analysis suggest that the key mutations and variants of SARS-CoV-2 may be reliably detected using a focused algorithm of biologically relevant SNPs. This highlights the potential for rapid in situ PCR genotyping to compliment or replace sequencing or to be utilized instead of sequences in settings where sequencing is not feasible, accessible or affordable. Rapid detection of variants with in situ PCR genotyping may facilitate a more effective COVID-19 diagnosis and treatment patient pathway.\n\nFundingThe study was funded by Primer Design (UK), with kind contributions from all academic partners.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Daryl Borley", - "author_inst": "Novacyt Group" - }, - { - "author_name": "R A Trevor", - "author_inst": "Novacyt Group" - }, - { - "author_name": "Alex Richter", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Stephen Kidd", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Nick Cortes", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Nathan Moore", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Alice Goring", - "author_inst": "Hampshire Hospitals NHS Foundation Trust" - }, - { - "author_name": "Prachi Teltumbde", - "author_inst": "Novacyt Group" - }, - { - "author_name": "Kate Templeton", - "author_inst": "Edinburgh Royal Infirmary" - }, - { - "author_name": "Seden Grippon", - "author_inst": "Novacyt Group" - }, - { - "author_name": "Paul Oladimeji", - "author_inst": "Novacyt Group" - }, - { - "author_name": "Aida Sanchez-Bretano", - "author_inst": "Novacyt Group" - }, - { - "author_name": "Andrew Dawson", - "author_inst": "Novacyt Group" - }, - { - "author_name": "Joanne Martin", - "author_inst": "Queen Mary University of London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.07.21256531", "rel_title": "Immunophenotyping and machine learning identify distinct immunotypes that predict COVID-19 clinical severity", @@ -753742,6 +757670,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.05.04.21256655", + "rel_title": "COVID-19 cases from the first local outbreak of SARS-CoV-2 B.1.1.7 variant in China presented more serious clinical features: a prospective, comparative cohort study", + "rel_date": "2021-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256655", + "rel_abs": "BackgroundThe SARS-CoV-2 B.1.1.7 variant which was first identified in the United Kingdom (U.K.) has increased sharply in numbers worldwide and was reported to be more contagious. On January 17, 2021, a COVID-19 clustered outbreak caused by B.1.1.7 variant occurred in a community in Daxing District, Beijing, China. Three weeks prior, another non-variant (lineage B.1.470) COVID-19 outbreak occurred in Shunyi District, Beijing. This study aimed to investigate the clinical features of B.1.1.7 variant infection.\n\nMethodsA prospective cohort study was conducted on COVID-19 cases admitted to Ditan hospital since January 2020. Data of 74 COVID-19 cases from two independent COVID-19 outbreaks in Beijing were extracted as study subjects from a Cloud Database established in Ditan hospital, which included 41 Shunyi cases (Shunyi B.1.470 group) and 33 Daxing cases (Daxing B.1.1.7 group) that have been hospitalized since December 25, 2020 and January 17, 2021, respectively. We conducted a comparison of the clinical characteristics, RT-qPCR results and genomic features between the two groups.\n\nFindingsCases from Daxing B.1.1.7 group (15 [45.5%] male; median age, 39 years [range, 30.5, 62.5]) and cases from Shunyi B.1.470 group (25 [61.0%] male; median age, 31 years [range, 27.5, 41.0]) had a statistically significant difference in median age (P =0.014). Seven clinical indicators of Daxing B.1.1.7 group were significantly higher than Shunyi B.1.470 group including patients having fever over 38{degrees}C (14/33 [46.43%] in Daxing B.1.1.7 group vs. 9/41 (21.95%) in Shunyi B.1.470 group [P = 0 .015]), C-reactive protein ([CRP, mg/L], 4.30 [2.45, 12.1] vs. 1.80, [0.85, 4.95], [P = 0.005]), Serum amyloid A ([SAA, mg/L], 21.50 [12.50, 50.70] vs. 12.00 [5.20, 26.95], [P = 0.003]), Creatine Kinase ([CK, U/L]), 110.50 [53.15,152.40] vs. 70.40 [54.35,103.05], [P = 0.040]), D-dimer ([DD, mg/L], 0.31 [0.20, 0.48] vs. 0.24 [0.17,0.31], [P = 0.038]), CD4+ T lymphocyte ([CD4+ T, mg/L], [P = 0.003]), and Ground-glass opacity (GGO) in lung (15/33 [45.45%] vs. 5/41 [12.20%], [P =0.001]). After adjusting for the age factor, B.1.1.7 variant infection was the risk factor for CRP (P = 0.045, Odds ratio [OR] 2.791, CI [1.025, 0.8610]), SAA (0.011, 5.031, [1.459, 17.354]), CK (0.034, 4.34, [0.05, 0.91]), CD4+ T (0.029, 3.31, [1.13, 9.71]), and GGO (0.005, 5.418, [1.656, 17.729]) of patients. The median Ct value of RT-qPCR tests of the N-gene target in the Daxing B.1.1.7 group was significantly lower than the Shunyi B.1.470 group (P=0.036). The phylogenetic analysis showed that only 2 amino acid mutations in spike protein were detected in B.1.470 strains while B.1.1.7 strains had 3 deletions and 7 mutations.\n\nInterpretationClinical features including a more serious inflammatory response, pneumonia and a possible higher viral load were detected in the cases infected with B.1.1.7 SARS-CoV-2 variant. It could therefore be inferred that the B.1.1.7 variant may have increased pathogenicity.\n\nFundingThe study was funded by the National Key Research and Development Program (grant nos.2020YFC0846200 and 2020YFC0848300) and National Natural Science Foundation of China (grant no. 82072295).", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Yang Song M.D.", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Ziruo Ge M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Shuping Cui M.Sc.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China and Peking University, Ditan Teaching Hospital, Beijing, Ch" + }, + { + "author_name": "Di Tian M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Gang Wan M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Shuangli Zhu B.Sc.", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Xianbo Wang M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Yu Wang M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Xiang Zhao M.D.", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Pan Xiang M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Yanli Xu M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Tingyu Zhang M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Long Liu M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Gang Liu M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Yanhai Wang M.Sc.", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Jianbo Tan M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Wei Zhang M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Wenbo Xu M.D.", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Zhihai Chen M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.04.21256635", "rel_title": "Visual Exploratory Analysis of COVID-19 Pandemic: One Year After the Outbreak", @@ -753815,85 +757834,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.05.21256712", - "rel_title": "Unified real-time environmental-epidemiological data for multiscale modeling of the COVID-19 pandemic", - "rel_date": "2021-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256712", - "rel_abs": "An impressive number of COVID-19 data catalogs exist. None, however, are optimized for data science applications, e.g., inconsistent naming and data conventions, uneven quality control, and lack of alignment between disease data and potential predictors pose barriers to robust modeling and analysis. To address this gap, we generated a unified dataset that integrates and implements quality checks of the data from numerous leading sources of COVID-19 epidemiological and environmental data. We use a globally consistent hierarchy of administrative units to facilitate analysis within and across countries. The dataset applies this unified hierarchy to align COVID-19 case data with a number of other data types relevant to understanding and predicting COVID-19 risk, including hydrometeorological data, air quality, information on COVID-19 control policies, and key demographic characteristics.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Hamada S. Badr", - "author_inst": "Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD 21218" - }, - { - "author_name": "Benjamin F. Zaitchik", - "author_inst": "Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218" - }, - { - "author_name": "Gaige H. Kerr", - "author_inst": "Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC 20052" - }, - { - "author_name": "Nhat-Lan Nguyen", - "author_inst": "Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA 22903" - }, - { - "author_name": "Yen-Ting Chen", - "author_inst": "Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA 22903" - }, - { - "author_name": "Patrick Hinson", - "author_inst": "Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA 22903" - }, - { - "author_name": "Josh M. Colston", - "author_inst": "Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA 22903" - }, - { - "author_name": "Margaret N. Kosek", - "author_inst": "Division of Infectious Diseases and International Health, University of Virginia School of Medicine, Charlottesville, VA 22903" - }, - { - "author_name": "Ensheng Dong", - "author_inst": "Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD 21218" - }, - { - "author_name": "Hongru Du", - "author_inst": "Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD 21218" - }, - { - "author_name": "Maximilian Marshall", - "author_inst": "Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD 21218" - }, - { - "author_name": "Kristen Nixon", - "author_inst": "Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD 21218" - }, - { - "author_name": "Arash Mohegh", - "author_inst": "Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC 20052" - }, - { - "author_name": "Daniel L. Goldberg", - "author_inst": "Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC 20052" - }, - { - "author_name": "Susan C. Anenberg", - "author_inst": "Department of Environmental and Occupational Health, Milken Institute School of Public Health, George Washington University, Washington, DC 20052" - }, - { - "author_name": "Lauren M. Gardner", - "author_inst": "Department of Civil and Systems Engineering, Johns Hopkins University, Baltimore, MD 21218" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.04.21256444", "rel_title": "Intentional and unintentional non-adherence to social distancing measures during COVID-19: A mixed-methods analysis.", @@ -755796,6 +759736,57 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.05.01.21256182", + "rel_title": "Modelling upper respiratory viral load dynamics of SARS-CoV-2", + "rel_date": "2021-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.01.21256182", + "rel_abs": "Relationships between viral load, severity of illness, and transmissibility of virus, are fundamental to understanding pathogenesis and devising better therapeutic and prevention strategies for COVID-19. Here we present within-host modelling of viral load dynamics observed in the upper respiratory tract (URT), drawing upon 2172 serial measurements from 605 subjects, collected from 17 different studies. We developed a mechanistic model to describe viral load dynamics and host response, and contrast this with simpler mixed-effects regression analysis of peak viral load and its subsequent decline. We observed wide variation in URT viral load between individuals, over 5 orders of magnitude, at any given point in time since symptom onset. This variation was not explained by age, sex, or severity of illness, and these variables were not associated with the modelled early or late phases of immune-mediated control of viral load. We explored the application of the mechanistic model to identify measured immune responses associated with control of viral load. Neutralizing antibody correlated strongly with modelled immune-mediated control of viral load amongst subjects who produced neutralizing antibody. Our models can be used to identify host and viral factors which control URT viral load dynamics, informing future treatment and transmission blocking interventions.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Joseph D Challenger", + "author_inst": "Imperial College London" + }, + { + "author_name": "Cher Y Foo", + "author_inst": "Imperial College London" + }, + { + "author_name": "Yue Wu", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ada WC Yan", + "author_inst": "Imperial College London" + }, + { + "author_name": "Mahdi Moradi Marjaneh", + "author_inst": "Imperial College London" + }, + { + "author_name": "Felicity Liew", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ryan S Thwaites", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lucy C Okell", + "author_inst": "Imperial College London" + }, + { + "author_name": "Aubrey J Cunnington", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.03.21256520", "rel_title": "The BNT162b2 mRNA vaccine against SARS-CoV-2 reprograms both adaptive and innate immune responses", @@ -756105,53 +760096,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dermatology" }, - { - "rel_doi": "10.1101/2021.05.04.21256575", - "rel_title": "SARS-CoV-2 infections and hospitalizations among immigrants in Norway: significance of occupation, household crowding, education, household income and medical risk. A nationwide register study", - "rel_date": "2021-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256575", - "rel_abs": "BackgroundAs in other countries, the coronavirus disease 2019 (COVID-19) pandemic has affected Norways immigrant population disproportionately with significantly higher infection rates and hospitalizations. The reasons for this are uncertain.\n\nMethodsThrough the national emergency preparedness register, BeredtC19, we have studied laboratory-confirmed infections with SARS-CoV-2 and related hospitalizations in the entire Norwegian population, by birth-country background for the period 15 June 2020 - 31 March 2021, excluding the first-wave due to limited test capacity and restrictive test criteria. Straightforward linkage of individual-level data allowed adjustment for demographics, socioeconomic factors (occupation, household crowding, education, and household income), and underlying medical risk for severe COVID-19 in regression models.\n\nResultsThe sample comprised 5.49 million persons, of which 0.91 million born outside of Norway, 82 532 confirmed cases, and 3088 hospitalizations. Confirmed infections in this period (per 100 000): foreign-born 3140, Norwegian-born with foreign-born parents 4799, Norwegian-born with Norwegian-born parent(s) 1011. Hospitalizations (per 100 000): foreign-born 147, Norwegian-born with foreign-born parents 47, Norwegian-born with Norwegian-born parent(s) 37. The addition of socioeconomic and medical factors to the base-model (age, sex, municipality of residence) attenuated excess infection rates by 12.0% and hospitalizations by 3.8% among foreign-born, and 10.9% and 46.2% respectively among Norwegian-born with foreign parents, compared to Norwegian-born with Norwegian-born parent(s).\n\nConclusionThere were large differences in infection rates and hospitalizations by country background, and these do not appear to be fully explained by socioeconomic and medical factors. Our results may have implications for health policy, including the targeting of mitigation strategies.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Angela S Labberton", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Anna A Godoy", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Ingeborg Hess Elgersma", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Bjorn Heine Strand", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Kjetil Telle", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Trude M Arnesen", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Karin Maria Nygard", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Thor Indseth", - "author_inst": "Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.05.21256716", "rel_title": "Preliminary Analysis of Safety and Immunogenicity of a SARS-CoV-2 Variant Vaccine Booster", @@ -757849,6 +761793,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.05.442782", + "rel_title": "Combination Respiratory Vaccine Containing Recombinant SARS-CoV-2 Spike and QuadrivalentSeasonal Influenza Hemagglutinin Nanoparticles with Matrix-M Adjuvant", + "rel_date": "2021-05-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.05.442782", + "rel_abs": "The 2019 outbreak of a severe respiratory disease caused by an emerging coronavirus, SARS-CoV-2, has spread globally with high morbidity and mortality. Co-circulating seasonal influenza has greatly diminished recently, but expected to return with novel strains emerging, thus requiring annual strain adjustments. We have developed a recombinant hemagglutinin (HA) quadrivalent nanoparticle influenza vaccine (qNIV) produced using an established recombinant insect cell expression system to produce nanoparticles. Influenza qNIV adjuvanted with Matrix-M was well-tolerated and induced robust antibody and cellular responses, notably against both homologous and drifted A/H3N2 viruses in Phase 1, 2, and 3 trials. We also developed a full-length SARS-CoV-2 spike protein vaccine which is stable in the prefusion conformation (NVX-CoV2373) using the same platform technology. In phase 3 clinical trials, NVX-CoV2373 is highly immunogenic and protective against the prototype strain and B.1.1.7 variant. Here we describe the immunogenicity and efficacy of a combination quadrivalent seasonal flu and COVID-19 vaccine (qNIV/CoV2373) in ferret and hamster models. The combination qNIV/CoV2373 vaccine produces high titer influenza hemagglutination inhibiting (HAI) and neutralizing antibodies against influenza A and B strains. The combination vaccine also elicited antibodies that block SARS-CoV-2 spike protein binding to the human angiotensin converting enzyme-2 (hACE2) receptor. Significantly, hamsters immunized with qNIV/CoV2373 vaccine and challenged with SARS-CoV-2 were protected against weight loss and were free of replicating SARS-CoV-2 in the upper and lower respiratory tract with no evidence of viral pneumonia. This study supports evaluation of qNIV/CoV2373 combination vaccine as a preventive measure for seasonal influenza and CoVID-19.\n\nHighlightsO_LICombination qNIV/CoV2373 vaccine induced protective hemagglutination inhibition (HAI) responses to seasonal influenza A and B unchanged when formulated with recombinant spike.\nC_LIO_LICombination qNIV/CoV2373 vaccine maintained clinical and virologic protection against experimental challenge with SARS-CoV-2.\nC_LIO_LICombination qNIV/CoV2373 vaccine showed no clinical or histological sign of enhanced disease following experimental challenge with SARS-CoV-2.\nC_LIO_LICombination qNIV/CoV2373 vaccine induced antibodies against SARS-CoV-2 neutralizing epitopes common between US-WA and B.1.352 variant.\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Micheal J Massare", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Nita Patel", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Bin Zhou", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Sonia Maciejewski", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Rhonda Flores", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Mimi Guebre-Xabier", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Jing-Hui Tian", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Alyse D Portnoff", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Louis Fries", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Vivek Shinde", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Larry R Ellingsworth", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Greg Glenn", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Gale Smith", + "author_inst": "Novavax, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.04.442701", "rel_title": "SARS-CoV-2 cell-to-cell infection is resistant to neutralizing antibodies", @@ -757938,61 +761949,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.05.05.442779", - "rel_title": "ProLung\u2122-budesonide Inhibits SARS-CoV-2 Replication and Reduces Lung Inflammation", - "rel_date": "2021-05-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.05.442779", - "rel_abs": "BackgroundInhaled budesonide benefits patients with COVID-19. ProLung-budesonide enables the sustained, low dose administration of budesonide within a delivery vehicle similar to lung surfactant. ProLung-budesonide may offer anti-inflammatory and protective effects to the lung in COVID-19, yet its effect on SARS-CoV-2 replication is unknown.\n\nObjectiveTo determine the efficacy of ProLung-budesonide against SARS-CoV-2 infection in vitro, evaluate its ability to decrease inflammation, and airway hyperresponsiveness in an animal model of lung inflammation.\n\nMethodsSARS-CoV-2-infected Vero 76 cells were treated with ProLung-budesonide ([0.03- 100 g/ml]) for 3 days, and virus yield in the supernatant was measured. Ovalbumin-sensitized C57BL/6 mice received aerosolized (a) ProLung-budesonide weekly, (b) only budesonide, either daily or weekly, or (c) weekly empty ProLung-carrier (without budesonide). All treatment groups were compared to sensitized untreated, or normal mice using histopathologic examination, electron microscopy (EM), airway hyperresponsiveness (AHR) to Methacholine (Mch) challenge, and eosinophil peroxidase activity (EPO) measurements in bronchioalveolar lavage (BAL).\n\nResultsProLung-budesonide showed significant inhibition on viral replication of SARS-CoV-2-infected cells with the selectivity index (SI) value > 24. Weekly ProLung-budesonide and daily budesonide therapy significantly decreased lung inflammation and EPO in BAL. ProLung-budesonide localized in type II pneumocytes, and was the only group to significantly decrease AHR, and EPO in BAL with Mch challenge\n\nConclusionsProLung-budesonide significantly inhibited viral replication in SARS-CoV-2 infected cells. It localized into type II pneumocytes, decreased lung inflammation, AHR and EPO activity with Mch challenge. This novel drug formulation may offer a potential inhalational treatment for COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Kameswari S Konduri", - "author_inst": "VGSK Technologies, Inc. Madison, WI" - }, - { - "author_name": "Ram Pattisapu", - "author_inst": "VGSK Technologies, Inc Madison, WI" - }, - { - "author_name": "Jogi Pattisapu", - "author_inst": "University of Central Florida, Orlando, FL" - }, - { - "author_name": "Girija G Konduri", - "author_inst": "Medical College of Wisconsin, Milwaukee, WI" - }, - { - "author_name": "John Zwetchkenbaum", - "author_inst": "VGSK Technologies, Inc, Madison, WI" - }, - { - "author_name": "Bidhan Roy", - "author_inst": "VGSK Technologies, Inc, Madison, WI" - }, - { - "author_name": "Monalisa Barman", - "author_inst": "VGSK Technologies, Inc, Madison, WI" - }, - { - "author_name": "Adria Frazier", - "author_inst": "University of the Pacific School of Dentistry, San Francisco, CA" - }, - { - "author_name": "Brett L Hurst", - "author_inst": "Utah State University, Logan, UT" - }, - { - "author_name": "Nejat Duzgunes", - "author_inst": "University of the Pacific School of Dentistry, San Francisco, CA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2021.05.05.442760", "rel_title": "SARS CoV-2 variant B.1.617.1 is highly pathogenic in hamsters than B.1 variant", @@ -759787,6 +763743,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.30.21256377", + "rel_title": "Disordered eating and self-harm as risk factors for poorer mental health during the COVID-19 pandemic: A population-based cohort study", + "rel_date": "2021-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.30.21256377", + "rel_abs": "BackgroundYoung adults and especially those with pre-existing mental health conditions, such as disordered eating and self-harm, appear to be at greater risk of developing metal health problems during the COVID-19 pandemic. However, it is unclear whether this increased risk is affected by any changes in lockdown restrictions, and whether any lifestyle changes could moderate this increased risk.\n\nMethodsIn a longitudinal UK-based birth cohort (The Avon Longitudinal Study of Parents and Children, ALSPAC) we assessed the relationship between pre-pandemic measures of disordered eating and self-harm and mental health during the COVID-19 pandemic in 2,657 young adults. Regression models examined the relationship between self-reported disordered eating, self-harm, and both disordered eating and self-harm at age 25 years and depressive symptoms, anxiety symptoms and mental wellbeing during a period of eased restrictions in the COVID-19 pandemic (May-July 2020) when participants were aged 27-29 years. Analyses were adjusted for sex, questionnaire completion date, pre-pandemic socioeconomic disadvantage and pre-pandemic mental health and wellbeing. We also examined whether lifestyle changes (sleep, exercise, alcohol, visiting green space, eating, talking with family/friends, hobbies, relaxation) in the initial UK lockdown (April-May 2020) moderated these associations.\n\nResultsPre-existing disordered eating, self-harm and comorbid disordered eating and self-harm were all associated with the reporting of a higher frequency of depressive symptoms and anxiety symptoms, and poorer mental wellbeing during the pandemic compared to individuals without disordered eating and self-harm. Associations remained when adjusting for pre-pandemic mental health measures. There was little evidence that interactions between disordered eating and self-harm exposures and lifestyle change moderators affected pandemic mental health and wellbeing.\n\nConclusionsYoung adults with pre-pandemic disordered eating, self-harm and comorbid disordered eating and self-harm were at increased risk for developing symptoms of depression, anxiety and poor mental wellbeing during the COVID-19 pandemic, even when accounting for pre-pandemic mental health. Lifestyle changes during the pandemic do not appear to alter this risk. A greater focus on rapid and responsive service provision is essential to reduce the impact of the pandemic on the mental health of these already vulnerable individuals.\n\nPlain English summaryThe aim of this project was to explore the mental health of young adults with disordered eating behaviours (such as fasting, vomiting/taking laxatives, binge-eating and excessive exercise) and self-harm during the COVID-19 pandemic. We analysed data from an established study that has followed children from birth (in 1991 and 1992) up to present day, including during the pandemic when participants were 28 years old. We looked at the relationship between disordered eating and/or self-harm behaviours from before the pandemic and mental health problems (symptoms of depression and anxiety) and mental wellbeing during the pandemic. We also explored whether there were any lifestyle changes (such as changes in sleep, exercise, visiting green space) that might be linked to better mental health and wellbeing in young adults with disordered eating and self-harm. We found that young adults with prior disordered eating and/or self-harm had more symptoms of depression and anxiety, and worse mental wellbeing than individuals without prior disordered eating or self-harm. However, lifestyle changes did not appear to affect mental health and wellbeing in these young adults. Our findings suggest that people with a history of disordered eating and/or self-harm were at high risk for developing mental health problems during the pandemic, and they will need help from mental health services.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Naomi Warne", + "author_inst": "University of Bristol" + }, + { + "author_name": "Jon Heron", + "author_inst": "University of Bristol" + }, + { + "author_name": "Becky Mars", + "author_inst": "University of Bristol" + }, + { + "author_name": "Alex Siu Fung Kwong", + "author_inst": "University of Bristol" + }, + { + "author_name": "Francesca Solmi", + "author_inst": "UCL" + }, + { + "author_name": "Rebecca Pearson", + "author_inst": "Univeristy of Bristol" + }, + { + "author_name": "Paul Moran", + "author_inst": "University of Bristol" + }, + { + "author_name": "Helen Bould", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.04.442648", "rel_title": "Immunolocalization studies of vimentin and ACE2 on the surface of cells exposed to SARS-CoV-2 Spike proteins", @@ -759948,45 +763951,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.03.442392", - "rel_title": "The method utilized to purify the SARS-CoV-2 N protein can affect its molecular properties", - "rel_date": "2021-05-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.03.442392", - "rel_abs": "One of the main structural proteins of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the nucleocapsid protein (N). The basic function of this protein is to bind genomic RNA and to form a protective nucleocapsid in the mature virion. The intrinsic ability of the N protein to interact with nucleic acids makes its purification very challenging. Therefore, typically employed purification methods appear to be insufficient for removing nucleic acid contamination. In this study, we present a novel purification protocol that enables the N protein to be prepared without any bound nucleic acids. We also performed comparative structural analysis of the N protein contaminated with nucleic acids and free of contamination and showed significant differences in the structural and phase separation properties of the protein. These results indicate that nucleic-acid contamination may severely affect molecular properties of the purified N protein. In addition, the notable ability of the N protein to form condensates whose morphology and behaviour suggest more ordered forms resembling gel-like or solid structures is described.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Aneta Tarczewska", - "author_inst": "Wroclaw University of Technology" - }, - { - "author_name": "Marta Kolonko-Adamska", - "author_inst": "Wroclaw University of Technology" - }, - { - "author_name": "Miros\u0142aw Zar\u0119bski", - "author_inst": "Jagiellonian University" - }, - { - "author_name": "Jerzy W Dobrucki", - "author_inst": "Jagiellonian University" - }, - { - "author_name": "Andrzej O\u017cyhar", - "author_inst": "Wroclaw University of Science and Technology" - }, - { - "author_name": "Beata Greb-Markiewicz", - "author_inst": "Wroclaw University of Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.04.30.21256331", "rel_title": "COVID-19 and acute kidney injury in German hospitals 2020", @@ -761357,6 +765321,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.04.21256298", + "rel_title": "Fatal cytokine release syndrome by an aberrant FLIP/STAT3 axis", + "rel_date": "2021-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256298", + "rel_abs": "Inflammatory responses rapidly detect pathogen invasion and mount a regulated reaction. However, dysregulated anti-pathogen immune responses can provoke life-threatening inflammatory pathologies collectively known as cytokine release syndrome (CRS), exemplified by key clinical phenotypes unearthed during the SARS-Cov-2 pandemic. The underlying pathophysiology of CRS remains elusive. We found that FLIP, a protein that controls caspase-8 death pathways, was highly expressed in myeloid cells of COVID-19 lungs. FLIP controlled CRS by fueling a STAT3-dependent inflammatory program. Indeed, constitutive expression of a viral FLIP homologue in myeloid cells triggered a STAT3-linked, progressive and fatal inflammatory syndrome in mice, characterized by elevated cytokine output, lymphopenia, lung injury and multiple organ dysfunctions that mimicked human CRS. As STAT3-targeting approaches relieved inflammation, immune disorders, and organ failures in these mice, targeted intervention towards this pathway could suppress the lethal CRS inflammatory state.\n\nOne sentence summaryFLIP-expressing myeloid cells are key drivers of CRS through aberrant overexpression of STAT3 pathway. STAT3-targeting is effective in mitigating CRS like severe COVID-19.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.05.04.21256489", "rel_title": "COVID-19 VACCINE PERCEPTIONS AND DIFFERENCES BY SEX, AGE, AND EDUCATION: FINDINGS FROM A CROSS-SECTIONAL ASSESSMENT OF 1367 COMMUNITY ADULTS IN ONTARIO", @@ -761399,20 +765377,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.05.04.21256537", - "rel_title": "Modeling and Predicting Antibody Durability for mRNA-1273 Vaccine for SARS-CoV-2 Variants", - "rel_date": "2021-05-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256537", - "rel_abs": "Recently, the antibody titer levels have been followed in 33 adults who received the mRNA-1273 vaccine for 6 months. With single dose estimated effectiveness of 92.1%, we combine this knowledge with corresponding antibody levels to model and estimate the long-term durability of mRNA-1273 vaccine. Additionally, we integrate studies about differences in antibody neutralization to SARS-CoV-2 variants to understand how variants can affect the durability of the vaccine.\n\nThe estimated days after first injection for binding antibodies to fall below levels of those from day 15 is 411 days. The estimated days after first injection to fall below the lower limit of detection of 20 GMTs is 327 days for pseudovirus neutralization and 461 days for live virus neutralization. Our model has pseudovirus neutralization against variant B.1.351 falling below 20 GMT on day 100; variant P.1 on day 202, variant B.1.429 on day 258; and variant B.1.1.7 on day 309.\n\nThe data used contains many limitations including the small sample size with older age bias, sensitivity of the neutralization assays, and limited data on variants. Still, we believe mRNA-1273 two dose vaccine can provide over a year of protection against COVID-19 from the initial D614G variant. It is likely by the second year, protection against COVID-19 will fall below single dose efficacy. Therefore, there should be consideration for a booster shot a year after the first set of vaccines. If there is an observed increase in variants with higher resistance such as B.1.351 and P.1, a booster vaccine against the newer variants should be considered to increase protection against resistant variants.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.04.21256001", "rel_title": "Does the elevated thrombosis risk of males relative to females help account for the excess male mortality observed in Covid-19? An observational study", @@ -762922,6 +766886,165 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.01.442279", + "rel_title": "Signaling through Fc\u03b3RIIA and the C5a-C5aR pathway mediates platelet hyperactivation in COVID-19", + "rel_date": "2021-05-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.01.442279", + "rel_abs": "Patients with COVID-19 present with a wide variety of clinical manifestations. Thromboembolic events constitute a significant cause of morbidity and mortality in patients infected with SARS-CoV-2. Severe COVID-19 has been associated with hyperinflammation and pre-existing cardiovascular disease. Platelets are important mediators and sensors of inflammation and are directly affected by cardiovascular stressors. In this report, we found that platelets from severely ill, hospitalized COVID-19 patients exhibit higher basal levels of activation measured by P-selectin surface expression, and have a poor functional reserve upon in vitro stimulation. Correlating clinical features to the ability of plasma from COVID-19 patients to stimulate control platelets identified ferritin as a pivotal clinical marker associated with platelet hyperactivation. The COVID-19 plasma-mediated effect on control platelets was highest for patients that subsequently developed inpatient thrombotic events. Proteomic analysis of plasma from COVID-19 patients identified key mediators of inflammation and cardiovascular disease that positively correlated with in vitro platelet activation. Mechanistically, blocking the signaling of the Fc{gamma}RIIa-Syk and C5a-C5aR pathways on platelets, using antibody-mediated neutralization, IgG depletion or the Syk inhibitor fostamatinib, reversed this hyperactivity driven by COVID-19 plasma and prevented platelet aggregation in endothelial microfluidic chamber conditions, thus identifying these potentially actionable pathways as central for platelet activation and/or vascular complications in COVID-19 patients. In conclusion, we reveal a key role of platelet-mediated immunothrombosis in COVID-19 and identify distinct, clinically relevant, targetable signaling pathways that mediate this effect. These studies have implications for the role of platelet hyperactivation in complications associated with SARS-CoV-2 infection.\n\nCover illustration O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY\n\nOne-sentence summaryThe Fc{gamma}RIIA and C5a-C5aR pathways mediate platelet hyperactivation in COVID-19", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Sokratis A. Apostolidis", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Amrita Sarkar", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Heather M. Giannini", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Rishi R. Goel", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Divij Mathew", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Aae Suzuki", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Amy E. Baxter", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Allison R. Greenplate", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Cecile Alanio", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Mohamed Abdel-Hakeem", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Derek A. Oldridge", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Josephine R. Giles", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jennifer E. Wu", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Zeyu Chen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Yinghui Jane Huang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ajinkya Pattekar", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sasikanth Manne", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Oliva Kuthuru", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jeanette Dougherty", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Brittany Weiderhold", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ariel R. Weisman", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Caroline A.G. Ittner", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sigrid Gouma", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Debora Dunbar", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ian Frank", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Alexander C. Huang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Laura A. Vella", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "- The UPenn COVID Processing Unit", + "author_inst": "-" + }, + { + "author_name": "John P. Reilly", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Scott E. Hensley", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Lubica Rauova", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Liang Zhao", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Nuala J. Meyer", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Mortimer Poncz", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Charles S. Abrams", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "E John Wherry", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.03.441080", "rel_title": "Human organoid systems reveal in vitro correlates of fitness for SARS-CoV-2 B.1.1.7", @@ -763119,57 +767242,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.05.02.442384", - "rel_title": "In silico and in vitro Demonstration of Homoharrintonine Antagonism of RBD-ACE2 Binding and its Anti-inflammatory and anti-thrombogenic Properties in a 3D human vascular lung model", - "rel_date": "2021-05-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.02.442384", - "rel_abs": "Since 2019 the world has seen severe onslaught of SARS-CoV-2 viral pandemic. There is an urgent need for drugs that can be used to either prevent or treat the potentially fatal disease COVD-19. To this end, we screened FDA approved antiviral drugs which could be repurposed for COVID-19 through molecular docking approach in the various active sites of receptor binding domain (RBD). The RBD domain of SARS-CoV-2 spike protein is a promising drug target due to its pivotal role in viral-host attachment. Specifically, we focussed on identifying antiviral drugs which could a) block the entry of virus into host cells, b) demonstrate anti-inflammatory and/or anti-thrombogenic properties. Drugs which poses both properties could be useful for prevention and treatment of the disease. While we prioritized a few antiviral drugs based on molecular docking, corroboration with in vitro studies including a new 3D human vascular lung model strongly supported the potential of Homoharringtonine, a drug approved for chronic myeloid leukaemia to be repurposed for COVID-19. This natural product drug not only antagonized the biding of SARS-CoV-2 spike protein RBD binding to human angiotensin receptor 2 (ACE-2) protein but also demonstrated for the first time anti-thrombogenic and anti-leukocyte adhesive properties in a human cell model system. Overall, this work provides an important lead for development of rapid treatment of COVID-19 and also establishes a screening paradigm using molecular modelling and 3D human vascular lung model of disease to identify drugs with multiple desirable properties for prevention and treatment of COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Shalini Saxena", - "author_inst": "INDRAS Pvt. Ltd" - }, - { - "author_name": "Kranti Meher", - "author_inst": "Reagene Innovations Pvt. Ltd." - }, - { - "author_name": "Madhuri Rotella", - "author_inst": "Reagene Innovations Pvt Ltd" - }, - { - "author_name": "Subhramanyam Vangala", - "author_inst": "Reagene Innovations Pvt Ltd" - }, - { - "author_name": "Satish Chandran", - "author_inst": "Reagene Innovations Pvt Ltd" - }, - { - "author_name": "Nikhil Malhotra", - "author_inst": "TechMahindra Ltd" - }, - { - "author_name": "Ratnakar Palakodeti", - "author_inst": "Tech Mahindra" - }, - { - "author_name": "Sreedhara Voleti", - "author_inst": "In Silico Discovery Research Academic Services (INDRAS) Pvt. Ltd" - }, - { - "author_name": "Uday Saxena", - "author_inst": "Reagene" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2021.05.01.442293", "rel_title": "ACE2 expression in rat brain: implications for COVID-19 associated neurological manifestations", @@ -764696,6 +768768,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.28.21256146", + "rel_title": "The causal effects of chronic air pollution on the intensity of COVID-19 disease: Some answers are blowing in the wind", + "rel_date": "2021-04-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.28.21256146", + "rel_abs": "The threats posed by COVID-19 have catalyzed a search by researchers across multiple disciplines for policy-relevant findings about critical risk factors. We contribute to this effort by providing causal estimates of the link between increased chronic ambient pollutant concentrations and the intensity of COVID-19 disease, as measured by deaths and hospitalizations in New York City from March through August, 2020. Given concerns about unobservable characteristics that contribute to both ambient air pollutant concentrations and the impacts of COVID-19 disease, we instrument for pollutant concentrations using the time spent downwind of nearby highways and estimate key causal relationships using two-stage least squares models. The causal links between increases in concentrations of our traffic-related air pollutants (PM2.5, NO2, and NO) and COVID-19 deaths are much larger than the correlations presented in recent observational studies. We find that a 0.16 g/m3 increase in average ambient PM2.5 concentration leads to an approximate 30% increase in COVID-19 deaths. This is the change in concentration associated with being downwind of a nearby highway. We see that this effect is mostly driven by residents with at least 75 years of age. In addition to emphasizing the importance of searching for causal relationships, our analysis highlights the value of increasing the density of pollution-monitoring networks and suggests potential benefits of further tightening of Clean Air Act amendments, as our estimated effects occur at concentrations well below thresholds set by the National Ambient Air Quality Standards.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Marc N Conte", + "author_inst": "Fordham University" + }, + { + "author_name": "Matthew Gordon", + "author_inst": "Yale University" + }, + { + "author_name": "Nicole Swartwood", + "author_inst": "Harvard T.H. Chan School" + }, + { + "author_name": "Rachel Wilwerding", + "author_inst": "Fordham University" + }, + { + "author_name": "Chu A. (Alex) Yu", + "author_inst": "Wake Forest University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.27.21256210", "rel_title": "U.S. Regional Differences in Physical Distancing: Evaluating Racial and Socioeconomic Divides During the COVID-19 Pandemic", @@ -764901,33 +769008,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.27.21256185", - "rel_title": "Pre-pandemic mental and physical health as predictors of COVID-19 vaccine hesitancy: evidence from a UK-wide cohort study", - "rel_date": "2021-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.27.21256185", - "rel_abs": "ImportanceAlthough several predictors of COVID-19 vaccine hesitancy have been identified, the role of physical health has not been well-examined, and the association with mental health is unknown.\n\nObjectiveTo examine the association of pre-pandemic mental health, physical health, and shielding with vaccine hesitancy after the announcement of the successful testing of the Oxford University/AstraZeneca vaccine.\n\nDesign, Setting, and ParticipantsWe used individual-level data from a pandemic-focused investigation (COVID Survey), a prospective cohort study nested within the UK Understanding Society (Main Survey) project. In the week immediately following the announcement of successful testing of the first efficacious inoculation (November/December 2020), data on vaccine intentionality were collected in 12,035 individuals aged 16-95 years. Pre-pandemic, study members had responded to enquiries about diagnoses of mental and physical health, completed the 12-item General Health Questionnaire for symptoms of psychological distress (anxiety and depression), and indicated whether they or someone in their household was shielding.\n\nMain outcome measuresSelf-reported intention to take up a vaccination for COVID-19. To summarise our results, we computed odds ratios with accompanying 95% confidence intervals for indices of health and shielding adjusted for selected covariates.\n\nResultsIn an analytical sample of 11,955 people (6741 women), 15.4% indicated that they were vaccine hesitant. Relative to their disease-free counterparts, shielding was associated with a 24% lower risk of being hesitant (odds ratio; 95% confidence interval: 0.76; 0.59, 0.96), after adjustment for a range of covariates which included age, education, and ethnicity. Corresponding results for cardiometabolic disease were 22% (0.78; 0.64, 0.95), and for respiratory disease were 26% (0.74; 0.59, 0.93). Having a pre-pandemic diagnosis of anxiety or depression, or a high score on the distress symptom scale, were all unrelated to the willingness to take up a vaccine.\n\nConclusions and relevancePeople who have been prioritised for COVID-19 vaccination owing to a physical condition are more likely to take it up. These effects were not apparent for indices of mental health.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "George David Batty", - "author_inst": "University College London" - }, - { - "author_name": "Ian Deary", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Drew Altschul", - "author_inst": "University of Edinburgh" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.27.21256196", "rel_title": "LUCAS: A highly accurate yet simple risk calculator that predicts survival of COVID-19 patients using rapid routine tests", @@ -766292,6 +770372,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.04.28.21255760", + "rel_title": "SARS-CoV-2 infections in nasal epithelial cells from smokers versus non-smokers", + "rel_date": "2021-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.28.21255760", + "rel_abs": "Whether smoking exacerbates Coronavirus disease 2019 is still debated. Ex-vivo Infection of reconstituted epithelial tissues from smoker versus non-smoker donors suggested comparable susceptibility to SARS-CoV-2 in epithelia from both groups.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Manel Essaidi-Laziosi", + "author_inst": "University of Geneva - Faculty of Medicine 1 rue Michel-Servet CH-1211 Geneva 4" + }, + { + "author_name": "Giulia Torriani", + "author_inst": "University of Geneva - Faculty of Medicine 1 rue Michel-Servet CH-1211 Geneva 4" + }, + { + "author_name": "Catia Alvarez", + "author_inst": "University of Geneva - Faculty of Medicine 1 rue Michel-Servet CH-1211 Geneva 4" + }, + { + "author_name": "Laurent Kaiser", + "author_inst": "University of Geneva Hospitals" + }, + { + "author_name": "Isabella Eckerle", + "author_inst": "University Hospitals of Geneva" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.27.21255023", "rel_title": "Large university with high COVID-19 incidence did not increase risk to non-student population", @@ -766509,65 +770624,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.25.21256049", - "rel_title": "Previously infected vaccinees broadly neutralize SARS-CoV-2 variants", - "rel_date": "2021-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.25.21256049", - "rel_abs": "We compared the serum neutralizing antibody titers before and after two doses of the BNT162b2 COVID-19 vaccine in ten individuals who recovered from SARS-CoV-2 infection prior to vaccination to 20 individuals with no history of infection, against clinical isolates of B.1.1.7, B.1.351, P.1, and the original SARS-CoV-2 virus. Vaccination boosted pre-existing levels of anti-SARS-CoV-2 spike antibodies 10-fold in previously infected individuals, but not to levels significantly higher than those of uninfected vaccinees. However, neutralizing antibody titers increased in previously infected vaccinees relative to uninfected vaccinees against every variant tested: 5.2-fold against B.1.1.7, 6.5-fold against B.1.351, 4.3-fold against P.1, and 3.4-fold against original SARS-CoV-2. Our study indicates that a first-generation COVID-19 vaccine provides broad protection from SARS-CoV-2variants in individuals with previous infection.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Hans C Leier", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Timothy A Bates", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Zoe L Lyski", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Savannah K McBride", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "David X Lee", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Felicity J Coulter", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "James R Goodman", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Zhengchun Lu", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Marcel E Curlin", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "William B Messer", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Fikadu G Tafesse", - "author_inst": "Oregon Health & Science University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.27.21256156", "rel_title": "Affordable and time-effective high throughput screening of SARS-CoV-2 variants using Denaturing High-Performance Liquid Chromatography analysis", @@ -768278,6 +772334,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.04.26.21255732", + "rel_title": "Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales", + "rel_date": "2021-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21255732", + "rel_abs": "BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation.\n\nMethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period.\n\nResultsRelative to participants in the least deprived areas, participants in the most deprived areas persistently exhibited elevated risk of exposure to vehicle sharing (aRR range across time points 1.73-8.52), public transport (aRR 3.13-5.73), work or education outside of the household (aRR 1.09-1.21), essential shops (aRR 1.09-1.13) and non-household contacts (aRR 1.15-1.19) across multiple survey periods.\n\nConclusionDifferential exposure to essential public activities in deprived communities is likely to contribute to inequalities in infection risk and outcomes during the COVID-19 pandemic. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Sarah Beale", + "author_inst": "University College London" + }, + { + "author_name": "Isobel Braithwaite", + "author_inst": "University College London" + }, + { + "author_name": "Annalan MD Navaratnam", + "author_inst": "University College London" + }, + { + "author_name": "Pia Hardelid", + "author_inst": "University College London" + }, + { + "author_name": "Alison Rodger", + "author_inst": "University College London; Royal Free London NHS Foundation Trust," + }, + { + "author_name": "Anna Aryee", + "author_inst": "University College London" + }, + { + "author_name": "Thomas Edward Byrne", + "author_inst": "University College London" + }, + { + "author_name": "Wing Lam Erica Fong", + "author_inst": "University College London" + }, + { + "author_name": "Ellen Fragaszy", + "author_inst": "University College London" + }, + { + "author_name": "Cyril Geismar", + "author_inst": "University College London" + }, + { + "author_name": "Jana Kovar", + "author_inst": "University College London" + }, + { + "author_name": "Vincent Nguyen", + "author_inst": "University College London" + }, + { + "author_name": "Parth Patel", + "author_inst": "University College London" + }, + { + "author_name": "Madhumita Shrotri", + "author_inst": "University College London" + }, + { + "author_name": "Robert W Aldridge", + "author_inst": "University College London" + }, + { + "author_name": "Andrew C Hayward", + "author_inst": "University College London" + }, + { + "author_name": "- Virus Watch Collaborative", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.25.21256067", "rel_title": "Trends of SARS-CoV-2 antibody prevalence in selected regions across Ghana", @@ -768471,29 +772610,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.26.21256108", - "rel_title": "Forecasting COVID-19 disease cases using the SARIMA-NNAR hybrid model", - "rel_date": "2021-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21256108", - "rel_abs": "BackgroundCOVID-19 is a new disease that is associated with high morbidity that has spread around the world. Credible estimating is crucial for control and prevention. Nowadays, hybrid models have become popular, and these models have been widely implemented. Better estimation accuracy may be attained using time-series models. Thus, our aim is to forecast the number of COVID-19 cases with time-series models.\n\nObjectiveUsing time-series models to predict deaths due to COVID-19.\n\nDesignSARIMA, NNAR, and SARIMA-NNAR hybrid time series models were used using the COVID-19 information of the Republic of Turkey Health Ministry.\n\nParticipantsWe analyzed data on COVID-19 in Turkey from March 11, 2020 to February 22, 2021.\n\nMain MeasuresDaily numbers of COVID-19 confirmed cases and deaths.\n\nMaterials and methodsWe fitted a seasonal autoregressive integrated moving average (SARIMA)-neural network nonlinear autoregressive (NNAR) hybrid model with COVID-19 monthly cases from March 11, 2020, to February 22, 2021, in Turkey. Additionally, a SARIMA model, an NNAR model, and a SARIMA-NNAR hybrid model were established for comparison and estimation.\n\nResultsThe RMSE, MAE, and MAPE values of the NNAR model were obtained the lowest in the training set and the validation set. Thus, the NNAR model demonstrates excellent performance whether in fitting or forecasting compared with other models.\n\nConclusionsThe NNAR model that fits this study is the most suitable for estimating the number of deaths due to COVID-19. Hence, it will facilitate the prevention and control of COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ibrahim Demir", - "author_inst": "Yildiz TechnicalUniversity" - }, - { - "author_name": "Murat Kirisci", - "author_inst": "Istanbul University-Cerrahpasa" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.26.21256103", "rel_title": "Professionals' views on the mental health problems and vulnerability of children and young people during the early phase of the COVID-19 pandemic", @@ -770176,6 +774292,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.19.21255709", + "rel_title": "Perceived public health threat a key factor for willingness to get the COVID-19 vaccine in Australia", + "rel_date": "2021-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255709", + "rel_abs": "BackgroundVaccination rollout against COVID-19 has begun across multiple countries worldwide. Although the vaccine is free, rollout might still be compromised by hesitancy or concerns about COVID-19 vaccines.\n\nMethodsWe conducted two online surveys of Australian adults in April (during national lockdown; convenience cross-sectional sample) and November (virtually no cases of COVID-19; nationally representative sample) 2020, prior to vaccine rollout. We asked about intentions to have a potential COVID-19 vaccine (If a COVID-19 vaccine becomes available, I will get it) and free-text responses (November only).\n\nResultsAfter adjustment for differences in sample demographics, the estimated proportion agreeing to a COVID-19 vaccine if it became available in April (n=1146) was 76.2%. In November (n=2034) this was estimated at 71.4% of the sample; additional analyses identified that the variation was driven by differences in perceived public health threat between April and November. Across both surveys, female gender, being younger, having inadequate health literacy and lower education were associated with reluctance to be vaccinated against COVID-19. Lower perceived susceptibility to COVID-19, belief that data on the efficacy of vaccines is largely made up, having lower confidence in government, and lower perception of COVID-19 as a public health threat, were also associated with reluctance to be vaccinated against COVID-19. The top three reasons for agreeing to vaccinate (November only) were to protect myself and others, moral responsibility, and having no reason not to get it. For those who were indifferent or disagreeing to vaccinate, safety concerns were the top reason, followed by indecision and lack of trust in the vaccine respectively.\n\nCONCLUSIONSThese findings highlight some factors related to willingness to accept a COVID-19 vaccine prior to one being available in Australia. Now that the vaccine is being offered, this study identifies key issues that can inform public health messaging to address vaccine hesitancy.\n\nHIGHLIGHTSO_LIPerceived public health threat is associated with intentions to vaccinate\nC_LIO_LIThose believing the efficacy of vaccines is made up were less willing to get vaccinated\nC_LIO_LITo protect myself and others was the top reason for getting the vaccine\nC_LIO_LISafety concerns was the top reason against getting the vaccine\nC_LI", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Rachael H Dodd", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Kristen Pickles", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Erin Cvejic", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Samuel Cornell", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Jennifer MJ Isautier", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Tessa Copp", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Brooke Nickel", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Carissa Bonner", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Carys Batcup", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Danielle M Muscat", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Julie Ayre", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Kirsten J McCaffery", + "author_inst": "The University of Sydney" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.19.21255714", "rel_title": "Antibody response after COVID-19 mRNA vaccination in relation to age, sex, and side effects", @@ -770385,25 +774564,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.19.21255768", - "rel_title": "Pharmacovigilance Analysis on Cerebrovascular Accidents and Coronavirus disease 2019 Vaccines", - "rel_date": "2021-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255768", - "rel_abs": "IntroductionRecently, there have been reports of cerebrovascular accidents (CVA) occurring in individuals who have received the Coronavirus disease 2019 (COVID-19) vaccine.\n\nObjectiveThe objective of this analysis was to determine if a statistically significant signal exists in post-marketing safety reports between CVA and the three COVID-19 vaccines being administered in the United States of America (Pfizer, Moderna, Janssen).\n\nMethodsA pharmacovigilance disproportionality analysis on adverse events reported with COVID-19 vaccines was conducted using data from Vaccine Adverse Event Reporting System.\n\nResultsA statistically significant signal was found between CVA events and each of the three COVID-19 vaccines (Pfizer/BioNTechs, Modernas and Janssens) in the VAERS database. Females and individuals of age 65 or older had higher number of case reports of CVA events with the COVID-19 vaccines. Females had also more COVID-19 adverse event reports in which a CVA was reported and resulted in the patient having permanent disability or death.\n\nLimitationsRandomized controlled trials are needed to further analyze this signal.\n\nConclusionPatients should be made aware of the risk-benefit and symptoms to watch out for that may indicate the onset of a CVA and informed to seek medical care as soon as possible if they develop these symptoms.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Pushkar Aggarwal", - "author_inst": "University of Cincinnati College of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.19.21255737", "rel_title": "When can we stop wearing masks? Agent-based modeling to identify when vaccine coverage makes nonpharmaceutical interventions for reducing SARS-CoV-2 infections redundant in indoor gatherings", @@ -771813,6 +775973,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.24.21256054", + "rel_title": "High proportion of post-acute sequelae of SARS-CoV-2 infection in individuals 1-6 months after illness and association with disease severity in an outpatient telemedicine population", + "rel_date": "2021-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.24.21256054", + "rel_abs": "BackgroundIndividuals with coronavirus disease 2019 (COVID-19) may have persistent symptoms following their acute illness. The prevalence and predictors of these symptoms, termed post-acute sequelae of SARS-CoV-2 (PASC), are not fully described.\n\nMethodsParticipants discharged from an outpatient telemedicine program for COVID-19 were emailed a survey (1-6 months after discharge) about ongoing symptoms, acute illness severity, and quality of life. Standardized telemedicine notes from acute illness were used for covariates (comorbidities and provider-assessed symptom severity). Bivariate and multivariable analyses were performed to assess predictors of persistent symptoms.\n\nResultsTwo hundred and ninety patients completed the survey, of whom 115 (39.7%) reported persistent symptoms including fatigue (n= 59, 20.3%), dyspnea on exertion (n=41, 14.1%), and mental fog (n=39, 13.5%) among others. Proportion of persistent symptoms did not differ based on duration since illness (<90 days: n=32, 37.2% versus >90 days: n=80, 40.4%, p = 0.61). Predictors of persistent symptoms included provider-assessed moderate-severe illness (aOR 3.24, 95% CI 1.75, 6.02), female sex (aOR 1.99 95% 0.98, 4.04; >90 days out: aOR 2.24 95% CI 1.01, 4.95), and middle age (aOR 2.08 95% CI 1.07, 4.03). Common symptoms associated with reports of worse physical health included weakness, fatigue, myalgias, and mental fog.\n\nConclusionsSymptoms following acute COVID-19 are common and may be predicted by factors during the acute phase of illness. Fatigue and neuropsychiatric symptoms figured prominently. Select symptoms seem to be particularly associated with perceptions of physical health following COVID-19 and warrant specific attention on future studies of PASC.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "James B O'Keefe", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "H. Caroline Minton", + "author_inst": "Rollins School of Public Health, Emory University" + }, + { + "author_name": "Mary Morrow", + "author_inst": "Emory Healthcare" + }, + { + "author_name": "Colin Johnson", + "author_inst": "Emory Healthcare" + }, + { + "author_name": "Miranda A Moore", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Ghazala A. D. O'Keefe", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Karima Benameur", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Jason Higdon", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Jessica K. Fairley", + "author_inst": "Emory University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.26.21256131", "rel_title": "SARS-CoV-2 subgenomic RNA kinetics in longitudinal clinical samples", @@ -771954,49 +776165,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2021.04.25.21256024", - "rel_title": "COVID-19 vaccine acceptance in older Syrian refugees: preliminary findings from an ongoing study", - "rel_date": "2021-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.25.21256024", - "rel_abs": "This study assesses COVID-19 vaccine intentions among a sample of Syrian refugees ([≥]50 years) beneficiaries of a humanitarian organization in Lebanon, and explores factors associated with vaccine refusal. The findings are part of an ongoing rotating 4-wave panel study. The sample was limited to participants from the first panel who completed a phone interview between January-February, 2021. Out 1,037 beneficiaries, almost a third (29%) reported no intention to vaccinate. Reasons for refusal were: newness of the vaccine (35%); preference to maintain precaution measures (21%); belief that COVID-19 vaccine is not essential (21%); and other reasons (23%). COVID-19 vaccine refusal was significantly associated with perceptions regarding vaccine safety (OR: 5.97; 95%CI: 4.03-8.84) and effectiveness (OR: 6.80; 95%CI:4.44-10.42) but did not differ by age, presence of chronic conditions, self-reported adherence to COVID-19 measures, and perceptions of susceptibility to and severity of COVID-19. Addressing vaccine hesitancy among Syrian refugees in Lebanon necessitates disseminating accurate, accessible, and culturally appropriate information about vaccine safety and effectiveness.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Noura El Salibi", - "author_inst": "American University of Beirut" - }, - { - "author_name": "Sawsan Abdulrahim", - "author_inst": "American University of Beirut" - }, - { - "author_name": "Maria El Haddad", - "author_inst": "American University of Beirut" - }, - { - "author_name": "Stephanie Bassil", - "author_inst": "Norwegian Refugee Council (NRC)" - }, - { - "author_name": "Zeina El Khoury", - "author_inst": "Norwegian Refugee Council (NRC)" - }, - { - "author_name": "Hala Ghattas", - "author_inst": "American University of Beirut" - }, - { - "author_name": "Stephen McCall", - "author_inst": "American University of Beirut" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.26.21255801", "rel_title": "The SARS-CoV2 pandemic explained via asymptomatic infection and susceptibility heterogeneity. Buenos Aires First Wave", @@ -773623,6 +777791,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.23.21255995", + "rel_title": "Regional opening strategies with commuter testing and containment of new SARS-CoV-2 variants", + "rel_date": "2021-04-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.23.21255995", + "rel_abs": "BackgroundDespite the vaccination process in Germany, a large share of the population is still susceptible to SARS-CoV-2. In addition, we face the spread of novel variants. Until we overcome the pandemic, reasonable mitigation and opening strategies are crucial to balance public health and economic interests.\n\nMethodsWe model the spread of SARS-CoV-2 over the German counties by a graph-SIR-type, metapopulation model with particular focus on commuter testing. We account for political interventions by varying contact reduction values in private and public locations such as homes, schools, workplaces, and other. We consider different levels of lockdown strictness, commuter testing strategies, or the delay of intervention implementation. We conduct numerical simulations to assess the effectiveness of the different intervention strategies after one month. The virus dynamics in the regions (German counties) are initialized randomly with incidences between 75-150 weekly new cases per 100,000 inhabitants (red zones) or below (green zones) and consider 25 different initial scenarios of randomly distributed red zones (between 2 and 20 % of all counties). To account for uncertainty, we consider an ensemble set of 500 Monte Carlo runs for each scenario.\n\nResultsWe find that the strength of the lockdown in regions with out of control virus dynamics is most important to avoid the spread into neighboring regions. With very strict lockdowns in red zones, commuter testing rates of twice a week can substantially contribute to the safety of adjacent regions. In contrast, the negative effect of less strict interventions can be overcome by high commuter testing rates. A further key contributor is the potential delay of the intervention implementation. In order to keep the spread of the virus under control, strict regional lockdowns with minimum delay and commuter testing of at least twice a week are advisable. If less strict interventions are in favor, substantially increased testing rates are needed to avoid overall higher infection dynamics.\n\nConclusionsOur results indicate that local containment of outbreaks and maintenance of low overall incidence is possible even in densely populated and highly connected regions such as Germany or Western Europe. While we demonstrate this on data from Germany, similar patterns of mobility likely exist in many countries and our results are, hence, generalizable to a certain extent.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Martin J Kuehn", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Daniel Abele", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Sebastian Binder", + "author_inst": "Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology (BRICS), Helmholtz Centre for Infection Research, Braunschweig, Germany" + }, + { + "author_name": "Kathrin Rack", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Margrit Klitz", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Jan Kleinert", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Jonas Gilg", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Luca Spataro", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Wadim Koslow", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Martin Siggel", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Michael Meyer-Hermann", + "author_inst": "Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology (BRICS), Helmholtz Centre for Infection Research, Braunschweig, Germany." + }, + { + "author_name": "Achim Basermann", + "author_inst": "German Aerospace Center, Institute for Software Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.22.21255941", "rel_title": "Predicting the end of Covid-19 infection for various countries using a stochastic agent-based model taking into account vaccination rates and the new mutant", @@ -773752,61 +777983,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.04.23.21255993", - "rel_title": "Depression during the COVID-19 pandemic amongst residents of homeless shelters in France.", - "rel_date": "2021-04-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.23.21255993", - "rel_abs": "BackgroundAccumulating evidence suggests that the COVID-19 pandemic has negatively affected global mental health and well-being. However, the impact amongst homeless persons has not been fully evaluated. The ECHO study reports factors associated with depression amongst the homeless population living in shelters in France during the Spring of 2020.\n\nMethodsInterview data were collected from 527 participants living in temporary and/or emergency accommodation following Frances first lockdown (02/05/20 - 07/06/20), in the metropolitan regions of Paris (74%), Lyon (19%) and Strasbourg (7%). Interviews were conducted in French, English, or with interpreters (33% of participants, [~]20 languages). Presence of depression was ascertained using the Patient Health Questionnaire (PHQ-9).\n\nResultsAmongst ECHO study participants, 30% had symptoms of moderate to severe depression (PHQ-9[≥] 10). Multivariate analysis revealed depression to be associated with being female (aOR: 2.15; CI: 1.26-3.69), being single (aOR: 1.60; CI: 1.01-2.52), having a chronic illness (aOR: 2.32; CI: 1.43:-3.78), facing food insecurity (aOR: 2.12; CI: 1.40-3.22) and participants region of origin. Persons born in African and Eastern Mediterranean regions showed levels of depression comparable to those of French participants (30-33%) but higher than migrants from European countries (14%). Reduced rates of depression were observed amongst participants aged 30-49 (aOR: 0.60; CI: 0.38-0.95) and over 50 (aOR: 0.28; CI: 0.13-0.64), compared to 18-29-year-olds.\n\nConclusionsOur results indicate high levels of depression among homeless persons during the COVID-19 pandemic. The value of these findings extends beyond the health crisis, as predicted future instability and economic repercussions could particularly impact the mental health of this vulnerable group.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Honor Scarlett", - "author_inst": "Pierre Louis Institute of Epidemiology and Public Health" - }, - { - "author_name": "Camille Davisse-Paturet", - "author_inst": "Pierre Louis Institute of Epidemiology and Public Health" - }, - { - "author_name": "Cecile Longchamps", - "author_inst": "Pierre Louis Institute of Epidemiology and Public Health" - }, - { - "author_name": "Tarik El Aarbaoui", - "author_inst": "Pierre Louis Institute of Epidemiology and Public Health" - }, - { - "author_name": "Cecile Allaire", - "author_inst": "French National Public Health Agency" - }, - { - "author_name": "Anne-Claire Colleville", - "author_inst": "French National Public Health Agency" - }, - { - "author_name": "Mary Convence-Arulthas", - "author_inst": "Pierre Louis Institute of Epidemiology and Public Health" - }, - { - "author_name": "Lisa Crouzet", - "author_inst": "Research on Healthcare Performance RESHAPE" - }, - { - "author_name": "Simon Ducarroz", - "author_inst": "Research on Healthcare Performance RESHAPE" - }, - { - "author_name": "Maria Melchior", - "author_inst": "Pierre Louis Institute of Epidemiology and Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.23.21256005", "rel_title": "Reopen or redistribute? Modeling years of life lost due to Covid-19, socioeconomic status, and non-pharmaceutical interventions", @@ -775221,6 +779397,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.21.21255874", + "rel_title": "Evaluation of the sensitivity, accuracy and currency of the Cochrane COVID-19 Study Register for supporting rapid evidence synthesis production", + "rel_date": "2021-04-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.21.21255874", + "rel_abs": "IntroductionThe Cochrane COVID-19 Study Register (CCSR) is a public, continually updated, curated database of COVID-19 study references. The aim of this study-based register is to support rapid and living evidence synthesis, including a project to build an evidence ecosystem of COVID-19 research (CEOsys). In November and December 2020 we conducted an evaluation of the CCSR for CEOsys, measured its performance and identified areas for improvement.\n\nMethodsFor the evaluation we generated a purposive sample of 286 studies from 20 reviews to calculate the CCSRs sensitivity (comprehensiveness), accuracy (correctly classified and linked studies) and currency (time to publish and process references).\n\nResultsThe CCSR had an overall sensitivity of 77.2%, with the highest sensitivity for interventional studies (94.4%) and lowest sensitivity for modelling studies (63.6%). The study register had 100% sensitivity for trial registry records, 86.5% for journal articles and 52.4% for preprints. 98.3% of references were correctly classified with regard to study type, and 93.4% with regard to study aim. 89% of studies were correctly linked. 81.4% of references were published to the register in under 30 days, with 0.5 day (median) for trial registry records, 2 days for journal articles and 56 days for preprints.\n\nConclusionThe CCSR had high sensitivity, accurate study classifications and short publishing times for journal articles and trial registry records. We identified that the CCSRs coverage and publishing times for preprints needed improvement. Finally, the evaluation illustrated the value of a study-based register for identifying additional study references for analysis in evidence synthesis.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Maria-Inti Metzendorf", + "author_inst": "Cochrane Metabolic and Endocrine Disorders Group, Institute of General Practice, Medical Faculty of the Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Robin M Featherstone", + "author_inst": "Cochrane, Editorial and Methods Department, London, United Kingdom" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.22.21255631", "rel_title": "Risk Profile of Thanksgiving Gatherers and Subsequent SARS-CoV2 Testing and Diagnosis", @@ -775398,41 +779597,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.21.21255876", - "rel_title": "Impact of national and regional lockdowns on COVID-19 epidemic waves: Application to the 2020 spring wave in France", - "rel_date": "2021-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.21.21255876", - "rel_abs": "Several countries have implemented lockdowns to control their COVID-19 epidemic. However, questions like \"where\" and \"when\" still require answers. We assessed the impact of national and regional lockdowns considering the French first epidemic wave of COVID-19 as a case study. In a regional lockdown scenario aimed at preventing intensive care units (ICU) saturation, almost all French regions would have had to implement a lockdown within 10 days and 96% of ICU capacities would have been used. For slowly growing epidemics, with a lower reproduction number, the expected delays between regional lockdowns increases. However, the public health costs associated with these delays tend to grow exponentially with time. In a quickly growing pandemic wave, defining the timing of lockdowns at a regional rather than national level delays by a few days the implementation of a nationwide lockdown but leads to substantially higher morbidity, mortality and stress on the healthcare system.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jonathan Roux", - "author_inst": "Univ Rennes, EHESP, REPERES - EA7449" - }, - { - "author_name": "Cl\u00e9ment Massonnaud", - "author_inst": "Univ Rennes, EHESP, REPERES - EA7449 & Rouen University Hospital" - }, - { - "author_name": "Vittoria Colizza", - "author_inst": "INSERM" - }, - { - "author_name": "Simon Cauchemez", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Pascal Cr\u00e9pey", - "author_inst": "Univ Rennes, EHESP, REPERES - EA 7449" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.21.21255841", "rel_title": "Maternal and child outcomes reported by breastfeeding women following mRNA COVID-19 vaccination", @@ -776751,6 +780915,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.22.21255952", + "rel_title": "COVID-19 pandemic: Analyzing of different pandemic control strategies using saturation models", + "rel_date": "2021-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.22.21255952", + "rel_abs": "Since December 2019, the world is confronted with the outbreak of the respiratory disease COVID-19. At the beginning of 2020, the COVID-19 epidemic evolved into a pandemic, which continues to this day. Within many countries, several control strategies or combinations of them, like restrictions (e.g. lockdown actions), medical care (e.g. development of vaccine or medicaments) and medical prevention (e.g. hygiene concept), were established with the goal to control the pandemic. Depending on the chosen control strategy, the COVID-19 spreading behavior slowed down or approximately stopped for a defined time range. This phenomenon is called saturation effect and can be described by saturation models: E.g. a fundamental approach is Verhulst (1838). The model parameter allows the interpretation of the spreading speed (growth) and the saturation effect in a sound way. This paper shows results of a research study of the COVID-19 spreading behavior and saturation effects depending on different pandemic control strategies in different countries and time phases based on Johns Hopkins University data base (2020). The study contains the analyzing of saturation effects related to short time periods, e.g. possible caused by lockdown strategies, geographical influences and medical prevention activities. The research study is focusing on reference countries like Germany, Japan, Denmark, Iceland, Ireland and Israel.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Stefan Bracke", + "author_inst": "University of Wuppertal, Germany" + }, + { + "author_name": "Lars Grams", + "author_inst": "University of Wuppertal, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.22.21255953", "rel_title": "COVID-19 pandemic: Analyzing of spreading behavior, the impact of restrictions and prevention measures in Germany and Japan.", @@ -776956,57 +781143,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.23.441151", - "rel_title": "Large-scale analysis of synonymous viral variants reveals global adaptation of the SARS-CoV-2 to the human codon usage", - "rel_date": "2021-04-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.23.441151", - "rel_abs": "Many large national and transnational studies have been dedicated to the analysis of SARS-CoV-2 genome, most of which focused on missense and nonsense mutations. However, approximately 30% of the SARS-CoV-2 variants are synonymous, therefore changing the target codon without affecting the corresponding protein sequence.\n\nBy performing a large-scale analysis of sequencing data generated from almost 400,000 SARS-CoV-2 samples, we show that silent mutations increasing the similarity of viral codons to the human ones tend to fixate in the viral genome over-time. This indicates that SARS-CoV-2 codon usage is adapting to the human host, likely improving its effectiveness in using the human aminoacyl-tRNA set through the accumulation of deceitfully neutral silent mutations.\n\nOne-Sentence SummarySynonymous SARS-CoV-2 mutations related to the activity of different mutational processes may positively impact viral evolution by increasing its adaptation to human codon usage.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Daniele Ramazzotti", - "author_inst": "Dept. of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy" - }, - { - "author_name": "Fabrizio Angaroni", - "author_inst": "Dept. of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy" - }, - { - "author_name": "Davide Maspero", - "author_inst": "Dept. of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy" - }, - { - "author_name": "Mario Mauri", - "author_inst": "Dept. of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy" - }, - { - "author_name": "Diletta Fontana", - "author_inst": "Dept. of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy" - }, - { - "author_name": "Marco Antoniotti", - "author_inst": "Dept. of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy" - }, - { - "author_name": "Elena Maria Elli", - "author_inst": "Hematology and Clinical Research Unit, San Gerardo Hospital, Monza, Italy" - }, - { - "author_name": "Alex Graudenzi", - "author_inst": "Inst. of Molecular Bioimaging and Physiology, Consiglio Nazionale delle Ricerche (IBFM- CNR), Segrate, Milan, Italy" - }, - { - "author_name": "Rocco Piazza", - "author_inst": "Dept. of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.04.19.20219949", "rel_title": "Resolutive results with oral corticosteroids for patients with COVID-19 in pulmonary inflammatory phase. Successful outpatient experience during the collapse of Belem do Para Health System - Brazil.", @@ -778701,6 +782837,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.19.21255727", + "rel_title": "Prolonged activation of nasal immune cell populations and development of tissue-resident SARS-CoV-2 specific CD8 T cell responses following COVID-19", + "rel_date": "2021-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255727", + "rel_abs": "The immune system plays a major role in Coronavirus Disease 2019 (COVID-19) pathogenesis, viral clearance and protection against re-infection. Immune cell dynamics during COVID-19 have been extensively documented in peripheral blood, but remain elusive in the respiratory tract. We performed minimally-invasive nasal curettage and mass cytometry to characterize nasal immune cells of COVID-19 patients during and 5-6 weeks after hospitalization. Contrary to observations in blood, no general T cell depletion at the nasal mucosa could be detected. Instead, we observed increased numbers of nasal granulocytes, monocytes, CD11c+ NK cells and exhausted CD4+ T effector memory cells during acute COVID-19 compared to age-matched healthy controls. These pro-inflammatory responses were found associated with viral load, while neutrophils also negatively correlated with oxygen saturation levels. Cell numbers mostly normalized following convalescence, except for persisting CD127+ granulocytes and activated T cells, including CD38+ CD8+ tissue-resident memory T cells. Moreover, we identified SARS-CoV-2 specific CD8+ T cells in the nasal mucosa in convalescent patients. Thus, COVID-19 has both transient and long-term effects on the immune system in the upper airway.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Anna H.E. Roukens", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Marion Konig", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Tim Dalebout", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Tamar Tak", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Shohreh Azimi", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Yvonne Kruize", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Cilia R. Pothast", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Renate S. Hagedoorn", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Sesmu M. Arbous", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Jaimie L.H. Zhang", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Maaike Verheij", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Corine Prins", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Anne M. Does van der", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Pieter S. Hiemstra", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Jutte J.C. Vries de", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Jacqueline J. Janse", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Meta Roestenberg", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Sebenzile K. Myeni", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Marjolein Kikkert", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Mirjam H.M. Heemskerk", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Maria Yazdanbakhsh", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Hermelijn H. Smits", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Simon P. Jochems", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "- BEAT-COVID group", + "author_inst": "" + }, + { + "author_name": "- COVID-19 LUMC group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.19.21255723", "rel_title": "B and T cell immune responses elicited by the BNT162b2 (Pfizer BioNTech) COVID-19 vaccine in nursing home residents", @@ -778898,89 +783149,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2021.04.20.21255596", - "rel_title": "Comparison of SARS-CoV-2 serological assays for use in epidemiological surveillance in Scotland", - "rel_date": "2021-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.20.21255596", - "rel_abs": "BackgroundSero-surveillance of SARS-CoV-2 is crucial to monitoring levels of population exposure and informing public health responses, but may be influenced by variability in performance between available assays.\n\nMethodsFive commercial immunoassays and a neutralising activity assay were used to detect antibodies to SARS-CoV-2 in routine primary care and paediatric samples collected during the first wave of the pandemic in NHS Lothian, Scotland as part of ongoing surveillance efforts. For each assay, sensitivity and specificity was calculated relative to consensus results and neutralising activity. Quantitative correlation was performed between serological and neutralising titres.\n\nResultsSeroprevalence ranged from 3.4-7.3 % in primary care patients and 3-5.9 % in paediatric patients according to different immunoassays. Neutralising activity was detectable in 2.8 % and 1.3 % respectively. Relative assay performance changed depending on comparison to immunoassay consensus versus neutralising activity and qualititative versus quantitative agreement. Cross-reactivity with endemic seasonal coronaviruses was confirmed by neutralising assay in false positives for one immunoassay. Presence of false positives for another assay was found specifically in paediatric but not adult samples.\n\nConclusionsFive serological assays show variable accuracy when applied to the general population, impacting seroprevalence estimates. Assay performance may also vary in detection of protective neutralising antibody levels. These aspects should be considered in assay selection and interpretation in epidemiological studies.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Lindsay McDonald", - "author_inst": "Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, Scotland" - }, - { - "author_name": "Helen Wise", - "author_inst": "Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, Scotland" - }, - { - "author_name": "Frauke Muecksch", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA" - }, - { - "author_name": "Daniel Poston", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA" - }, - { - "author_name": "Sally Mavin", - "author_inst": "Scottish Microbiology Reference Laboratory, NHS Highland, Inverness, Scotland" - }, - { - "author_name": "Kate Templeton", - "author_inst": "Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, Scotland" - }, - { - "author_name": "Elizabeth Furrie", - "author_inst": "Ninewells Hospital and Medical School, NHS Tayside, Dundee, Scotland" - }, - { - "author_name": "Claire Richardson", - "author_inst": "University Hospital Monklands, NHS Lanarkshire, Airdrie, Scotland" - }, - { - "author_name": "Jacqueline McGuire", - "author_inst": "University Hospital Monklands, NHS Lanarkshire, Airdrie, Scotland" - }, - { - "author_name": "Lisa Jarvis", - "author_inst": "Scottish National Blood Transfusion Service, The Jack Copland Centre, Edinburgh, Scotland" - }, - { - "author_name": "Kristen Malloy", - "author_inst": "Scottish National Blood Transfusion Service, The Jack Copland Centre, Edinburgh, Scotland" - }, - { - "author_name": "Andrew McAuley", - "author_inst": "Public Health Scotland, Glasgow, Scotland; School of Health & Life Sciences, Glasgow Caledonian University, Glasgow, Scotland" - }, - { - "author_name": "Norah Palmateer", - "author_inst": "Public Health Scotland, Glasgow, Scotland; School of Health & Life Sciences, Glasgow Caledonian University, Glasgow, Scotland" - }, - { - "author_name": "Elizabeth Dickson", - "author_inst": "Public Health Scotland, Glasgow, Scotland" - }, - { - "author_name": "Theodora Hatziioannou", - "author_inst": "Laboratory of Retrovirology, The Rockefeller University, New York, New York, USA" - }, - { - "author_name": "Paul Bieniasz", - "author_inst": "The Rockefeller University, New York, New York, USA" - }, - { - "author_name": "Sara Jenks", - "author_inst": "Royal Infirmary of Edinburgh, NHS Lothian, Edinburgh, Scotland" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.17.21255548", "rel_title": "Preexisting and new-onset diabetes in patients with COVID-19 pneumonia", @@ -780634,6 +784802,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.20.21255350", + "rel_title": "When can we safely return to normal? A novel method for identifying safe levels of NPIs in the context of COVID-19 vaccinations", + "rel_date": "2021-04-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.20.21255350", + "rel_abs": "Over the course of the COVID-19 pandemic, governing bodies and individuals have relied on a variety of non-pharmaceutical interventions (NPIs) to control the transmission of SARS-CoV-2, which posed an acute threat to individuals well-being and consistently impacted economic activities in many countries worldwide. NPIs have been implemented at varying levels of severity and in response to widely-divergent perspectives of risk tolerance. Now, concurrently with the introduction of multiple SARS-CoV-2 vaccines, the world looks optimistically to a \"return to normality\". In this work, we propose a multi-disciplinary approach, combining transmission modeling with control and optimization theory, to examine how risk tolerance and vaccination rates will impact the safe return to normal behavior over the next few months. To this end, we consider a version of the Susceptible-Exposed-Infected-Recovered transmission model that accounts for hospitalizations, vaccinations, and loss of immunity. We then propose a novel control approach to calibrate the necessary level of NPIs at various geographical levels to guarantee that the number of hospitalizations does not exceed a given risk tolerance (i.e., a maximum allowable threshold). Our model and control objectives are calibrated and tailored for the state of Colorado, USA. Our results suggest that: (i) increasing risk tolerance can decrease the number of days required to discontinue all NPIs; (ii) increasing risk tolerance inherently increases COVID-19 deaths even in the context of vaccination; (iii) if the vaccination uptake in the population is 70% or less, then return to normal behavior within the next year may newly stress the healthcare system. Furthermore, by using a multi-region model accounting for travel, our simulations predict that: (iv) relaxation should take into account regional heterogeneity in transmission and travel; and (v) premature relaxation of NPIs, even if restricted only to low-density regions, will lead to exceeding hospitalization limits even when highly-populated regions implement full-closures. Although the simulations are performed for the state of Colorado, the proposed model of transmission and control methods are applicable to any area worldwide and can be utilized at any geographical granularity.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Gianluca Bianchin", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Emiliano Dall'Anese", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Jorge Ivan Poveda", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Andrea Buchwald", + "author_inst": "University of Colorado Anschutz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.21.440801", "rel_title": "Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania", @@ -780739,29 +784938,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.04.18.440376", - "rel_title": "GIVE Statistic for Goodness of Fit in Instrumental Variables Models with Application to COVID Data", - "rel_date": "2021-04-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.18.440376", - "rel_abs": "Since COVID-19 outbreak, scientists have been interested to know whether there is any impact of the Bacillus Calmette-Guerin (BCG) vaccine against COVID-19 mortality or not. It becomes more relevant as a large population in the world may have latent tuberculosis infection (LTBI), for which a person may not have active tuberculosis but persistent immune responses stimulated by Mycobacterium tuberculosis antigens, and that means, both LTBI and BCG generate immunity against COVID-19. In order to understand the relationship between LTBI and COVID-19 mortality, this article proposes a measure of goodness of fit, viz., Goodness of Instrumental Variable Estimates (GIVE) statistic, of a model obtained by Instrumental Variables estimation. The GIVE helps in finding the appropriate choice of instruments, which provides a better fitted model. In the course of study, the large sample properties of the GIVE statistic are investigated. As indicated before, the COVID-19 data is analysed using the GIVE statistic, and moreover, simulation studies are also conducted to show the usefulness of the GIVE statistic.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Subhra Sankar Dhar", - "author_inst": "IIT Kanpur" - }, - { - "author_name": "Shalabh", - "author_inst": "IIT Kanpur" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.04.21.440783", "rel_title": "Deep time course proteomics of SARS-CoV and SARS-CoV-2-infected human lung epithelial cells (Calu-3) reveals strong induction of interferon-stimulated gene (ISG) expression by SARS-CoV-2 in contrast to SARS-CoV", @@ -782384,6 +786560,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.14.21255448", + "rel_title": "Gender Differences in Health Protective Behaviors During the COVID-19 Pandemic in Taiwan: An Empirical Study", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255448", + "rel_abs": "IntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection produces more severe symptoms and a higher mortality in men than in women. The role of biological sex in the immune response to SARS-CoV-2 is believed to explain this sex disparity. However, the contribution of gender factors that influence health protective behaviors and therefore health outcomes, remains poorly explored.\n\nMethodsWe assessed the contributions of gender in attitudes towards the COVID-19 pandemic, using a hypothetical influenza pandemic data from the 2014 Taiwan Social Change Survey. Participants were selected through a stratified, three-stage probability proportional-to-size sampling from across the nation, to fill in questionnaires that asked about their perception of the hypothetical pandemic, and intention to adopt health protective behaviors.\n\nResultsA total of 1,990 participants (median age 45.92 years, 49% women) were included. Significant gender disparities (p<0.001) were observed. The risk perception of pandemic (OR=1.28, 95% CI=1.21-1.35, p<0.001), older age (1.06, 95%=1.05-1.07, p<0.001), female gender (OR = 1.18, 95% CI = 1.09{square}1.27, p<0.001), higher education (OR=1.10, 95% CI=1.06-1.13, p<0.001), and larger family size (OR=1.09, 95% CI=1.06-1.15, p<0.001) were positively associated with health protective behaviors. The risk perception of pandemic (OR=1.25, 95% CI=1.15-1.36), higher education (OR=1.07, 95% CI=1.02-1.13, p<0.05), being married (OR=1.17, 95% CI=1.01-1.36, p<0.05), and larger family size (OR=1.33, 95% CI=1.25-1.42, p<0.001), were positively associated with intention to receive a vaccine. However, female gender was negatively associated with intention to receive a vaccine (OR=0.85, 95% CI=0.75-0.90, p<0.01) and to comply with contact-tracing (OR=0.95, 95% CI=0.90-1.00, p<0.05) compared to men. Living with children was also negatively associated with intention to receive vaccines (OR=0.77, 95% CI=0.66-0.90, p<0.001).\n\nConclusionThis study unveils gender differences in risk perception, health protective behaviors, vaccine hesitancy, and compliance with contact-tracing using a hypothetical viral pandemic. Gender-specific health education raising awareness of health protective behaviors may be beneficial to prevent future pandemics.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jasmine Tan", + "author_inst": "School of Medicine, National Taiwan University, Taipei, Taiwan" + }, + { + "author_name": "Yilin Yoshida", + "author_inst": "Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA" + }, + { + "author_name": "Kevin Sheng-Kai Ma", + "author_inst": "Department of Life Science, National Taiwan University, Taipei, Taiwan" + }, + { + "author_name": "Franck Mauvais-Jarvis", + "author_inst": "Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.14.21255490", "rel_title": "Expectant parents' perceptions of healthcare and support during COVID-19 in the UK: A thematic analysis.", @@ -782593,117 +786800,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2021.04.19.21255730", - "rel_title": "The impact of COVID-19 on the oncologic outcomes of 3236 patients undergoing ColoRectal Cancer surgery in Northern Italy in 2019 and 2020 (COVID-CRC): results of a multicentric comparative cohort study.", - "rel_date": "2021-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255730", - "rel_abs": "ObjectiveThis study compared all patients undergoing surgery for colorectal cancer in 20 hospitals of Northern Italy in 2019 versus 2020, in order to evaluate whether COVID-19-related delays in the execution of colorectal cancer screening resulted in more advanced cancers at diagnosis and worse clinical outcomes.\n\nDesignA retrospective multicentric cohort analysis of patients who underwent surgery for colorectal cancer in March-December 2019 (2019) versus March-December 2020 (2020). The independent predictors of disease stage (oncologic stage, associated symptoms, clinical T4 stage, metastasis) and postoperative outcome (surgical complications, palliative surgery, 30-day death) were evaluated using logistic regression.\n\nResultsThe sample consisted of 1755 patients operated in 2019, and 1481 in 2020 (both mean ages 69.6 years). The proportions of cancers with symptoms, clinical T4 stage, liver and lung metastases in 2019 and 2020 were, respectively: 80.8% vs 84.5%; 6.2% vs 8.7%; 10.2% vs 10.3%; and 3.0% vs 4.4%. The proportions of surgical complications, palliative surgery, and death in 2019 and 2020 were, respectively: 34.4%vs 31.9%; 5.0% vs 7.5%; and 1.7% vs 2.4%. At multivariate analysis, as compared with 2019, cancers in 2020 were significantly more likely to be symptomatic (Odds Ratio - OR: 1.36, 95% Confidence Interval - CI: 1.09-1.69), in clinical T4 stage (OR: 1.38; 1.03-1.85), with multiple liver metastases (OR: 2.21; 1.24-3.94), but less likely to cause surgical complications (OR: 0.79; 0.68-0.93).\n\nConclusionsColorectal cancer patients who had surgery between March and December 2020 had an increased risk of more advanced disease in terms of associated symptoms, cancer location, clinical T4 stage, and number of liver metastases.\n\nSHORT SUMMARY BOX\n\nWhat is already known about this subject?A specific search regarding the correlation between colorectal cancer oncologic outcomes and COVID-19 showed a few modeling studies which reported the predictions of the potential impact of the diagnostic delays (due to the reduction of the screening programs) on the survival of patients affected by colorectal cancer. However, no study reported any real-life evidence regarding the correlation between the COVID-19 outbreak and the deteriorations of the oncologic outcomes of patients with colorectal cancer.\n\nWhat are the new findings?The present study showed that patients who had surgery for colorectal cancer between March and December 2020 had an increased risk of more advanced disease in terms of associated symptoms, cancer location, clinical T4 stage, and number of liver metastases, than patients who had surgery between March and December 2019.\n\nHow might it impact on clinical practice in the foreseeable future?The present study confirmed that the backlogs of the screening programs have had, and probably will have, detrimental effects on the oncologic outcomes of patients affected by colorectal cancer. Increased resources should be placed in order to reactivate and enhance the screening programs, and to reduce the risk of colorectal cancer patients to be diagnosed with advanced cancer in the next future.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Matteo Rottoli", - "author_inst": "Alma Mater Studiorum University of Bologna" - }, - { - "author_name": "Gianluca Pellino", - "author_inst": "Department of Advanced Medical and Surgical Sciences, Universita degli Studi della Campania \"Luigi Vanvitelli\", Naples, Italy" - }, - { - "author_name": "Antonino Spinelli", - "author_inst": "Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy" - }, - { - "author_name": "Maria E Flacco", - "author_inst": "Department of Medical Sciences, University of Ferrara, Ferrara, Italy" - }, - { - "author_name": "Lamberto Manzoli", - "author_inst": "Department of Medical Sciences, University of Ferrara, Ferrara, Italy" - }, - { - "author_name": "Mario Morino", - "author_inst": "AOU Citta della Salute e della Scienza, Turin, Italy" - }, - { - "author_name": "Salvatore Pucciarelli", - "author_inst": "Department of Surgical, Oncological, and Gastroenterological Sciences, University of Padua, Padua, Italy" - }, - { - "author_name": "Elio Jovine", - "author_inst": "Division of General and Emergency Surgery, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy" - }, - { - "author_name": "Moh'd Abu Hilal", - "author_inst": "Fondazione Poliambulanza Hospital, Brescia, Italy" - }, - { - "author_name": "Riccardo Rosati", - "author_inst": "Department of Gastrointestinal Surgery, IRCCS San Raffaele Scientific Institute and San Raffaele Vita-Salute University, Milan, Italy" - }, - { - "author_name": "Alessandro Ferrero", - "author_inst": "Ospedale Mauriziano Umberto I, Turin, Italy" - }, - { - "author_name": "Andrea Pietrabissa", - "author_inst": "Department of Surgery, University of Pavia and Fondazione IRCCS Policlinico San Matteo, Pavia, Italy" - }, - { - "author_name": "Marcello Guaglio", - "author_inst": "Department of Surgery, Colorectal Surgery Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy" - }, - { - "author_name": "Nicolo' de Manzini", - "author_inst": "Surgical Clinic Unit, University Hospital of Trieste, Trieste, Italy" - }, - { - "author_name": "Pierluigi Pilati", - "author_inst": "UOC Chirurgia Oncologica Esofago e vie digestive, Istituto Oncologico Veneto (IOV-IRCCS), Padua, Italy" - }, - { - "author_name": "Elisa Cassinotti", - "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico Milano - Universita' degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Giusto Pignata", - "author_inst": "ASST Spedali Civili di Brescia, Brescia, Italy" - }, - { - "author_name": "Orlando Goletti", - "author_inst": "Chirurgia Generale Humanitas Gavazzeni Bergamo, Italy" - }, - { - "author_name": "Enrico Opocher", - "author_inst": "ASST Santi Paolo e Carlo, Dipartimento di scienze della salute - Universita' degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Piergiorgio Danelli", - "author_inst": "ASST Fatebenefratelli Sacco, Milano; Dipartimento di Scienze Biomediche e Cliniche, Universita' degli Studi di Milano, Milan, Italy" - }, - { - "author_name": "Gianluca M Sampietro", - "author_inst": "Divisione di Chirurgia Generale ed Epato-Bilio-Pancreatica. ASST Rhodense. Ospedale di Rho, Monumento ai Caduti, Rho, Milan, Italy" - }, - { - "author_name": "Stefano Olmi", - "author_inst": "Chirurgia Generale ed Oncologica, Policlinico San Marco GSD, Zingonia, Bergamo, Italy" - }, - { - "author_name": "Nazario Portolani", - "author_inst": "Department of Clinical and Experimental Sciences, Surgical Clinic, University of Brescia, Italy" - }, - { - "author_name": "Gilberto Poggioli", - "author_inst": "Department of Medical and Surgical Sciences, Alma Mater Studiorum University of Bologna, Bologna, Italy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2021.04.14.21255457", "rel_title": "The evaluation of a novel tool to remotely assess visual acuity in chronic uveitis patients during the COVID-19 pandemic", @@ -784118,6 +788214,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.14.21255512", + "rel_title": "Assessing the Mortality Impact of the COVID-19 Pandemic in Florida State Prisons", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255512", + "rel_abs": "BackgroundThe increased risk of COVID-19 infection among incarcerated individuals due to environmental hazards is well known and recent studies have highlighted the higher rates of infection and mortality prisoners in the United States face due to COVID-19. However, the impact of COVID-19 on all-cause mortality rates in incarcerated populations has not been studied.\n\nMethodsUsing data reported by the Florida Department of Corrections on prison populations and mortality events we conducted a retrospective cohort study of all individuals incarcerated in Florida state prisons between 2015 and 2020. We calculated excess deaths by estimating age-specific expected deaths from mortality trends in 2015 through 2019 and taking the difference between observed and expected deaths during the pandemic period. We calculated life table measures using standard demographic techniques and assessed significant yearly changes using bootstrapping.\n\nFindingsThe Florida Department of Corrections reported 510 total deaths from March 1, 2020 to December 31, 2020 among the state prison population. This was 42% higher (rate ratio 1.42, 95% CI 1.15 to 1.89) than the expected number of deaths in light of mortality rates for previous years. Reported COVID-19 deaths in a month were positively correlated with estimated excess deaths (80.4%, p <.01). Using age-specific mortality estimates, we found that life expectancy at age 20 declined by 4 years (95% CI 2.06-6.57) between 2019 and 2020 for the Florida prison population.\n\nInterpretationThe Florida prison population saw a significant increase in all-cause mortality during the COVID-19 pandemic period, leading to a decrease in life expectancy of more than four years. Life years lost by the Florida prison population were likely far greater than those lost by the general United States population, as reported by other studies. This difference in years lost highlights the need for increased interventions to protect vulnerable incarcerated populations during pandemics.\n\nFundingVital Projects Fund, Arnold Ventures, US Centers for Disease Control, Eunice Kennedy Shriver National Institute of Child Health and Human Development", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Neal Marquez", + "author_inst": "University of Washington" + }, + { + "author_name": "Aaron Littman", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Victoria Rossi", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Michael Everett", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Erika Tyagi", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Hope Johnson", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Sharon Dolovich", + "author_inst": "University of California Los Angeles" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.14.21255476", "rel_title": "Geographic and demographic heterogeneity of SARS-CoV-2 diagnostic testing in Illinois, USA, March to December 2020", @@ -784359,37 +788498,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.18.21255699", - "rel_title": "INTRANASAL APPLICATION OF LACTOCOCCUS LACTIS W 136 BACTERIA EARLY IN COVID 19 INFECTION MAY HAVE A BENEFICIAL IMMUNOMODULATORY EFFECT: A PROOF-OF-CONCEPT STUDY", - "rel_date": "2021-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.18.21255699", - "rel_abs": "JustificationStimulation of early innate anti-viral responses during the early phase of SARS-COV-2 infection oxygen may improve evolution of illness and late pulmonary complications. This may be possible using a TLR agonist such as a probiotic bacterium possessing desirable immunomodulatory properties.\n\nMethodWe performed a non-contact, open-label, prospective randomized clinical trial comparing intranasally applied Lactococcus lactis W136 with saline irrigation alone in patients within 96 hours of diagnosis of SARS-COV-2 infection not requiring supplemental oxygen.\n\nResultsTwenty-three of a planned forty participants aged 18-59 without comorbidities were recruited. Irrigation with intranasal L lactis W136 twice-daily for fourteen days of was associated with a nasal response characterised by increase in the symptom of Facial and Throat pain/discomfort, and with a lesser severity in symptoms of i) Fatigue ii) Olfactory dysfunction and iii) Breathlessness. Safety and tolerability were good, with no acute infections or severe deteriorations.\n\nInterpretationFacial and throat pain may correspond to postulated mechanism of action corresponding to activation of innate defences with antiviral effects and may explain the potentially protective effects seen. Intranasal L lactis W136 irrigations may thus represent a potentially inexpensive, safe, and easily scalable non-antigen based therapeutic for the continuing global SARS-COV-2 pandemic.\n\nData availability statementData is available on request from the senior author, Dr Desrosiers: martin-yvon.desrosiers.med@ssss.gouv.qc.ca\n\nFundingThis work was supported with internal funds from the Desrosiers laboratory at the Centre de Recherche du Centre Hospitaller de lUniversite de Montreal (CRCHUM).\n\nCompeting InterestsDr Desrosiers holds equity in Probionase Therapies inc., Which commercialises Lactococcus lactis W136 for chronic rhinosinusitis.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Leandra Mfuna Endam", - "author_inst": "Centre de Recherche Centre Hospitalier Universite de Montreal (CRCHUM)" - }, - { - "author_name": "Cecile Tremblay", - "author_inst": "Centre Hospitalier Universite de Montreal (CHUM)" - }, - { - "author_name": "Ali Filali", - "author_inst": "Centre de Recherche Centre Hospitalier Universite de Montreal (CRCHUM)" - }, - { - "author_name": "Martin Yvon Desrosiers", - "author_inst": "Centre Hospitalier Universite de Montreal (CHUM)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.19.21255441", "rel_title": "Early treatment with nitazoxanide prevents worsening of mild and moderate COVID-19 and subsequent hospitalization", @@ -786448,6 +790556,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.13.21255396", + "rel_title": "Ultra-fast, high throughput and inexpensive detection of SARS-CoV-2 seroconversion", + "rel_date": "2021-04-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255396", + "rel_abs": "A technique allowing high throughput, fast and low-cost quantitative analysis of human IgG antibodies reacting to SARS-CoV-2 antigens will be required to understand the levels of protecting antibodies in the population raised in response to infections and/or to immunization. We described previously a fast, simple, and inexpensive Ni2+ magnetic bead immunoassay which allowed detection of human antibodies reacting against the SARS-CoV-2 nucleocapsid protein using a minimal amount of serum or blood. A major drawback of the previously described system was that it only processed 12 samples simultaneously. Here we describe a manually operating inexpensive 96 well plate magnetic extraction / homogenization process which allows high throughput analysis delivering results of 96 samples in chromogenic format in 12 minutes or in fluorescent ultrafast format which takes only 7 minutes. We also show that His tag antigen purification can be performed on the fly while loading antigens to the Ni2+ magnetic beads in a process which takes only 12 min reducing the pre analytical time and cost. Finally, we show that the magnetic bead immunoassay is antigen flexible and can be performed using either Nucleocapsid, Spike or Spike RBD. The method performed with low inter and intra assay variability using different antigens and detection modes and was able to deliver >99.5% specificity and >95% sensitivity for a cohort of 203 pre pandemic and 63 COVID-19 positive samples.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Marcelo S Conzentino Sr.", + "author_inst": "UFPR" + }, + { + "author_name": "Tatiele P.C. Santos Sr.", + "author_inst": "UFPR" + }, + { + "author_name": "Khaled Selim", + "author_inst": "Tubingen University" + }, + { + "author_name": "Berenike Wagner", + "author_inst": "Tubingen University" + }, + { + "author_name": "Janette T Alford", + "author_inst": "Tubingen University" + }, + { + "author_name": "Nelli Deobald", + "author_inst": "Tubingen University" + }, + { + "author_name": "Nigella M Paula", + "author_inst": "UFPR" + }, + { + "author_name": "Fabiane G.M Rego Sr.", + "author_inst": "UFPR" + }, + { + "author_name": "Dalila L Zanette", + "author_inst": "Fiocruz" + }, + { + "author_name": "Mateus N Aoki", + "author_inst": "Fiocruz" + }, + { + "author_name": "Jeanine M Nardin", + "author_inst": "Hospital Erasto Gaerthener" + }, + { + "author_name": "Maria C.C Huergo", + "author_inst": "Prefeitura Municipal de Guaratuba" + }, + { + "author_name": "Rodrigo A Reis", + "author_inst": "UFPR" + }, + { + "author_name": "Luciano Huergo Sr.", + "author_inst": "UFPR" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.12.21255330", "rel_title": "Identification of natural SARS-CoV-2 infection in seroprevalence studies among vaccinated populations", @@ -786629,37 +790808,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.13.21255395", - "rel_title": "How disease risk awareness modulates transmission: coupling infectious disease models with behavioral dynamics", - "rel_date": "2021-04-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255395", - "rel_abs": "Epidemiological models often assume that individuals do not change their behavior or that those aspects are implicitly incorporated in parameters in the models. Typically these assumption is included in the contact rate between infectious and susceptible individuals. For example models incorporate time variable contact rates to account for the effect of behavior or other interventions than in general terms reduce transmission. However, adaptive behaviors are expected to emerge and to play an important role in the transmission dynamics across populations. Here, we propose a theoretical framework to couple transmission dynamics with behavioral dynamics due to infection awareness. We first model the dynamics of social behavior by using a game theory framework. Then we coupled the model with an epidemiological model that captures the disease dynamics by assuming that individuals are more aware of that epidemiological state (i.e. fraction of infected individuals) and reduces their contacts. Our results from a mechanistic modeling framework show that as individuals increase their awareness the steady-state value of the final fraction of infected individuals in a susceptible-infected-susceptible (SIS) model decreases. We also extend our results to a spatial framework, incorporating a spatially-defined theoretical contact network (social network) and we made the awareness parameter dependent on a global or local contact structure. Our results show that even when individuals increase their awareness of the disease, the spatial structure itself defines the steady state solution of the system, in which more connected networks (networks with random or constant degree distributions) results in a population with no change in their behavior. Our work then shows that explicitly incorporating dynamics about the behavioral response dynamics might significantly change the predicted course of the epidemic and therefore highlights the importance of accounting for this source of variation in the epidemiological models.\n\nAuthor summaryWe present a theoretical framework for coupling traditional epidemiological models with a behavioral dynamical model in the form of a game-theoretical setting. Here, individual payoffs are assumed to be coupled with the force of infection (FOI) and the transmission probability, which is proportional to the individuals behavior. Our approach studies the temporal dynamics of a mechanistic epidemiological model (SIS) coupled with a prisoners dilemma framework, then we extended the results to an SIS model implemented on a network (social network) using three types of networks: Scale-free, Watts-Strogatz or small world and grid networks. Our results show that behavior can change the final fraction of infected individuals and the fraction of cooperators or individuals who voluntarily take actions to reduce their transmission in the system. In addition, when the dynamics were studied on a contact network we found that the topology of this network plays an essential role in controlling individuals behavior. Specifically, our results show that as the network gets more connected (i.e. degree distribution is random or uniform (Watts-Strogatz or grid networks respectively) disease spread is faster and therefore individuals are not obligated to cooperate. However, when the dynamics are studied in a scale free contact network, as degree distribution follows a power-law, we show that similarly as the mechanistic ODEs model individuals cooperate so their transmission probability is reduced.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jaime Cascante-Vega", - "author_inst": "Universidad de los Andes" - }, - { - "author_name": "Samuel Torres-Florez", - "author_inst": "Universidad de los Andes" - }, - { - "author_name": "Juan Cordovez", - "author_inst": "Universidad de los Andes" - }, - { - "author_name": "Mauricio Santos-Vega", - "author_inst": "Universidad de los Andes" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.12.21255363", "rel_title": "Assessing the Risk of Cascading COVID-19 Outbreaks from Prison-to-Prison Transfers", @@ -788266,6 +792414,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.13.21255384", + "rel_title": "Outcomes of COVID-19 infection in patients treated with Clozapine.", + "rel_date": "2021-04-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255384", + "rel_abs": "BackgroundClozapine, an antipsychotic, is associated with increased susceptibility to infection with COVID-19, compared to other antipsychotics.\n\nAimsTo investigate associations between clozapine treatment and increased risk of adverse outcomes of COVID-19, namely COVID-related hospitalisation and intensive care treatment, and death, among patients taking antipsychotics with schizophrenia-spectrum disorders.\n\nMethodUsing data from South London and Maudsley NHS Foundation Trust (SLAM) clinical records, via the Clinical Record Interactive Search system, we identified 157 individuals who had an ICD-10 diagnosis of schizophrenia-spectrum disorders, were taking antipsychotics at the time of the COVID-19 pandemic in the UK, and had a laboratory-confirmed COVID-19 infection. The following health outcomes were measured: COVID-related hospitalisation, COVID-related intensive care treatment death. We tested associations between clozapine treatment and each outcome using logistic regression models, adjusting for gender, age, ethnicity, neighbourhood deprivation, obesity, smoking status, diabetes, asthma, bronchitis and hypertension using propensity scores.\n\nResultsIn the 157 individuals who developed COVID while on antipsychotics, there were 44 COVID-related hospitalisations, 13 COVID-related intensive care treatments and 13 deaths of any cause during the follow-up period. In the unadjusted analysis, there was no significant association between clozapine and any of the outcomes and there remained no associations following adjusting for the confounding variables.\n\nConclusionsIn our sample of patients with COVID-19 and schizophrenia-spectrum disorders, we found no evidence that clozapine treatment puts patients at increased risk of hospitalisation, intensive care treatment or death, compared to any other antipsychotic treatment. However, further research should be considered in larger samples to confirm this.\n\nConflict of interestRDH has received research funding from Roche, Pfizer, Janssen, and Lundbeck. DFF has received research funding from Janssen and Lundbeck. JHM has received research funding from Lundbeck. JTT has received research funding from Bristol-Meyers-Squibb. RS declares research support in the last 36 months from Janssen, GSK and Takeda.\n\nEthics statementThe research was conducted under ethical approval reference 18/SC/0372 from Oxfordshire Research Ethics Committee C.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Risha Govind", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "Daniela Fonseca de Freitas", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "Megan Pritchard", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "Mizanur Khondoker", + "author_inst": "Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, UK." + }, + { + "author_name": "James T Teo", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "Robert Stewart", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "Richard D. Hayes", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "James H. MacCabe", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.04.13.21255413", "rel_title": "The impact of population mobility on COVID-19 incidence and socioeconomic disparities at the sub-city level in 314 Latin American cities", @@ -788471,65 +792666,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.04.16.21255647", - "rel_title": "Prospective predictive performance comparison between Clinical Gestalt and validated COVID-19 mortality scores.", - "rel_date": "2021-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.16.21255647", - "rel_abs": "BackgroundMost COVID-19 mortality scores were developed in the early months of the pandemic and now available evidence-based interventions have helped reduce its lethality. It has not been evaluated if the original predictive performance of these scores holds true nor compared it against Clinical Gestalt predictions. We tested the current predictive accuracy of six COVID-19 scores and compared it with Clinical Gestalt predictions.\n\nMethods200 COVID-19 patients were enrolled in a tertiary hospital in Mexico City between September and December 2020. Clinical Gestalt predictions of death (as a percentage) and LOW-HARM, qSOFA, MSL-COVID-19, NUTRI-CoV and NEWS2 were obtained at admission. We calculated the AUC of each score and compared it against Clinical Gestalt predictions and against their respective originally reported value.\n\nResults106 men and 60 women aged 56+/-9 and with confirmed COVID-19 were included in the analysis. The observed AUC of all scores was significantly lower than originally reported; LOW-HARM 0.96 (0.94-0.98) vs 0.76 (0.69-0.84), qSOFA 0.74 (0.65-0.81) vs 0.61 (0.53-0.69), MSL-COVID-19 0.72 (0.69-0.75) vs 0.64 (0.55-0.73) NUTRI-CoV 0.79 (0.76-0.82) vs 0.60 (0.51-0.69), NEWS2 0.84 (0.79-0.90) vs 0.65 (0.56-0.75), Neutrophil-Lymphocyte ratio 0.74 (0.62-0.85) vs 0.65 (0.57-0.73). Clinical Gestalt predictions were non-inferior to mortality scores (AUC=0.68 (0.59-0.77)). Adjusting the LOW-HARM score with locally derived likelihood ratios did not improve its performance. However, some scores performed better than Clinical Gestalt predictions when clinicians confidence of prediction was <80%.\n\nConclusionNo score was significantly better than Clinical Gestalt predictions. Despite its subjective nature, Clinical Gestalt has relevant advantages for predicting COVID-19 clinical outcomes.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Adrian Soto-Mota", - "author_inst": "National Institute of Medical Sciences and Nutrition Salvador Zubiran" - }, - { - "author_name": "Braulio A. Marfil-Garza", - "author_inst": "CHRISTUS-LatAm Hub Center of Excellence and Innovation" - }, - { - "author_name": "Santiago Castiello", - "author_inst": "The University of Oxford" - }, - { - "author_name": "Erick Martinez-Rodriguez", - "author_inst": "National Institute of Medical Sciences and Nutrition Salvador Zubiran" - }, - { - "author_name": "Daniel Carrillo-Vazquez", - "author_inst": "National Institute of Medical Sciences and Nutrition Salvador Zubiran" - }, - { - "author_name": "Hiram Tadeo Espinoza", - "author_inst": "National Institute of Medical Sciences and Nutrition Salvador Zubiran" - }, - { - "author_name": "Jessica Paola Guerrero-Cabrera", - "author_inst": "National Institute of Medical Sciences and Nutrition Salvador Zubiran" - }, - { - "author_name": "Francisco Eduardo Dardon-Fierro", - "author_inst": "National Institute of Medical Sciences and Nutrition Salvador Zubiran" - }, - { - "author_name": "Juan Manuel Escobar Valderrama", - "author_inst": "National Institute of Medical Sciences and Nutrition Salvador Zubiran" - }, - { - "author_name": "Jorge Alanis-Mendizabal", - "author_inst": "National Institute of Medical Sciences and Nutrition Salvador Zubiran" - }, - { - "author_name": "Juan Gutierrez-Mejia", - "author_inst": "National Institute of Medical Sciences and Nutrition Salvador Zubiran" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.17.21255651", "rel_title": "Feasibility and accuracy of a novel saliva sampling method for large-scale SARS-CoV-2 screening in children < 12 years of age", @@ -790028,6 +794164,129 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.04.13.21255139", + "rel_title": "Strong anti-viral responses in pediatric COVID-19 patients in South Brazil", + "rel_date": "2021-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255139", + "rel_abs": "Epidemiological evidence that COVID-19 manifests as a milder disease in children compared to adults has been reported by numerous studies, but the mechanisms underlying this phenomenon have not been characterized. It is still unclear how frequently children get infected, and/or generate immune responses to SARS-CoV-2. We have performed immune profiling of pediatric and adult COVID-19 patients in Brazil, producing over 38 thousand data points, asking if cellular or humoral immune responses could help explain milder disease in children. In this study, pediatric COVID-19 patients presented high viral titers. Though their non-specific immune profile was dominated by naive, non-activated lymphocytes, their dendritic cells expressed high levels of HLA-DR and were low in CX3CR1, indicating competence to generate immune responses that are not targeted to inflamed tissue. Finally, children formed strong specific antibody and T cell responses for viral structural proteins. Childrens T cell responses differed from adults in that their CD8+ TNF+ T cell responses were low for S peptide but significantly higher against N and M peptide pools. Altogether, our data support a scenario in which SARS-CoV-2 infected children may contribute to transmission, though generating strong and differential responses to the virus that might associate with protection in pediatric COVID-19 presentation.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Tiago Fazolo", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Karina Lima", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Julia C. Fontoura", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Priscila Oliveira de Souza", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Gabriel Hilario", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Renata Zorzetto", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Luiz Rodrigues Jr.", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Veridiane Maria Pscheidt", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Jayme Ferreira Neto", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Alisson F. Haubert", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Izza Gambin", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Aline C. Oliveira", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Raissa S. Mello", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Matheus Gutierrez", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Rodrigo Benedetti Gassen", + "author_inst": "Center for Transplantation Sciences, Department of Surgery, Massachusetts" + }, + { + "author_name": "Ivaine Tais Sauthier Sartor", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Gabriela Oliveira Zavaglia", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Ingrid Rodrigues Fernandes", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Fernanda Hammes Varela", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "M\u00e1rcia Polese-Bonatto", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Thiago J. Borges", + "author_inst": "Center for Transplantation Sciences, Department of Surgery, Massachusetts" + }, + { + "author_name": "Sidia Maria Callegari-Jacques", + "author_inst": "Departamento de Estat\u00edstica, Universidade Federal do Rio Grande do Sul" + }, + { + "author_name": "Marcela Santos Correa da Costa", + "author_inst": "Coordena\u00e7\u00e3o-Geral do Programa Nacional de Imuniza\u00e7\u00f5es - Departamento de Imuniza\u00e7\u00f5es e Doen\u00e7as Transmiss\u00edveis - Secretaria de Vigil\u00e2ncia em Sa\u00fade - Minist\u00e9rio da" + }, + { + "author_name": "Jaqueline de Araujo Schwartz", + "author_inst": "Coordena\u00e7\u00e3o-Geral do Programa Nacional de Imuniza\u00e7\u00f5es - Departamento de Imuniza\u00e7\u00f5es e Doen\u00e7as Transmiss\u00edveis - Secretaria de Vigil\u00e2ncia em Sa\u00fade - Minist\u00e9rio da" + }, + { + "author_name": "Marcelo Comerlato Scotta", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Renato T. Stein", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Cristina Bonorino", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.04.10.21254878", "rel_title": "Preparations of Dutch emergency departments for the COVID-19 pandemic: a questionnaire-based study", @@ -790125,53 +794384,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.12.21255149", - "rel_title": "Clumpiness: Modeling the Impact of Social Dynamics on COVID-19 Spread", - "rel_date": "2021-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.12.21255149", - "rel_abs": "We present an agent based simulation model configured for exploring the dynamics of disease spread in the context of agents that group together through homophily, the principle of \"like attracts like\". To study the properties of this model, we introduce two novel social network inter-connectivity measures, \"clumpiness\" and \"hoprank,\" that are the same basic concept defined at global and local levels, respectively. The measures may be computed from samples of readily available demographic data, and are useful for measuring probabilistic packet transmission through social networks. In three studies we apply clumpiness to measure the effects, on COVID-19 transmission, caused by social networks of both homophilic physical proximity and homophilic information replication. The particular characteristic we are interested in about disease transmission is herd immunity, the percentage of a population that has to be immune in order to prevent infection from spreading to those who are not. Two studies demonstrate innovations measuring herd immunity levels and predicting future outbreak locations, procedures relevant to epidemiological control policy. In the first study, we look at how homophilic physical proximity networks form natural bubbles that act as frictive surfaces that affect the speed of transmission of packets and influence herd immunity levels. In the second study, we test clumpiness in homophilic proximity social networks as a predictor of future infection outbreaks at the level of individual schools, restaurants, and workplaces. Our third study demonstrates that protective social bubbles form naturally from homophilic information replication networks, and enhance the natural bubbles that come from the homophilic physical proximity networks. Accurate description of this information environment lays the foundation for epidemiological messaging policy formation.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ben Goertzel", - "author_inst": "SingularityNET Foundation" - }, - { - "author_name": "Cassio Pennachin", - "author_inst": "SingularityNET Foundation" - }, - { - "author_name": "Deborah Duong", - "author_inst": "SingularityNET Foundation" - }, - { - "author_name": "Matthew Ikl\u00e9", - "author_inst": "SingularityNET Foundation" - }, - { - "author_name": "Michael Duncan", - "author_inst": "SingularityNET Foundation" - }, - { - "author_name": "James Boyd", - "author_inst": "The Millennium Project" - }, - { - "author_name": "Andr\u00e9 Senna", - "author_inst": "SingularityNET Foundation" - }, - { - "author_name": "Ramon Dur\u00e3es", - "author_inst": "SingularityNET Foundation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.12.21255205", "rel_title": "The impact of COVID-19 upon the delivery of exercise services within cystic fibrosis clinics in the United Kingdom", @@ -791718,6 +795930,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.08.21255118", + "rel_title": "The association between loneliness during the COVID-19 pandemic and psychological distress", + "rel_date": "2021-04-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21255118", + "rel_abs": "The purpose of this study was to examine the association between loneliness and psychological distress during the COVID-19 pandemic in Japan. We conducted a cross-sectional, online study from 22 to 26 December 2020. A total of 27,036 participants, all employed at the time of the survey, were included in the analysis. Participants were asked if they felt loneliness in a single-item question. The Kessler 6 (K6) was used to assess psychological distress defined as K6 scores of 5 or higher, and 13 or higher. The odds ratios (ORs) of psychological distress associated with loneliness were estimated using a multilevel logistic model nested in the prefecture of residence, with adjustment for age, sex, marital status, equivalent income, educational level, smoking, alcohol consumption, job type, number of workplace employees, and cumulative incidence rate of COVID-19 in the prefecture. Communication with friends, acquaintances, and family was strongly associated with psychological distress, so we adjusted for these factors and eating meals alone. Results showed a significant association between loneliness and psychological distress (OR = 36.62, 95%CI = 32.95-40.69). Lack of friends to talk to, lack of acquaintances to ask for help, and lack of people to communicate with through social networking sites were all strongly associated with psychological distress, as were family time and solitary eating. Even after adjusting for these factors, loneliness was still strongly associated with psychological distress (OR = 29.36, 95%CI = 26.44-32.98). The association between loneliness during the COVID-19 pandemic and psychological distress indicates the need for intervention.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yusuke Konno", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Masako Nagata", + "author_inst": "Department of Occupational Health Practice and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Jap" + }, + { + "author_name": "Ayako Hino", + "author_inst": "Department of Mental Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" + }, + { + "author_name": "Seiichiro Tateishi", + "author_inst": "Department of Occupational Medicine, School of Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" + }, + { + "author_name": "Mayumi Tsuji", + "author_inst": "Department of Environmental Health, School of Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" + }, + { + "author_name": "Akira Ogami", + "author_inst": "Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan, Kitakyushu, Japa" + }, + { + "author_name": "Reiji Yoshimura", + "author_inst": "Department of Psychiatry, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" + }, + { + "author_name": "Shinya Matsuda", + "author_inst": "Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" + }, + { + "author_name": "Yoshihisa Fujino", + "author_inst": "University of Occupational and Environmental Health, Japan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.04.09.21255215", "rel_title": "Impacts of COVID-19 on sick leave", @@ -791907,61 +796170,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.13.21255393", - "rel_title": "Facemask usage during the COVID-19 pandemic among people with primary ciliary dyskinesia: a participatory project", - "rel_date": "2021-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255393", - "rel_abs": "BackgroundFacemasks help prevent transmission of SARS-CoV-2 and are particularly important for people with chronic respiratory disease such as primary ciliary dyskinesia (PCD). We studied the usage of facemasks and its consequences among people with PCD in an international context.\n\nMethodsWe used data from COVID-PCD, an international observational cohort study which collects longitudinal data from people with PCD during the COVID-19 pandemic via weekly online questionnaires. An online questionnaire investigating use of facemasks was posted in October 2020. It asked about frequency of facemask usage in different public places, problems experienced with use of facemasks, affordability of masks, and beliefs regarding their effectiveness.\n\nResults282 participants (50%) completed the questionnaire. Participants came from 27 different countries; median age was 32 years (interquartile range 17-48), and 63% were female. Almost all wore a facemask whenever they left their house. In addition, many avoided public places altogether. For example, 159 (57%) did not use public transport at all, 108 (39%) always wore a facemask in public transport, 4 (1%) sometimes, and 7 (3%) never. 81% agreed with the statement that facemasks protect the person who wears the mask, and 91% agreed that facemasks protect others. One third reported that it was uncomfortable to wear a mask because of their runny nose, 31% because of cough, and 22% because of difficulty breathing. Participants less often wore facemasks in public when there was no national requirement. Only two persons had a personal exemption from wearing a facemask prescribed by a physician.\n\nConclusionsThis international study found that people with PCD carefully shield themselves, and most wear facemasks everywhere in public. People who did not wear facemasks in public came from countries without a national facemask requirement. National policies mandating facemask use in public are important for universal use to protect high-risk populations from SARS-CoV-2 infections.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Eva Sophie Lunde Pedersen", - "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Switzerland" - }, - { - "author_name": "Eugenie NR Collaud", - "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Switzerland" - }, - { - "author_name": "Rebeca Mozun", - "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Switzerland" - }, - { - "author_name": "Katie Dexter", - "author_inst": "PCD Family Support Group, London, United Kingdom" - }, - { - "author_name": "Catherine Kruljac", - "author_inst": "PCD Australia Primary Ciliary Dyskinesia, Altona Victoria, Australia" - }, - { - "author_name": "Hansruedi Silberschmidt", - "author_inst": "Verein Kartagener Syndrom und Primaere Ciliaere Dyskinesie, Deutschland, Wetzikon, Switzerland" - }, - { - "author_name": "- COVID-PCD patient advisory group", - "author_inst": "" - }, - { - "author_name": "Jane S Lucas", - "author_inst": "Primary Ciliary Dyskinesia Centre, NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom; Universit" - }, - { - "author_name": "Myrofora Goutaki", - "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Switzerland; Paediatric Respiratory Medicine, Children's University Hospital of Bern, Universit" - }, - { - "author_name": "Claudia E. Kuehni", - "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Switzerland; Paediatric Respiratory Medicine, Children's University Hospital of Bern, Universit" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.12.21255365", "rel_title": "Association between comorbidities and death from COVID-19 in different age groups", @@ -793524,6 +797732,109 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.04.13.439641", + "rel_title": "Spike Protein Targeting \"Nano-Glue\" that Captures and Promotes SARS-CoV-2 Elimination", + "rel_date": "2021-04-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.13.439641", + "rel_abs": "The global emergency caused by the SARS-CoV-2 pandemics can only be solved with adequate preventive and therapeutic strategies, both currently missing. The electropositive Receptor Binding Domain (RBD) of SARS-CoV-2 spike protein with abundant {beta}-sheet structure serves as target for COVID-19 therapeutic drug design. Here, we discovered that ultrathin 2D CuInP2S6 (CIPS) nanosheets as a new agent against SARS-CoV-2 infection, which also able to promote viral host elimination. CIPS exhibits extremely high and selective binding capacity with the RBD of SARS-CoV-2 spike protein, with consequent inhibition of virus entry and infection in ACE2-bearing cells and human airway epithelial organoids. CIPS displays nano-viscous properties in selectively binding with spike protein (KD < 1 pM) with negligible toxicity in vitro and in vivo. Further, the CIPS-bound SARS-CoV-2 was quickly phagocytosed and eliminated by macrophages, suggesting CIPS could be successfully used to capture and facilitate the virus host elimination with possibility of triggering anti-viral immunization. Thus, we propose CIPS as a promising nanodrug for future safe and effective anti-SARS-CoV-2 therapy, as well as for use as disinfection agent and surface coating material to constrain the SARS-CoV-2 spreading.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Guofang Zhang", + "author_inst": "Laboratory of Immunology and Nanomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Yalin Cong", + "author_inst": "University of Chinese Academy of Science" + }, + { + "author_name": "Guoli Cao", + "author_inst": "Laboratory of Immunology and Nanomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Liang Li", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Peng Yu", + "author_inst": "School of Materials Science and Engineering, Sun Yat-sen University" + }, + { + "author_name": "Qingle Song", + "author_inst": "Laboratory of Immunology and Nanomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Ke Liu", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Jing Qu", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Jing Wang", + "author_inst": "State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University" + }, + { + "author_name": "Wei Xu", + "author_inst": "CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and Natio" + }, + { + "author_name": "Shumin Liao", + "author_inst": "Department of Otolaryngology, The Seventh Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Yunping Fan", + "author_inst": "Department of Otolaryngology, The Seventh Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Yufeng Li", + "author_inst": "CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and Natio" + }, + { + "author_name": "Guocheng Wang", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Lijing Fang", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Yanzhong Chang", + "author_inst": "College of Life Science, Hebei Normal University" + }, + { + "author_name": "Yuliang Zhao", + "author_inst": "Research Unit of Nanoscience and Technology, Chinese Academy of Medical Sciences" + }, + { + "author_name": "Diana Boraschi", + "author_inst": "The Institute of Biochemistry and Cell Biology, National Research Council" + }, + { + "author_name": "Hongchang Li", + "author_inst": "Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences" + }, + { + "author_name": "Chunying Chen", + "author_inst": "CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and Natio" + }, + { + "author_name": "Liming Wang", + "author_inst": "CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and Natio" + }, + { + "author_name": "Yang Li", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.04.14.439793", "rel_title": "Neuropilin-1 Mediates SARS-CoV-2 Infection in Bone Marrow-derived Macrophages", @@ -793701,37 +798012,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.13.439743", - "rel_title": "Dynamic Profiling of Binding and Allosteric Propensities of the SARS-CoV-2 Spike Protein with Different Classes of Antibodies: Mutational and Perturbation-Based Scanning Reveal Allosteric Duality of Functionally Adaptable Hotspots", - "rel_date": "2021-04-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.13.439743", - "rel_abs": "Structural and biochemical studies of the SARS-CoV-2 spike complexes with highly potent antibodies have revealed multiple conformation-dependent epitopes and a broad range of recognition modes linked to different neutralization responses In this study, we combined atomistic simulations with mutational and perturbation-based scanning approaches to perform in silico profiling of binding and allosteric propensities of the SARS-CoV-2 spike protein residues in complexes with B38, P2B-2F6, EY6A and S304 antibodies representing three different classes. Conformational dynamics analysis revealed that binding-induced modulation of soft modes can elicit the unique protein response to different classes of antibodies. Mutational scanning heatmaps and sensitivity analysis revealed the binding energy hotspots for different classes of antibodies that are consistent with the experimental deep mutagenesis, showing that differences in the binding affinity caused by global circulating variants in spike positions K417, E484 and N501 are relatively moderate and may not fully account for the observed antibody resistance effects. Through functional dynamics analysis and perturbation-response scanning of the SARS-CoV-2 spike protein residues in the unbound form and antibody-bound forms, we examine how antibody binding can modulate allosteric propensities of spike protein residues and determine allosteric hotspots that control signal transmission and global conformational changes. These results show that residues K417, E484, and N501 targeted by circulating mutations correspond to a group of versatile allosteric centers in which small perturbations can modulate collective motions, alter the global allosteric response and elicit binding resistance. We suggest that SARS-CoV-2 S protein may exploit plasticity of specific allosteric hotspots to generate escape mutants that alter response to antibody binding without compromising activity of the spike protein.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Gennady M Verkhivker", - "author_inst": "Chapman University School of Pharmacy" - }, - { - "author_name": "Steve Agajanian", - "author_inst": "Chapman University" - }, - { - "author_name": "Deniz Yazar Oztas", - "author_inst": "Chapman University" - }, - { - "author_name": "Grace Gupta", - "author_inst": "Chapman University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.04.14.439719", "rel_title": "INO-4800 DNA Vaccine Induces Neutralizing Antibodies and T cell Activity Against Global SARS-CoV-2 Variants", @@ -795122,6 +799402,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.11.21253563", + "rel_title": "Impact of COVID -19 on Depression and Anxiety among Healthcare Professionals in Abu Dhabi", + "rel_date": "2021-04-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.11.21253563", + "rel_abs": "COVID-19 have affected Healthcare workers is many ways. One of the important areas is the psychological impact. The aim of this study is to examine the effects of the COVID-19 outbreak on the mental health of healthcare Professionals (HCP). A cross-sectional study was conducted between April 11th, and July 23rd, 2020, to assess depression and anxiety of healthcare workers, during the COVID-19 pandemic. An online, self-administered, anonymous questionnaire evaluated 1,268 HCP. More than half of the participants reported symptoms of anxiety (51.5%). Mild anxiety was reported in 28.8% of participating HCP, and 12.68 % of the participants registered moderate anxiety scores, while 9.95 % reported severe anxiety. Depression symptoms were revealed in 38.3 % of participating providers. Among all participates, 4.3 % and 2.7 % reported moderately severe and severe depression, accordingly, while 22.5%, and 8.8 % of the participating health care providers documented mild and moderate depression. The high prevalence of anxiety and depression recorded among HCP during the pandemic suggests that mental health intervention and support are necessary to ensure the psychological well-being of HCP.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Amal Alzarooni", + "author_inst": "Ambulatory health care,Abu Dhabi Health Services Company, UAE" + }, + { + "author_name": "Aljazia Alghfeli", + "author_inst": "Ambulatory health care, Abu Dhabi Health Services Company, AE" + }, + { + "author_name": "Hamda Alremeithi", + "author_inst": "Ambulatory health care,Abu Dhabi Health Services Company , UAE" + }, + { + "author_name": "Roqayah Al Madhaani,", + "author_inst": "Ambulatory Healthcare Services,Abu Dhabi Health Services Company, UAE" + }, + { + "author_name": "Latifa Al Ketbi,", + "author_inst": "Ambulatory Healthcare Services, Abu Dhabi Health Services Company, UAE" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.09.21255179", "rel_title": "SARS-CoV-2 UK, South African and Brazilian Variants in Karachi- Pakistan", @@ -795339,49 +799654,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.04.09.21255131", - "rel_title": "Early and ongoing importations of SARS-CoV-2 in Canada", - "rel_date": "2021-04-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.09.21255131", - "rel_abs": "Tracking the emergence and spread of SARS-CoV-2 is critical to inform public health interventions. Phylodynamic analyses have quantified SARS-CoV-2 migration on global and local scales1-5, yet they have not been applied to determine transmission dynamics in Canada. We quantified SARS-CoV-2 migration into, within, and out of Canada in the context of COVID-19 travel restrictions. To minimize sampling bias, global sequences were subsampled with probabilities corrected for their countries monthly contribution to global new diagnoses. A time-scaled maximum likelihood tree was used to estimate most likely ancestral geographic locations (country or Canadian province), enabling identification of sublineages, defined as introduction events into Canada resulting in domestic transmission. Of 402 Canadian sublineages identified, the majority likely originated from the USA (54%), followed by Russia (7%), India (6%), Italy (6%), and the UK (5%). International introductions were mostly into Ontario (39%) and Quebec (38%). Among Pango lineages6, B.1 was imported at least 191 separate times from 11 different countries. Introduction rates peaked in late March then diminished but were not eliminated following national interventions including restrictions on non-essential travel. We further identified 1,380 singleton importations, international importations that did not result in further sampled transmission, whereby representation of lineages and location were comparable to sublineages. Although proportion of international transmission decreased over time, this coincided with exponential growth of within-province transmission - in fact, total number of sampled transmission events from international or interprovincial sources increased from winter 2020 into spring 2020 in many provinces. Ontario, Quebec, and British Columbia acted as sources of transmission more than recipients, within the caveat of higher sequence representation. We present strong evidence that international introductions and interprovincial transmission of SARS-CoV-2 contributed to the Canadian COVID-19 burden throughout 2020, despite initial reductions mediated by travel restrictions in 2020. More stringent border controls and quarantine measures may have curtailed introductions of SARS-CoV-2 into Canada and may still be warranted.\n\nSignificance StatementBy analyzing SARS-CoV-2 genomes from Canada in the context of the global pandemic, we illuminate the extent to which the COVID-19 burden in Canada was perpetuated by ongoing international importations and interprovincial transmission throughout 2020. Although travel restrictions enacted in March 2020 reduced the importation rate and proportion of transmission from abroad across all Canadian provinces, SARS-CoV-2 introductions from the USA, India, Russia, and other nations were detectable through the summer and fall of 2020.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Angela McLaughlin", - "author_inst": "Bioinformatics, University of British Columbia, British Columbia, Canada; British Columbia Centre for Excellence in HIV/AIDS, British Columbia, Canada" - }, - { - "author_name": "Vincent Montoya", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, British Columbia, Canada" - }, - { - "author_name": "Rachel L Miller", - "author_inst": "Bioinformatics, University of British Columbia, British Columbia, Canada; British Columbia Centre for Excellence in HIV/AIDS, British Columbia, Canada" - }, - { - "author_name": "Gideon J Mordecai", - "author_inst": "Department of Medicine, University of British Columbia, British Columbia, Canada" - }, - { - "author_name": "Michael Worobey", - "author_inst": "Department of Ecology and Evolution, University of Arizona, Arizona, United States" - }, - { - "author_name": "Art FY Poon", - "author_inst": "Department of Pathology and Laboratory Medicine, Western University, Ontario, Canada" - }, - { - "author_name": "Jeffrey B Joy", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, British Columbia, Canada; Bioinformatics, University of British Columbia, British Columbia, Canada; Departme" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.09.21254250", "rel_title": "Improving SARS-CoV-2 cumulative incidence estimation through mixture modelling of antibody levels", @@ -797104,6 +801376,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.09.21255161", + "rel_title": "The PUPPY Study - Protocol for a Longitudinal Mixed Methods Study Exploring Problems Coordinating and Accessing Primary Care for Attached and Unattached Patients Exacerbated During the COVID-19 Pandemic Year", + "rel_date": "2021-04-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.09.21255161", + "rel_abs": "BackgroundThe COVID-19 pandemic significantly disrupted primary care in Canada, with many walk-in clinics and family practices initially closing or being perceived as inaccessible, pharmacies remaining open with restrictions on patient interactions, rapid uptake of virtual care, and reduced referrals for lab tests, diagnostics, and specialist care. The PUPPY Study (Problems Coordinating and Accessing Primary Care for Attached and Unattached Patients Exacerbated During the COVID-19 Pandemic Year) seeks to understand the impact of COVID-19 across the quadruple aim of primary care, with particular focus on the impacts on patients without attachment to a regular provider and those with chronic health conditions.\n\nObjectiveThe PUPPY Study objective is to understand the impact of COVID-19 across the quadruple aim of primary care.\n\nMethodsThe PUPPY study builds on an existing research program exploring patients access and attachment to primary care, pivoted to adapt to the emerging COVID-19 context. We will undertake a longitudinal mixed methods study to understand critical gaps in primary care access and coordination, comparing data pre- and post-pandemic in three Canadian provinces (Quebec, Ontario, and Nova Scotia). Multiple data sources will be used including: a policy review; qualitative interviews with primary care policymakers, providers (i.e., family physicians, nurse practitioners, and pharmacists), and patients (N=120); and medication prescribing and healthcare billings. The findings will inform the strengthening of primary care during and beyond the COVID-19 pandemic.\n\nResultsFunding was provided by the Canadian Institutes of Health Research COVID-19 Rapid Funding Opportunity Grant. Ethical approval to conduct this study was granted in Ontario (Queens Health Sciences & Affiliated Teaching Hospitals Research Ethics Board, file number 6028052; Western University Health Sciences Research Ethics Board, project 116591; University of Toronto Health Sciences Research Ethics Board, protocol number 40335), Quebec (Centre integre universitaire de sante et de services sociaux de lEstrie, project number 2020-3446) and Nova Scotia (Nova Scotia Health Research Ethics Board, file number 1024979).\n\nConclusionsThis is the first study of its kind exploring the impacts of COVID-19 on primary care systems, with particular focus on the issues of patients attachment and access to primary care. Through a multi-stakeholder, cross-jurisdictional approach, the PUPPY Study will generate findings and implications for future policy and practice.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Emily Gard Marshall", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Mylaine Breton", + "author_inst": "Universite de Sherbrooke" + }, + { + "author_name": "Benoit Cossette", + "author_inst": "Universite de Sherbrooke" + }, + { + "author_name": "Jennifer Isenor", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Maria Mathews", + "author_inst": "Western University" + }, + { + "author_name": "Caitlyn Ayn", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Melanie Ann Smithman", + "author_inst": "Universite de Sherbrooke" + }, + { + "author_name": "David Stock", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Eliot Frymire", + "author_inst": "Queen's University" + }, + { + "author_name": "Lynn Edwards", + "author_inst": "Nova Scotia Health" + }, + { + "author_name": "Michael Green", + "author_inst": "Queen's University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2021.04.08.21255046", "rel_title": "COVID-19 and mortality risk in patients with psychiatric disorders", @@ -797345,57 +801676,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.08.21254779", - "rel_title": "Immunogenicity of SARS-CoV-2 Vaccine in Dialysis", - "rel_date": "2021-04-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21254779", - "rel_abs": "BackgroundPatients receiving maintenance dialysis represent a high risk, immune-compromised population with 15-25% COVID mortality rate who were unrepresented in clinical trials evaluated for mRNA vaccines emergency use authorization.\n\nMethodAll patients receiving maintenance dialysis that received two doses of SARS-CoV-2 mRNA vaccines with antibody test results drawn [≥]14 days after the second dose, as documented in the electronic health record through March 18, 2021 were included. We report seroresponse based on levels of immunoglobulin-G against the receptor binding domain of the S1 subunit of SARS-CoV-2 spike antigen (seropositive [≥]2) using FDA-approved semi-quantitative chemiluminescent assay (ADVIA Centaur(R) XP/XPT COV2G).\n\nResultsAmong 186 dialysis patients from 32 clinics in 8 states tested 23{+/-}8 days after receiving 2 vaccine doses, mean age was 68{+/-}12 years, with 47% women, 21% Black, 26% residents in long-term care facilities and 97% undergoing in-center hemodialysis. Overall seropositive rate was 165/186 (88.7%) with 70% at maximum titer and with no significant difference in seropositivity between BNT162b2/Pfizer (N=148) and mRNA-1273/Moderna (N=18) vaccines (88.1% vs. 94.4%, p=0.42). Among patients with COVID-19 history, seropositive rate was 38/38 (100%) with 97% at maximum titer.\n\nConclusionMost patients receiving maintenance dialysis were seropositive after two doses of BNT162b2/Pfizer or mRNA-1273/Moderna vaccine. Early evidence suggests that vaccinated dialysis patients with prior COVID-19 develop robust antibody response. These results support an equitable and aggressive vaccination strategy for eligible dialysis patients, regardless of age, sex, race, ethnicity, or disability, to prevent the extremely high morbidity and mortality associated with COVID-19 in this high risk population.\n\nSignificanceIn this retrospective observational evaluation of SARS-CoV-2 mRNA vaccine response defined by detectable levels of immunoglobulin-G against the receptor binding domain of the S1 subunit of SARS-CoV-2 spike antigen of [≥]2 in serum of patients receiving maintenance dialysis, 165/186 (88.7%) were found to be seropositive (with 70% at maximum titer) at least 14 days after completing the second dose. No significant differences were observed by race or other subgroup or by vaccine manufacturer. Therefore, an equitable and aggressive vaccination strategy for all eligible maintenance dialysis patients, regardless of age, sex, race, ethnicity, or disability, is warranted to prevent the extremely high morbidity and mortality associated with COVID-19 in this high risk population.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Eduardo Lacson Jr.", - "author_inst": "Dialysis Clinic Inc./Tufts Medical Center" - }, - { - "author_name": "Christos P Argyropoulos", - "author_inst": "University of New Mexico" - }, - { - "author_name": "Harold J Manley", - "author_inst": "Dialysis Clinic, Inc." - }, - { - "author_name": "Gideon Aweh", - "author_inst": "Dialysis Clinic, Inc." - }, - { - "author_name": "Andrew I Chin", - "author_inst": "University of California Davis" - }, - { - "author_name": "Loay H Salman", - "author_inst": "Albany Medical College" - }, - { - "author_name": "Caroline M Hsu", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Doug S Johnson", - "author_inst": "Dialysis Clinic, Inc." - }, - { - "author_name": "Daniel E Weiner", - "author_inst": "Tufts Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2021.04.08.21255108", "rel_title": "High coverage COVID-19 mRNA vaccination rapidly controls SARS-CoV-2 transmission in Long-Term Care Facilities", @@ -798882,6 +803162,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.09.439260", + "rel_title": "Nosocomial Pseudomonas aeruginosaregulates alginate biosynthesis and Type VI secretion system during adaptive and convergent evolution for coinfection in critically ill COVID-19 patients", + "rel_date": "2021-04-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.09.439260", + "rel_abs": "COVID-19 pandemic has caused millions of death globally and caused huge impact on the health of infected patients. Shift in the lung microbial ecology upon such viral infection often worsens the disease and increases host susceptibility to secondary infections. Recent studies have indicated that bacterial coinfection is an unignorable factor contributing to the aggravation of COVID-19 and posing great challenge to clinical treatments. However, there is still a lack of in-depth investigation on the coinfecting bacteria in COVID-19 patients for better treatment of bacterial coinfection. With the knowledge that Pseudomonas aeruginosa is one of the top coinfecting pathogens, we analyzed the adaptation and convergent evolution of nosocomial P. aeruginosa isolated from two critical COVID-19 patients in this study. We sequenced and compared the genomes and transcriptomes of P. aeruginosa isolates longitudinally and parallelly for its evolutionary traits. P. aeruginosa overexpressed alginate and attenuated Type VI secretion system (T6SS) during coinfection for excessive biofilm formation and suppressed virulence. Results of bacterial competition assay and macrophage cytotoxicity test indicated that P. aeruginosa reduced its virulence towards both prokaryotic competitors and eukaryotic host through inhibiting its T6SS during evolution. P. aeuginosa T6SS is thus one of the reasons for its advantage to cause coinfection in COVID-19 patients while the attenuation of T6SS could cause a shift in the microecological composition in the lung. Our study will contribute to the development of therapeutic measures and the discovery of novel drug target to eliminate P. aeruginosa coinfection in COVID-19 patient.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Zhao Cai", + "author_inst": "School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Xiangke Duan", + "author_inst": "School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Han Zhang", + "author_inst": "School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Shuhong Han", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China" + }, + { + "author_name": "Kaiwei Yu", + "author_inst": "School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Yingdan Zhang", + "author_inst": "School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Yang Liu", + "author_inst": "Medical Research Center, Southern University of Science and Technology Hospital" + }, + { + "author_name": "Liang Yang", + "author_inst": "School of Medicine, Southern University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.10.439275", "rel_title": "CoVac501, a self-adjuvanting peptide vaccine conjugated with TLR7 agonists, against SARS-CoV-2 induces protective immunity", @@ -799143,61 +803470,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.04.07.21254925", - "rel_title": "Antibody Responses in Elderly Residential Care Persons following COVID-19 mRNA Vaccination", - "rel_date": "2021-04-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.07.21254925", - "rel_abs": "ObjectiveCOVID-19 disproportionately impacts older adults residing at long-term care facilities. Data regarding antibody response to COVID-19 vaccines in this population is limited. Our objective was to quantify the presence and magnitude of antibody response in older, vaccinated residents at assisted living, personal care, and independent living facilities.\n\nDesignA cross-sectional quality improvement study was conducted March 15 - April 1, 2021 in the Pittsburgh region.\n\nSetting and PopulationParticipants were volunteers at assisted living, personal care, and independent living facilities, who received mRNA COVID-19 vaccine. Conditions that obviate immune responses were exclusionary criteria.\n\nMethodsSera were collected to measure IgG anti-SARS-CoV-2 antibody level with reflex to total anti-SARS-CoV-2 immunoglobulin levels. Descriptive statistics, Pearson correlation coefficients, and multiple linear regression analysis were performed to evaluate relationships between factors potentially associated with antibody levels.\n\nResultsAll participants (N=70) had received two rounds of vaccination for COVID-19 and were found to have antibodies to SARS-CoV-2. There was wide variation in relative levels of antibodies as determined by extinction coefficients. Antibody levels trended lower in male sex, advanced age, steroid medications, and longer length of time from vaccination.\n\nConclusions and ImplicationsHigher functioning long-term care residents mounted detectable antibody responses when vaccinated with COVID-19 mRNA-based vaccines. This study provides preliminary information on level of population risk of assisted living, personal care, and independent living residents which can inform reopening strategies. Data suggests some degree of immunity is present during the immediate period following vaccination. However, protective effects of such vaccination programs remain to be determined in larger studies. Clinical protection is afforded not just by pre-formed antibody levels, but by ongoing adaptive immunity, which is known to be decreased in older individuals. Thus, the implications of these levels of antibodies in preventing COVID-19 disease must be determined by clinical follow-up.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "David A Nace", - "author_inst": "Division of Geriatric Medicine, School of Medicine, University of Pittsburgh" - }, - { - "author_name": "Kevin E Kip", - "author_inst": "Clinical Analytics, University of Pittsburgh Medical Center" - }, - { - "author_name": "Octavia M Peck Palmer", - "author_inst": "Department of Pathology, University of Pittsburgh" - }, - { - "author_name": "Michael R Shurin", - "author_inst": "Department of Pathology, University of Pittsburgh" - }, - { - "author_name": "Katie Mulvey", - "author_inst": "Clinical Laboratory, University of Pittsburgh Medical Center" - }, - { - "author_name": "Melissa Crandall", - "author_inst": "Clinical Laboratory, University of Pittsburgh Medical Center" - }, - { - "author_name": "April L Kane", - "author_inst": "Senior Services, University of Pittsburgh Medical Center" - }, - { - "author_name": "Amy Lukanski", - "author_inst": "Wolff Center, University of Pittsburgh Medical Center" - }, - { - "author_name": "Paula L Kip", - "author_inst": "Wolff Center, University of Pittsburgh Medical Center" - }, - { - "author_name": "Alan L Wells", - "author_inst": "Department of Pathology, University of Pittsburgh and Clinical Laboratory, University of Pittsburgh Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.04.07.21254206", "rel_title": "Cardiac Surgery during the Covid-19 Pandemic: Evidence from the first wave", @@ -800660,6 +804932,149 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.04.05.21254834", + "rel_title": "Performance of Repeat BinaxNOW SARS-CoV-2 Antigen Testing in a Community Setting, Wisconsin, November-December 2020", + "rel_date": "2021-04-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254834", + "rel_abs": "Repeating the BinaxNOW antigen test for SARS-CoV-2 by two groups of readers within 30 minutes resulted in high concordance (98.9%) in 2,110 encounters. BinaxNOW test sensitivity was 77.2% (258/334) compared to real-time reverse transcription-polymerase chain reaction. Repeating antigen testing on the same day did not significantly improve test sensitivity while specificity remained high.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Melisa M. Shah", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Phillip P. Salvatore", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Laura Ford", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Emiko Kamitani", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Melissa J. Whaley", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Kaitlin Mitchell", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Dustin W. Currie", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Clint N. Morgan", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Hannah E. Segaloff", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Shirley Lecher", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Tarah Somers", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Miriam E. Van Dyke", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "John Paul Bigouette", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Augustina Delaney", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Juliana DaSilva", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Michelle O'Hegarty", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Lauren Boyle-Estheimer", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Fatima Abdirizak", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Sandor E. Karpathy", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jennifer Meece", + "author_inst": "Marshfield Clinic Research Institute" + }, + { + "author_name": "Lynn Ivanic", + "author_inst": "Marshfield Clinic Research Institute" + }, + { + "author_name": "Kimberly Goffard", + "author_inst": "Winnebago County Health Department" + }, + { + "author_name": "Doug Gieryn", + "author_inst": "Winnebago County Health Department" + }, + { + "author_name": "Alana Sterkel", + "author_inst": "Wisconsin State Laboratory of Hygiene" + }, + { + "author_name": "Allen Bateman", + "author_inst": "Wisconsin State Laboratory of Hygiene" + }, + { + "author_name": "Juliana Kahrs", + "author_inst": "University of Wisconsin-Oshkosh" + }, + { + "author_name": "Kimberly Langolf", + "author_inst": "University of Wisconsin-Oshkosh" + }, + { + "author_name": "Tara Zochert", + "author_inst": "University of Wisconsin-Oshkosh" + }, + { + "author_name": "Nancy W. Knight", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Christopher H. Hsu", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Hannah L. Kirking", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jacqueline E. Tate", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.04.21254881", "rel_title": "Neutralization of SARS-CoV-2 variants by convalescent and vaccinated serum", @@ -800905,29 +805320,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.06.21255039", - "rel_title": "An extended SEIARD model for COVID-19 vaccination in Mexico: analysis and forecast", - "rel_date": "2021-04-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.06.21255039", - "rel_abs": "In this study, we propose and analyse an extended SEIARD model with vaccination. We compute the control reproduction number [R]c of our model and study the stability of equilibria. We show that the set of disease-free equilibria is locally asymptotically stable when [R]c < 1 and unstable when [R]c > 1, and we provide a sufficient condition for its global stability. Furthermore, we perform numerical simulations using the reported data of COVID-19 infections and vaccination in Mexico to study the impact of different vaccination, transmission and efficacy rates on the dynamics of the disease.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "\u00c1ngel G. C. P\u00e9rez", - "author_inst": "Universidad Aut\u00f3noma de Yucat\u00e1n" - }, - { - "author_name": "David Adeyemi Oluyori", - "author_inst": "Ahmadu Bello University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.06.21254958", "rel_title": "The demographic and geographic impact of the COVID pandemic in Bulgaria and Eastern Europe in 2020", @@ -802226,6 +806618,205 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.06.438709", + "rel_title": "Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape", + "rel_date": "2021-04-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.06.438709", + "rel_abs": "An ideal anti-SARS-CoV-2 antibody would resist viral escape1-3, have activity against diverse SARS-related coronaviruses4-7, and be highly protective through viral neutralization8-11 and effector functions12,13. Understanding how these properties relate to each other and vary across epitopes would aid development of antibody therapeutics and guide vaccine design. Here, we comprehensively characterize escape, breadth, and potency across a panel of SARS-CoV-2 antibodies targeting the receptor-binding domain (RBD), including S3094, the parental antibody of the late-stage clinical antibody VIR-7831. We observe a tradeoff between SARS-CoV-2 in vitro neutralization potency and breadth of binding across SARS-related coronaviruses. Nevertheless, we identify several neutralizing antibodies with exceptional breadth and resistance to escape, including a new antibody (S2H97) that binds with high affinity to all SARS-related coronavirus clades via a unique RBD epitope centered on residue E516. S2H97 and other escape-resistant antibodies have high binding affinity and target functionally constrained RBD residues. We find that antibodies targeting the ACE2 receptor binding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency, but we identify one potent RBM antibody (S2E12) with breadth across sarbecoviruses closely related to SARS-CoV-2 and with a high barrier to viral escape. These data highlight functional diversity among antibodies targeting the RBD and identify epitopes and features to prioritize for antibody and vaccine development against the current and potential future pandemics.", + "rel_num_authors": 46, + "rel_authors": [ + { + "author_name": "Tyler N Starr", + "author_inst": "Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA" + }, + { + "author_name": "Nadine Czudnochowski", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Fabrizia Zatta", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Young-Jun Park", + "author_inst": "Department of Biochemistry, University of Washington, Seattle, WA 98195, USA" + }, + { + "author_name": "Zhuoming Liu", + "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA" + }, + { + "author_name": "Amin Addetia", + "author_inst": "Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA" + }, + { + "author_name": "Dora Pinto", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Martina Beltramello", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Patrick Hernandez", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Allison J Greaney", + "author_inst": "Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98" + }, + { + "author_name": "Roberta Marzi", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "William G Glass", + "author_inst": "Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA" + }, + { + "author_name": "Ivy Zhang", + "author_inst": "Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional PhD Pro" + }, + { + "author_name": "Adam S Dingens", + "author_inst": "Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA" + }, + { + "author_name": "John E Bowen", + "author_inst": "Department of Biochemistry, University of Washington, Seattle, WA 98195, USA" + }, + { + "author_name": "Jason A Wojcechowskyj", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Anna De Marco", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Laura E Rosen", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Jiayi Zhou", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Martin Montiel-Ruiz", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Hannah Kaiser", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Heather Tucker", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Michael P. Housley", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Julia Di Iulio", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Gloria Lombardo", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Maria Agostini", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Nicole Sprugasci", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Katja Culap", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Stefano Jaconi", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Marcel Meury", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Exequiel Dellota", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Elisabetta Cameroni", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Tristan I Croll", + "author_inst": "Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, CB2 0XY, UK" + }, + { + "author_name": "Jay C Nix", + "author_inst": "Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA" + }, + { + "author_name": "Colin Havenar-Daughton", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Amalio Telenti", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Florian A Lempp", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Matteo Samuele Pizzuto", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "John D Chodera", + "author_inst": "Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA" + }, + { + "author_name": "Christy M Hebner", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Sean PJ Whelan", + "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA" + }, + { + "author_name": "Herbert W Virgin", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; D" + }, + { + "author_name": "David Veesler", + "author_inst": "Department of Biochemistry, University of Washington, Seattle, WA 98195, USA" + }, + { + "author_name": "Davide Corti", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98" + }, + { + "author_name": "Gyorgy Snell", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.07.438806", "rel_title": "Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of nsp5 Main Protease", @@ -802475,89 +807066,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.04.07.438804", - "rel_title": "Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of Nsp3 Papain-like Protease", - "rel_date": "2021-04-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.07.438804", - "rel_abs": "The COVID-19 pandemic has emerged as the biggest life-threatening disease of this century. Whilst vaccination should provide a long-term solution, this is pitted against the constant threat of mutations in the virus rendering the current vaccines less effective. Consequently, small molecule antiviral agents would be extremely useful to complement the vaccination program. The causative agent of COVID-19 is a novel coronavirus, SARS-CoV-2, which encodes at least nine enzymatic activities that all have drug targeting potential. The papain-like protease (PLpro) contained in the nsp3 protein generates viral non-structural proteins from a polyprotein precursor, and cleaves ubiquitin and ISG protein conjugates. Here we describe the expression and purification of PLpro. We developed a protease assay that was used to screen a custom chemical library from which we identified Dihydrotanshinone I and Ro 08-2750 as compounds that inhibit PLpro in protease and isopeptidase assays and also inhibit viral replication in cell culture-based assays.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Lee A Armstrong", - "author_inst": "The University of Dundee" - }, - { - "author_name": "Rupert Beale", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Ganka Bineva-Todd", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Berta Canal", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "John FX Diffley", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Lucy S Drury", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Michael Howell", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Yogesh Kulathu", - "author_inst": "The University of Dundee" - }, - { - "author_name": "Karim Labib", - "author_inst": "The University of Dundee" - }, - { - "author_name": "Chew Theng Lim", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Jennifer Milligan", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Eiko Ozono", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Kang Wei Tan", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Florian Weissmann", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Mary Wu", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Theresa U Zeisner", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Jingkun Zeng", - "author_inst": "The Francis Crick Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.04.07.438811", "rel_title": "Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of Nsp15 Endoribonuclease", @@ -804600,6 +809108,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.01.21254798", + "rel_title": "Female-male differences in COVID vaccine adverse events have precedence in seasonal flu shots: a potential link to sex-associated baseline gene expression patterns", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.01.21254798", + "rel_abs": "Nearly 150 million doses of FDA-authorized COVID vaccines have been administered in the United States. Sex-based differences of adverse events remain poorly understood, mandating the need for real-world investigation from Electronic Health Records (EHRs) and broader epidemiological data sets. Based on an augmented curation of EHR clinical notes of 31,064 COVID-vaccinated individuals (19,321 females and 11,743 males) in the Mayo Clinic, we find that nausea and vomiting were documented significantly more frequently in females than males after both vaccine doses (nausea: RRDose 1 = 1.67, pDose 1 <0.001, RRDose 2 = 2.2, pDose 1 < 0.001; vomiting: RRDose 1 = 1.58, pDose 1 < 0.001, RRDose 2 = 1.88, pDose 1 = 3.4x10-2). Conversely, fever, fatigue, and lymphadenopathy were more common in males after the first dose vaccination (fever RR = 0.62; p = 8.65x10-3; fatigue RR = 0.86, p = 2.89x10-2; lymphadenopathy RR = 0.61, p = 3.45x10-3). Analysis of the Vaccine Adverse Events Reporting System (VAERS) database further confirms that nausea comprises a larger fraction of total reports among females than males (RR: 1.58; p<0.001), while fever comprises a larger fraction of total reports among males than females (RR: 0.84; p<0.001). Importantly, increased reporting of nausea and fever among females and males, respectively, is also observed for prior influenza vaccines in the VAERS database, establishing that these differences are not unique to the recently developed COVID-19 vaccines. Investigating the mechanistic basis underlying these clinical findings, an analysis of bulk RNA-sequencing data from 12,158 human blood samples (8626 female, 3532 male) reveals 85 genes that are not only significantly different in their gene expression between females and males at baseline, but also have established literature-based associations to COVID-19 as well as the vaccine-related adverse events of clinical consequence. The NLRP3 inflammasome and the NR3C1 glucocorticoid receptor emerge as particularly promising baseline links to sex-associated vaccine adverse events, warranting targeted investigation of these signaling pathways and associated cell types. From a public health standpoint, our clinical findings shall aid in educating patients on the sex-associated risks they should expect for COVID-19 vaccines and also promote better clinical management of vaccine-associated adverse events.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "AJ Venkatakrishnan", + "author_inst": "nference" + }, + { + "author_name": "Praveen Kumar-M", + "author_inst": "nference" + }, + { + "author_name": "Eli Silvert", + "author_inst": "nference" + }, + { + "author_name": "Enrique Garcia-Rivera", + "author_inst": "nference" + }, + { + "author_name": "Mariola Szenk", + "author_inst": "nference" + }, + { + "author_name": "Rohit Suratekar", + "author_inst": "nference Labs" + }, + { + "author_name": "Patrick Lenehan", + "author_inst": "nference" + }, + { + "author_name": "Emily Lindemer", + "author_inst": "nference" + }, + { + "author_name": "John C OHoro", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Amy W Williams", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew D Badley", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Abinash Virk", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Melanie D Swift", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Gregory J Gores", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Venky Soundararajan", + "author_inst": "nference" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.05.21254897", "rel_title": "No Evidence of Infectious SARS-CoV-2 in Human Milk: Analysis of a Cohort of 110 Lactating Women", @@ -804733,45 +809316,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.04.04.21254903", - "rel_title": "Monitoring carbon dioxide to quantify the risk of indoor airborne transmission of COVID-19", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.04.21254903", - "rel_abs": "A new guideline for mitigating indoor airborne transmission of COVID-19 prescribes a limit on the time spent in a shared space with an infected individual (Bazant and Bush, 2021). Here, we rephrase this safety guideline in terms of occupancy time and mean exhaled carbon dioxide concentration in an indoor space, thereby enabling the use of CO2 monitors in the risk assessment of airborne transmission of respiratory diseases. While CO2 concentration is related to airborne pathogen concentration (Rudnick and Milton, 2003), the guideline developed here accounts for the different physical processes affecting their evolution, such as enhanced pathogen production from vocal activity and pathogen removal via face-mask use, filtration, sedimentation and deactivation. Critically, transmission risk depends on the total infectious dose, so necessarily depends on both the pathogen concentration and exposure time. The transmission risk is also modulated by the fractions of susceptible, infected and immune persons within a population, which evolve as the pandemic runs its course. A mathematical model is developed that enables a prediction of airborne transmission risk from real-time CO2 measurements. Illustrative examples of implementing our guideline are presented using data from CO2 monitoring in university classrooms and office spaces.\n\nO_TEXTBOXImpact StatementThere is mounting scientific evidence that COVID-19 is primarily transmitted through indoor airborne transmission, as arises when a susceptible person inhales virus-laden aerosol droplets exhaled by an infectious person. A safety guideline to limit indoor airborne transmission (Bazant and Bush, 2021) has recently been derived that complements the public health guidelines on surface cleaning and social distancing. We here recast this safety guideline in terms of total inhaled carbon dioxide, as can be readily monitored in most indoor spaces. Our approach paves the way for optimizing air handling systems by balancing health and financial concerns, informs policy for safely re-opening schools and businesses as the pandemic runs its course, and may be applied quite generally in the mitigation of airborne respiratory illnesses, including influenza.\n\nC_TEXTBOX", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Martin Z. Bazant", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Ousmane Kodio", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Alexander E. Cohen", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Kasim Khan", - "author_inst": "none" - }, - { - "author_name": "Zongyu Gu", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "John W. M. Bush", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.01.21254783", "rel_title": "Trust boosts recovery of countries from COVID-19", @@ -806378,6 +810922,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.02.21254809", + "rel_title": "Risk factors for severity on admission and the disease progression during hospitalization in a large cohort of COVID-19 patients in Japan", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.02.21254809", + "rel_abs": "ObjectivesTo investigate the risk factors contributing to severity on admission. Additionally, risk factors on worst severity and fatality were studied. Moreover, factors were compared based on three points: early severity, worst severity, and fatality.\n\nDesignA observational cohort study utilizing data entered in a Japan nationwide COVID-19 inpatient registry, COVIREGI-JP.\n\nSettingAs of August 31, 2020, 7,546 cases from 780 facilities have been registered. Participating facilities cover a wide range of hospitals where COVID-19 patients are admitted in Japan.\n\nParticipantsParticipants who had a positive test result on any applicable SARS-CoV-2 diagnostic tests, and were admitted to participating healthcare facilities. A total of 3,829 cases were identified from January 16 to May 31, 2020, of which 3,376 cases were included in this study.\n\nPrimary and secondary outcoe measuresPrimary outcome was severe or non-severe on admission, determined by the requirement of mechanical ventilation or oxygen therapy, SpO2, or respiratory rate. Secondary outcome was the worst severity during hospitalization, judged by the requirement of oxygen and/or IMV/ECMO.\n\nResultsRisk factors for severity on admission were older age, male, cardiovascular disease, chronic respiratory disease, diabetes, obesity, and hypertension. Cerebrovascular disease, liver disease, renal disease or dialysis, solid tumor, and hyperlipidemia did not influence severity on admission; however it influenced worst severity. Fatality rates for obesity, hypertension, and hyperlipidemia were relatively lower.\n\nConclusionsThis study segregated the comorbidities driving severity and death. It is possible that risk factors for severity on admission, worst severity, and fatality are not consistent and may be propelled by different factors. Specifically, while hypertension, hyperlipidemia, and obesity had major effect on worst severity, their impact was mild on fatality in the Japanese population. Some studies contradict our results; therefore, detailed analyses, considering in-hospital treatments, are needed for validation.\n\nTrial registrationUMIN000039873. https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000045453\n\nStrengths and limitations of this studyO_LIIn this article, we studied the disease progression of COVID-19, by comparing the risk factors on three points: early severity, worst severity, and fatality.\nC_LIO_LIOur results are useful from a public health perspective, as we provide risk factors for predicting the severity on admission and disease progression from patients background factors.\nC_LIO_LIThis study pointed out the possibility that risk factors of the severity on admission, worst severity, and fatality are not consistent and may be propelled by different factors.\nC_LIO_LIOur data were collected from hundreds of healthcare facilities; thus data accuracy may be questionable.\nC_LIO_LIAlso, treatment type, dosage, duration, and combination varied immensely across the facilities and we did not consider treatments prior to and during hospitalization in the analysis.\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Mari Terada", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Hiroshi Ohtsu", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Sho Saito", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Kayoko Hayakawa", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Shinya Tsuzuki", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Yusuke Asai", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Nobuaki Matsunaga", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Satoshi Kutsuna", + "author_inst": "National Centre for Global Health and Medicine" + }, + { + "author_name": "Wataru Sugiura", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "National Center for Global Health and Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.01.21254755", "rel_title": "Rapid screening for variants of concern in routine SARS-CoV-2 PCR diagnostics", @@ -806539,61 +811138,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.04.05.21254924", - "rel_title": "Phylogenetic estimates of SARS-CoV-2 introductions into Washington State", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254924", - "rel_abs": "BackgroundThe first confirmed case of SARS-CoV-2 in North America was identified in Washington state on January 21, 2020. We aimed to quantify the number and temporal trends of out-of-state introductions of SARS-CoV-2 into Washington.\n\nMethodsWe conducted a phylogenetic analysis of 11,422 publicly available whole genome SARS-CoV-2 sequences from GISAID sampled between December 2019 and September 2020. We used maximum parsimony ancestral state reconstruction methods on time-calibrated phylogenies to enumerate introductions/exports, their likely geographic source (e.g. US, non-US, and between eastern and western Washington), and estimated date of introduction. To incorporate phylogenetic uncertainty into our estimates, we conducted 5,000 replicate analyses by generating 25 random time-stratified samples of non-Washington reference sequences, 20 random polytomy resolutions, and 10 random resolutions of the reconstructed ancestral state.\n\nResultsWe estimated a minimum 287 separate introductions (median, range 244-320) into Washington and 204 exported lineages (range 188-227) of SARS-CoV-2 out of Washington. Introductions began in mid-January and peaked on March 29, 2020. Lineages with the Spike D614G variant accounted for the majority (88%) of introductions. Overall, 61% (range 55-65%) of introductions into Washington likely originated from a source elsewhere within the US, while the remaining 39% (range 35-45%) likely originated from outside of the US. Intra-state transmission accounted for 65% and 28% of introductions into eastern and western Washington, respectively.\n\nConclusionsThere is phylogenetic evidence that the SARS-CoV-2 epidemic in Washington is continually seeded by a large number of introductions, and that there was significant inter- and intra-state transmission. Due to incomplete sampling our data underestimate the true number of introductions.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Diana M Tordoff", - "author_inst": "University of Washington, Department of Epidemiology, Seattle, WA" - }, - { - "author_name": "Alexander L Greninger", - "author_inst": "University of Washington, Department of Laboratory Medicine & Pathology, Seattle, WA" - }, - { - "author_name": "Pavitra Roychoudhury", - "author_inst": "University of Washington, Department of Laboratory Medicine & Pathology, Seattle, WA" - }, - { - "author_name": "Lasata Shrestha", - "author_inst": "University of Washington, Department of Laboratory Medicine & Pathology, Seattle, WA" - }, - { - "author_name": "Hong Xie", - "author_inst": "University of Washington, Department of Laboratory Medicine & Pathology, Seattle, WA" - }, - { - "author_name": "Keith R Jerome", - "author_inst": "Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA" - }, - { - "author_name": "Nathan Breit", - "author_inst": "University of Washington, Department of Laboratory Medicine & Pathology, Seattle, WA" - }, - { - "author_name": "Meei-Li Huang", - "author_inst": "University of Washington, Department of Laboratory Medicine & Pathology, Seattle, WA" - }, - { - "author_name": "Mike Famulare", - "author_inst": "Institute for Disease Modeling, Seattle, WA" - }, - { - "author_name": "Joshua T Herbeck", - "author_inst": "Institute for Disease Modeling, Seattle, WA; International Clinical Research Center, University of Washington, Department of Global Health, Seattle, WA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.04.21253205", "rel_title": "Molecular Profiling of COVID-19 Autopsies Uncovers Novel Disease Mechanisms", @@ -808148,6 +812692,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.05.438465", + "rel_title": "The Up state of the SARS-COV-2 Spike homotrimer favors an increased virulence for new variants", + "rel_date": "2021-04-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.05.438465", + "rel_abs": "The COVID-19 pandemic has spread widely worldwide. However, as soon as the vaccines were released - the only scientifically verified and efficient therapeutic option thus far - a few mutations combined into variants of SARS-CoV-2 that are more transmissible and virulent emerged raising doubts about their efficiency. Therefore, this work aims to explain possible molecular mechanisms responsible for the increased transmissibility and the increased rate of hospitalizations related to the new variants. A combination of theoretical methods was employed. Constant-pH Monte Carlo simulations were carried out to quantify the stability of several spike trimeric structures at different conformational states and the free energy of interactions between the receptor binding domain (RBD) and Angiotensin Converting Enzyme 2 (ACE2) for the most worrying variants. Electrostatic epitopes were mapped using the PROCEEDpKa method. These analyses showed that the increased virulence is more likely to be due to the improved stability to the S trimer in the opened state (the one in which the virus can interact with the cellular receptor ACE2) than due to alterations in the complexation RBD-ACE2, once the increased observed in the free energy values is small. Conversely, the South African variant (B.1.351), when compared with the wild type SARS-CoV-2, is much more stable in the opened state (either with one or two RBDs in the up position) than in the closed state (with the three RBDs in the down position). Such results contribute to the understanding of the natural history of disease and also to indicate possible strategies to both develop new therapeutic molecules and to adjust the vaccine doses for a higher production of B cells antibodies.\n\nGraphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Carolina Correa Giron", + "author_inst": "Universidade Federal do Triangulo Mineiro" + }, + { + "author_name": "Aatto Laaksonen", + "author_inst": "Stockholm University" + }, + { + "author_name": "Fernando Luis Barroso da Silva", + "author_inst": "University of Sao Paulo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.04.05.438500", "rel_title": "An Autoantigen-ome from HS-Sultan B-Lymphoblasts Offers a Molecular Map for Investigating Autoimmune Sequelae of COVID-19", @@ -808337,109 +812908,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.02.21252580", - "rel_title": "Therapeutic application of alpha-1-antitrypsin in COVID-19", - "rel_date": "2021-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.02.21252580", - "rel_abs": "RationaleThe treatment options for COVID-19 patients are sparse and do not show sufficient efficacy. Alpha-1-antitrypsin (AAT) is a multi-functional host-defense protein with anti-proteolytic and anti-inflammatory activities.\n\nObjectivesThe aim of the present study was to evaluate whether AAT is a suitable candidate for treatment of COVID-19.\n\nMethodsAAT and inflammatory markers were measured in the serum of COVID-19 patients. Human cell cultures were employed to determine the cell-based anti-protease activity of AAT and to test whether AAT inhibits the host cell entry of vesicular stomatitis virus (VSV) particles bearing the spike (S) protein of SARS-CoV-2 and the replication of authentic SARS-CoV-2. Inhaled and / or intravenous AAT was applied to nine patients with mild-to-moderate COVID-19.\n\nMeasurements and Main ResultsThe serum AAT concentration in COVID-19 patients was increased as compared to control patients. The relative AAT concentrations were decreased in severe COVID-19 or in non-survivors in ratio to inflammatory blood biomarkers. AAT inhibited serine protease activity in human cell cultures, the uptake of VSV-S into airway cell lines and the replication of SARS-CoV-2 in human lung organoids. All patients, who received AAT, survived and showed decreasing respiratory distress, inflammatory markers, and viral load.\n\nConclusionAAT has anti-SARS-CoV-2 activity in human cell models, is well tolerated in patients with COVID-19 and together with its anti-inflammatory properties might be a good candidate for treatment of COVID-19.\n\nFundingThis work was supported by grants of the Rolf M. Schwiete Stiftung, the Saarland University, the BMBF, the State of Lower Saxony, and The State of Saarland.\n\nScientific Knowledge on the SubjectCOVID-19 is caused by \"severe acute respiratory syndrome coronavirus 2\" (SARS-CoV-2) and is a serious global health threat. Efficacious treatments are not available and there are no drugs that can prevent progression towards respiratory and extra-pulmonary organ failure. AAT has been studied in vitro and has activity against SARS-CoV-2. We searched PubMed and Google Scholar using the search terms \"COVID-19\", \"SARS-CoV-2\", \"therapy\", and \"-1-antitrypsin\" (AAT) for research published in 2020 and 2021.\n\nWhat This Study Adds to the FieldThis study shows the results of a translational program with a focus on the biology of AAT in COVID-19. The data show that there is a relative deficiency of AAT in relation to systemic inflammation. AAT inhibits serine protease activity in human airway cells and the replication of SARS-CoV-2 in human lung organoids. Inhaled and / or intravenous application of AAT in nine patients was associated with clinical stabilization. The findings of this exploratory study suggest that AAT has a mechanistic role in the pathophysiology of COVID-19 based on its anti-inflammatory and anti-viral activities. This offers the possibility to test and develop AAT application for treatment of different phenotypes or stages of COVID-19, including severe, inflammatory courses or early stages. Inhaled treatment could be an option to administer AAT non-invasively in early stages.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Felix Ritzmann", - "author_inst": "Saarland University" - }, - { - "author_name": "Praneeth Chitirala", - "author_inst": "Saarland University" - }, - { - "author_name": "Yiwen Yao", - "author_inst": "Saarland University" - }, - { - "author_name": "Nadine Krueger", - "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" - }, - { - "author_name": "Markus Hoffmann", - "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" - }, - { - "author_name": "Wei Zuo", - "author_inst": "Tongji University" - }, - { - "author_name": "Frank Lammert", - "author_inst": "Saarland University Medical Center" - }, - { - "author_name": "Sigrun Smola", - "author_inst": "Saarland University Medical Center" - }, - { - "author_name": "Nastasja Seiwert", - "author_inst": "Saarland University Medical Center" - }, - { - "author_name": "Naveh Tov", - "author_inst": "Kamada Ltd." - }, - { - "author_name": "Noga Alagem", - "author_inst": "Kamada Ltd." - }, - { - "author_name": "Bahareh Mozafari", - "author_inst": "Saarland University" - }, - { - "author_name": "Katharina Guenther", - "author_inst": "Saarland University" - }, - { - "author_name": "Martina Seibert", - "author_inst": "Saarland University" - }, - { - "author_name": "Sabrina Hoersch", - "author_inst": "Saarland University Medical Center" - }, - { - "author_name": "Thomas Volk", - "author_inst": "Saarland University Medical Center" - }, - { - "author_name": "Philipp M. Lepper", - "author_inst": "Saarland University" - }, - { - "author_name": "Guy Danziger", - "author_inst": "Saarland University" - }, - { - "author_name": "Stefan Poehlmann", - "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" - }, - { - "author_name": "Christoph Beisswenger", - "author_inst": "Saarland University" - }, - { - "author_name": "Christian Herr", - "author_inst": "Saarland University" - }, - { - "author_name": "Robert Bals", - "author_inst": "Saarland University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.27.21254373", "rel_title": "Statins Are Associated with Improved 28-day Mortality in Patients Hospitalized with SARS-CoV-2 Infection", @@ -810026,6 +814494,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.06.438634", + "rel_title": "Plasma microbiome in COVID-19 subjects: an indicator of gut barrier defects and dysbiosis", + "rel_date": "2021-04-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.06.438634", + "rel_abs": "The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal (GI) symptoms. We asked whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n=30) and healthy control (n=16) were collected during hospitalization. Plasma microbiome was analyzed using 16S rRNA sequencing, metatranscriptomic analysis, and gut permeability markers including FABP-2, PGN and LPS in both patient cohorts. Almost 65% (9 out 14) COVID-19 patients showed abnormal presence of gut microbes in their bloodstream. Plasma samples contained predominately Proteobacteria, Firmicutes, and Actinobacteria. The abundance of gram-negative bacteria (Acinetobacter, Nitrospirillum, Cupriavidus, Pseudomonas, Aquabacterium, Burkholderia, Caballeronia, Parabhurkholderia, Bravibacterium, and Sphingomonas) was higher than the gram-positive bacteria (Staphylococcus and Lactobacillus) in COVID-19 subjects. The levels of plasma gut permeability markers FABP2 (1282{+/-}199.6 vs 838.1{+/-}91.33; p=0.0757), PGN (34.64{+/-}3.178 vs 17.53{+/-}2.12; p<0.0001), and LPS (405.5{+/-}48.37 vs 249.6{+/-}17.06; p=0.0049) were higher in COVID-19 patients compared to healthy subjects. These findings support that the intestine may represent a source for bacteremia and may contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Ram Prasad", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Michael John Patton", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Jason L Floyd", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Cristiano P Vieira", + "author_inst": "Univeristy of Alabama at Birmingham" + }, + { + "author_name": "Seth D. Fortmann", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Mariana DuPont", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Angie Harbour", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Jeremy R Chen See", + "author_inst": "WrightLabs LLC" + }, + { + "author_name": "Justin Wright", + "author_inst": "Wright Labs LLC" + }, + { + "author_name": "Regina Lamendella", + "author_inst": "Juniata College" + }, + { + "author_name": "Bruce R. Stevens", + "author_inst": "University of Florida College of Medicine" + }, + { + "author_name": "Maria B. Grant", + "author_inst": "University of Alabama- Birmingham" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.05.438537", "rel_title": "High-Potency Polypeptide-based Interference for Coronavirus Spike Glycoproteins", @@ -810239,77 +814770,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.04.06.438614", - "rel_title": "Altered O-glycosylation Level of SARS-CoV-2 Spike Protein by Host O-glycosyltransferase Strengthens Its Trimeric Structure", - "rel_date": "2021-04-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.06.438614", - "rel_abs": "The trimeric spike protein (S) mediates host-cell entry and membrane fusion of SARS-CoV-2. S protein is highly glycosylated, whereas its O-glycosylation is still poorly understood. Herein, we site-specifically examine the O-glycosylation of S protein through a mass spectrometric approach with HCD-triggered-ETD model. We identify 15 high-confidence O-glycosites and at least 10 distinct O-glycan structures on S protein. Peptide microarray assays prove that human ppGalNAc-T6 actively participates in O-glycosylation of S protein. Importantly, the upregulation of ppGalNAc-T6 expression can profoundly enhance the O-glycosylation level by generating new O-glycosites and increasing both O-glycan heterogeneity and intensities. Further molecular dynamics simulations reveal that the O-glycosylation on the protomer-interface regions, which are mainly modified by ppGalNAc-T6, can potentially stabilize the trimeric S protein structure. Our work provides deep molecular insights of how viral infection harnesses the host O-glycosyltransferases to dynamically regulate the O-glycosylation level of the viral envelope protein responsible for membrane fusion.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Zhijue Xu", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Xin Ku", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Jiaqi Tian", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Han Zhang", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Jingli Hou", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Can Zhang", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Jingjing Shi", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Yang Li", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Hiroyuki Kaji", - "author_inst": "National Institute of Advanced Industrial Science and Technology (AIST)" - }, - { - "author_name": "Sheng-ce Tao", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Atsushi Kuno", - "author_inst": "National Institute of Advanced Industrial Science and Technology (AIST)" - }, - { - "author_name": "Wei Yan", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Lin-Tai Da", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Yan Zhang", - "author_inst": "Shanghai Jiao Tong University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.04.06.437914", "rel_title": "Uneven growth of SARS-CoV-2 clones evidenced by more than 500,000 whole-genome sequences", @@ -812012,6 +816472,121 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.02.438288", + "rel_title": "An emerging SARS-CoV-2 mutant evading cellular immunity and increasing viral infectivity", + "rel_date": "2021-04-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.02.438288", + "rel_abs": "During the current SARS-CoV-2 pandemic that is devastating the modern societies worldwide, many variants that naturally acquire multiple mutations have emerged. Emerging mutations can affect viral properties such as infectivity and immune resistance. Although the sensitivity of naturally occurring SARS-CoV-2 variants to humoral immunity has recently been investigated, that to human leukocyte antigen (HLA)-restricted cellular immunity remains unaddressed. Here we demonstrate that two recently emerging mutants in the receptor binding domain of the SARS-CoV-2 spike protein, L452R (in B.1.427/429) and Y453F (in B.1.298), can escape from the HLA-24-restricted cellular immunity. These mutations reinforce the affinity to viral receptor ACE2, and notably, the L452R mutation increases protein stability, viral infectivity, and potentially promotes viral replication. Our data suggest that the HLA-restricted cellular immunity potentially affects the evolution of viral phenotypes, and the escape from cellular immunity can be a further threat of the SARS-CoV-2 pandemic.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC=\"FIGDIR/small/438288v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (45K):\norg.highwire.dtl.DTLVardef@153428forg.highwire.dtl.DTLVardef@136ca5aorg.highwire.dtl.DTLVardef@1ee490org.highwire.dtl.DTLVardef@2fe478_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Chihiro Motozono", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Mako Toyoda", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Jiri Zahradnik", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Terumasa Ikeda", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Akatsuki Saito", + "author_inst": "University of Miyazaki" + }, + { + "author_name": "Toong Seng Tan", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Isaac Ngare", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Hesham Nasser", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Izumi Kimura", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Keiya Uriu", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Yusuke Kosugi", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Shiho Torii", + "author_inst": "Osaka University" + }, + { + "author_name": "Akiko Yonekawa", + "author_inst": "Kyushu University" + }, + { + "author_name": "Nobuyuki Shimono", + "author_inst": "Kyushu University" + }, + { + "author_name": "Yoji Nagasaki", + "author_inst": "Kyushu Medical Center" + }, + { + "author_name": "Rumi Minami", + "author_inst": "Kyushu Medical Center" + }, + { + "author_name": "Takashi Toya", + "author_inst": "Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital" + }, + { + "author_name": "Noritaka Sekiya", + "author_inst": "Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital" + }, + { + "author_name": "Takasuke Fukuhara", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Yoshiharu Matsuura", + "author_inst": "Osaka University" + }, + { + "author_name": "Gideon Schreiber", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "- The Genotype to Phenotype Japan (G2P-Japan) consortium", + "author_inst": "-" + }, + { + "author_name": "So Nakagawa", + "author_inst": "Tokai University School of Medicine" + }, + { + "author_name": "Takamasa Ueno", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Kei Sato", + "author_inst": "Institute of Medical Science, The University of Tokyo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.04.438420", "rel_title": "Rational Selection of PCR Primer/Probe Design Sites for SARS-CoV-2", @@ -812173,61 +816748,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.19.21253989", - "rel_title": "Comprehensive assessment of humoral response after Pfizer BNT162b2 mRNA Covid-19 vaccination: a three-case series", - "rel_date": "2021-04-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253989", - "rel_abs": "BackgroundSince universal vaccination is a pillar against coronavirus disease 2019 (COVID-19), monitoring anti-SARS-CoV-2 neutralizing antibodies is essential for deciphering post-vaccination immune response.\n\nMethodsThree healthcare workers received 30 g BNT162b2 mRNA Covid-19 Vaccine, followed by a second identical dose, 21 days afterwards. Venous blood was drawn at baseline and at serial intervals, up to 63 days afterwards, for assessing total immunoglobulins (Ig) anti-RBD (receptor binding domain), IgG anti-S1/S2, IgG anti-RBD, IgM anti-RBD, IgM anti-N/S1 and IgA anti-S1.\n\nResultsAll subjects were SARS-CoV-2 seronegative at baseline. Total Ig anti-RBD, IgG anti-S1/S2 and IgG anti-RBD levels increased between 91-368 folds until 21 days after the first vaccine dose, then reached a plateau. The levels raised further after the second dose (by [~]30-, [~]8- and [~]8-fold, respectively), peaking at day 35, but then slightly declining and stabilizing [~]50 days after the first dose. IgA anti-S1 levels increased between 7-11 days after the first dose, slightly declined before the second dose, after which levels augmented by [~]24-fold from baseline. The anti-RBD and anti-N/S1 IgM kinetics were similar to that of anti-S1 IgA, though displaying substantially weaker increases and modest peaks, only 4 to 7-fold higher than baseline. Highly significant inter-correlation was noted between total Ig anti-RBD, anti-S1/S2 and anti-RBD IgG (all r=0.99), whilst other anti-SARS-CoV-2 antibodies displayed lower, though still significant, correlations. Serum spike protein concentration was undetectable at all time points.\n\nConclusionsBNT162b2 mRNA vaccination generates a robust humoral immune response, especially involving IgG and IgA, magnified by the second vaccine dose.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Elisa Danese", - "author_inst": "Section of Clinical Biohemistry, University of Verona" - }, - { - "author_name": "Martina Montagnana", - "author_inst": "Section of Clinical Biohemistry, University of Verona" - }, - { - "author_name": "Gian Luca Salvagno", - "author_inst": "Section of Clinical Biohemistry, University of Verona" - }, - { - "author_name": "Matteo Gelati", - "author_inst": "Section of Clinical Biohemistry, University of Verona" - }, - { - "author_name": "Denise Peserico", - "author_inst": "Section of Clinical Biohemistry, University of Verona" - }, - { - "author_name": "Laura Pighi", - "author_inst": "Section of Clinical Biochemistry, University of Verona" - }, - { - "author_name": "Simone De Nitto", - "author_inst": "Section of Clinical Biochemistry, University of Verona" - }, - { - "author_name": "Brandon Michael Henry", - "author_inst": "Cincinnati Children's Hospital Medical Center" - }, - { - "author_name": "Stefano Porru", - "author_inst": "Section of Occupational Medicine, University of Verona" - }, - { - "author_name": "Giuseppe Lippi", - "author_inst": "Section of Clinical Biochemistry, University of Verona" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.30.21254353", "rel_title": "Using PARIHS framework to design a community-based COVID-19 intervention in rural Ghana", @@ -813858,6 +818378,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.02.438155", + "rel_title": "An immunoinformatics approach to study the epitopes contributed by Nsp13 of SARS-CoV-2", + "rel_date": "2021-04-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.02.438155", + "rel_abs": "The on-going coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2 has infected hundreds of millions of people and killed more than two million people worldwide. Currently, there are no effective drugs available for treating SARS-CoV-2 infections; however, vaccines are now being administered worldwide to control this virus. In this study, we have studied SARS-CoV-2 helicase, Nsp13, which is critical for viral replication. We compared the Nsp13 sequences reported from India with the first reported sequence from Wuhan province, China to identify and characterize the mutations occurring in this protein. To correlate the functional impact of these mutations, we characterised the most prominent B cell and T cell epitopes contributed by Nsp13. Our data revealed twenty-one epitopes, which exhibited high antigenicity, stability and interactions with MHC class-I and class-II molecules. Subsequently, the physiochemical properties of these epitopes were also analysed. Furthermore, several of these Nsp13 epitopes harbour mutations, which were further characterised by secondary structure and per-residue disorderness, stability and dynamicity predictions. Altogether, we report the candidate epitopes of Nsp13 that may help the scientific community to understand the evolution of SARS-CoV-2 variants and their probable implications.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sushant Kumar", + "author_inst": "Patna University" + }, + { + "author_name": "Gajendra Kumar Azad", + "author_inst": "Patna University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.04.02.438204", "rel_title": "Discovery and in-vitro evaluation of potent SARS-CoV-2 entry inhibitors", @@ -813983,41 +818526,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, - { - "rel_doi": "10.1101/2021.03.29.21254233", - "rel_title": "Estimating the strength of selection for new SARS-CoV-2 variants", - "rel_date": "2021-04-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254233", - "rel_abs": "Controlling the SARS-CoV-2 pandemic becomes increasingly challenging as the virus adapts to human hosts through the continual emergence of more transmissible variants. Simply observing that a variant is increasing in frequency is relatively straightforward, but more sophisticated methodology is needed to determine whether a new variant is a global threat and the magnitude of its selective advantage. We present three methods for quantifying the strength of selection for new and emerging variants of SARS-CoV-2 relative to the background of contemporaneous variants. These methods range from a detailed model of dynamics within one country to a broad analysis across all countries, and they include alternative explanations such as migration and drift. We find evidence for strong selection favoring the D614G spike mutation and B.1.1.7 (Alpha), weaker selection favoring B.1.351 (Beta), and no advantage of R.1 after it spreads beyond Japan. Cutting back data to earlier time horizons reveals large uncertainty very soon after emergence, but that estimates of selection stabilize after several weeks. Our results also show substantial heterogeneity among countries, demonstrating the need for a truly global perspective on the molecular epidemiology of SARS-CoV-2.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Christiaan H van Dorp", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Emma E Goldberg", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Nicolas Hengartner", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Ruian Ke", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Ethan Obie Romero-Severson", - "author_inst": "Los Alamos National Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.30.21254652", "rel_title": "Short-term antibody response and tolerability of one dose of BNT162b2 vaccine in patients receiving hemodialysis", @@ -816012,6 +820520,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.28.21254496", + "rel_title": "SARS-CoV-2 infections in children and adolescents with rheumatic musculoskeletal diseases: data from the National Pediatric Rheumatology Database in Germany", + "rel_date": "2021-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.28.21254496", + "rel_abs": "ObjectivesDue to their underlying disease as well as therapeutic immunosuppression, children and adolescents with rheumatic and musculoskeletal diseases (RMD) may be at higher risk for a severe course or worse outcome of COVID-19, and SARS-CoV2 infection may trigger a flare of the RMD. To address these issues, a specific SARS-CoV-2 questionnaire was implemented in the National Pediatric Rheumatology Database (NPRD) in Germany.\n\nMethodsDemographic, clinical and treatment data from juvenile patients with RMD as well as data about SARS-CoV-2 infection like test date and method, clinical characteristics, disease course, outcome and impact on the disease activity of the RMD documented on this questionnaire were analyzed.\n\nResultsFrom April 17th, 2020, to February 14th, 2021, data were collected from 79 patients (53% female) with RMD with median age of 14 years, diagnosed with juvenile idiopathic arthritis (57%), autoinflammatory (23%) and connective tissue disease (8%). Sixty-one patients (77%) received disease-modifying antirheumatic drugs (DMARDs), 43% biologic DMARDs, and 9% systemic glucocorticoids. Sixty patients (76%) developed symptoms of COVID-19. Disease severity was mild and outcome was good in the majority of patients. Two patients were hospitalized, one of whom required intensive care and died of cardiorespiratory failure. In 84% of SARS-CoV-2-positive patients, no relevant increase in disease activity of the RMD was observed.\n\nConclusionsIn our cohort, COVID-19 in juvenile patients with RMD under various medications was mild with good outcome in the majority of cases. SARS-CoV-2 infection does not appear to have a relevant impact on disease activity of the underlying condition.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Claudia Sengler", + "author_inst": "German Rheumatism Research Center, Epidemiology Unit, Berlin, Germany" + }, + { + "author_name": "Sascha Eulert", + "author_inst": "German Rheumatism Research Center, Epidemiology Unit, Berlin, Germany" + }, + { + "author_name": "Martina Niewerth", + "author_inst": "German Rheumatism Research Center, Epidemiology Unit, Berlin, Germany" + }, + { + "author_name": "Kirsten Minden", + "author_inst": "German Rheumatism Research Center, Epidemiology Unit, Berlin, Germany" + }, + { + "author_name": "Gerd Horneff", + "author_inst": "Asklepios Klinik St. Augustin, Allgemeine Kinder- und Jugendmedizin, Sankt Augustin, Germany" + }, + { + "author_name": "Jasmin B Kuemmerle-Deschner", + "author_inst": "Tuebingen University Hospital, Department of Pediatric and Adolescent Medicine, Tuebingen, Germany" + }, + { + "author_name": "Caroline Siemer", + "author_inst": "Deutsches Zentrum fuer Kinder- und Jugendrheumatologie, Garmisch-Partenkirchen, Germany" + }, + { + "author_name": "Rainer Berendes", + "author_inst": "Kinderkrankenhaus St. Marien, Landshut, Germany" + }, + { + "author_name": "Hermann Girschick", + "author_inst": "Krankenhaus im Friedrichshain, Klinik fuer Kinder- und Jugendmedizin, Berlin, Germany" + }, + { + "author_name": "Regina Huehn", + "author_inst": "Universitaetsklinikum Halle (Saale), Klinik fuer Kinder- und Jugendmedizin, Haale (Saale), Germany" + }, + { + "author_name": "Michael Borte", + "author_inst": "Klinikum St. Georg, Klinik fuer Kinder- und Jugendmedizin, Leipzig, Germany" + }, + { + "author_name": "Anton Hospach", + "author_inst": "Olgahospital and Women`s Clinic, Paediatrie 2 - Allgemeine und spezielle Paediatrie, Stuttgart, Germany" + }, + { + "author_name": "Wolfgang Emminger", + "author_inst": "Universitaetskinderklinik Wien, Wien, Austria" + }, + { + "author_name": "Jakob Peter Armann", + "author_inst": "University Hospital and Medical Faculty Carl Gustav Carus, Technische Uni" + }, + { + "author_name": "Ariane Klein", + "author_inst": "Asklepios Klinik St. Augustin, Allgemeine Kinder- und Jugendmedizin, Sankt Augustin, Germany" + }, + { + "author_name": "Tilmann Kallinich", + "author_inst": "Charite - Universitaetsmedizin Berlin, Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Berlin, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2021.03.29.21254538", "rel_title": "Half year longitudinal seroprevalence of SARS-CoV-2-antibodies and rule compliance in German hospital employees", @@ -816185,33 +820772,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2021.03.29.21254589", - "rel_title": "Impact of COVID-19 pandemic on rare diseases- A case study on thalassaemia patients in Bangladesh", - "rel_date": "2021-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254589", - "rel_abs": "ObjectivesThalassaemia is a life-threatening rare disease, which requires regular blood transfusion and medical care. The information on how thalassaemia patients are affected during the unprecedented COVID-19 crisis is scarce. This study aimed to assess the impact of the COVID-19 pandemic on the blood transfusion and healthcare access of thalassaemia patients at the community level in Bangladesh.\n\nMethodsA cross-sectional study was conducted among thalassaemia patients registered in a community-based thalassaemia registry in Jamapur, Bangladesh.\n\nResultsAs compared to pre-COVID-19 time, the number of blood transfusions among patients under the thalassaemia registry was significantly reduced during COVID-19 pandemic (190 units versus 81 units). In addition, the median number of red cell transfusions per patient was dropped significantly from 4 units to one unit. Over 80% of patient had no access to healthcare services at all during the early phase of the pandemic.\n\nConclusionsEmergency response with appropriate mitigative measures must be a priority for addressing an acute shortage of blood supply in situations like COVID-19 pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mohammad Sorowar Hossain", - "author_inst": "Biomedical Research Foundation, Dhaka, Bangladesh" - }, - { - "author_name": "Farhana Runa", - "author_inst": "Biomedical Research Foundation, Dhaka, Bangladesh" - }, - { - "author_name": "Abdullah Al Mosabbir", - "author_inst": "Biomedical Research Foundation, Dhaka, Bangladesh" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2021.03.29.21254563", "rel_title": "Improved performance of saliva for the detection of the B.1.351 variant in South Africa", @@ -817538,6 +822098,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.29.21254590", + "rel_title": "Use of portable air cleaners to reduce aerosol transmission on a hospital COVID-19 ward", + "rel_date": "2021-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254590", + "rel_abs": "ObjectiveTo study the airflow, transmission and clearance of aerosols in the clinical spaces of a hospital ward that had been used to care for patients with COVID-19, and to examine the impact of portable air cleaners on aerosol clearance.\n\nDesignObservational study\n\nSettingA single ward of a tertiary public hospital in Melbourne Australia\n\nInterventionGlycerine-based aerosol was used as a surrogate for respiratory aerosols. The transmission of aerosols from a single patient room into corridors and a nurses station in the ward was measured. The rate of clearance of aerosols was measured over time from the patient room, nurses station and ward corridors with and without air cleaners (also called portable HEPA filters).\n\nResultsAerosols rapidly travelled from the patient room into other parts of the ward. Air cleaners were effective in increasing the clearance of aerosols from the air in clinical spaces and reducing their spread to other areas. With two small domestic air cleaners in a single patient room of a hospital ward, 99% of aerosols could be cleared within 5.5 minutes.\n\nConclusionAir cleaners may be useful in clinical spaces to help reduce the risk of healthcare acquired acquisition of respiratory viruses that are transmitted via aerosols. They are easy to deploy and are likely to be cost effective in a variety of healthcare settings", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Kirsty Lee Buising", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Robyn Schofield", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Louis Irving", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Melita Keywood", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + }, + { + "author_name": "Ashley Stevens", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Nick Keogh", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Grant Skidmore", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Imogen Wadlow", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Kevin Kevin", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Behzad Rismanchi", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Amanda Wheeler", + "author_inst": "Australian Catholic University" + }, + { + "author_name": "Ruhi Humphries", + "author_inst": "Commonwealth Scientific and Industrial research Organization" + }, + { + "author_name": "Marion Kainer", + "author_inst": "Western Health" + }, + { + "author_name": "Forbes McGain", + "author_inst": "Western Health" + }, + { + "author_name": "Jason Monty", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Caroline Marshall", + "author_inst": "The University of Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.29.21254509", "rel_title": "Genetic associations with severe COVID-19", @@ -817659,33 +822298,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.31.437823", - "rel_title": "Linking Diabetes mellitus to SARS-CoV-2 infection through differential targeting of the microRNAs in the Pancreas tissue", - "rel_date": "2021-03-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.31.437823", - "rel_abs": "Coronavirus Disease 2019 (COVID-19) severity and Diabetes mellitus affect each other bidirectionally. The plus-sense single-stranded RNA (+ssRNA) genome of the SARS-CoV-2 virus can be targeted and suppressed by the host cells microRNAs (miRNAs). Using the differential gene expression analysis between the mock-infected and the SARS-CoV-2-infected pancreatic tissue, we report five Diabetes-associated genes that are upregulated due to SARS-CoV-2 infection in the hESC pancreas tissues. Ten miRNAs regulating these five genes can potentially target the SARS-CoV-2 genome. We hypothesize that the SARS-CoV-2 genome copies in the infected human pancreas cell compete with the host cells native genes in being regulated by the native miRNAs. It leads to the reduced miRNA-regulation and, thus, the upregulation of the Diabetes-associated native genes. Thus, the resultant new-onset or elevated Diabetic symptoms may worsen the condition of COVID-19 patients.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Bhavya", - "author_inst": "Bioinformatics, MMV, Institute of Science, Banaras Hindu University" - }, - { - "author_name": "Ekta Pathak", - "author_inst": "Bioinformatics, MMV, Institute of Science, Banaras Hindu University" - }, - { - "author_name": "Rajeev Mishra", - "author_inst": "Bioinformatics, MMV, Institute of Science, Banaras Hindu University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.03.31.437907", "rel_title": "A spatial multi-scale fluorescence microscopy toolbox discloses entry checkpoints of SARS-CoV-2 variants in VeroE6 cells", @@ -819364,6 +823976,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.27.21254480", + "rel_title": "Assessing the impact of widespread respirator use in curtailing COVID-19 transmission in the United States", + "rel_date": "2021-03-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.27.21254480", + "rel_abs": "Dynamic models are used to assess the impact of three types of face masks-cloth masks, surgical/procedure masks and respirators-in controlling the COVID-19 pandemic in the United States. We showed that the pandemic would have failed to establish in the US if a nationwide mask mandate, based on using respirators with moderately-high compliance, had been implemented during the first two months of the pandemic. The other mask types would fail to prevent the pandemic from becoming established. When mask usage compliance is low to moderate, respirators are far more effective in reducing disease burden. Using data from the third wave, we showed that the epidemic could be eliminated in the US if at least 40% of the population consistently wore respirators in public. Surgical masks can also lead to elimination, but requires compliance of at least 55%. Daily COVID-19 mortality could be eliminated in the US by June or July 2021 if 95% of the population opted for either respirators or surgical masks from the beginning of the third wave. We showed that the prospect of effective control or elimination of the pandemic using mask-based strategy is greatly enhanced if combined with other nonpharmaceutical interventions (NPIs) that significantly reduce the baseline community transmission. By slightly modifying the model to include the effect of a vaccine against COVID-19 and waning vaccine-derived and natural immunity, this study shows that the waning of such immunity could trigger multiple new waves of the pandemic in the US. The number, severity and duration of the projected waves depend on the quality of mask type used and the level of increase in the baseline levels of other NPIs used in the community during the onset of the third wave of the pandemic in the US. Specifically, no severe fourth or subsequent wave of the pandemic will be recorded in the US if surgical masks or respirators are used, particularly if the mask-use strategy is combined with an increase in the baseline levels of other NPIs. This study further emphasizes the role of human behavior towards masking on COVID-19 burden, and highlights the urgent need to maintain a healthy stockpile of highly-effective respiratory protection, particularly respirators, to be made available to the general public in times of future outbreaks or pandemics of respiratory diseases that inflict severe public health and socio-economic burden on the population.\n\nAuthor summaryWe developed and used dynamic models to assess the role of highly-effective face coverings on the control and mitigation of the COVID-19 pandemic in the US. The study indicates that implementing and sustaining mask mandates is useful in containing diseases like COVID-19. Additionally, the study suggests that prioritizing the use of respirators is more effective in combating the disease than using other mask types. Specifically, the COVID-19 pandemic would have been prevented from being established in the US if four in every five Americans started wearing respirators during the first two months of the pandemic. The study further shows that COVID-19 can be eliminated in the US if a universal masking strategy that emphasizes respirators, requiring only 23% compliance, is combined with other nonpharmaceutical interventions that can reduce community transmission by 20%. Furthermore, the daily COVID-19 death rate can be completely suppressed by June 2021 if 95% of the population consistently use respirators. The elimination will extend to January 2022 if cloth masks were adopted instead. We conclude that stockpiling and distributing highly-efficient face coverings, notably respirators, will be vital in effectively curtailing future epidemics and pandemics of respiratory diseases.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Calistus N Ngonghala", + "author_inst": "University of Florida" + }, + { + "author_name": "James R Knitter", + "author_inst": "The University of Arizona, College of Medicine, Tucson" + }, + { + "author_name": "Lucas Marinacci", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Matthew H Bonds", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Abba B Gumel", + "author_inst": "Arizona State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.26.21254429", "rel_title": "Forecasting the Spreading Trajectory of the COVID-19 Pandemic", @@ -819493,69 +824140,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.26.21253712", - "rel_title": "A Novel Diagnostic Test to Screen SARS-CoV-2 Variants Containing E484K and N501Y Mutations", - "rel_date": "2021-03-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21253712", - "rel_abs": "Spike protein mutations E484K and N501Y carried by SARS-CoV-2 variants have been associated with concerning changes of the virus, including resistance to neutralizing antibodies and increased transmissibility. While the concerning variants are fast spreading in various geographical areas, identification and monitoring of these variants is lagging far behind, due in large part to the slow speed and insufficient capacity of viral sequencing. In response to the unmet need for a fast and efficient screening tool, we developed a single-tube duplex molecular assay for rapid and simultaneous identification of E484K and N501Y mutations from nasopharyngeal swab (NS) samples within 2.5 h from sample preparation to report. Using this tool, we screened a total of 435 clinical NS samples collected from COVID patients at 8 hospitals within the Hackensack Meridian Health network in New Jersey. While B.1.351 and P.1 variants were absent from the current study, our data revealed a dramatic increase in the frequency of E484K over time, underscoring the need for continuous epidemiological monitoring.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Yanan Zhao", - "author_inst": "CDI, hackensack meridian health" - }, - { - "author_name": "Annie Lee", - "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health" - }, - { - "author_name": "Kaelea Composto", - "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health" - }, - { - "author_name": "Marcus H Cunninghan", - "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health" - }, - { - "author_name": "Jose R Mediavilla", - "author_inst": "Hackensack Meridian Health Center for Discovery and Innovation" - }, - { - "author_name": "Samantha Fennessey", - "author_inst": "New York Genomic Center" - }, - { - "author_name": "Andre Corvelo", - "author_inst": "New York Genomic Center" - }, - { - "author_name": "Kar Fai Chow", - "author_inst": "Hackensack University Medical Center" - }, - { - "author_name": "Michael C Zody", - "author_inst": "New York Genomic Center" - }, - { - "author_name": "Liang Chen", - "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health" - }, - { - "author_name": "Barry N. Kreiswirth", - "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health" - }, - { - "author_name": "David S Perlin", - "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.27.21254483", "rel_title": "Relative burdens of the COVID-19, malaria, tuberculosis and HIV/AIDS epidemics in sub-Saharan Africa in 2020", @@ -821150,6 +825734,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.26.21254427", + "rel_title": "Assessment of serological assays for identifying high titer convalescent plasma", + "rel_date": "2021-03-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254427", + "rel_abs": "The COVID-19 pandemic has been accompanied by the largest mobilization of therapeutic convalescent plasma (CCP) in over a century. Initial identification of high titer units was based on dose-response data using the Ortho VITROS IgG assay. The proliferation of SARS-CoV-2 serological assays and non-uniform application has led to uncertainty about their interrelationships. The purpose of this study was to establish correlations and analogous cutoffs between commercially available serological tests (Ortho, Abbott, Roche), a spike ELISA, and a virus neutralization assay using convalescent plasma from a cohort of 79 donors from April 2020. Relationships relative to FDA-approved cutoffs under the CCP EUA were identified by linear regression and receiver operator characteristic curves. Relative to the Ortho VITROS assay, the r2 of the Abbott, Roche, the anti-Spike ELISA and the neutralizing assay were 0.58, 0.5, 0.82, and 0.44, respectively. The best correlative index for establishing high-titer units was 3.82 S/C for the Abbott, 10.89 COI for the Roche, 1:1,202 for the anti-Spike ELISA, and 1:200 by the neutralization assay. The overall agreement using derived cutoffs compared to the CCP EUA Ortho VITROS cutoff of 9.5 was 92.4% for Abbott, 84.8% for Roche, 87.3% for the anti-S ELISA and 78.5% for the neutralization assay. Assays based on antibodies against the nucleoprotein (Roche, Abbott) and neutralizing antibody tests were positively associated with the Ortho assay, although their ability to distinguish FDA high-titer specimens was imperfect. The resulting relationships help reconcile results from the large body of serological data generated during the COVID-19 pandemic.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Christopher W. Farnsworth", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Brett Case", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Karl Hock", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Rita E Chen", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Jane O'Halloran", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Rachel Presti", + "author_inst": "Wash U" + }, + { + "author_name": "Charles William Goss", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Adriana M Rauseo", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Ali Ellebedy", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Elitza S Theel", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Michael Diamond", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Jeffrey P Henderson", + "author_inst": "Washington University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.27.21254471", "rel_title": "Estimation of SARS-CoV-2 antibody prevalence through integration of serology and incidence data", @@ -821255,65 +825902,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.03.26.21254367", - "rel_title": "Emergence of a SARS-CoV-2 E484K variant of interest in Arizona", - "rel_date": "2021-03-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254367", - "rel_abs": "SARS-CoV-2 is locked in a high-stakes arms race between the dynamics of rising population immunity and escape mutations. The E484K mutation in the spike protein reduces neutralization by post-vaccination sera and monoclonal antibody therapeutics. We detected the emergence of an E484K harboring variant B.1.243.1 from a common circulating variant (B.1.243) in the United States. In contrast to other instances when the E484K mutation was acquired independently in the parental lineage, genomic surveillance indicates that the B.1.243.1 variant of interest is in the process of being established in Arizona and beginning to cross state borders to New Mexico and Texas. Genomic, epidemiologic and phylogenetic evidence indicates that the B.1.243.1 variant of interest is poised to emerge. These findings demonstrate the critical need to continue tracking SARS-CoV-2 in real-time to inform public health strategies, diagnostics, medical countermeasures and vaccines.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Peter T Skidmore", - "author_inst": "Arizona State University" - }, - { - "author_name": "Emily A Kaelin", - "author_inst": "Arizona State University" - }, - { - "author_name": "LaRinda A Holland", - "author_inst": "Arizona State University" - }, - { - "author_name": "Rabia Maqsood", - "author_inst": "Arizona State University" - }, - { - "author_name": "Lily I Wu", - "author_inst": "Arizona State University" - }, - { - "author_name": "Nicholas J Mellor", - "author_inst": "Arizona State University" - }, - { - "author_name": "Joy M Blain", - "author_inst": "Arizona State University" - }, - { - "author_name": "Valerie Harris", - "author_inst": "Arizona State University" - }, - { - "author_name": "Joshua LaBaer", - "author_inst": "Arizona State University" - }, - { - "author_name": "Vel Murugan", - "author_inst": "Arizona State University" - }, - { - "author_name": "Efrem S Lim", - "author_inst": "Arizona State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.24.21254277", "rel_title": "Emergence and spread of SARS-CoV-2 lineages B.1.1.7 and P.1 in Italy", @@ -823036,6 +827624,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.17.21253847", + "rel_title": "Femtomolar SARS-CoV-2 Antigen Detection Using the Microbubbling Digital Assay with Smartphone Readout Enables Antigen Burden Quantitation and Dynamics Tracking", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253847", + "rel_abs": "BackgroundLittle is known about the dynamics of SARS-CoV-2 antigen burden in respiratory samples in different patient populations at different stages of infection. Current rapid antigen tests cannot quantitate and track antigen dynamics with high sensitivity and specificity in respiratory samples.\n\nMethodsWe developed and validated an ultra-sensitive SARS-CoV-2 antigen assay with smartphone readout using the Microbubbling Digital Assay previously developed by our group, which is a platform that enables highly sensitive detection and quantitation of protein biomarkers. A computer vision-based algorithm was developed for microbubble smartphone image recognition and quantitation. A machine learning-based classifier was developed to classify the smartphone images based on detected microbubbles. Using this assay, we tracked antigen dynamics in serial swab samples from COVID patients hospitalized in ICU and immunocompromised COVID patients.\n\nResultsThe limit of detection (LOD) of the Microbubbling SARS-CoV-2 Antigen Assay was 0.5 pg/mL (10.6 fM) recombinant nucleocapsid (N) antigen or 4000 copies/mL inactivated SARS-CoV-2 virus in nasopharyngeal (NP) swabs, comparable to many rRT-PCR methods. The assay had high analytical specificity towards SARS-CoV-2. Compared to EUA-approved rRT-PCR methods, the Microbubbling Antigen Assay demonstrated a positive percent agreement (PPA) of 97% (95% confidence interval (CI), 92-99%) in symptomatic individuals within 7 days of symptom onset and positive SARS-CoV-2 nucleic acid results, and a negative percent agreement (NPA) of 97% (95% CI, 94-100%) in symptomatic and asymptomatic individuals with negative nucleic acid results. Antigen positivity rate in NP swabs gradually decreased as days-after-symptom-onset increased, despite persistent nucleic acid positivity of the same samples. The computer vision and machine learning-based automatic microbubble image classifier could accurately identify positives and negatives, based on microbubble counts and sizes. Total microbubble volume, a potential marker of antigen burden, correlated inversely with Ct values and days-after-symptom-onset. Antigen was detected for longer periods of time in immunocompromised patients with hematologic malignancies, compared to immunocompetent individuals. Simultaneous detectable antigens and nucleic acids may indicate the presence of replicating viruses in patients with persistent infections.\n\nConclusionsThe Microbubbling SARS-CoV-2 Antigen Assay enables sensitive and specific detection of acute infections, and quantitation and tracking of antigen dynamics in different patient populations at various stages of infection. With smartphone compatibility and automated image processing, the assay is well-positioned to be adapted for point-of-care diagnosis and to explore the clinical implications of antigen dynamics in future studies.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Hui Chen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Zhao Li", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sheng Feng", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Anni Wang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Melissa Richard-Greenblatt", + "author_inst": "Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania" + }, + { + "author_name": "Emily Hutson", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Stefen Andrianus", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Laurel Glaser", + "author_inst": "Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania" + }, + { + "author_name": "Kyle G Rodino", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jianing Qian", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Dinesh Jayaraman", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ronald Collman", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Abigail L Glascock", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Frederic Bushman", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jae Seung Lee", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sara Cherry", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Alejandra Fausto", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Susan R Weiss", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Hyun Koo", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Patricia M Corby", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Una ODoherty", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Alfred L Garfall", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Dan T Vogl", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Edward A Stadtmauer", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ping Wang", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.21.21254061", "rel_title": "Quantitative SARS-CoV-2 anti-spike responses to Pfizer-BioNTech and Oxford-AstraZeneca vaccines by previous infection status", @@ -823269,105 +827972,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.03.21.21254072", - "rel_title": "Hyperglycemia in Acute COVID-19 is Characterized by Adipose Tissue Dysfunction and Insulin Resistance", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.21.21254072", - "rel_abs": "COVID-19 has proven to be a metabolic disease resulting in adverse outcomes in individuals with diabetes or obesity. Patients infected with SARS-CoV-2 and hyperglycemia suffer from longer hospital stays, higher risk of developing acute respiratory distress syndrome (ARDS), and increased mortality compared to those who do not develop hyperglycemia. Nevertheless, the pathophysiological mechanism(s) of hyperglycemia in COVID-19 remains poorly characterized. Here we show that insulin resistance rather than pancreatic beta cell failure is the prevalent cause of hyperglycemia in COVID-19 patients with ARDS, independent of glucocorticoid treatment. A screen of protein hormones that regulate glucose homeostasis reveals that the insulin sensitizing adipokine adiponectin is reduced in hyperglycemic COVID-19 patients. Hamsters infected with SARS-CoV-2 also have diminished expression of adiponectin. Together these data suggest that adipose tissue dysfunction may be a driver of insulin resistance and adverse outcomes in acute COVID-19.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Moritz Reiterer", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Mangala Rajan", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Nicolas Gomez-Banoy", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Jennifer D Lau", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Luis G Gomez-Escobar", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Ankit Gilani", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Sergio Alvarez-Mullet", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Evan T Sholle", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Vasuretha Chandar", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Yaron Bram", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Katherine Hoffman", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Alfonso Rubio-Navarro", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Skyler Uhl", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Alpana P Shukla", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Parag Goyal", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Benjamin R tenOever", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Laura Alonso", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Robert E Schwartz", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Edward J Schenck", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Monika M Safford", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "James C Lo", - "author_inst": "Weill Cornell Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2021.03.21.21253968", "rel_title": "Characteristics of Long Covid: findings from a social media surve", @@ -825010,6 +829614,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.23.21254169", + "rel_title": "COVID-19 antibody seroprevalence in Duhok, Kurdistan Region, Iraq: A population-based study", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254169", + "rel_abs": "ObjectiveThis population-based study aimed to evaluate the seroprevalence of antibodies to SARS-CoV-2 in Duhok City, Kurdistan Region of Iraq.\n\nMethodsWe analyzed the national COVID-19 database that contains data regarding COVID-19 testing, management, and clinical outcomes in Duhok. For this study, different subdistricts within each district of Duhok were considered distinct clusters. Blood samples were collected from and questionnaires were administered to eligible and consenting participants who were members of different families from the subdistricts. Immunoassays were conducted to detect antibodies against SARS-CoV-2, and the associations between certain variables were investigated.\n\nResultsThe average number cases of COVID-19 before November 2020 was 23141 {+/-} 4364, which was significantly higher than the average number of cases between November 2020 and February 2021 (3737 {+/-} 2634; P = 0.001). A total of 743 individuals agreed to participate and were enrolled in the study. Among the participants, 465/743 (62.58%) were found to have antibodies against severe acute respiratory syndrome coronavirus 2. Among the participants with antibodies, 262/465 (56.34%) denied having any history of COVID-19-related symptoms. The most common symptom was fever (81.77%), followed by myalgia (81.28%). We found that antibody levels increased steadily with age (Pearson correlation coefficient = 0.117; P = 0.012). A significant association was found between antibody levels and the presence of symptoms (P = 0.023; odds ratio = 1.0023; 95% confidence interval = 1.0002-1.0061).\n\nConclusionsA significant reduction in the number of COVID-19 cases was observed. This might be due to the high prevalence of SARS-CoV-2 antibodies in Duhok. However, infection-prevention measures should be followed as it remains unclear whether acquired immunity is protective against reinfection. It expected that the infection rates during the next wave will not be as high as the first wave due to the high infection rate in the society.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Nawfal R Hussein", + "author_inst": "Department of Biomolecular Sciences, College of Medicine, University of Zakho" + }, + { + "author_name": "Amer Balatay", + "author_inst": "Department of pharmacology and clinical pharmacy, College of pharmacy, University of Duhok, Kurdistan Region, Iraq" + }, + { + "author_name": "Ibrahim A Naqid", + "author_inst": "Department of Biomedical Sciences, College of Medicine, University of Zakho, Kurdistan Region, Iraq" + }, + { + "author_name": "Shakir A Jamal", + "author_inst": "Department of Biomedical Sciences, College of Medicine, University of Zakho, Kurdistan Region, Iraq" + }, + { + "author_name": "Narin A Rasheed", + "author_inst": "Akre Technical Institute, Duhok Polytechnic University, Duhok, Kurdistan Region, Iraq" + }, + { + "author_name": "Alind N Ahmed", + "author_inst": "Azadi Teaching Hospital, Duhok, Kurdistan Region of Iraq" + }, + { + "author_name": "Reving S Salih", + "author_inst": "Azadi Teaching Hospital, Duhok, Kurdistan Region of Iraq" + }, + { + "author_name": "Ahmed S Mahdi", + "author_inst": "Childhood Friends Hospital of Amedi, Kurdistan Region of Iraq" + }, + { + "author_name": "Sabeeha A Mansour", + "author_inst": "Azadi Teaching Hospital, Duhok, Kurdistan Region of Iraq" + }, + { + "author_name": "Shaveen Mahdi", + "author_inst": "Duhok Maternity Hospital, Duhok, Kurdistan Region of Iraq" + }, + { + "author_name": "Nashwan Ibrahim", + "author_inst": "Department of Surgery, College of Medicine, University of Duhok, Kurdistan Region, Iraq" + }, + { + "author_name": "Dildar H Musa", + "author_inst": "Department of Surgery, College of Medicine, University of Duhok, Kurdistan Region, Iraq" + }, + { + "author_name": "Zana SM Saleem", + "author_inst": "Department of Medicine, College of Medicine, University of Duhok, Duhok, Kurdistan Region of Iraq" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.23.21253460", "rel_title": "Serological profiles of pan-coronavirus-specific responses in COVID-19 patients using a multiplexed electro-chemiluminescence-based testing platform", @@ -825167,49 +829838,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.23.21254054", - "rel_title": "Tocilizumab in hospitalized COVID-19 patients: A meta-analysis of randomized controlled trials", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254054", - "rel_abs": "BackgroundTo date, only dexamethasone has been shown to reduce mortality in COVID-19 patients. Tocilizumab has been recently added to the treatment guidelines for hospitalized COVID-19 patients, but data remains conflicting.\n\nMethodsElectronic databases such as MEDLINE, EMBASE and Cochrane central were searched from March 1, 2020, until February 28th, 2021, for randomized controlled trials evaluating the efficacy of tocilizumab in hospitalized COVID-19 patients. The outcomes assessed were all-cause mortality at 28 days, mechanical ventilation, and time to discharge.\n\nResultsEight studies (with 6,311 patients) were included in the analysis. In total, 3,267 patients received tocilizumab, and 3,044 received standard care/placebo. Pooled analysis showed a significantly decreased risk of all-cause mortality at 28 days (RR 0.90, 95% CI 0.83-0.97, p=0.009) and progression to mechanical ventilation (RR 0.79, 95% CI 0.70-0.90, p=0.0002) in the tocilizumab arm compared to standard therapy or placebo. In addition, there was a trend towards improved median time to hospital discharge (RR 1.18, 95% CI 1.05-1.34, p=0.007).\n\nConclusionsTocilizumab therapy improves outcomes of mortality and need for mechanical ventilation, in hospitalized patients with COVID-19 infection compared with standard therapy or placebo. Our findings suggest the efficacy of tocilizumab therapy in hospitalized COVID-19 patients and strengthen the concept that tocilizumab is a promising therapeutic intervention to improve mortality and morbidity in COVID-19 patients.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Vijairam Selvaraj", - "author_inst": "The Miriam Hospital" - }, - { - "author_name": "Mohammad Saud Khan", - "author_inst": "The Miriam Hospital" - }, - { - "author_name": "Chirag Bavishi", - "author_inst": "Rhode Island Hospital" - }, - { - "author_name": "Kwame Dapaah-Afriyie", - "author_inst": "The Miriam Hospital" - }, - { - "author_name": "Arkadiy Finn", - "author_inst": "The Miriam Hospital" - }, - { - "author_name": "Amos Lal", - "author_inst": "Mayo Clinic Rochester" - }, - { - "author_name": "Elefterios Mylonakis", - "author_inst": "Brown University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.23.21253885", "rel_title": "Expansion of Cytotoxic CD4+ T cells in the lungs in severe COVID-19", @@ -826552,6 +831180,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2021.03.23.21254207", + "rel_title": "Association between the physical work environment and work functioning impairment while working from home under the COVID-19 pandemic in Japanese workers", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254207", + "rel_abs": "ObjectiveThis study examined the relationship between the physical work environment and work functioning impairment while working from home in the context of rapid changes associated with the COVID-19 pandemic.\n\nMethodsThis cross-sectional study of internet monitors was conducted between December 22 and 26, 2020. Of a total of 33,302 participants, 5,760 who worked from home at least 1 day a month, excluding those who met the exclusion criteria, were included in the analysis. A binary subjective assessment of the physical work environment while working from home was used as an exposure factor. We examined 9 items related to the physical work environment, including level of illuminance and use of suitable desks and chairs, traditionally recommended for health and safety management when working at a desk. The number of non-conformities to 7 items was also used as an exposure factor. The presence of severe work functioning impairment was measured using the Work Functioning impairment Scale (WFun), a self-reported outcome measure of the degree of work functioning impairment. Odds ratios of severe work functioning impairment were estimated using mixed-effects logistic regression analysis with the prefecture of residence as a random effect.\n\nResultsMultivariate analysis showed that the odds ratio of severe work functioning impairment was significantly higher among those who indicated \"No\" to all recommended items except for \"I work at a desk/chair for office use.\" The highest odds ratio of work functioning impairment was associated with a \"No\" response to \"There is enough light to do my work\" (aOR: 2.02, 95%CI: 1.73-2.35, p<0.01). Our results also suggest the presence of a dose-response relationship between the number of non-conformities to recommendations for work environments while working from home and work functioning impairment.\n\nConclusionsOur findings suggest that it is important for both companies and individual workers to create a work environment that prevents negative health outcomes and improves productivity while working from home.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Makoto Okawara", + "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Tomohiro Ishimaru", + "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Seiichiro Tateishi", + "author_inst": "Department of Occupational Medicine, School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Ayako Hino", + "author_inst": "Department of Mental Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Mayumi Tsuji", + "author_inst": "Department of Environmental Health, School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Kazunori Ikegami", + "author_inst": "Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Masako Nagata", + "author_inst": "Department of Occupational Health Practice and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Jap" + }, + { + "author_name": "Shinya Matsuda", + "author_inst": "Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Yoshihisa Fujino", + "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.03.25.21254314", "rel_title": "Automatic identification of risk factors for SARS-CoV-2 positivity and severe clinical outcomes of COVID-19 using Data Mining and Natural Language Processing", @@ -826701,81 +831380,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.26.21254391", - "rel_title": "Vaccine effectiveness of the first dose of ChAdOx1 nCoV-19 and BNT162b2 against SARS-CoV-2 infection in residents of Long-Term Care Facilities (VIVALDI study)", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254391", - "rel_abs": "BackgroundThe effectiveness of SARS-CoV-2 vaccines in frail older adults living in Long-Term Care Facilities (LTCFs) is uncertain. We estimated protective effects of the first dose of ChAdOx1 and BNT162b2 vaccines against infection in this population.\n\nMethodsCohort study comparing vaccinated and unvaccinated LTCF residents in England, undergoing routine asymptomatic testing (8 December 2020 - 15 March 2021). We estimated the relative hazard of PCR-positive infection using Cox proportional hazards regression, adjusting for age, sex, prior infection, local SARS-CoV-2 incidence, LTCF bed capacity, and clustering by LTCF.\n\nResultsOf 10,412 residents (median age 86 years) from 310 LTCFs, 9,160 were vaccinated with either ChAdOx1 (6,138; 67%) or BNT162b2 (3,022; 33%) vaccines. A total of 670,628 person days and 1,335 PCR-positive infections were included. Adjusted hazard ratios (aHRs) for PCR-positive infection relative to unvaccinated residents declined from 28 days following the first vaccine dose to 0{middle dot}44 (0{middle dot}24, 0{middle dot}81) at 28-34 days and 0{middle dot}38 (0{middle dot}19, 0{middle dot}77) at 35-48 days. Similar effect sizes were seen for ChAdOx1 (aHR 0{middle dot}32 [0{middle dot}15-0{middle dot}66] and BNT162b2 (aHR 0{middle dot}35 [0{middle dot}17, 0{middle dot}71]) vaccines at 35-48 days. Mean PCR cycle threshold values were higher, implying lower infectivity, for infections [≥]28 days post-vaccination compared with those prior to vaccination (31{middle dot}3 vs 26{middle dot}6, p<0{middle dot}001).\n\nInterpretationThe first dose of BNT162b2 and ChAdOx1 vaccines was associated with substantially reduced SARS-CoV-2 infection risk in LTCF residents from 4 weeks to at least 7 weeks.\n\nFundingUK Government Department of Health and Social Care.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe conducted a systematic search for studies which evaluated SARS-CoV-2 vaccine effectiveness in residents of long-term care facilities (LTCFs) published between 01/01/2020 and 11/03/2021. We used variations of search terms for \"COVID-19\" AND \"vaccine effectiveness\" OR \"vaccine efficacy\" AND \"care homes\" OR \"long term care facilities\" OR \"older people\" on Ovid MEDLINE and MedRxiv. We identified one pre-print article regarding LTCFs in Denmark, which reported that a single dose of BNT162b was ineffective against SARS-CoV-2 infection in residents, however, participants received the second vaccine dose 24 days following the first dose on average, which is likely to be too soon to capture the protective effects of a single vaccine dose. Additionally, we identified two pre-print reports of studies evaluating vaccine effectiveness against symptomatic infection and hospitalisation amongst older adults in the community. The first of these found 81% vaccine effectiveness against COVID-19-related hospitalisation at 28-34 days following a single dose of BNT162b or ChAdOx1 in [≥]80-year-olds. The second of these found vaccine effectiveness against symptomatic infection of 60% at 28-34 days and 73% at 35+ days following a single dose of ChAdOx1 in [≥]70-year-olds. No studies were identified that focused on the effectiveness of a single vaccine dose against infection amongst LTCF residents at more than 4 weeks post-vaccination, a particularly important question in the context of the UK policy decision to extend the dose interval beyond 3 weeks.\n\nAdded value of this studyWe conducted a prospective cohort study of 10,412 residents aged [≥]65 years, from 310 LTCFs across England, to investigate the protective effect of the first dose of the ChAdOx1 and BNT162b vaccines against SARS-CoV-2 infection in frail older adults. We retrieved results from routine monthly PCR testing, as well as outbreak and clinical testing for SARS-CoV-2, thereby capturing data on asymptomatic as well as symptomatic infections, which we linked to vaccination records. We estimated vaccine effectiveness to be 56% (19-76%) at 28-34 days, and 62% (23-81%) at 35-48 days following a single dose of ChAdOx1 or BNT162. Our findings suggest that the risk of SARS-CoV-2 infection is substantially reduced from 28 days following the first dose of either vaccine and that this effect is maintained for at least 7 weeks, with similar protection offered by both vaccine types. We also found that PCR cycle threshold (Ct) values, which are negatively associated with the ability to isolate virus, were significantly higher in infections occurring at [≥] 28days post vaccination compared to those occurring in the unvaccinated period, suggesting that vaccination may reduce onward transmission of SARS-CoV-2 in breakthrough infections. To the best of our knowledge, our findings constitute the first real-world evidence on vaccine effectiveness against infection for ChAdOx1, in any age group. We can also infer that both vaccines are effective against the B.1.1.7 variant, because our analysis period coincided with the rapid emergence of B.1.1.7 in England during the second wave of the pandemic.\n\nImplications of all the available evidenceOur findings add to the growing body of evidence on the protective effect of the BNT162b vaccines in residents of LTCFs and demonstrate the effectiveness of ChAdOx1 in this vulnerable population. Evaluating single-dose vaccine efficacy has become increasingly important in light of extended dosing intervals that have been implemented in order to maximise vaccine coverage across high-risk groups. Further work is required to evaluate the effectiveness of the first vaccine dose after 8-12 weeks, as well as following the second dose, and to evaluate the long-term impact of vaccination on SARS-CoV-2 infection, transmission and mortality in LTCFs. This will inform policy decisions regarding the ongoing need for disease control measures in LTCF such as visitor restrictions, which continue to have a detrimental impact on the wellbeing of residents, their relatives, and staff.\n\nSupplementary material attached.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Madhumita Shrotri", - "author_inst": "University College London" - }, - { - "author_name": "Maria Krutikov", - "author_inst": "University College London" - }, - { - "author_name": "Tom Palmer", - "author_inst": "University College London" - }, - { - "author_name": "Rebecca Giddings", - "author_inst": "University College London" - }, - { - "author_name": "Borscha Azmi", - "author_inst": "University College London" - }, - { - "author_name": "Sathyavani Subbarao", - "author_inst": "Public Health England" - }, - { - "author_name": "Christopher Fuller", - "author_inst": "University College London" - }, - { - "author_name": "Aidan Irwin-Singer", - "author_inst": "Department of Health and Social Care, UK" - }, - { - "author_name": "Daniel Davies", - "author_inst": "Palantir Technologies UK Ltd" - }, - { - "author_name": "Gokhan Tut", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Jamie Lopez Bernal", - "author_inst": "Public Health England" - }, - { - "author_name": "Paul Moss", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Andrew Hayward", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Copas", - "author_inst": "University College London" - }, - { - "author_name": "Laura Shallcross", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.24.20208835", "rel_title": "Importance of serological testing in the convalescence phase in patients with pulmonary impairment due to COVID 19 - a health care workers analysis", @@ -828046,6 +832650,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.24.21254046", + "rel_title": "Sudden rise in COVID-19 case fatality among young and middle-aged adults in the south of Brazil after identification of the novel B.1.1.28.1 (P.1) SARS-CoV-2 strain: analysis of data from the state of Parana", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21254046", + "rel_abs": "Brazil is currently suffering a deadly surge of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, which has been attributed to the spread of a new strain known as P.1 (B.1.1.28.1). In this investigation, we analyzed coronavirus disease 2019 (COVID-19) public health data from Parana, the largest state in southern half of Brazil, between September 1, 2020 and March 17, 2021, to evaluate recent trends in case fatality rates in different age groups. A total of 553,518 cases of SARS-CoV-2, 8,853 currently registered as fatal, were finally included in our analysis. All age groups showed either decline or stabilization of the case fatality rates (CFRs) between September 2020 and January 2021. In February 2021, an increase in CFR for almost all age groups could be instead observed. All groups above 20 years of age showed statistically significant increases in CFR when diagnosed in February 2021 as opposed to January 2021. Patients aged 20-29 years experienced a tripling of their CFR, from 0.04% to 0.13%, while those aged 30-39, 40-49, 50-59 experienced approximate CFR doubling. Individuals between 20 and 29 years of age whose diagnosis was made in February 2021 had an over 3-fold higher risk of death compared to those diagnosed in January 2021 (Risk Ratio (RR): 3.15 [95%CI: 1.52-6.53], p<0.01), while those aged 30-39, 40-49, 50-59 years experienced 93% (1.93 [95%CI:1.31-2.85], p<0.01), 110% (RR: 2.10 [95%CI:1.62-2.72], p<0.01), and 80% (RR: 1.80 [95%CI:1.50-2.16], p<0.01) increases in risk of death, respectively. Notably, the observed CFR increase coincided with the second consecutive month of declining number of diagnosed SARS-CoV-2 cases. Taken together, these preliminary findings suggest significant increases in CFR in young and middle-aged adults after identification of a novel SARS-CoV-2 strain circulating in Brazil, and this should raise public health alarms, including the need for more aggressive local and regional public health interventions and faster vaccination.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Maria Helena Santos de Oliveira", + "author_inst": "Federal University of Parana" + }, + { + "author_name": "Giuseppe Lippi", + "author_inst": "University of Verona" + }, + { + "author_name": "Brandon Michael Henry", + "author_inst": "Cincinnati Children's Hospital Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.24.21254254", "rel_title": "Dental mitigation strategies to reduce aerosolization of SARS-CoV-2", @@ -828271,133 +832902,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.24.21253489", - "rel_title": "Factors associated with COVID-19 vaccine receipt at two integrated healthcare systems in New York City: A Cross sectional study of healthcare workers", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21253489", - "rel_abs": "ObjectivesTo examine factors associated with COVID-19 vaccine receipt among healthcare workers, including healthcare worker job type, race, and gender, as well as the role of vaccine confidence in decisions to vaccinate, and to better understand specific concerns related to COVID-19 vaccination among healthcare workers.\n\nDesignCross-sectional anonymous survey among front-line, support service, and administrative healthcare workers.\n\nSettingTwo large integrated healthcare systems (one private and one public) in New York City during the initial rollout of the COVID-19 vaccine among healthcare workers.\n\nParticipants1,933 healthcare workers, including nurses, physicians, allied health professionals, environmental services staff, researchers, and administrative staff.\n\nMain Outcome MeasuresThe primary outcome was COVID-19 vaccine receipt during the initial rollout of the vaccine among healthcare workers.\n\nResultsAmong 1,933 healthcare workers who had been offered the vaccine, 81% had received the vaccine at the time of the survey. Receipt was lower among Black (58%) compared with White (91%) healthcare workers; and lower among Hispanic (69%) compared with non-Hispanic (84%) healthcare workers. Among healthcare workers with concerns about COVID-19 vaccine safety, 65% received the vaccine. Among healthcare workers who agreed with the statement that the vaccine is important to protect family members, 86% were vaccinated. Of those who disagreed, 25% received the vaccine. Across all participants, 27% expressed concern about being experimented on with the COVID-19 vaccine. In a multivariable analysis, concern about being experimented on with the COVID-19 vaccine, concerns about COVID-19 vaccine safety, lack of influenza vaccine receipt, disagreeing that COVID-19 vaccination is important to protect family members, and Black race were independently associated with COVID-19 vaccine non-receipt. Over 70% of all healthcare workers responded that they had been approached for vaccine advice multiple times by family, community members, and patients.\n\nConclusionsOur data demonstrated high overall receipt among healthcare workers. Even among healthcare workers with concerns about COVID-19 vaccine safety, side effects, or being experimented on, over 50% received the vaccine. Attitudes around the importance of COVID-19 vaccination to protect others played a large role in healthcare workers decisions to vaccinate. We observed striking inequities in COVID-19 vaccine receipt, particularly affecting Black and Hispanic workers. Further research is urgently needed in developing strategies with healthcare workers to address issues related to vaccine equity and uptake in the context of systemic racism and barriers to care. This is particularly important given the influence healthcare workers have in vaccine decision-making conversations in their communities.\n\nSUMMARY BOXES\n\nWhat is already known?O_LIHigh uptake of effective COVID-19 vaccines among healthcare workers is critical to pandemic response.\nC_LIO_LIIn studies of potential COVID-19 vaccine acceptance prior to COVID-19 vaccine availability, people who identified as Black were less likely to indicate they would accept the vaccine.\nC_LIO_LIUnderstanding reasons why some healthcare workers chose not to get the COVID-19 vaccine will help us develop interventions to improve COVID-19 vaccine confidence among healthcare workers and in their communities.\nC_LI\n\nWhat this study addsO_LIWe demonstrate high receipt of COVID-19 vaccines in the initial rollout among healthcare workers.\nC_LIO_LIAttitudes around the importance of COVID-19 vaccination to protect others played a large role in healthcare workers decisions to vaccinate.\nC_LIO_LIWe observed substantially lower rates of receipt among Black and Hispanic healthcare workers, independent of differences in vaccine-related beliefs. A quarter of healthcare workers expressed concerns about being experimented on. These results suggest systemic racism may be a critical barrier to equitable vaccination.\nC_LIO_LIOur results highlight that healthcare workers of all types, including those with non-patient-facing roles, play an important role as sources of COVID-19 vaccine information in their communities.\nC_LI", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Kristin Oliver", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Anant Raut", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA, Possible, Kathmandu, Nepal" - }, - { - "author_name": "Stanley Pierre", - "author_inst": "NYC Health and Hospitals / Queens Hospital Center, NY, USA" - }, - { - "author_name": "Leopolda Silvera", - "author_inst": "NYC Health and Hospitals / Elmhurst Hospital Center, Queens, NY, USA" - }, - { - "author_name": "Alexander Boulos", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Alyssa Gale", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Aaron Baum", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Ashley Chory", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Nichola Davis", - "author_inst": "NYC Health + Hospitals/ Office of Ambulatory Care and Population Health" - }, - { - "author_name": "Amy Freeman", - "author_inst": "NYU Grossman School of Medicine, New York, NY, USA" - }, - { - "author_name": "Crispin Goytia", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Andrea Hamilton", - "author_inst": "NYC Health and Hospitals / Queens Hospital Center, NY, USA" - }, - { - "author_name": "Carol Horowitz", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Nadia Islam", - "author_inst": "NYU Grossman School of Medicine, New York, NY, USA" - }, - { - "author_name": "Jessica Jeavons", - "author_inst": "NYC DOHMH" - }, - { - "author_name": "Janine Knudsen", - "author_inst": "NYU Grossman School of Medicine, New York, NY, USA, NYC Health and Hospitals / Bellevue Hospital Center, NY, USA, NYC DOHMH" - }, - { - "author_name": "Sheng Li", - "author_inst": "City University of New York, New York, NY, USA" - }, - { - "author_name": "Jenna Lupi", - "author_inst": "NYC Health and Hospitals / Office of Population Health" - }, - { - "author_name": "Roxanne Martin", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Sheela Maru", - "author_inst": "NYC Health and Hospitals / Elmhurst Hospital Center, Queens, NY, USA, Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Ismail Nabeel", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Dina Pimenova", - "author_inst": "NYU Grossman School of Medicine, New York, NY, USA" - }, - { - "author_name": "Anya Romanoff", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Nina Schwalbe", - "author_inst": "Mailman School of Public Health, Columbia University" - }, - { - "author_name": "Nita Vangeepuram", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Rachel Vreeman", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Joseph Masci", - "author_inst": "NYC Health and Hospitals / Elmhurst Hospital Center, Queens, NY, USA, Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Duncan Maru", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.24.21251900", "rel_title": "Trends in clinical characteristics and associations of severe non-respiratory events related to SARS-CoV-2", @@ -830163,6 +834667,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.25.436930", + "rel_title": "Genomic surveillance and phylodynamic analyses reveal emergence of novel mutation and co-mutation patterns within SARS-CoV2 variants prevalent in India", + "rel_date": "2021-03-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.25.436930", + "rel_abs": "Emergence of distinct viral clades has been observed in SARS-CoV2 variants across the world and India. Identification of the genomic diversity and the phylodynamic profiles of the prevalent strains of the country are critical to understand the evolution and spread of the variants. We performed whole-genome sequencing of 54 SARS-CoV2 strains collected from COVID-19 patients in Kolkata, West Bengal during August to October 2020. Phylogeographic and phylodynamic analyses were performed using these 54 and other sequences from India and abroad available in GISAID database. Spatio-temporal evolutionary dynamics of the pathogen across various regions and states of India over three different time periods in the year 2020 were analyzed. We estimated the clade dynamics of the Indian strains and compared the clade specific mutations and the co-mutation patterns across states and union territories of India over the time course. We observed that GR, GH and G (GISAID) or 20B and 20A (Nextstrain) clades were the prevalent clades in India during middle and later half of the year 2020. However, frequent mutations and co-mutations observed within the major clades across time periods do not show much overlap, indicating emergence of newer mutations in the viral population prevailing in the country. Further, we explored the possible association of specific mutations and co-mutations with the infection outcomes manifested within the Indian patients.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Nupur Biswas", + "author_inst": "CSIR-IICB" + }, + { + "author_name": "Priyanka Mallick", + "author_inst": "CSIR-IICB" + }, + { + "author_name": "Sujay Krishna Maity", + "author_inst": "CSIR-IICB" + }, + { + "author_name": "Debaleena Bhowmik", + "author_inst": "CSIR-IICB" + }, + { + "author_name": "Arpita Ghosh Mitra", + "author_inst": "MEDICA Superspeciality Hospital, Kolkata, West Bengal, India" + }, + { + "author_name": "Soumen Saha", + "author_inst": "MEDICA Superspeciality Hospital, Kolkata, West Bengal, India" + }, + { + "author_name": "Aviral Roy", + "author_inst": "MEDICA Superspeciality Hospital, Kolkata, West Bengal, India" + }, + { + "author_name": "Partha Chakrabarti", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "Sandip Paul", + "author_inst": "CSIR-IICB" + }, + { + "author_name": "Saikat Chakrabarti", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.03.25.437046", "rel_title": "Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring", @@ -830332,53 +834891,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.25.437083", - "rel_title": "Target Capture Sequencing of SARS-CoV-2 Genomes Using the ONETest Coronaviruses Plus", - "rel_date": "2021-03-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.25.437083", - "rel_abs": "BackgroundGenomic sequencing is important to track and monitor genetic changes in SARS-CoV-2. We introduce a target capture next-generation sequencing methodology, the ONETest Coronaviruses Plus, to sequence SARS-CoV-2 genomes and select genes of other respiratory viruses simultaneously.\n\nMethodsWe applied the ONETest on 70 respiratory samples (collected in Florida, USA between May and July, 2020), in which SARS-CoV-2 had been detected by a qualitative PCR assay. For 48 (69%) of the samples, we also applied the ARTIC protocol for Illumina sequencing. All the libraries were sequenced as 2x150 nucleotide reads on an Illumina instrument. The ONETest data were analyzed using an in-house pipeline and the ARTIC data using a published pipeline to produce consensus SARS-CoV-2 genome sequences, to which lineages were assigned using pangolin.\n\nResultsOf the 70 ONETest libraries, 45 (64%) had a complete or near-complete SARS-CoV-2 genome sequence (> 29,000 bases and with > 90% of its bases covered by at least 10 reads). Of the 48 ARTIC libraries, 25 (52%) had a complete or near-complete SARS-CoV-2 genome sequence.\n\nIn 24 out of 34 (71%) samples in which both the ONETest and ARTIC sequences were complete or near-complete and in which lineage could be assigned to both the ONETest and ARTIC sequences, the SARS-CoV-2 lineage identified was the same.\n\nConclusionsThe ONETest can be used to sequence the SARS-CoV-2 genomes in archived samples and thereby enable detection of circulating and emerging SARS-CoV-2 variants. Target capture approaches, such as the ONETest, are less prone to loss of sequence coverage probably due to amplicon dropouts encountered in amplicon approaches, such as ARTIC. With its added value of characterizing other major respiratory pathogens, although not assessed in this study, the ONETest can help to better understand the epidemiology of infectious respiratory disease in the post COVID-19 era.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Shing Hei Zhan", - "author_inst": "Fusion Genomics Corporation" - }, - { - "author_name": "Sepideh M Alamouti", - "author_inst": "Fusion Genomics Corporation" - }, - { - "author_name": "Brian S Kwok", - "author_inst": "Fusion Genomics Corporation" - }, - { - "author_name": "Meng-Hsun Lee", - "author_inst": "Fusion Genomics Corporation" - }, - { - "author_name": "Jaswinder Khattra", - "author_inst": "Fusion Genomics Corporation" - }, - { - "author_name": "Habib Daneshpajouh", - "author_inst": "Fusion Genomics Corporation" - }, - { - "author_name": "Herbert J Houck", - "author_inst": "University of Florida College of Medicine" - }, - { - "author_name": "Kenneth H Rand", - "author_inst": "University of Florida College of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.03.25.436935", "rel_title": "COVID-19: A need for new rather than repurposed antiviral drugs.", @@ -831829,6 +836341,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.22.21254134", + "rel_title": "Relationship between COVID-19 pandemic and ecological, economic, and social characteristics", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21254134", + "rel_abs": "COVID-19 pandemic had huge impacts on the global world, with both a negative impact on society and economy, but a positive one on nature. But this universal effect resulted in different infection rates from country to country. We analyzed the relationship between the pandemic and ecological, economic, and social characteristics. All of these data were collected in 140 countries at 6 time points. Correlations were studied using univariate and multivariate regression models.\n\nThe world was interpreted as a single global ecosystem consisting of ecosystem units representing countries. We first studied 140 countries around the world together, and infection rates were related to per capita GDP, Ecological Footprint, median age, urban population, and Biological Capacity, globally. We then ranked 140 countries by infection rate and created 4 equal groups, each with 35 countries. In the first group, the infection rate was very high and was related to the Ecological Footprint (consumption) and GDP per capita (production). This group is dominated by developed countries and their ecological characteristics have proven to be particularly significant. In groups 2, 3, and 4, infection rates were high, moderate, and low, and were primarily associated with median age and urban population.\n\nIn the scientific discussion, we have interpreted why infection is high in developed countries. Sustainable ecosystems are balanced, unlike the ecosystems of developed countries. According to science, the resilience and health of both natural ecosystems and humans are closely linked to the world of microbial communities. Our results suggest that both the economy and society need to be in harmony with nature, creating sustainable ecosystems in developed countries as well.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Attila Muranyi", + "author_inst": "Institute for Soil Science and Agricultural Chemistry, Hungarian Academy of Sciences" + }, + { + "author_name": "Balint Varga", + "author_inst": "Department of Computer Science, Institute of Mathematics, Eotvos Lorand University, Budapest, Hungary" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.20.21253892", "rel_title": "Intention of Healthcare Workers to Receive COVID-19 Vaccine: A Cross-Sectional Survey in 10 Countries in Eastern Mediterranean Region", @@ -832046,45 +836581,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2021.03.24.436620", - "rel_title": "B.1.526 SARS-CoV-2 variants identified in New York City are neutralized by vaccine-elicited and therapeutic monoclonal antibodies", - "rel_date": "2021-03-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.24.436620", - "rel_abs": "DNA sequence analysis recently identified the novel SARS-CoV-2 variant B.1.526 that is spreading at an alarming rate in the New York City area. Two versions of the variant were identified, both with the prevalent D614G mutation in the spike protein together with four novel point mutations and with an E484K or S477N mutation in the receptor binding domain, raising concerns of possible resistance to vaccine-elicited and therapeutic antibodies. We report that convalescent sera and vaccine-elicited antibodies retain full neutralizing titer against the S477N B.1.526 variant and neutralize the E484K version with a modest 3.5-fold decrease in titer as compared to D614G. The E484K version was neutralized with a 12-fold decrease in titer by the REGN10933 monoclonal antibody but the combination cocktail with REGN10987 was fully active. The findings suggest that current vaccines and therapeutic monoclonal antibodies will remain protective against the B.1.526 variants. The findings further support the value of wide-spread vaccination.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Hao Zhou", - "author_inst": "Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA" - }, - { - "author_name": "Belinda M. Dcosta", - "author_inst": "Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA" - }, - { - "author_name": "Marie I. Samanovic", - "author_inst": "NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA" - }, - { - "author_name": "Mark J. Mulligan", - "author_inst": "NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA" - }, - { - "author_name": "Nathaniel R. Landau", - "author_inst": "Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA" - }, - { - "author_name": "Takuya Tada", - "author_inst": "Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.03.23.436684", "rel_title": "Isolation and Characterization of Cross-Neutralizing Coronavirus Antibodies from COVID-19+ Subjects", @@ -833461,6 +837957,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.14.21253532", + "rel_title": "Epicardial adipose tissue thickness is associated with increased severity and mortality related to SARS-CoV-2 infection", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.14.21253532", + "rel_abs": "BACKGROUNDIncreased adiposity and visceral obesity have been linked to adverse COVID-19 outcomes. The amount of epicardial adipose tissue (EAT) may have relevant implications given its proximity to the heart and lungs. Here, we explored the role of EAT in increasing the risk for COVID-19 adverse outcomes.\n\nMETHODSWe included 748 patients with COVID-19 attending a reference center in Mexico City. EAT thickness, sub-thoracic and extra-pericardial fat were measured using thoracic CT scans. We explored the association of each thoracic adipose tissue compartment with COVID-19 mortality and severe COVID-19 (defined as mortality and need for invasive mechanical ventilation), according to the presence or absence of obesity. Mediation analyses evaluated the role of EAT in facilitating the effect of age, body mass index and cardiac troponin levels with COVID-19 outcomes.\n\nRESULTSEAT thickness was associated with increased risk of COVID-19 mortality (HR 1.18, 95%CI 1.01-1.39) independent of age, gender, comorbid conditions and BMI. Increased EAT was associated with lower SpO2 and PaFi index and higher levels of cardiac troponins, D-dimer, fibrinogen, C-reactive protein, and 4C severity score, independent of obesity. EAT mediated 13.1% (95%CI 3.67-28.0%) and 5.1% (95%CI 0.19-14.0%) of the effect of age and 19.4% (95%CI 4.67-63.0%) and 12.8% (95%CI 0.03-46.0%) of the effect of BMI on requirement for intubation and mortality, respectively. EAT also mediated the effect of increased cardiac troponins on myocardial infarction during COVID-19.\n\nCONCLUSIONEAT is an independent risk factor for severe COVID-19 and mortality independent of obesity. EAT partly mediates the effect of age and BMI and increased cardiac troponins on adverse COVID-19 outcomes.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Roopa Mehta", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Omar Yaxmehen Bello-Chavolla", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Leonardo Mancillas-Adame", + "author_inst": "Facultad de Medicina, Universidad Autonoma de Nuevo Leon" + }, + { + "author_name": "Marcela Rodr\u00edguez-Flores", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Natalia Ram\u00edrez-Pedraza", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Bethsabel Rodr\u00edguez-Encinas", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Carolina Isabel P\u00e9rez-Carri\u00f3n", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Mar\u00eda Isabel Jasso-\u00c1vila", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Jorge Valladares-Garcia", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Pablo Esteban Vanegas-Cedillo", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Diana Hern\u00e1ndez-Ju\u00e1rez", + "author_inst": "dianaheez@hotmail.com" + }, + { + "author_name": "Arsenio Vargas-V\u00e1zquez", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Neftali Eduardo Antonio-Villa", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Monica Chapa-Ibarguengoitia", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Paloma Almeda-Vald\t\u00e9s", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Daniel Elias-Lopez", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Arturo Galindo-Fraga", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Alfonso Gulias-Herrero", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Alfredo Ponce de Leon", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Jose Sifuentes-Osornio", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Carlos A. Aguilar-Salinas", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "endocrinology" + }, { "rel_doi": "10.1101/2021.03.16.21253652", "rel_title": "Within-Day Variability of SARS-CoV-2 RNA in Municipal Wastewater Influent During Periods of Varying COVID-19 Prevalence and Positivity", @@ -833566,77 +838161,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.16.21252974", - "rel_title": "Molecular Epidemiology of SARS-CoV-2 in Cyprus", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21252974", - "rel_abs": "Whole genome sequencing of viral specimens following molecular diagnosis is a powerful analytical tool of molecular epidemiology that can critically assist in resolving chains of transmission, identifying of new variants or assessing pathogen evolution and allows a real-time view into the dynamics of a pandemic. In Cyprus, the first two cases of COVID-19 were identified on March 9, 2020 and since then 33,567 confirmed cases and 230 deaths were documented. In this study, viral whole genome sequencing was performed on 133 SARS-CoV-2 positive samples collected between March 2020 and January 2021. Phylogenetic analysis was conducted to evaluate the genomic diversity of circulating SARS-CoV-2 lineages in Cyprus. 15 different lineages were identified that clustered into three groups associated with the spring, summer and autumn/winter wave of SARS-CoV2 incidence in Cyprus, respectively. The majority of the Cypriot samples belonged to the B.1.258 lineage first detected in September that spread rapidly and largely dominated the autumn/winter wave with a peak prevalence of 86% during the months of November and December. The B.1.1.7 UK variant (VOC-202012/01) was identified for the first time at the end of December and spread rapidly reaching 37% prevalence within one month. Overall, we describe the changing pattern of circulating SARS-CoV-2 lineages in Cyprus since the beginning of the pandemic until the end of January 2021. These findings highlight the role of importation of new variants through travel towards the emergence of successive waves of incidence in Cyprus and demonstrate the importance of genomic surveillance in determining viral genetic diversity and the timely identification of new variants for guiding public health intervention measures.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jan Richter", - "author_inst": "Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus" - }, - { - "author_name": "Pavlos Fanis", - "author_inst": "Molecular Genetics, Function & Therapy Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus" - }, - { - "author_name": "Christina Tryfonos", - "author_inst": "Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus" - }, - { - "author_name": "Dana Koptides", - "author_inst": "Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus" - }, - { - "author_name": "George Krashias", - "author_inst": "Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus" - }, - { - "author_name": "Stavros Bashiardes", - "author_inst": "Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus" - }, - { - "author_name": "Andreas Hadjisavvas", - "author_inst": "Cancer Genetics, Therapeutics & Ultrastructural Pathology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus" - }, - { - "author_name": "Maria Loizidou", - "author_inst": "Cancer Genetics, Therapeutics & Ultrastructural Pathology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus" - }, - { - "author_name": "Anastasis Oulas", - "author_inst": "Bioinformatics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus" - }, - { - "author_name": "Denise Alexandrou", - "author_inst": "Medical and Public Health Services, Ministry of Health, Nicosia, Cyprus" - }, - { - "author_name": "Olga Kalakouta", - "author_inst": "Medical and Public Health Services, Ministry of Health, Nicosia, Cyprus" - }, - { - "author_name": "Mihalis I Panayiotidis", - "author_inst": "Cancer Genetics, Therapeutics & Ultrastructural Pathology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus" - }, - { - "author_name": "George M Spyrou", - "author_inst": "Bioinformatics Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus" - }, - { - "author_name": "Christina Christodoulou", - "author_inst": "Molecular Virology Department, Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.15.21253582", "rel_title": "SARS-CoV-2 pandemic dynamics and infection tracing in Denmark", @@ -835427,6 +839951,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.21.21254047", + "rel_title": "Factors influencing COVID-19 vaccination uptake in an elderly sample in Poland", + "rel_date": "2021-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.21.21254047", + "rel_abs": "BackgroundsThis research represents an investigation into potential predictors for the uptake of the COVID-19 vaccination in Poland, following the instigation of policies to encourage the over-seventies to be vaccinated.\n\nMethodsIndividuals participated in cross-sectional structured interviews. 1427 respondents were questioned for determining vaccination uptake, revealing attitudes regarding vaccination, where information was sourced from, health status and behavior, demographics and socio-economic profiles.\n\nResultsSelected predictors for acceptance of the vaccination were: being talked through the importance of the vaccination and potential side-effects by a medical professional; sharing living space with others; having a high ranking occupation; suffering from chronic illnesses; being able to access medical services by driving or walking rather than using public transport or relying on others. Those who opted not to be vaccinated most frequently justify their decision by saying that they were concerned about the efficacy of the vaccine or that they were worried about side-effects.\n\nConclusionsIt appears that the current nationwide campaign has successfully raised awareness regarding the vaccine, but this research indicates that a more information-based campaign, focusing on evidence of the vaccines efficacy and the non-serious nature of all side-effects, could lead to improved uptake of the COVID-19 vaccine.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Marta Malesza", + "author_inst": "University of Economics and Human Sciences in Warsaw" + }, + { + "author_name": "Magdalena Bozym", + "author_inst": "Military Academy Hospital, Warsaw, Poland" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.21.21254068", "rel_title": "Determinants of COVID-19 outcomes: A systematic review.", @@ -835532,165 +840079,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.18.21253888", - "rel_title": "Long Covid in adults discharged from UK hospitals after Covid-19: A prospective, multicentre cohort study using the ISARIC WHO Clinical Characterisation Protocol.", - "rel_date": "2021-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.18.21253888", - "rel_abs": "Structured AbstractO_ST_ABSObjectivesC_ST_ABSThe long-term consequences of severe Covid-19 requiring hospital admission are not well characterised. The objective of this study was to establish the long-term effects of Covid-19 following hospitalisation and the impact these may have on patient reported outcome measures.\n\nDesignA multicentre, prospective cohort study with at least 3 months follow-up of participants admitted to hospital between 5th February 2020 and 5th October 2020.\n\nSetting31 hospitals in the United Kingdom.\n\nParticipants327 hospitalised participants discharged alive from hospital with confirmed/high likelihood SARS-CoV-2 infection.\n\nMain outcome measures and comparisonsThe primary outcome was self-reported recovery at least ninety days after initial Covid-19 symptom onset. Secondary outcomes included new symptoms, new or increased disability (Washington group short scale), breathlessness (MRC Dyspnoea scale) and quality of life (EQ5D-5L). We compared these outcome measures across age, comorbidity status and in-hospital Covid-19 severity to identify groups at highest risk of developing long-term difficulties. Multilevel logistic and linear regression models were built to adjust for the effects of patient and centre level risk factors on these outcomes.\n\nResultsIn total 53.7% (443/824) contacted participants responded, yielding 73.8% (327/443) responses with follow-up of 90 days or more from symptom onset. The median time between symptom onset of initial illness and completing the participant questionnaire was 222 days (Interquartile range (IQR) 189 to 269 days). In total, 54.7% (179/327) of participants reported they did not feel fully recovered. Persistent symptoms were reported by 93.3% (305/325) of participants, with fatigue the most common (82.8%, 255/308), followed by breathlessness (53.5%, 175/327). 46.8% (153/327) reported an increase in MRC dyspnoea scale of at least one grade. New or worse disability was reported by 24.2% (79/327) of participants. Overall (EQ5D-5L) summary index was significantly worse at the time of follow-up (median difference 0.1 points on a scale of 0 to 1, IQR: -0.2 to 0.0). Females under the age of 50 years were five times less likely to report feeling recovered (adjusted OR 5.09, 95% CI 1.64 to 15.74), were more likely to have greater disability (adjusted OR 4.22, 95% CI 1.12 to 15.94), twice as likely to report worse fatigue (adjusted OR 2.06, 95% CI 0.81 to 3.31) and seven times more likely to become more breathless (adjusted OR 7.15, 95% CI 2.24 to 22.83) than men of the same age.\n\nConclusionsSurvivors of Covid-19 experienced long-term symptoms, new disability, increased breathlessness, and reduced quality of life. These findings were present even in young, previously healthy working age adults, and were most common in younger females. Policymakers should fund further research to identify effective treatments for long-Covid and ensure healthcare, social care and welfare support is available for individuals with long-Covid.\n\nSection 1: What is already known on this topicO_LILong-term symptoms after hospitalisation for Covid-19 have been reported, but it is not clear what impact this has on quality of life.\nC_LIO_LIIt is not known which patient groups are most likely to have long-term persistent symptoms following hospitalisation for Covid-19, or if this differs by disease severity.\nC_LI\n\nSection 2: What this study addsO_LIMore than half of patients reported not being fully recovered 7 months after onset of Covid-19 symptoms.\nC_LIO_LIPreviously healthy participants and those under the age of 50 had higher odds of worse long-term outcomes compared to older participants and those with comorbidities.\nC_LIO_LIYounger women and those with more severe acute disease in-hospital had the worst long-term outcomes.\nC_LIO_LIPolicy makers need to ensure there is long-term support for people experiencing long-Covid and should plan for lasting long-term population morbidity. Funding for research to understand mechanisms underlying long-Covid and identify potential interventions for testing in randomised trials is urgently required.\nC_LI", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Louise Sigfrid", - "author_inst": "ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK" - }, - { - "author_name": "Tom M Drake", - "author_inst": "Centre for Medical Informatics, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Ellen Pauley", - "author_inst": "University of Edinburgh Medical School, Edinburgh, UK." - }, - { - "author_name": "Edwin C Jesudason", - "author_inst": "NHS Lothian, Edinburgh, UK," - }, - { - "author_name": "Piero Olliaro", - "author_inst": "ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK." - }, - { - "author_name": "Wei Shen Lim", - "author_inst": "Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, UK." - }, - { - "author_name": "Annelise Gillesen", - "author_inst": "ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK." - }, - { - "author_name": "Colin Berry", - "author_inst": "Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK" - }, - { - "author_name": "David Lowe", - "author_inst": "NHS Greater Glasgow and Clyde, Emergency Department, Glasgow, UK" - }, - { - "author_name": "Joanne McPeake", - "author_inst": "School of Medicine, Dentistry and Nursing, University of Glasgow, UK" - }, - { - "author_name": "Nazir Lone", - "author_inst": "Usher Institute, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Muge Cevik", - "author_inst": "University of St Andrews" - }, - { - "author_name": "Daniel Munblit", - "author_inst": "Sechenov First Moscow State Medical University, Imperial College London, Imperial College London, RSMU" - }, - { - "author_name": "Anna Casey", - "author_inst": "Medical Student, Brighton and Sussex Medical School, UK" - }, - { - "author_name": "Peter Bannister", - "author_inst": "Brighton & Sussex Medical School, Brighton, UK" - }, - { - "author_name": "Clark D Russell", - "author_inst": "Centre for Inflammation Research, University of Edinburgh, UK" - }, - { - "author_name": "Lynsey Goodwin", - "author_inst": "Institute of Infection, Veterinary and Ecological Studies, Univeristy of Liverpool. Tropical and Infectious Diseases Unit, North Manchester General Hospital, De" - }, - { - "author_name": "Antonia Ho", - "author_inst": "University of Glasgow, Glasgow, UK" - }, - { - "author_name": "Lance Turtle", - "author_inst": "NIHR Health Protection Research Unit in emerging and zoonotic infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L" - }, - { - "author_name": "Margret E O'Hara", - "author_inst": "Long COVID Support, Birmingham, UK" - }, - { - "author_name": "Claire Hastie", - "author_inst": "Long COVID Support, Birmingham, UK" - }, - { - "author_name": "Chloe Donohue", - "author_inst": "Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK" - }, - { - "author_name": "Rebecca Spencer", - "author_inst": "Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK." - }, - { - "author_name": "Cara Donegan", - "author_inst": "Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK." - }, - { - "author_name": "Alison Gummery", - "author_inst": "Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK." - }, - { - "author_name": "Janet Harrison", - "author_inst": "National Institute of Health Research (NIHR) Health Protection research Unit in Emerging and Zoonotic Infections, Liverpool, UK. 2. Institute of Infection and G" - }, - { - "author_name": "Hayley Hardwick", - "author_inst": "National Institute of Health Research (NIHR) Health Protection research Unit in Emerging and Zoonotic Infections, Liverpool, UK. 2. Institute of Infection and G" - }, - { - "author_name": "Claire E Hastie", - "author_inst": "Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK." - }, - { - "author_name": "Gail Carson", - "author_inst": "ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK." - }, - { - "author_name": "Laura Merson", - "author_inst": "ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK" - }, - { - "author_name": "John Kenneth Baillie", - "author_inst": "Roslin Institute, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Peter Openshaw", - "author_inst": "National Heart and Lung Institute, Imperial College, London UK." - }, - { - "author_name": "Ewen M Harrison", - "author_inst": "Director Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK." - }, - { - "author_name": "Annemarie Docherty", - "author_inst": "Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK. 2. Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Malcolm G Semple", - "author_inst": "Health Protection Research Unit In Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK 2. " - }, - { - "author_name": "Janet T Scott", - "author_inst": "MRC-University of Glasgow Center for Virus research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.21.21253978", "rel_title": "Detection of Mutations Associated with Variants of Concern Via High Throughput Sequencing of SARS-CoV-2 Isolated from NYC Wastewater", @@ -837525,6 +841913,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.03.19.21253425", + "rel_title": "COVID 19 Vaccine Perceptions in the New York State Intellectual and Developmental Disabilities Community", + "rel_date": "2021-03-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253425", + "rel_abs": "BackgroundPeople with intellectual and developmental disabilities (IDD) are at disproportionate risk for severe COVID-19 outcomes, particularly those living in congregate care settings. Yet, there is limited data on vaccine perceptions in the disability community.\n\nObjectiveTo explore COVID-19 vaccine perceptions in individuals with IDD, their family members, and those who work with them, to inform a statewide vaccine information and messaging project.\n\nMethodsA national survey, adapted for the IDD community, was distributed to a convenience sample of IDD organizations throughout New York State, in five languages. Constructs included vaccine intention, reasons for vaccine hesitancy, and trusted sources of vaccine information. Zip code data were used to map respondent location and vaccine preferences.\n\nResultsOf n= 825 respondents, approximately 75% intended to or had received the vaccine, across roles (i.e., people with disabilities, family members, direct care workers) and racial/ethnic groups. Greater vaccine hesitancy was reported in younger individuals and those making decisions on behalf of a person with IDD. Concerns included side effects and the swiftness of vaccine development. Black and Hispanic participants had heightened concerns about being an \"experiment\" for the vaccine. Trusted sources of information included healthcare providers and family members. Respondents who intended/got the vaccine were distributed throughout the state.\n\nConclusionsVaccine preferences in this New York State disability community sample align with national data. Identified concerns suggest the need for community education that addresses misperceptions. Age and race differences in perspectives highlight the need for tailored education, delivered by trusted messengers.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Suzannah Iadarola", + "author_inst": "University of Rochester Medical Center, Director, Strong Center for Developmental Disabilities" + }, + { + "author_name": "Joanne Siegel", + "author_inst": "Einstein College of Medicine-Montefiore Medical Center" + }, + { + "author_name": "Qi Gao", + "author_inst": "Einstein College of Medicine" + }, + { + "author_name": "Kathleen McGrath", + "author_inst": "Einstein College of Medicine" + }, + { + "author_name": "Karen Bonuck", + "author_inst": "Einstein College of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.21.21254048", "rel_title": "Factors informing healthcare workers' willingness to work during the COVID-19 pandemic", @@ -837662,73 +842085,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.19.21253950", - "rel_title": "Limit of detection in different matrices of nineteen commercially available rapid antigen tests for the detection of SARS-CoV-2", - "rel_date": "2021-03-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253950", - "rel_abs": "In the context of the coronavirus disease 2019 (COVID-19) pandemic there has been an increase of the use of antigen-detection rapid diagnostic tests (Ag-RDT). The performance of Ag-RDT vary greatly between manufacturers and evaluating their analytical limit of detection (LOD) has become high priority. Here we describe a manufacturer-independent evaluation of the LOD of 19 marketed Ag-RDT using live SARS-CoV-2 spiked in different matrices: direct culture supernatant, a dry swab, and a swab in Amies. Additionally, the LOD using dry swab was investigated after 7 days storage at -80{degrees}C of the SARS-CoV-2 serial dilutions. An LOD of {approx} 5.0 x 102 pfu/ml (1.0 x 106 genome copies/ml) in culture media is defined as acceptable by the World Health Organization. Fourteen of nineteen Ag-RDTs (ActiveXpress, Espline, Excalibur, Innova, Joysbio, Mologic, NowCheck, Orient, PanBio, RespiStrip, Roche, Standard-F, Standard-Q and Sure-Status) exceeded this performance criteria using direct culture supernatant applied to the Ag-RDT. Six Ag-RDT were not compatible with Amies media and a decreased sensitivity of 2 to 20-fold was observed for eleven tests on the stored dilutions at -80{degrees}C for 7 days. Here, we provide analytical sensitivity data to guide appropriate test and sample type selection for use and for future Ag-RDT evaluations.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Ana I Cubas Atienzar", - "author_inst": "Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, L3 5QA, UK" - }, - { - "author_name": "Konstantina Kontogianni", - "author_inst": "Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, L3 5QA, UK" - }, - { - "author_name": "Thomas Edwards", - "author_inst": "Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, L3 5QA, UK" - }, - { - "author_name": "Dominic Wooding", - "author_inst": "Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, L3 5QA, UK" - }, - { - "author_name": "Kate Buist", - "author_inst": "Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, L3 5QA, UK" - }, - { - "author_name": "Caitlin R Thompson", - "author_inst": "Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, L3 5QA, UK" - }, - { - "author_name": "Christopher T Williams", - "author_inst": "Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, L3 5QA, UK" - }, - { - "author_name": "Lisa Baldwin", - "author_inst": "Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, L3 5QA, UK" - }, - { - "author_name": "Ian Patterson", - "author_inst": "Liverpool School of Tropical Medicine, Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Diseases, Liverpool, L3 5QA, UK" - }, - { - "author_name": "Grant Hughes", - "author_inst": "Liverpool School of Tropical Medicine, Departments of Vector Biology and Tropical Disease Biology, Centre for Neglected Tropical Diseases, Liverpool, L3 5QA, UK" - }, - { - "author_name": "Camille Escadafal", - "author_inst": "FIND, Foundation for Innovative New Diagnostics, Geneva, Switzerland" - }, - { - "author_name": "Jilian Sacks", - "author_inst": "FIND, Foundation for Innovative New Diagnostics, Geneva, Switzerland" - }, - { - "author_name": "Emily R Adams", - "author_inst": "Liverpool School of Tropical Medicine, Centre for Drugs and Diagnostics, Liverpool, L3 5QA, UK" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.20.21254021", "rel_title": "Changes in HIV Treatment Differentiated Care Utilization During the COVID-19 Pandemic in Zambia", @@ -839515,6 +843871,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2021.03.19.21253962", + "rel_title": "The effects of physical distancing and lockdown to restrain SARS-CoV-2 outbreak in the Italian Municipality of Cogne", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253962", + "rel_abs": "The outbreak of SARS-CoV-2 started in Wuhan, China, and is now a pandemic. An understanding of the prevalence and contagiousness of the disease, and of whether the strategies used to contain it to date have been successful, is important for understanding future containment strategies. One strategy for controlling the spread of SARS-CoV-2 is to adopt strong social distancing policies. The Municipality of Cogne (I), adopted strict lockdown rules from March 4, 2020 up to May 18, 2020. This first wave of the pandemic impressed by the extremely low impact of the SARS-CoV-2 on the locals, compared to the number accused on all the Italian territory. Starting from October 2020 up to the end of December, when the second wave hit Italy and Cogne territory, heavier effects were observed. In order to cast light on the effectiveness of the adopted strategy 74,5% of the local population underwent to a blood screening to detect IgM and IgG antibodies and after six months all the people tested positive were again investigated to establish the longitudinal changes in antibodies level. Moreover, within the context of this survey a rare and interesting case of secondary infection has been identified and here presented.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Gianpiero Gervino", + "author_inst": "University of Torino" + }, + { + "author_name": "Fabio Truc", + "author_inst": "University of Torino" + } + ], + "version": "1", + "license": "cc0_ng", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.03.18.21253881", "rel_title": "A Prospective Study of Long-Term Outcomes Among Hospitalized COVID-19 Patients with and without Neurological Complications", @@ -839948,49 +844327,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.18.21253903", - "rel_title": "Development and validation of the long covid symptom and impact tools, a set of patient-reported instruments constructed from patients' lived experience", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.18.21253903", - "rel_abs": "ObjectivesTo develop and validate patient-reported instruments, based on patients lived experiences, for monitoring the symptoms and impact of long covid.\n\nDesignThe long covid Symptom and Impact Tools (ST and IT) were constructed from the answers to a survey with open-ended questions to 492 patients with long covid. Validation of the tools involved adult patients with suspected or confirmed covid-19 and symptoms extending over three weeks after onset. Construct validity was assessed by examining the relations of the ST and IT scores with health related quality of life (EQ-5D-5L), function (PCFS, post-covid functional scale), and perceived health (MYMOP2). Reliability was determined by a test-retest. The \"patient acceptable symptomatic state\" (PASS) was determined by the percentile method.\n\nResultsValidation involved 1022 participants (55% with confirmed covid-19, 79% female and 12.5% hospitalised for covid-19). The long covid ST and IT scores were strongly correlated with the EQ-5D-5L (rs = -0.45 and rs = -0.59 respectively), the PCFS (rs = -0.39 and rs = -0.55), and the MYMOP2 (rs = -0.40 and rs = -0.59). Reproducibility was excellent with an interclass correlation coefficient of 0.83 (95% confidence interval 0.80 to 0.86) for the ST score and 0.84 (0.80 to 0.87) for the IT score. In total, 793 (77.5%) patients reported an unacceptable symptomatic state, thereby setting the PASS for the long covid IT score at 30 (28 to 33).\n\nConclusionsThe long covid ST and IT tools, constructed from patients lived experiences, provide the first validated and reliable instruments for monitoring the symptoms and impact of long covid.\n\nShort summaryWe developed the long covid Symptom and Impact Tools (ST and IT) from the experiences of 492 patients, captured during a survey with open-ended questions, and assessed their validity and reliability in a sample of 1022 patients with long covid.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Viet-Thi Tran", - "author_inst": "Universite de Paris" - }, - { - "author_name": "Carolina Riveros", - "author_inst": "Assistance Publique Hopitaux de Paris" - }, - { - "author_name": "Berangere Clepier", - "author_inst": "Patient" - }, - { - "author_name": "Moise Desvarieux", - "author_inst": "Columbia University" - }, - { - "author_name": "Camille Collet", - "author_inst": "Patient" - }, - { - "author_name": "Youri Yordanov", - "author_inst": "Sorbonne Universite" - }, - { - "author_name": "Philippe Ravaud", - "author_inst": "philippe.ravaud@aphp.fr" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.17.21252922", "rel_title": "Assessing the utility of lymphocyte count to diagnose COVID-19", @@ -842045,6 +846381,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.19.21253974", + "rel_title": "Data-driven estimate of SARS-CoV-2 herd immunity threshold in populations with individual contact pattern variations", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253974", + "rel_abs": "The development of efficacious vaccines has made it possible to envision mass vaccination programs aimed at suppressing SARS-CoV-2 transmission around the world. Here we use a data-driven age-structured multilayer representation of the population of 34 countries to estimate the disease induced immunity threshold, accounting for the contact variability across individuals. We show that the herd immunization threshold of random (un-prioritized) mass vaccination programs is generally larger than the disease induced immunity threshold. We use the model to test two additional vaccine prioritization strategies, transmission-focused and age-based, in which individuals are inoculated either according to their behavior (number of contacts) or infection fatality risk, respectively. Our results show that in the case of a sterilizing vaccine the behavioral strategy achieves herd-immunity at a coverage comparable to the disease-induced immunity threshold, but it appears to have inferior performance in averting deaths than the risk vaccination strategy. The presented results have potential use in defining the effects that the heterogeneity of social mixing and contact patterns has on herd immunity levels and the deployment of vaccine prioritization strategies.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Dan Lu", + "author_inst": "University of Zaragoza" + }, + { + "author_name": "Alberto Aleta", + "author_inst": "ISI Foundation" + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington" + }, + { + "author_name": "Romualdo Pastor-Satorras", + "author_inst": "Universitat Politecnica de Catalunya" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Northeastern University" + }, + { + "author_name": "Yamir Moreno", + "author_inst": "University of Zaragoza" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.18.21253931", "rel_title": "A convergence based assessment of relative differences in age-stratified susceptibility and infectiousness for SARS-CoV-2 variants of B.1.1.7 lineage", @@ -842238,77 +846613,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.03.17.21253739", - "rel_title": "Adapting French COVID-19 vaccination campaign duration to variant dissemination", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253739", - "rel_abs": "BackgroundThe outbreak of SARS-CoV-2 virus has caused a major international health crisis with serious consequences in terms of public health and economy. In France, two lockdown periods were decided in 2020 to avoid the saturation of intensive care units (ICU) and an increase in mortality. The rapid dissemination of variant SARS-CoV-2 VOC 202012/01 has strongly influenced the course of the epidemic. Vaccines have been rapidly developed. Their efficacy against the severe forms of the disease has been established, and their efficacy against disease transmission is under evaluation. The aim of this paper is to compare the efficacy of several vaccination strategies in the presence of variants in controlling the COVID-19 epidemic through population immunity.\n\nMethodsAn agent-based model was designed to simulate with different scenarios the evolution of COVID-19 pandemic in France over 2021 and 2022. The simulations were carried out ignoring the occurrence of variants then taking into account their diffusion over time. The expected effects of three Non-Pharmaceutical Interventions (Relaxed-NPI, Intensive-NPI, and Extended-NPI) to limit the epidemic extension were compared. The expected efficacy of vaccines were the values recently estimated in preventing severe forms of the disease (75% and 94%) for the current used vaccines in France (Pfizer-BioNTech and Moderna since January 11, 2021, and AstraZeneca since February 2, 2021). All vaccination campaigns reproduced an advanced age-based priority advised by the Haute Autorite de Sante. Putative reductions of virus transmission were fixed at 0, 50, 75 and 90%. The effects of four vaccination campaign durations (6-month, 12-month, 18-month and 24-month) were compared.\n\nResultsIn the absence of vaccination, the presence of variants led to reject the Relaxed-NPI because of a high expected number of deaths (170 to 210 thousands) and the significant overload of ICUs from which 35 thousand patients would be deprived. In comparison with the situation without vaccination, the number of deaths was divided by 7 without ICU saturation with a 6-month vaccination campaign. A 12-month campaign would divide the number of death by 3 with Intensive-NPI and by 6 with Extended-NPI (the latter being necessary to avoid ICU saturation). With 18-month and 24-month vaccination campaigns without Extended-NPI, the number of deaths and ICU admissions would explode.\n\nConclusionAmong the four compared strategies the 6-month vaccination campaign seems to be the best response to changes in the dynamics of the epidemic due to the variants. The race against the COVID-19 epidemic is a race of vaccination strategy. Any further vaccination delay would increase the need of strengthened measures such as Extended-NPI to limit the number of deaths and avoid ICU saturation.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Simon Pageaud", - "author_inst": "Univ Lyon, Universit\u00e9 Claude Bernard Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie Evolutive, UMR5558, F-69621, Villeurbanne, France; P\u00f4le Sant\u00e9 Publique, " - }, - { - "author_name": "Nicolas Ponthus", - "author_inst": "Univ Lyon, Ecole Centrale de Lyon, ENTPE, CNRS, Laboratoire de Tribologie et Dynamique des Syst\u00e8mes LTDS, UMR5513, F-69134, Ecully, France" - }, - { - "author_name": "Romain Gauchon", - "author_inst": "Univ Lyon, Universit\u00e9 Claude Bernard Lyon 1, Laboratoire de Sciences Actuarielle et Financi\u00e8re LSAF, ISFA, F-69007, Lyon, France" - }, - { - "author_name": "Catherine Pothier", - "author_inst": "Univ Lyon, INSA-Lyon, CNRS, Laboratoire d'InfoRmatique en Image et Syst\u00e8mes d'information LIRIS, UMR5205, F-69621, Villeurbanne, France" - }, - { - "author_name": "Christophe Rigotti", - "author_inst": "Univ Lyon, INSA-Lyon, CNRS, Laboratoire d'InfoRmatique en Image et Syst\u00e8mes d'information LIRIS, UMR5205, F-69621, Villeurbanne, France; INRIA, Grenoble-Rh\u00f4ne-A" - }, - { - "author_name": "Anne Eyraud-Loisel", - "author_inst": "Univ Lyon, Universit\u00e9 Claude Bernard Lyon 1, Laboratoire de Sciences Actuarielle et Financi\u00e8re LSAF, ISFA, F-69007, Lyon, France" - }, - { - "author_name": "Jean-Pierre Bertoglio", - "author_inst": "Univ Lyon, Ecole Centrale de Lyon, CNRS, Laboratoire de M\u00e9canique des Fluides et d'Acoustique LMFA, UMR5509, F-69130, Ecully, France" - }, - { - "author_name": "Alexis Bienven\u00fce", - "author_inst": "Univ Lyon, Universit\u00e9 Claude Bernard Lyon 1, Laboratoire de Sciences Actuarielle et Financi\u00e8re LSAF, ISFA, F-69007, Lyon, France" - }, - { - "author_name": "Fran\u00e7ois Gueyffier", - "author_inst": "Univ Lyon, Universit\u0107 Claude Bernard Lyon 1, CNRS, Laboratoire de Biom\u0107trie et Biologie Evolutive, UMR5558, F-69621, Villeurbanne, France; P\u00f4le Sant\u0107 Publique, " - }, - { - "author_name": "Philippe Vanhems", - "author_inst": "Public Health, Epidemiology and Eco-Evolution of Infectious Diseases, CIRI, Centre International de Recherche en Infectiologie, Univ Lyon, Inserm, U1111, Univer" - }, - { - "author_name": "Nicolas Leboisne", - "author_inst": "Univ Lyon, Universit\u00e9 Claude Bernard Lyon 1, Laboratoire de Sciences Actuarielle et Financi\u00e8re LSAF, ISFA, F-69007, Lyon, France" - }, - { - "author_name": "Jean Iwaz", - "author_inst": "Univ Lyon, Universit\u00e9 Claude Bernard Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie Evolutive, UMR5558, F-69621, Villeurbanne, France; Service de Biostatis" - }, - { - "author_name": "St\u00e9phane Loisel", - "author_inst": "Univ Lyon, Universit\u00e9 Claude Bernard Lyon 1, Laboratoire de Sciences Actuarielle et Financi\u00e8re LSAF, ISFA, F-69007, Lyon, France" - }, - { - "author_name": "Pascal Roy", - "author_inst": "Univ Lyon, Universit\u00e9 Claude Bernard Lyon 1, CNRS, Laboratoire de Biom\u00e9trie et Biologie Evolutive, UMR5558, F-69621, Villeurbanne, France; Service de Biostatis" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.16.21253742", "rel_title": "Modelling the population-level protection conferred by COVID-19 vaccination", @@ -843587,6 +847891,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.16.21253731", + "rel_title": "The Spike-specific IgA in milk commonly-elicited after SARS-Cov-2 infection is concurrent with a robust secretory antibody response, exhibits neutralization potency strongly correlated with IgA binding, and is highly durable over time", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253731", + "rel_abs": "Approximately 10% of infants will experience COVID-19 illness requiring advanced care (1). A potential mechanism to protect this population could be provided by passive immunity through the milk of a previously infected mother. We and others have reported on the presence of SARS-CoV-2-specific antibodies in human milk (2-5). We now report the prevalence of SARS-CoV-2 IgA in the milk of 75 COVID-19-recovered participants, and find that 88% of samples are positive for Spike-specific IgA. In a subset of these samples, 95% exhibited robust IgA activity as determined by endpoint binding titer, with 50% considered high-titer. These IgA positive specimens were also positive for Spike-specific antibodies bearing the secretory component. Levels of IgA antibodies and antibodies bearing secretory component were shown to be strongly positively correlated. The secretory IgA response was dominant among the milk samples tested compared to the IgG response, which was present in 75% of samples and found to be of high-titer in only 13% of cases. Our IgA durability analysis using 28 paired samples, obtained 4-6 weeks and 4-10 months after infection, found that all samples exhibited persistently significant Spike-specific IgA, with 43% of donors exhibiting increasing IgA titers over time. Finally, COVID-19 and pre-pandemic control milk samples were tested for the presence of neutralizing antibodies; 6 of 8 COVID-19 samples exhibited neutralization of Spike-pseudotyped VSV (IC50 range, 2.39 - 89.4ug/mL) compared to 1 of 8 controls. IgA binding and neutralization capacities were found to be strongly positively correlated. These data are highly relevant to public health, not only in terms of the protective capacity of these antibodies for breastfed infants, but also for the potential use of such antibodies as a COVID-19 therapeutic, given that secretory IgA is highly stable not only in milk and the infant mouth and gut, but in all mucosa including the gastrointestinal tract, upper airway, and lungs (6).", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alisa Fox", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jessica Marino", + "author_inst": "University of California, Merced" + }, + { + "author_name": "Fatima Amanat", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kasopefoluwa Y. Oguntuyo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jennifer Hahn-Holbrook", + "author_inst": "University of California, Merced" + }, + { + "author_name": "Benhur Lee", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Susan Zolla-Pazner", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Rebecca L Powell", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.03.17.21252673", "rel_title": "Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater; a use-case in the metropolitan area of Thessaloniki, Greece", @@ -843732,157 +848087,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.19.21253964", - "rel_title": "Longitudinal assessment of diagnostic test performance over the course of acute SARS-CoV-2 infection", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253964", - "rel_abs": "What is already known about this topic?Diagnostic tests and sample types for SARS-CoV-2 vary in sensitivity across the infection period.\n\nWhat is added by this report?We show that both RTqPCR (from nasal swab and saliva) and the Quidel SARS Sofia FIA rapid antigen tests peak in sensitivity during the period in which live virus can be detected in nasal swabs, but that the sensitivity of RTqPCR tests rises more rapidly in the pre-infectious period. We also use empirical data to estimate the sensitivities of RTqPCR and antigen tests as a function of testing frequency.\n\nWhat are the implications for public health practice?RTqPCR tests will be more effective than rapid antigen tests at identifying infected individuals prior to or early during the infectious period and thus for minimizing forward transmission (provided results reporting is timely). All modalities, including rapid antigen tests, showed >94% sensitivity to detect infection if used at least twice per week. Regular surveillance/screening using rapid antigen tests 2-3 times per week can be an effective strategy to achieve high sensitivity (>95%) for identifying infected individuals.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Rebecca L Smith", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Laura L Gibson", - "author_inst": "University of Massachusetts Medical School" - }, - { - "author_name": "Pamela P Martinez", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Ruian Ke", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Agha Mirza", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Madison Conte", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Nicholas Gallagher", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Abigail Conte", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Leyi Wang", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Rick Fredrickson", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Darci C Edmonson", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Melinda E Baughman", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Karen K Chiu", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Hannah Choi", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Tor W Jensen", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Kevin R Scardina", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Shannon Bradley", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Stacy L Gloss", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Crystal Reinhart", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Jagadeesh Yedetore", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Alyssa N Owens", - "author_inst": "University of Massachusetts Medical School" - }, - { - "author_name": "John Broach", - "author_inst": "UMass Memorial Medical Center" - }, - { - "author_name": "Bruce Barton", - "author_inst": "University of Massachusetts Medical School" - }, - { - "author_name": "Peter Lazar", - "author_inst": "University of Massachusetts Medical School" - }, - { - "author_name": "Darcy Henness", - "author_inst": "Carle Foundation Hospital" - }, - { - "author_name": "Todd Young", - "author_inst": "Carle Foundation Hospital" - }, - { - "author_name": "Alastair Dunnett", - "author_inst": "Carle Foundation Hospital" - }, - { - "author_name": "Matthew L Robinson", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Heba H Mostafa", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Andrew Pekosz", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Yukari C Manabe", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "William J Heetderks", - "author_inst": "National Institute for Biomedical Imaging and Bioengineering" - }, - { - "author_name": "David D McManus", - "author_inst": "University of Massachusetts Medical School" - }, - { - "author_name": "Christopher B Brooke", - "author_inst": "University of Illinois at Urbana-Champaign" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.18.21253861", "rel_title": "Hospitalization of mild cases of community-acquired pneumonia decreased more than severe ones during the COVID-19 epidemic", @@ -845537,6 +849741,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.13.21253527", + "rel_title": "PD-1highCXCR5-CD4+ Peripheral Helper T (Tph) cells Promote Tissue-Homing Plasmablasts in COVID-19", + "rel_date": "2021-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.13.21253527", + "rel_abs": "A dysregulated immune response against coronavirus-2 (SARS-CoV-2) plays a critical role in the outcome of patients with coronavirus disease 2019 (COVID-19). A significant increase in circulating plasmablasts is characteristic of COVID-19 though the underlying mechanisms and its prognostic implications are not known. Here, we demonstrate that in the acute phase of COVID-19, activated PD-1highCXCR5-CD4+ T cells, peripheral helper T cells, (Tph) are significantly increased and promote inflammatory tissue-homing plasmablasts in patients with stable but not severe COVID-19. Analysis of scRNA-seq data revealed that plasmablasts in stable patients express higher levels of tissue-homing receptors including CXCR3. The increased Tph cells exhibited \"B cell help\" signatures similar to that of circulating T follicular helper (cTfh) cells and promoted B cell differentiation in vitro. Compared with cTfh cells, Tph cells produced more IFN{gamma}, inducing tissue-homing chemokine receptors on plasmablasts. Finally, expansion of activated Tph cells was correlated with the frequency of CXCR3+ plasmablasts in the acute phase of patients with stable disease. Our results demonstrate a novel role for Tph cells in acute viral immunity by inducing ectopic, antibody secreting plasmablasts.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Hiromitsu Asashima", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Subhasis Mohanty", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Michela Comi", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "William E Ruff", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Kenneth B Hoehn", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Patrick Wong", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Inessa Cohen", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Sarah Coffey", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Khadir Raddassi", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Omkar Chaudhary", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Avraham Unterman", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Brinda Emu", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Steven H Kleinstein", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Ruth R Montgomery", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Charles S Dela Cruz", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Naftali Kaminski", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Albert C Shaw", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "David A Hafler", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Tomokazu S Sumida", + "author_inst": "Yale School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.03.15.21253619", "rel_title": "COVID-19 with early neurological and cardiac thromboembolic phenomena--timeline of incidence and clinical features", @@ -845670,57 +849969,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.14.21253561", - "rel_title": "Female gender and knowing a person positive for COVID-19 significantly increases fear levels in the Cuban population", - "rel_date": "2021-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.14.21253561", - "rel_abs": "The objective of this study was to explore the relationship between sociodemographic factors and fear of COVID-19 in a Cuban population. A web-based study with a cross-sectional design was conducted. The sample comprised 1145 participants. To explore fear, the Fear of COVID-19 Scale was used. Our results suggest that women were more likely to experience medium to high levels fear compared to men. Additionally, knowing a person positive to COVID-19 significantly increases fear levels in Cuban participants.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Yunier Broche-Perez", - "author_inst": "Universidad Central Marta Abreu de Las Villas" - }, - { - "author_name": "Zoylen Fernandez-Fleites", - "author_inst": "Universidad Central Marta Abreu de Las Villas" - }, - { - "author_name": "Evelyn Fernandez-Castillo", - "author_inst": "Universidad Central Marta Abreu de Las Villas" - }, - { - "author_name": "Elizabeth Jimenez-Puig", - "author_inst": "Universidad Central Marta Abreu de Las Villas" - }, - { - "author_name": "Dunia M Ferrer-Lozano", - "author_inst": "Universidad Central Marta abreu de Las Villas" - }, - { - "author_name": "Annia E Vizcaino- Escobar", - "author_inst": "Universidad Central Marta Abreu de Las Villas" - }, - { - "author_name": "Lesnay Martinez-Rodriguez", - "author_inst": "Universidad Central Marta Abreu de Las Villas" - }, - { - "author_name": "Reinier Martin-Gonzalez", - "author_inst": "Universidad Central Marta Abreu de Las Villas" - }, - { - "author_name": "Boris C Rodriguez-Martin", - "author_inst": "Funcacion RECAL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.03.14.21253548", "rel_title": "Characterizing altruistic motivation in potential volunteers for SARS-CoV-2 challenge trials", @@ -847283,6 +851531,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.16.435705", + "rel_title": "Identification of ACE2 mutations that modulate SARS-CoV-2 spike binding across multiple mammalian species", + "rel_date": "2021-03-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.16.435705", + "rel_abs": "Understanding how SARS-CoV-2 interacts with different mammalian angiotensin-converting enzyme II (ACE2) cell entry receptors elucidates determinants of virus transmission and facilitates development of vaccines for humans and animals. Yeast display-based directed evolution identified conserved ACE2 mutations that increase spike binding across multiple species. Gln42Leu increased ACE2-spike binding for human and four of four other mammalian ACE2s; Leu79Ile had a effect for human and three of three mammalian ACE2s. These residues are highly represented, 83% for Gln42 and 56% for Leu79, among mammalian ACE2s. The above findings can be important in protecting humans and animals from existing and future SARS-CoV-2 variants.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Pete Heinzelman", + "author_inst": "UW-Madison" + }, + { + "author_name": "Jonathan Greenhalgh", + "author_inst": "University of Wisconsin--Madison" + }, + { + "author_name": "Philip A Romero", + "author_inst": "UW-Madison" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.03.16.434488", "rel_title": "SARS-CoV-2 Spike receptor-binding domain with a G485R mutation in complex with human ACE2", @@ -847464,89 +851739,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.03.17.435637", - "rel_title": "Epigallocatechin Gallate from Green Tea Effectively Blocks Infection of SARS-CoV-2 and New Variants by Inhibiting Spike Binding to ACE2 Receptor", - "rel_date": "2021-03-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.17.435637", - "rel_abs": "As the COVID-19 pandemic rages on, the new SARS-CoV-2 variants have emerged in the different regions of the world. These newly emerged variants have mutations in their spike (S) protein that may confer resistance to vaccine-elicited immunity and existing neutralizing antibody therapeutics. Therefore, there is still an urgent need of safe, effective, and affordable agents for prevention/treatment of SARS-CoV-2 and its variant infection. Here, we demonstrated that green tea beverage (GTB) or its major ingredient, epigallocatechin gallate (EGCG), were highly effective in inhibiting infection of live SARS-CoV-2 and human coronavirus (HCoV OC43). In addition, infection of the pseudoviruses with spikes of the new variants (UK-B.1.1.7, SA-B.1.351, and CA-B.1.429) was efficiently blocked by GTB or EGCG. Among the 4 active green tea catechins at noncytotoxic doses, EGCG was the most potent in the action against the viruses. The highest inhibitory activity was observed when the viruses or the cells were pre-incubated with EGCG prior to the infection. Mechanistic studies revealed that EGCG blocked infection at the entry step through interfering with the engagement of the receptor binding domain (RBD) of the viral spikes to angiotensin-converting enzyme 2 (ACE2) receptor of the host cells. These data support further clinical evaluation and development of EGCG as a novel, safe, and cost-effective natural product for prevention/treatment of SARS-CoV-2 transmission and infection.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Jinbiao Liu", - "author_inst": "Temple University Lewis Katz School of Medicine" - }, - { - "author_name": "Brittany H Bodnar", - "author_inst": "Temple University Lewis Katz School of Medicine" - }, - { - "author_name": "Feng-Zhen Meng", - "author_inst": "Temple University Lewis Katz School of Medicine" - }, - { - "author_name": "Adil Khan", - "author_inst": "Temple University Lewis Katz School of Medicine" - }, - { - "author_name": "Xu Wang", - "author_inst": "Temple University Lewis Katz School of Medicine" - }, - { - "author_name": "Guangxiang George Luo", - "author_inst": "University of Alabama at Birmingham School of Medicine" - }, - { - "author_name": "Sami Saribas", - "author_inst": "Temple University Lewis Katz School of Medicine" - }, - { - "author_name": "Tao Wang", - "author_inst": "University of Nebraska-Lincoln" - }, - { - "author_name": "Saroj Chandra Lohani", - "author_inst": "University of Nebraska-Lincoln" - }, - { - "author_name": "Peng Wang", - "author_inst": "Temple University Lewis Katz School of Medicine" - }, - { - "author_name": "Zhengyu Wei", - "author_inst": "Temple University Lewis Katz School of Medicine" - }, - { - "author_name": "Jinjun Luo", - "author_inst": "Temple University Lewis Katz School of Medicine" - }, - { - "author_name": "Lina Zhou", - "author_inst": "Temple University Lewis Katz School of Medicine" - }, - { - "author_name": "Jianguo Wu", - "author_inst": "Jinan University" - }, - { - "author_name": "Qingsheng Li", - "author_inst": "University of Nebraska-Lincoln" - }, - { - "author_name": "Wenhui Hu", - "author_inst": "Temple University Lewis Katz School of Medicine" - }, - { - "author_name": "Wenzhe Ho", - "author_inst": "Temple University Lewis Katz School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.16.435741", "rel_title": "Structural basis of anti-SARS-CoV-2 activity of hydroxychloroquine: specific binding to NTD/CTD and disruption of LLPS of N protein", @@ -849509,6 +853701,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.11.21253404", + "rel_title": "COVID-19 Underreporting and its Impact on Vaccination Strategies", + "rel_date": "2021-03-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253404", + "rel_abs": "We present a novel methodology for the stable rate estimation of hospitalization and death related to the Corona Virus Disease 2019 (COVID-19) using publicly available reports from various distinct communities. These rates are then used to estimate underreported infections on the corresponding areas by making use of reported daily hospitalizations and deaths. The impact of underreporting infections on vaccination strategies is estimated under different disease-transmission scenarios using a Susceptible-Exposed-Infective-Removed-like (SEIR) epidemiological model.\n\nOne sentence SummaryUsing a novel methodology, we estimate COVID-19 underreporting from public data, quantifying its impact on vaccination.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vinicius V. L. Albani", + "author_inst": "Universidade Federal de Santa Catarina" + }, + { + "author_name": "Jennifer Loria", + "author_inst": "Instituto Nacional de Matematica Pura e Aplicada and Universidad de Costa Rica" + }, + { + "author_name": "Eduardo Massad", + "author_inst": "Fundacao Getulio Vargas" + }, + { + "author_name": "Jorge P. Zubelli", + "author_inst": "Khalifa University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.12.21253000", "rel_title": "Novel highly divergent SARS-CoV-2 lineage with the Spike substitutions L249S and E484K", @@ -849742,61 +853965,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.12.435191", - "rel_title": "A novel soluble ACE2 protein totally protects from lethal disease caused by SARS-CoV-2 infection", - "rel_date": "2021-03-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.12.435191", - "rel_abs": "Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) uses full-length angiotensin converting enzyme 2 (ACE2), which is membrane bound, as its initial cell contact receptor preceding viral entry. Here we report a human soluble ACE2 variant fused with a 5kD albumin binding domain (ABD) and bridged via a dimerization motif hinge-like 4-cysteine dodecapeptide, which we term ACE2 1-618-DDC-ABD. This protein is enzymatically active, has increased duration of action in vivo conferred by the ABD-tag, and displays 20-30-fold higher binding affinity to the SARS-CoV-2 receptor binding domain than its des-DDC monomeric form (ACE2 1-618-ABD) due to DDC-linked dimerization. ACE2 1-618-DDC-ABD was administered for 3 consecutive days to transgenic k18-hACE2 mice, a model that develops lethal SARS-CoV-2 infection, to evaluate the preclinical preventative/ therapeutic value for COVID-19. Mice treated with ACE2 1-618-DDC-ABD developed a mild to moderate disease for the first few days assessed by a clinical score and modest weight loss. The untreated control animals, by contrast, became severely ill and had to be sacrificed by day 6/7 and lung histology revealed extensive pulmonary alveolar hemorrhage and mononuclear infiltrates. At 6 days, mortality was totally prevented in the treated group, lung histopathology was improved and viral titers markedly reduced. This demonstrates for the first time in vivo the preventative/ therapeutic potential of a novel soluble ACE2 protein in a preclinical animal model.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Luise Hassler", - "author_inst": "Division of Nephrology/Hypertension, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois" - }, - { - "author_name": "Jan Wysocki", - "author_inst": "Division of Nephrology/Hypertension, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois" - }, - { - "author_name": "Ian Gelarden", - "author_inst": "Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois" - }, - { - "author_name": "Anastasia Tomatsidou", - "author_inst": "Department of Microbiology, The University of Chicago, Chicago, Illinois and Ricketts Regional Biocontainment Laboratory, University of Chicago, Lemont, Illinoi" - }, - { - "author_name": "Haley Gula", - "author_inst": "Department of Microbiology, The University of Chicago, Chicago, Illinois and Ricketts Regional Biocontainment Laboratory, University of Chicago, Lemont, Illinoi" - }, - { - "author_name": "Vlad Nicoleascu", - "author_inst": "Department of Microbiology, The University of Chicago, Chicago, Illinois and Ricketts Regional Biocontainment Laboratory, University of Chicago, Lemont, Illinoi" - }, - { - "author_name": "Glenn Randall", - "author_inst": "Department of Microbiology, The University of Chicago, Chicago, Illinois and Ricketts Regional Biocontainment Laboratory, University of Chicago, Lemont, Illinoi" - }, - { - "author_name": "Jack Henkin", - "author_inst": "Center for Developmental Therapeutics, Northwestern University, Evanston, IL, USA" - }, - { - "author_name": "Anjana Yeldandi", - "author_inst": "Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois" - }, - { - "author_name": "Daniel Batlle", - "author_inst": "Division of Nephrology/Hypertension, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, Illinois" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pathology" - }, { "rel_doi": "10.1101/2021.03.15.433877", "rel_title": "A map of direct SARS-CoV-2 protein interactions implicates specific human host processes", @@ -851843,6 +856011,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.12.21253484", + "rel_title": "Limits of lockdown: characterising essential contacts during strict physical distancing", + "rel_date": "2021-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253484", + "rel_abs": "COVID-19 has exposed health inequalities within countries and globally. The fundamental determining factor behind an individuals risk of infection is the number of social contacts they make. In many countries, physical distancing measures have been implemented to control transmission of SARS-CoV-2, reducing social contacts to a minimum. Characterising unavoidable social contacts is key for understanding the inequalities behind differential risks and planning vaccination programmes. We utilised an existing English longitudinal birth cohort, which is broadly representative of the wider population (n=6807), to explore social contact patterns and behaviours when strict physical distancing measures were in place during the UKs first lockdown in March-May 2020. Essential workers, specifically those in healthcare, had 4.5 times as many contacts as non-essential workers [incident rate ratio = 4.42 (CI95%: 3.88-5.04)], whilst essential workers in other sectors, mainly teaching and the police force had three times as many contacts [IRR = 2.84 (2.58-3.13)]. The number of individuals in a household, which is conflated by number of children, increases essential social contacts by 40%. Self-isolation effectively reduces numbers of contacts outside of the home, but not entirely. Together, these findings will aid the interpretation of epidemiological data and impact the design of effective SARS-CoV-2 control strategies, such as vaccination, testing and contact tracing.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Amy C Thomas", + "author_inst": "University of Bristol" + }, + { + "author_name": "Leon Danon", + "author_inst": "University of Bristol" + }, + { + "author_name": "Hannah Christensen", + "author_inst": "University of Bristol" + }, + { + "author_name": "Kate Northstone", + "author_inst": "University of Bristol" + }, + { + "author_name": "Daniel Smith", + "author_inst": "University of Bristol" + }, + { + "author_name": "Emily J Nixon", + "author_inst": "University of Bristol" + }, + { + "author_name": "Adam Trickey", + "author_inst": "University of Bristol" + }, + { + "author_name": "Gibran Hemani", + "author_inst": "University of Bristol" + }, + { + "author_name": "Sarah Sauchelli", + "author_inst": "NIHR Bristol Biomedical Research Centre, University of Bristol" + }, + { + "author_name": "Adam Finn", + "author_inst": "University of Bristol" + }, + { + "author_name": "Nicholas J Timpson", + "author_inst": "University of Bristol" + }, + { + "author_name": "Ellen Brooks-Pollock", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.12.21253493", "rel_title": "Seroprevalence of Antibodies to SARS-CoV-2 among Health Care Workers in Kenya", @@ -852164,45 +856395,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.13.21253499", - "rel_title": "Awake prone position in adult nonintubated patients with acute hypoxaemic respiratory failure secondary to COVID-19:A multi-centre feasibility randomized controlled trial", - "rel_date": "2021-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.13.21253499", - "rel_abs": "BackgroundThe primary manifestation of Corona Virus Disease -2019 (COVID-19) is acute hypoxic respiratory failure secondary to pneumonia and/or acute respiratory distress syndrome. Prone position has been shown to improve outcomes in ventilated patients with moderate to severe acute respiratory distress syndrome. The feasibility and safety of awake prone positioning and its impact on outcomes if any, in non-intubated patients with mild to moderate acute respiratory distress syndrome secondary to COVID-19 is unknown. Results of the observational studies published thus far in this pandemic have been conflicting. In this context, we conducted a multi-centre, parallel group, randomised controlled feasibility study on awake prone positioning in non-intubated patients with COVID-19 pneumonia requiring supplemental oxygen.\n\nMethods60 patients diagnosed with acute hypoxic respiratory failure secondary to COVID -19 pneumonia requiring 4 or more litres of oxygen to maintain a saturation of [≥] 92% were recruited in this study. Thirty patients each were randomised to either standard care or awake prone group. Patients randomised to the standard care were allowed to change their position as per comfort and patients randomized to the prone group were encouraged to self-prone for at least 6 hours a day. The primary outcome was the proportion of patients adhering to the protocol in each group. Secondary outcomes include failure of therapy leading to escalation of respiratory support, number of hours prone, maximum hours of continuous prone positioning in a day, length of stay in ICU, ICU mortality, total number of patients needing intubation and adverse events.\n\nResultsIn the prone group, 43% (13 out of 30) of patients were able to self-prone for 6 or more hours a day. The median maximum prone duration per session was 2 hours. In the supine group, 47% (14 out of 30) were completely supine and 53% spent some hours in the prone position, but none exceeded 6 hours. There was no significant difference in any of the secondary outcomes between the two groups and there were no adverse events.\n\nInterpretationAwake proning in non-intubated patients with acute hypoxic respiratory failure is feasible and safe under clinical trial conditions. The results of our feasibility study will potentially help in the design of larger definitive trials to address this key knowledge gap.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Devachandran Jayakumar", - "author_inst": "Apollo Speciality Hospital - OMR, Chennai, India" - }, - { - "author_name": "Pratheema Ramachandran", - "author_inst": "Apollo Speciality Hospital - OMR, Chennai, India" - }, - { - "author_name": "Ebenezer Rabindrarajan", - "author_inst": "Apollo Speciality Hospital - Vanagaram, Chennai, India" - }, - { - "author_name": "Bharathkumar Tirupakuzhi Vijayaraghavan", - "author_inst": "Apollo Hospital, Chennai, India" - }, - { - "author_name": "Ramakrishnan Nagarajan", - "author_inst": "Apollo Hospital, Chennai, India" - }, - { - "author_name": "Ramesh Venkataraman", - "author_inst": "Apollo Hospital, Chennai, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.03.12.21253490", "rel_title": "Serum Vitamin D levels are associated with increased COVID-19 severity markers and mortality independent of visceral adiposity", @@ -853845,6 +858037,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.10.21253260", + "rel_title": "Analytical and clinical performances of a SARS-CoV-2 S-RBD IgG assay: comparison with neutralization titers", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253260", + "rel_abs": "BackgroundSARS-CoV-2 serology presents an important role in understanding the virus epidemiology, in vaccine prioritization strategies and in convalescent plasma therapy. Immunoassays performances have to be accurately evaluated and correlated with neutralizing antibodies to be used as a surrogate measure of neutralizing activity. We investigate the analytical and clinical performance of a SARS-CoV-2 RBD IgG assay, automated on a high throughput platform, and the correlation of the antibodies (Ab) levels with the plaque reduction neutralization (PRNT50) Ab titers.\n\nMethodsA series of 546 samples were evaluated by SARS-CoV-2 RBD IgG assay (Snibe diagnostics), including 171 negative and 168 positive SARS-CoV-2 subjects and a further group of 207 subjects of the COVID-19 family clusters follow-up cohort.\n\nResultsAssay precision was acceptable at low and medium levels; linearity was excellent in all the measurement range. Considering specimens collected after 14 days post symptoms onset, overall sensitivity and specificity were 99.0% and 92.5%, respectively. A total of 281 leftover samples results of the PRNT50 test were available. An elevated correlation was obtained between the SARS-CoV-2 RBD IgG assay and the PRNT50 titer at univariate (rho = 0.689) and multivariate (rho = 0.712) analyses.\n\nConclusionsSARS-CoV-2 S-RBD IgG assay achieves elevated analytical and clinical performances, and a strong correlation with sera neutralization activity.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Andrea Padoan", + "author_inst": "university of padova" + }, + { + "author_name": "Francesco Bonfante", + "author_inst": "Istituto Zooprofilattico sperimentale delle venezie, legnaro, italy" + }, + { + "author_name": "Chiara Cosma", + "author_inst": "Department of Laboratory medicine, University-hospital of padova, italy" + }, + { + "author_name": "Costanza Di Chiara", + "author_inst": "Department of women's and children's health, university of padova" + }, + { + "author_name": "Laura Sciacovelli", + "author_inst": "Department of Laboratory Medicine, University-Hospital of Padova" + }, + { + "author_name": "Matteo Pagliari", + "author_inst": "Istituto zooprofilattico sperimentale delle venezie, legnaro, italy" + }, + { + "author_name": "Alessio Bortolami", + "author_inst": "Istituto zooprofilattico sperimentale delle venezie, legnaro, italy" + }, + { + "author_name": "Paola Costenaro", + "author_inst": "Department for Women's and Children's Health, University of Padova, Italy" + }, + { + "author_name": "Giulia Musso", + "author_inst": "Department of Laboratory Medicine, University-Hospital of Padova, Italy" + }, + { + "author_name": "Daniela Basso", + "author_inst": "University of Padova" + }, + { + "author_name": "Mario Plebani", + "author_inst": "University of Padova" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.10.21252711", "rel_title": "An In-House ELISA for SARS-CoV-2 RBD uncovers elevatedimmune response at higher altitudes", @@ -854030,33 +858281,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.09.21253198", - "rel_title": "Efficacy of SARS-CoV-2 Repeat Testing to Control Spread in Residential College Populations", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253198", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWUniversities have turned to SARS-CoV-2 models to examine campus reopening strategies 1-9. While these studies have explored a variety of modeling techniques, all have relied on simulated data. Here, we use an empirical proximity network of college freshmen 10, ascertained using smartphone Bluetooth, to simulate the spread of the virus. We investigate the role of testing, isolation, mask wearing, and social distancing in the presence of implementation challenges and imperfect compliance. Here we show that while frequent testing can drastically reduce spread if mask wearing and social distancing are not widely adopted, testing has limited impact if they are ubiquitous. Furthermore, even moderate levels of immunity can significantly reduce new infections, especially when combined with other interventions. Our findings suggest that while testing and isolation are powerful tools, they have limited benefit if other interventions are widely adopted. If universities can attain high levels of masking and social distancing, they may be able to relax testing frequency to once every two to four weeks.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Hali L Hambridge", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Rebecca Kahn", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Jukka-Pekka Onnela", - "author_inst": "Harvard T.H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.09.21252450", "rel_title": "Rapid screening for SARS-CoV-2 variants of concern in clinical and environmental samples using nested RT-PCR assays targeting key mutations of the Spike protein", @@ -855671,6 +859895,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.10.21253322", + "rel_title": "A Dynamical Map to Describe Covid-19 Epidemics", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253322", + "rel_abs": "Nonlinear dynamics perspective is an interesting approach to describe COVID-19 epidemics, providing information to support strategic decisions. This paper proposes a dynamical map to describe COVID-19 epidemics based on the classical susceptible-exposed-infected-recovered (SEIR) differential model, incorporating vaccinated population. On this basis, the novel map represents COVID-19 discrete-time dynamics by adopting three populations: infected, cumulative infected and vaccinated. The map promotes a dynamical description based on algebraic equations with a reduced number of variables and, due to its simplicity, it is easier to perform parameter adjustments. In addition, the map description allows analytical calculations of useful information to evaluate the epidemic scenario, being important to support strategic decisions. In this regard, it should be pointed out the estimation of the number death cases, infectious rate and the herd immunization point. Numerical simulations show the model capability to describe COVID-19 dynamics, capturing the main features of the epidemic evolution. Reported data from Germany, Italy and Brazil are of concern showing the map ability to describe different scenario patterns that include multi-wave and plateaus behaviors. The effect of vaccination is analyzed considering different campaign strategies, showing its importance to control the epidemics.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Eduardo Villela M. dos Reis", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Marcelo A. Savi", + "author_inst": "Universidade Federal do Rio de Janeiro" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.10.21253259", "rel_title": "Evaluation of Measles Surveillance System amidst Covid 19 pandemic in Asutifi North District, Ahafo Region, Ghana.", @@ -855824,65 +860071,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.10.21253299", - "rel_title": "SARS-CoV-2 Serology Status Detected by Commercialized Platforms Distinguishes Previous Infection and Vaccination Adaptive Immune Responses", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253299", - "rel_abs": "BackgroundThe severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected over 110 million individuals and led to 2.5 million deaths worldwide. As more individuals are vaccinated, the clinical performance and utility of SARS-CoV-2 serology platforms needs to be evaluated.\n\nMethodsThe ability of four commercial SARS-CoV-2 serology platforms to detect previous infection or vaccination were evaluated using a cohort of 53 SARS-CoV-2 PCR-positive patients, 89 SARS-CoV-2-vaccinated healthcare workers (Pfizer or Moderna), and 127 SARS-CoV-2 negative patients. Serology results were compared to a cell based SARS-CoV-2 pseudovirus (PSV) neutralizing antibodies assay.\n\nResultsThe Roche S-(spike) antibody and Diazyme neutralizing antibodies (NAbs) assays detected adaptive immune response in 100.0% and 90.1% of vaccinated individuals who received two-doses of vaccine (initial and booster), respectively. The Roche N-(nucleocapsid) antibody assay and Diazyme IgG assay did not detect adaptive immune response in vaccinated individuals. The Diazyme Nabs assay correlated with the PSV SARS-CoV-2 ID50 neutralization titers (R2= 0.70), while correlation of the Roche S-antibody assay was weaker (R2= 0.39). Median PSV SARS-CoV-2 ID50 titers more than doubled in vaccinated individuals who received two-doses of the Moderna vaccine (ID50: 597) compared to individuals that received a single dose (ID50: 284).\n\nConclusionsThe Roche S-antibody and Diazyme NAbs assays robustly detected adaptive immune responses in SARS-CoV-2 vaccinated individuals and SARS-CoV-2 infected individuals. The Diazyme NAbs assay strongly correlates with the PSV SARS-CoV-2 NAbs in vaccinated individuals. Understanding the reactivity of commercially available serology platforms is important when distinguishing vaccination response versus natural infection.\n\nSummaryThe Roche S (spike protein)-antibody and Diazyme neutralizing-antibodies (NAbs) assays were evaluated for their clinical utility in the detection of SARS-CoV-2 related adaptive immune responses by testing SARS-CoV-2 PCR-confirmed patients, SARS-CoV-2-vaccinated individuals, and SARS-CoV-2-negative individuals. Commercial serology results were compared to results generated using a cell-based SARS-CoV-2 pseudovirus (PSV) NAbs assay and previously validated SARS-CoV-2 commercial serology assays (Roche N (nucleocapsid protein) antibody and Diazyme IgG). We demonstrate that the Roche S-antibody and Diazyme NAbs assays detected adaptive immune response in SARS-CoV-2 vaccinated individuals and the presence of SARS-CoV-2 PSV NAbs. The Roche S-antibody assay had an observed positive percent agreement (PPA) of 100% for individuals who received two doses of the Pfizer or Moderna vaccine. By contrast, the Roche N assay and Diazyme IgG assay did not detect vaccine adaptive immune responses. Our findings also indicate that the Diazyme NAbs assay correlates strongly with the levels of SARS-CoV-2 ID50 neutralization titers using the PSV Nab assay in vaccinated individuals.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Raymond T Suhandynata", - "author_inst": "UCSD" - }, - { - "author_name": "Nicholas J Bevins", - "author_inst": "UCSD" - }, - { - "author_name": "Jenny T Tran", - "author_inst": "The Scripps Research Institution" - }, - { - "author_name": "Deli Huang", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Melissa A Hoffman", - "author_inst": "Vividion Therapeutics" - }, - { - "author_name": "Kyle Lund", - "author_inst": "UCSD" - }, - { - "author_name": "Michael J Kelner", - "author_inst": "UCSD" - }, - { - "author_name": "Ronald W McLawhon", - "author_inst": "UCSD" - }, - { - "author_name": "Steven L Gonias", - "author_inst": "UCSD" - }, - { - "author_name": "David Nemazee", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Robert L Fitzgerald", - "author_inst": "UCSD" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.10.21253285", "rel_title": "A tale of three SARS-CoV-2 variants with independently acquired P681H mutations in New York State", @@ -857201,6 +861389,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.11.21253367", + "rel_title": "SARS-CoV-2 specific immune-signature in direct contacts of COVID-19 cases protect them from contracting disease: A Retrospective Study", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253367", + "rel_abs": "The response to SARS-CoV-2 is largely impacted by the level of exposure and the status of immunity. The nature of protection shown by direct contacts of COVID-19 positive patients is quite intriguing to note. We aimed to study the immune differences reinforcing contact individuals in circumventing the disease. Our observation showed direct contacts of PCR positive patients developed elevated neutralizing antibody titres and cytokine levels. On the other hand, single cell data revealed differential usage of V(D)J genes and unique BCR clonotypes imparting protective immune signatures.\n\nTopicsserologic tests, immunoglobulin a, immunoglobulin g, immunoglobulin m, antibody titre; cytokine levels; virus neutralization; V(D)J sequencing; BCR clonotypes", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Sunil K. Raghav", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Kaushik Sen", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Arup Ghosh", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Sudeshna Datta", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Abdul Ahad", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Atimukta Jha", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Sanchari Chatterjee", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Sandhya Suranjika", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Soumya Sengupta", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Gargee Bhattacharya", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Omprakash Shriwas", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Kiran Avula", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Jayasingh Kshatri", + "author_inst": "ICMR-Regional Medical Research Center" + }, + { + "author_name": "Punit Prasad", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Ajay K. Parida", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.09.21253218", "rel_title": "An observational cohort study on the incidence of SARS-CoV-2 infection and B.1.1.7 variant infection in healthcare workers by antibody and vaccination status", @@ -857590,53 +861853,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.09.21253220", - "rel_title": "Leg-heel chest compression as an alternative for medical professionals in times of COVID-19", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253220", - "rel_abs": "ObjectiveTo evaluate leg-heel chest compression without previous training as an alternative for medical professionals and its effects on distance to potential aerosol spread during chest compression.\n\nMethods20 medical professionals performed standard manual chest compression followed by leg-heel chest compression after a brief instruction on a manikin. We compared percentage of correct chest compression position, percentage of full chest recoil, percentage of correct compression depth, average compression depth, percentage of correct compression rate and average compression rate between both methods. In a second approach, potential aerosol spread during chest compression was visualized.\n\nResultsThere was no significant difference between manual and leg-heel compression. The distance to potential aerosol spread could have been increased by leg-heel method.\n\nConclusionUnder special circumstances like COVID-19-pandemic, leg-heel chest compression may be an effective alternative without previous training compared to manual chest compression while markedly increasing the distance to the patient.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Matthias Ott", - "author_inst": "Klinikum Stuttgart" - }, - { - "author_name": "Alexander Krohn", - "author_inst": "Klinikum Stuttgart" - }, - { - "author_name": "Laurence H. Bilfield", - "author_inst": "Cleveland, Ohio" - }, - { - "author_name": "Florian Dengler", - "author_inst": "Klinikum Stuttgart" - }, - { - "author_name": "Christina Jaki", - "author_inst": "Klinikum Stuttgart" - }, - { - "author_name": "Fabian Echterdiek", - "author_inst": "Klinikum Stuttgart" - }, - { - "author_name": "Tobias Schilling", - "author_inst": "Klinikum Stuttgart" - }, - { - "author_name": "Johannes Heymer", - "author_inst": "Klinikum Stuttgart" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2021.03.11.21253380", "rel_title": "Comparing COVID-19 risk factors in Brazil using machine learning: the importance of socioeconomic, demographic and structural factors", @@ -858854,6 +863070,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.11.434841", + "rel_title": "Antibody responses to SARS-CoV-2 mRNA vaccines are detectable in saliva", + "rel_date": "2021-03-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.11.434841", + "rel_abs": "Vaccines are critical for curtailing the COVID-19 pandemic (1, 2). In the USA, two highly protective mRNA vaccines are available: BNT162b2 from Pfizer/BioNTech and mRNA-1273 from Moderna (3, 4). These vaccines induce antibodies to the SARS-CoV-2 S-protein, including neutralizing antibodies (NAbs) predominantly directed against the Receptor Binding Domain (RBD) (1-4). Serum NAbs are induced at modest levels within [~]1 week of the first dose, but their titers are strongly boosted by a second dose at 3 (BNT162b2) or 4 weeks (mRNA-1273) (3, 4). SARS-CoV-2 is most commonly transmitted nasally or orally and infects cells in the mucosae of the respiratory and to some extent also the gastrointestinal tract (5). Although serum NAbs may be a correlate of protection against COVID-19, mucosal antibodies might directly prevent or limit virus acquisition by the nasal, oral and conjunctival routes (5). Whether the mRNA vaccines induce mucosal immunity has not been studied. Here, we report that antibodies to the S-protein and its RBD are present in saliva samples from mRNA-vaccinated healthcare workers (HCW). Within 1-2 weeks after their second dose, 37/37 and 8/8 recipients of the Pfizer and Moderna vaccines, respectively, had S-protein IgG antibodies in their saliva, while IgA was detected in a substantial proportion. These observations may be relevant to vaccine-mediated protection from SARS-CoV-2 infection and disease.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Thomas J. Ketas", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Devidas Chaturbhuj", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Victor Cruz Portillo", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Erik Francomano", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Encouse Golden", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Sharanya Chandrasekhar", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Gargi Debnath", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Randy Diaz Tapia", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Anila Yasmeen", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Wilhem Leconet", + "author_inst": "Genmab" + }, + { + "author_name": "Zhen Zhao", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Philip J.M. Brouwer", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Melissa M. Cushing", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Rogier Sanders", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Albert Cupo", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Per Johan Klasse", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Silvia C. Formenti", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "John P. Moore", + "author_inst": "Weill Cornell Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.11.434937", "rel_title": "SARS-CoV-2 comprehensive receptor profiling: mechanistic insight to drive new therapeutic strategies", @@ -859011,29 +863314,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.08.21253144", - "rel_title": "Factors influencing COVID rates at local authority level and contribution of variation in vaccine coverage", - "rel_date": "2021-03-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21253144", - "rel_abs": "We have undertaken a piece of rapid analysis of the most recent COVID-19 weekly rates to examine commonalities across areas with rates exceeding twice the national average. Our preliminary findings point towards an association between higher case rates and deprivation with implications for health inequalities. Furthermore, we also observed an association between higher case rates and lower rates of vaccination. More analysis is needed to further explore these linkages and help fuel what should be an urgent narrative around the need to tackle health inequalities in the COVID era.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rachel Cullum", - "author_inst": "Suffolk County Council" - }, - { - "author_name": "Padmanabhan Badrinath", - "author_inst": "Suffolk County Council" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.10.434828", "rel_title": "Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants", @@ -860807,6 +865087,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.09.21252764", + "rel_title": "A High Rate of COVID-19 Vaccine Hesitancy Among Arabs: Results of a Large-scale Survey", + "rel_date": "2021-03-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21252764", + "rel_abs": "In this study, we present the results of the first large-scale multinational study (36,220 participants) that measures vaccine hesitancy among Arab-speaking subjects. Our analysis shows a significant rate of vaccine hesitancy among Arabs in and outside the Arab region (83% and 81%, respectively). The most cited reasons for hesitancy are concerns about side effects and distrust in healthcare policies, vaccine expedited production, published studies and vaccine producing companies. We also found that female participants, participants 30-59 year-old, those with no chronic diseases, those with lower-level of academic education, and those who do not know the type of vaccine authorized in their countries are more hesitant to receive COVID-19 vaccination. On the other hand, participants who regularly receive the influenza vaccine, health care workers, and those from countries with higher rates of COVID-19 infections showed more vaccination willingness. Interactive representation of our results is posted on our project website at https://mainapp.shinyapps.io/CVHAA.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Eyad A. Qunaibi", + "author_inst": "Department of Pharmaceutical Sciences, Jerash Private University, Jerash, Jordan" + }, + { + "author_name": "Mohamed Helmy", + "author_inst": "Agency for Science, Research and Technology" + }, + { + "author_name": "Iman Basheti", + "author_inst": "Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman, Jordan" + }, + { + "author_name": "Iyad Sultan", + "author_inst": "King Hussein Cancer Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.08.21253141", "rel_title": "COVID-19 is associated with multiple sclerosis exacerbations that are prevented by disease modifying therapies", @@ -861048,53 +865359,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.08.21253065", - "rel_title": "Impact of previous COVID-19 on immune response after a single dose of BNT162b2 SARS-CoV-2 vaccine", - "rel_date": "2021-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21253065", - "rel_abs": "Immune response after a single-dose of BNT162b2 vaccine is markedly increased in health care workers with previous SARS-CoV2 exposure, as assessed by positive SARS-CoV2 IgG, particularly after moderate-severe COVID-19. These data may inform the priority of the boosting mRNA second dose in times of vaccine shortage.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Maria Velasco", - "author_inst": "Hospital Universitario Fundacion Alcorcon" - }, - { - "author_name": "Maria Isabel Galan", - "author_inst": "Hospital Universitario Fundacion Alcorcon" - }, - { - "author_name": "Maria Luisa Casas", - "author_inst": "Hospital Universitario Fundacion Alcorcon" - }, - { - "author_name": "Elia Perez-Fernandez", - "author_inst": "Hospital Universitario Fundacion Alcorcon" - }, - { - "author_name": "Diana Martinez-Ponce", - "author_inst": "Hospital Universitario Fundacion Alcorcon" - }, - { - "author_name": "Beatriz Gonzalez-Pinyeiro", - "author_inst": "Hospital Universitario Fundacion Alcorcon" - }, - { - "author_name": "Virgilio Castilla", - "author_inst": "Hospital Universitario Fundacion Alcorcon" - }, - { - "author_name": "Carlos Guijarro", - "author_inst": "Hospital Universitario Fundacion Alcorcon" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.10.434722", "rel_title": "Structure and dynamics of the SARS-CoV-2 envelope protein monomer", @@ -863265,6 +867529,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.08.21252839", + "rel_title": "Transmission of SARS-CoV-2 by children attending school. Interim report on an observational, longitudinal sampling study of infected children, contacts, and the environment", + "rel_date": "2021-03-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21252839", + "rel_abs": "BackgroundAssessing transmission of SARS-CoV-2 by children in schools is of critical importance to inform public health action. We assessed frequency of acquisition of SARS-CoV-2 by contacts of children with COVID-19 in schools and households, as well as the amount of virus shed into the air and onto fomites in both settings.\n\nMethodsCases of COVID-19 in children in London schools were identified via notification. Weekly sampling for 3-4 weeks and PCR testing for SARS-CoV-2 of immediate classroom contacts (the \"bubble\"), non-bubble school contacts, and household contacts was undertaken supported by genome sequencing, along with surface and air sampling in the school and home environment.\n\nResultsWithin schools, secondary transmission was not detected in 28 individual bubble contacts, representing 10 distinct bubble classes. Across 8 non-bubble classes, 3/62 pupils tested positive- all three were asymptomatic and tested positive in one setting on the same day, unrelated to the original index case. In contrast, the secondary attack rate in naive household contacts was 14.3% (5/35) rising to 19.1% (9/47) when considering all household contacts. Environmental contamination with SARS-CoV-2 was rare in schools, regardless of school type; fomite SARS-CoV-2 RNA was identified in 4/189 (2.1%) samples in bubble classrooms, 2/127 (1.6%) samples in non-bubble classrooms, and 5/130 (3.8%) samples in washrooms. This contrasted with fomites in households, where SARS-CoV-2 RNA was identified in 60/248 (24.2%) bedroom samples, 66/241 (27.4%) communal room samples, and 21/188 (11.2%) bathroom samples. Air sampling identified SARS-CoV-2 RNA in just 1/68 (1.5%) of school air samples, compared with 21/85 (24.7%) of air samples taken in homes.\n\nSummaryThe low levels of environmental contamination in schools are consistent with low transmission frequency and adequate levels of cleaning and ventilation in schools during the period of study. Secondary transmission in schools was rare. The high frequency of secondary transmission in households associated with evident viral shedding throughout the home suggests a need to improve advice to households with infection in children in order to prevent onward community spread by sibling and adult contacts. The data highlight that transmission from children is very likely to occur when precautions are reduced.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Rebecca Cordery", + "author_inst": "Public Health England" + }, + { + "author_name": "Lucy Reeves", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jie Zhou", + "author_inst": "Imperial College London" + }, + { + "author_name": "Aileen G. Rowan", + "author_inst": "Imperial College London" + }, + { + "author_name": "Patricia Watber", + "author_inst": "Imperial College London" + }, + { + "author_name": "Carolina Rosadas", + "author_inst": "Imperial College London" + }, + { + "author_name": "Michael Andrew Crone", + "author_inst": "Imperial College London" + }, + { + "author_name": "Marko Storch", + "author_inst": "Imperial College London" + }, + { + "author_name": "Paul Freemont", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lucy Mosscrop", + "author_inst": "Imperial College London" + }, + { + "author_name": "Alice Cowley", + "author_inst": "Public Health England" + }, + { + "author_name": "Gina Zelent", + "author_inst": "Public Health England" + }, + { + "author_name": "Kate Bisset", + "author_inst": "Public Health England" + }, + { + "author_name": "Holly LeBlond", + "author_inst": "Public Health England" + }, + { + "author_name": "Sadie Regmi", + "author_inst": "Public Health England" + }, + { + "author_name": "Christian Buckingham", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ramlah Junaideen", + "author_inst": "Imperial College London" + }, + { + "author_name": "Nadia Abdulla", + "author_inst": "Imperial College London" + }, + { + "author_name": "Joseph Eliahoo", + "author_inst": "Imperial College London" + }, + { + "author_name": "Miranda Mindlin", + "author_inst": "Public Health England" + }, + { + "author_name": "Theresa Lamagni", + "author_inst": "Public Health England" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Imperial College London" + }, + { + "author_name": "Graham P Taylor", + "author_inst": "Imperial College London" + }, + { + "author_name": "Shiranee Sriskandan", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.08.21252200", "rel_title": "Vaccine effectiveness after 1st and 2nd dose of the BNT162b2 mRNA Covid-19 Vaccine in long-term care facility residents and healthcare workers - a Danish cohort study", @@ -863466,73 +867841,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.03.08.434499", - "rel_title": "The N501Y spike substitution enhances SARS-CoV-2 transmission", - "rel_date": "2021-03-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.08.434499", - "rel_abs": "Beginning in the summer of 2020, a variant of SARS-CoV-2, the cause of the COVID-19 pandemic, emerged in the United Kingdom (UK). This B.1.1.7 variant increased rapidly in prevalence among sequenced strains, attributed to an increase in infection and/or transmission efficiency. The UK variant has 19 nonsynonymous mutations across its viral genome including 8 substitutions or deletions in the spike protein, which interacts with cellular receptors to mediate infection and tropism. Here, using a reverse genetics approach, we show that, of the 8 individual spike protein substitutions, only N501Y exhibited consistent fitness gains for replication in the upper airway in the hamster model as well as primary human airway epithelial cells. The N501Y substitution recapitulated the phenotype of enhanced viral transmission seen with the combined 8 UK spike mutations, suggesting it is a major determinant responsible for increased transmission of this variant. Mechanistically, the N501Y substitution improved the affinity of the viral spike protein for cellular receptors. As suggested by its convergent evolution in Brazil and South Africa, our results indicate that N501Y substitution is a major adaptive spike mutation of major concern.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Yang Liu", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Jianying Liu", - "author_inst": "UTMB" - }, - { - "author_name": "Kenneth S. Plante", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Jessica A. Plante", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Xuping Xie", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Xianwen Zhang", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Zhiqiang Ku", - "author_inst": "Institute of Molecular Medicine" - }, - { - "author_name": "Zhiqiang An", - "author_inst": "The University of Texas Health Science Center at Houston" - }, - { - "author_name": "Dionna Scharton", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Craig Schindewolf", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Vineet D Menachery", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Scott C. Weaver", - "author_inst": "University of Texas Medical Branch" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.08.434433", "rel_title": "Systemic Tissue and Cellular Disruption from SARS-CoV-2 Infection revealed in COVID-19 Autopsies and Spatial Omics Tissue Maps", @@ -865703,6 +870011,33 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.03.06.434059", + "rel_title": "Structural Analysis of Spike Protein Mutations in an Emergent SARS-CoV-2 Variant from the Philippines", + "rel_date": "2021-03-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.06.434059", + "rel_abs": "A SARS-CoV-2 lineage designated as P.3 with multiple signature mutations in the Spike protein region was recently reported with cases from the Central Visayas Region of the Philippines. Whole genome sequencing revealed that the 33 samples under this lineage all contain the E484K, N501Y, and P681H Spike mutations previously found in variants of concern (VOC) such as the B.1.351, the P.1 and B.1.1.7 variants first reported in South Africa, Brazil, and the United Kingdom, respectively. The possible implications of the mutations found in the Spike protein of P.3 were analyzed for their potential effects on structure, stability, and molecular surface character. The analysis suggests that these mutations could significantly impact the possible interactions of the Spike protein with the ACE2 receptor and neutralizing antibodies, and warrants further clinical investigation. Some of the mutations affecting the N and C terminal domains may have effects on Spike monomer and trimer stability. This report provides insights on relevant targets for the design of future diagnostics, therapeutics and vaccines against the evolving SARS-CoV-2 variants in the Philippines.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Neil Andrew David Bascos", + "author_inst": "University of the Philippines Diliman" + }, + { + "author_name": "Denise Mirano-Bascos", + "author_inst": "University of the Philippines Diliman" + }, + { + "author_name": "Cynthia Palmes Saloma", + "author_inst": "University of the Philippines" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.03.08.434390", "rel_title": "Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses", @@ -865824,53 +870159,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.03.04.21252889", - "rel_title": "We also deserve help during the pandemic: The effect of the COVID-19 pandemic on foreign domestic workers in Hong Kong", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252889", - "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic poses particular challenges for migrant workers around the world. This study explores the unique experiences of foreign domestic workers (FDWs) in Hong Kong, and how COVID-19 impacted their health and economic wellbeing. Interviews with FDWs (n = 15) and key informants (n = 3) were conducted between May and August 2020. FDWs reported a dual-country experience of the pandemic, where they expressed concerns about local transmission risks as well as worries about their family members in their home country. Changes to their current work situation included how their employers treated them, as well as their employment status. FDWs also cited blind spots in the Hong Kong policy response that also affected their experience of the pandemic, including a lack of support from the Hong Kong government. Additional support is needed to mitigate the particularly negative effects of the pandemic on FDWs.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ingrid D Lui", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Nimisha Vandan", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Sara E. Davies", - "author_inst": "Griffith University" - }, - { - "author_name": "Sophie Harman", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Rosemary Morgan", - "author_inst": "Johns Hopkins University Bloomberg School of Public Health" - }, - { - "author_name": "Julia Smith", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Clare Wenham", - "author_inst": "London School of Economics and Political Science (LSE)" - }, - { - "author_name": "Karen Ann Gr\u00e9pin", - "author_inst": "University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.26.21252096", "rel_title": "Self-reported real-world safety and reactogenicity of COVID-19 vaccines: An international vaccine-recipient survey.", @@ -867261,6 +871549,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.04.21252658", + "rel_title": "SARS-CoV-2-specific T Cell Memory is Sustained in COVID-19 Convalescents for 8 Months with Successful Development of Stem Cell-like Memory T Cells", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252658", + "rel_abs": "Memory T cells contribute to rapid viral clearance during re-infection, but the longevity and differentiation of SARS-CoV-2-specific memory T cells remain unclear. We conducted direct ex vivo assays to evaluate SARS-CoV-2-specific CD4+ and CD8+ T cell responses in COVID-19 convalescents up to 254 days post-symptom onset (DPSO). Here, we report that memory T cell responses were maintained during the study period. In particular, we observed sustained polyfunctionality and proliferation capacity of SARS-CoV-2-specific T cells. Among SARS-CoV-2-specific CD4+ and CD8+ T cells detected by activation-induced markers, the proportion of stem cell-like memory T (TSCM) cells increased, peaking at approximately 120 DPSO. Development of TSCM cells was confirmed by SARS-CoV-2-specific MHC-I multimer staining. Considering the self-renewal capacity and multipotency of TSCM cells, our data suggest that SARS-CoV-2-specific T cells are long-lasting after recovery from COVID-19. The current study provides insight for establishing an effective vaccination program and epidemiological measurement.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Jae Hyung Jung", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Min-Seok Rha", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Moa Sa", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Hee Kyoung Choi", + "author_inst": "Korea University College of Medicine, Ansan Hospital" + }, + { + "author_name": "Ji Hoon Jeon", + "author_inst": "Korea University College of Medicine, Ansan Hospital" + }, + { + "author_name": "Hyeri Seok", + "author_inst": "Korea University College of Medicine, Ansan Hospital" + }, + { + "author_name": "Dae Won Park", + "author_inst": "Korea University College of Medicine, Ansan Hospital" + }, + { + "author_name": "Su-Hyung Park", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Hye Won Jeong", + "author_inst": "Chungbuk National University College of Medicine" + }, + { + "author_name": "Won Suk Choi", + "author_inst": "Korea University College of Medicine, Ansan Hospital" + }, + { + "author_name": "Eui-Cheol Shin", + "author_inst": "Korea Advanced Institute of Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.04.21252528", "rel_title": "Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England", @@ -867594,49 +871941,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.05.21249174", - "rel_title": "Serological surveys to estimate cumulative incidence of SARS-CoV-2 infection in adults (Sero-MAss study), Massachusetts, July-August 2020", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.05.21249174", - "rel_abs": "BackgroundThe SARS-CoV-2 pandemic is an unprecedented global health crisis. The state of Massachusetts was especially impacted during the initial stages; however, the extent of asymptomatic transmission remains poorly understood due to limited asymptomatic testing in the \"first wave.\" To address this gap, a geographically representative and contact-free seroprevalence survey was conducted in July-August 2020, to estimate prior undetected SARS-CoV-2 infections.\n\nMethodsStudents, faculty, librarians and staff members at the University of Massachusetts, Amherst without a previous COVID-19 diagnosis were invited to participate in this study along with one member of their household in June 2020. Two separate sampling frames were generated from administrative lists: all undergraduates and their household members (primary sampling group) were randomly selected with probability proportional to population size. All staff, faculty, graduate students and librarians (secondary sampling group) were selected as a simple random sample. After informed consent and a socio-behavioral survey, participants were mailed test kits and asked to return self-collected dried blood spot (DBS) samples. Samples were analyzed via ELISA for anti-SARS-CoV-2 IgG antibodies, and then IgM antibodies if IgG-positive. Seroprevalence estimates were adjusted for survey non-response. Binomial models were used to assess factors associated with seropositivity in both sample groups separately.\n\nResultsApproximately 27,000 persons were invited via email to assess eligibility. Of the 1,001 individuals invited to participate in the study, 762 (76%) returned blood samples for analysis. In the primary sampling group 548 returned samples, of which 230 enrolled a household member. Within the secondary sampling group of 214 individuals, 79 enrolled a household member. In the primary sample group, 36 (4.6%) had IgG antibodies detected for an estimated weighed prevalence for this population of 5.3% (95% CI: 3.5 to 8.0). In the secondary sampling group, 10 (3.4%) of 292 individuals had IgG antibodies detected for an estimated adjusted prevalence of 4.0% (95% CI: 2.2 to 7.4). No samples were IgM positive. No association was found in either sample group between seropositivity and self-reported work duties or customer-facing hours. In the primary sampling group, self-reported febrile illness since Feb 2020, male sex, and minority race (Black or American Indian/Alaskan Native) were associated with seropositivity. No factors except geographic regions within the state were associated with evidence of prior SARS-CoV-2 infection in the secondary sampling group.\n\nInterpretationThis study provides insight into the seroprevalence of university-related populations and their household members across the state of Massachusetts during the summer of 2020 of the pandemic and helps to fill a critical gap in estimating the levels of sub-clinical and asymptomatic infection. Estimates like these can be used to calibrate models that estimate levels of population immunity over time to inform public health interventions and policy.\n\nFundingUMass Faculty Fund (A Lover); UMass Faculty Discretionary Funds (N Reich); UMass Institute for Applied Life Science \"Midigrant\" (#169076; A. Lover); and D. Alfandari was supported by grants from the USPHS (R24OD021485).", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Teah Snyder", - "author_inst": "University of Massachusetts- Amherst" - }, - { - "author_name": "Johanna Ravenhurst", - "author_inst": "University of Massachusetts-Amherst" - }, - { - "author_name": "Estee Y. Cramer", - "author_inst": "University of Massachusetts- Amherst" - }, - { - "author_name": "Nicholas Reich", - "author_inst": "University of Massachusetts- Amherst" - }, - { - "author_name": "Laura B Balzer", - "author_inst": "University of Massachusetts- Amherst" - }, - { - "author_name": "Dominique Alfandari", - "author_inst": "University of Massachusetts- Amherst" - }, - { - "author_name": "Andrew A. Lover", - "author_inst": "University of Massachusetts- Amherst" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.05.21252946", "rel_title": "Higher COVID-19 vaccination rates are linked to decreased county-level COVID-19 incidence across USA", @@ -869195,6 +873499,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.03.06.21253058", + "rel_title": "Low Dose Regimens of BNT162b2 mRNA Vaccine Exceed SARS-Cov-2 Correlate of Protection Estimates for Symptomatic Infection, in those 19-55 Years of Age", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.06.21253058", + "rel_abs": "BackgroundAn exact correlate of protection (CoP) is not yet known for symptomatic COVID-19. However, it is still possible to show a new vaccine regimen exceeds an unknown CoP, provided the regimen shows an equivalent or greater immunological response in all measured indicators relative to the immunological response elicited by a clinically proven vaccine regimen. The principle of comparing immunogenicity between regimens is what the FDA, EMA, and Access Consortium use to authorize modifications to the vaccines for VOC, without requiring clinical efficacy studies before implementation. It is logical to apply the same principle to modifying vaccine doses if the data is available to do so. A two dose 30ug regimen of BNT162b2 has strong clinical evidence of efficacy, as does a single dose 30 ug regimen. The immunological markers for these regimens have been profiled in detail in Phase 1 and 2 trial data.\n\nMethodsThe immunological profile (including binding antibodies, viral neutralization, cytokine profiles, and CD4 and 8 expansion) of the 2 dose 30ug BNT162b2 vaccine is examined, referred to as a highly conservative CoP estimate. The single dose 30 ug BNT162b2 immunological profile is also examined, a tenable CoP estimate. Data from the phase 1 and 2 trials are examined to see if alternate regimens meet or exceed the level of each immune marker measured, relative to the regimens listed above that have proven clinical efficacy.\n\nResultsFor adults aged 19-55, a 2 dose 10ug BNT162b2 regimen elicits a comparable response to the standard 30 ug dose for each immune indicator, with viral neutralization nearly an order of magnitude greater than the tenable CoP estimate. Similarly, a single dose 10ug BNT 162b2 regimen or a two dose 1ug BNT 162b2 regimen equals or exceeds the immunogenicity of a single 30 ug dose.\n\nConclusionIf it is reasonable for the FDA, EMA, and Access Consortium to approve vaccine modifications without a clinical trial based on immunogenicity data, three alternate low dose regimens were identified that meet the requirements of having comparable immunogenicity relative to a protocol that has proven clinical efficacy. Immediate implementation of these lower dose regimens should be considered as they have major implications in alleviating vaccine supply, as well as improving vaccine side effect profile, and lowering total cost of vaccination.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Graham Jurgens", + "author_inst": "Unaffiliated" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.03.06.21252964", "rel_title": "Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data", @@ -869324,29 +873647,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.04.21252885", - "rel_title": "Prevalence of vitamin D is not associated with the COVID-19 epidemic in Europe. A judicial update of the existing evidence.", - "rel_date": "2021-03-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252885", - "rel_abs": "BackgroundCOVID-19 has emerged as a global pandemic, affecting nearly 104 million people worldwide as of February 4th 2021. In previous published studies, the association between the mean Vit D status of each country and COVID-19 infection rate, and mortality among the adult population in European countries was examined. The aim of this study was to re-examine the relationship between the Vit D status of each country and COVID-19 infection, recovery, and mortality using updated data and a different methodological approach.\n\nMethodsInformation only form the last decade on Vit D concentration/deficiency for each country was retrieved through literature search on PubMed(R) database. As of February, 4th 2021, COVID-19 infections and mortalities per one million population as well as total recoveries were extracted from the Worldometer website. The association between vitamin D deficiency and COVID-19 infection, recovery, and mortality were explored using correlation coefficients and scatterplots.\n\nFindingsThe prevalence of vitamin D deficiency among European countries ranged from 6.0 (Finland) to 75.5% (Turkey), with several countries facing more than 50% of vitamin D deficiency among their population. Non-significant correlations were observed between the number of COVID-19 infections (r=0.190; p=0.374), recoveries (rs=0.317, p=0.131), and mortalities (r=0.129; p=0.549) per one million population, with the prevalence of vitamin D deficiency.\n\nInterpretationPrevalence of vitamin D deficiency was not significantly associated with either number of infections, recoveries or mortality rate of COVID-19 among European countries. Thus, it is an important parameter to be considered when implementing preventive measures to face COVID-19.\n\nFundingNone", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Dimitra Rafailia Bakaloudi", - "author_inst": "Laboratory of Hygiene, Social & Preventive Medicine and Medical Statistics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki" - }, - { - "author_name": "Michail Chourdakis", - "author_inst": "Laboratory of Hygiene, Social & Preventive Medicine and Medical Statistics, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nutrition" - }, { "rel_doi": "10.1101/2021.03.03.21252868", "rel_title": "Comparison of clinical course and outcomes of critically ill patients with SARS-CoV2 infection managed in traditional ICU and \"Flex\" ICU during the surge of the pandemic in the Bronx.", @@ -871301,6 +875601,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.02.21252766", + "rel_title": "Self-reported symptoms, self-reported viral testing result and seroprevalence of SARS CoV-2 among a community sample in Essex County New Jersey: A brief report.", + "rel_date": "2021-03-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252766", + "rel_abs": "BackgroundSARS-CoV-2, the virus that causes COVID-19, has rapidly spread globally beginning in late 2019. Early areas impacted by this pandemic in the US include Essex County, New Jersey. Beyond understanding the prevalence of active infections and deaths, it is important to understand the true burden of infection in the community, as indicated by seroprevalence of antibodies directed to the virus. Understanding the spectrum of disease is key to the effectiveness of primary prevention and control measures and the design of interventions against transmission of infection.\n\nMethodsWe utilized venue-based-sampling (VBS), implemented by a community partner, to sample members of the community in Essex County. In VBS the venues are randomized as a proxy for randomizing the attendees of the venues. We asked standard demographic questions, questions about symptoms and PCR testing and previous antibody testing. Participants provide a blood sample collected by finger stick with the Neoteryx Mitra Collection device. Samples were tested using a novel ELISA based approached developed by our team.\n\nResultsFrom September 15, 2020 to December 22, 2020, we conducted 92 randomly selected sampling events where we approached 1349 individuals for screening. Of these, 924 consented and had complete data for analysis. Only 6.5% of the sample reported any COVID-19 like symptoms while 45.9% had sought out a COVID-19 test. In total 13 (1.4%) participants received a positive SARS-CoV-2 PCR test result. While 33 participants (2.6%) sought a SARS-CoV-2 antibody test, only 0.5% of the sample reported a positive antibody result. Testing in this study identified 83 (9.0%) participants positive for SARS-CoV-2 antibodies.\n\nConclusionWe recruited a large sample of the population of Essex County, New Jersey using VBS, electronic surveys, novel sample collection and lab methods. Our findings suggest that the burden of SARS-Cov-2 is slightly more than six times than that suggested by PCR testing. This burden is higher than most estimates obtained through studies of remnant blood samples from hospitals (4.2%), samples from staff at a public-school system (2.9%), and residents of a California county recruited with targeted Facebook ads (1.5%). (9-11) Moreover, with only 6.5% of the sample reporting any COVID-19-like symptoms, our finding suggests that the number of asymptomatic persons may be close to 1.5 times greater than anyone reporting symptoms.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Henry F Raymond", + "author_inst": "School of Public Health, Rutgers University" + }, + { + "author_name": "Pratik Datta", + "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark NJ" + }, + { + "author_name": "Rahul Ukey", + "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark NJ" + }, + { + "author_name": "Peng Wang", + "author_inst": "School of Public Health, Rutgers University, Piscataway, NJ" + }, + { + "author_name": "Richard J Martino", + "author_inst": "School of Public Health, Rutgers University, Piscataway, NJ" + }, + { + "author_name": "Kristen D Krause", + "author_inst": "School of Public Health, Rutgers University, Piscataway, NJ" + }, + { + "author_name": "Corey Rosmarin-DeStefano", + "author_inst": "North Jersey Community Research Initiative, Newark, NJ" + }, + { + "author_name": "Abraham Pinter", + "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark NJ" + }, + { + "author_name": "Perry N Halkitis", + "author_inst": "School of Public Health, Rutgers University, Piscataway, NJ" + }, + { + "author_name": "Maria L Gennaro", + "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark NJ" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.03.21252809", "rel_title": "Sharing positive changes made during COVID-19 national lockdown: a multi-method co-production study", @@ -871410,45 +875765,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.03.21252464", - "rel_title": "Covid-19 impact on Parkinson's Disease patients treated by drugs or deep brain stimulation", - "rel_date": "2021-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.03.21252464", - "rel_abs": "PurposeCovid-19 has affected all people, especially those with chronic diseases, including Parkinsons Disease (PD). Covid-19 may affect both motor and neuropsychiatric symptoms of PD patients. We intend to evaluate different aspects of Covid-19 impact on PD patients.\n\nMethods647 PD patients were evaluated in terms of PD-related and Covid-19-related clinical presentations in addition to past medical history during the pandemic through an online questioner. They were compared with an age-matched control group consist of 673 individuals and a sample of the normal population consist of 1215 individuals.\n\nResultsThe prevalence of Covid-19 in PD patients was 11.28%. The mortality was 1.23% among PD patients. The prevalence of Covid-19 in PD patients who undergone DBS was 18.18%. No significant association was found between the duration of disease and the prevalence of Covid-19. A statistically significant higher prevalence of Covid-19 in PD patients who had direct contact with SARS-CoV-19 infected individuals was found. No statistically significant association has been found between the worsening of motor symptoms and Covid-19. PD patients and the normal population may differ in the prevalence of some psychological disorders, including anxiety and sleeping disorders, and Covid-19 may affect the psychological status.\n\nConclusionPD patients possibly follow tighter preventive protocols, which lead to lower prevalence and severity of Covid-19 and its consequences in these patients. Although it seems Covid-19 does not affect motor and psychological aspects of PD as much as it was expected, more accurate evaluations are suggested in order to clarify such effects.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Mehri Salari", - "author_inst": "Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehra" - }, - { - "author_name": "Masoud Etemadifar", - "author_inst": "Department of Functional Neurosurgery, Medical School, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Alireza Zali", - "author_inst": "Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehra" - }, - { - "author_name": "Zahra Aminzade", - "author_inst": "School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Parsa Farsinejad", - "author_inst": "Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehra" - }, - { - "author_name": "Sepand Tehrani Fateh", - "author_inst": "Shahid Beheshti University of Medical Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2021.03.03.21252815", "rel_title": "Economic Benefits of COVID-19 Screening Tests with a Vaccine Rollout", @@ -873035,6 +877351,77 @@ "type": "confirmatory results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.03.05.434152", + "rel_title": "Scalable, Micro-Neutralization Assay for Qualitative Assessment of SARS-CoV-2 (COVID 19) Virus-Neutralizing Antibodies in Human Clinical Samples", + "rel_date": "2021-03-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.05.434152", + "rel_abs": "As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic was expanding, it was clear that effective testing for the presence of neutralizing antibodies in the blood of convalescent patients would be critical for development of plasma-based therapeutic approaches. To address the need for a high-quality neutralization assay against SARS-CoV-2, a previously established fluorescence reduction neutralization assay (FRNA) against Middle East respiratory syndrome coronavirus (MERS-CoV) was modified and optimized. The SARS-CoV-2 FRNA provides a quantitative assessment of a large number of infected cells through use of a high-content imaging system. Because of this approach, and the fact that it does not involve subjective interpretation, this assay is more efficient and more accurate than other neutralization assays. In addition, the ability to set robust acceptance criteria for individual plates and specific test wells provided further rigor to this assay. Such agile adaptability avails use with multiple virus variants. By February 2021, the SARS-CoV-2 FRNA had been used to screen over 5,000 samples, including acute and convalescent plasma or serum samples and therapeutic antibody treatments, for SARS-CoV-2 neutralizing titers.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Michael R Holbrook", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Richard S Bennett", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Elena N Postnikova", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Janie Liang", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Robin Gross", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Dawn Gerhardt", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Shalamar Georgia-Clark", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Yingyun Cai", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Shuiqinq Yu", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Lindsay Marron", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Greg Kocher", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Steven Mazur", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Saurabh Dixit", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Vladimir V Lukin", + "author_inst": "Kearney" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.05.434119", "rel_title": "SARS-CoV-2-host chimeric RNA-sequencing reads do not necessarily signify virus integration into the host DNA", @@ -873280,69 +877667,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.03.03.21252830", - "rel_title": "Saliva testing is accurate for early-stage and presymptomatic COVID-19", - "rel_date": "2021-03-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.03.21252830", - "rel_abs": "BackgroundAlthough nasopharyngeal (NP) samples have been considered the gold standard for COVID-19 testing, variability in viral load across different anatomical sites could theoretically cause NP samples to be less sensitive than saliva or nasal samples in certain cases. Self-collected samples also have logistical advantages over NP samples, making them amenable to population-scale screening.\n\nMethodsTo evaluate sampling alternatives for population screening, we collected NP, saliva, and nasal samples from two cohorts with varied levels and types of symptoms.\n\nResultsIn a mixed cohort of 60 symptomatic and asymptomatic participants, we found that saliva had 88% concordance with NP when tested in the same testing lab (n = 41), and 68% concordance when tested in different testing labs (n = 19). In a second cohort of 20 participants hospitalized for COVID-19, saliva had 74% concordance with NP tested in the same testing lab, but detected virus in two participants that tested negative with NP on the same day. Medical record review showed that the saliva-based testing sensitivity was related to the timing of symptom onset and disease stage.\n\nConclusionsWe find that no sample site will be perfectly sensitive for COVID-19 testing in all situations, and the significance of negative results will always need to be determined in the context of clinical signs and symptoms. Saliva retained high clinical sensitivity while allowing easier collection, minimizing the exposure of healthcare workers and need for personal protective equipment, and making it a viable option for population-scale testing.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Abigail J Johnson", - "author_inst": "Division of Epidemiology and Community Health, School of Public Health, University of Minnesota" - }, - { - "author_name": "Shannon Zhou", - "author_inst": "BioTechnology Institute, College of Biological Sciences, University of Minnesota" - }, - { - "author_name": "Susan L Hoops", - "author_inst": "Department of Computer Science and Engineering, University of Minnesota" - }, - { - "author_name": "Benjamin Hillmann", - "author_inst": "Department of Computer Science and Engineering, University of Minnesota" - }, - { - "author_name": "Matthew Schomaker", - "author_inst": "M Health Fairview, Minneapolis" - }, - { - "author_name": "Robyn Kincaid", - "author_inst": "M Health Fairview, Minneapolis" - }, - { - "author_name": "Jerry Daniel", - "author_inst": "University of Minnesota Genomics Center, University of Minnesota" - }, - { - "author_name": "Kenneth Beckman", - "author_inst": "Department of Laboratory Medicine and Pathology, Division of Molecular Pathology and Genomics, University of Minnesota" - }, - { - "author_name": "Daryl M Gohl", - "author_inst": "Department of Genetics, Cell Biology, and Development, University of Minnesota" - }, - { - "author_name": "Sophia Yohe", - "author_inst": "Department of Laboratory Medicine and Pathology, Division of Molecular Pathology and Genomics, University of Minnesota" - }, - { - "author_name": "Dan Knights", - "author_inst": "Department of Computer Science and Engineering, University of Minnesota" - }, - { - "author_name": "Andrew C Nelson", - "author_inst": "Department of Laboratory Medicine and Pathology, Division of Molecular Pathology and Genomics, University of Minnesota" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.04.21252877", "rel_title": "Comparing SARS-CoV-2 case rates between pupils, teachers and the general population: results from Ger-many", @@ -874945,6 +879269,197 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.02.21252420", + "rel_title": "Delayed rise of oral fluid antibodies, elevated BMI, and absence of early fever correlate with longer time to SARS-CoV-2 RNA clearance in an longitudinally sampled cohort of COVID-19 outpatients", + "rel_date": "2021-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252420", + "rel_abs": "BackgroundSustained molecular detection of SARS-CoV-2 RNA in the upper respiratory tract (URT) in mild to moderate COVID-19 is common. We sought to identify host and immune determinants of prolonged SARS-CoV-2 RNA detection.\n\nMethodsNinety-five outpatients self-collected mid-turbinate nasal, oropharyngeal (OP), and gingival crevicular fluid (oral fluid) samples at home and in a research clinic a median of 6 times over 1-3 months. Samples were tested for viral RNA, virus culture, and SARS-CoV-2 and other human coronavirus antibodies, and associations were estimated using Cox proportional hazards models.\n\nResultsViral RNA clearance, as measured by SARS-CoV-2 RT-PCR, in 507 URT samples occurred a median (IQR) 33.5 (17-63.5) days post-symptom onset. Sixteen nasal-OP samples collected 2-11 days post-symptom onset were virus culture positive out of 183 RT-PCR positive samples tested. All participants but one with positive virus culture were negative for concomitant oral fluid anti-SARS-CoV-2 antibodies. The mean time to first antibody detection in oral fluid was 8-13 days post-symptom onset. A longer time to first detection of oral fluid anti-SARS-CoV-2 S antibodies (aHR 0.96, 95% CI 0.92-0.99, p=0.020) and BMI [≥] 25kg/m2 (aHR 0.37, 95% CI 0.18-0.78, p=0.009) were independently associated with a longer time to SARS-CoV-2 viral RNA clearance. Fever as one of first three COVID-19 symptoms correlated with shorter time to viral RNA clearance (aHR 2.06, 95% CI 1.02-4.18, p=0.044).\n\nConclusionsWe demonstrate that delayed rise of oral fluid SARS-CoV-2-specific antibodies, elevated BMI, and absence of early fever are independently associated with delayed URT viral RNA clearance.", + "rel_num_authors": 44, + "rel_authors": [ + { + "author_name": "Annukka A. R. Antar", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Tong Yu", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Nora Pisnic", + "author_inst": "The Johns Hopkins University Bloomberg School of Medicine" + }, + { + "author_name": "Razvan Azamfirei", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Jeffrey A Tornheim", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Diane M. Brown", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Kate Kruczynski", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Justin P. Hardick", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Thelio Sewell", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Minyoung Jang", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Taylor Church", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Samantha N. Walch", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Carolyn Reuland", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Vismaya S. Bachu", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Kirsten Littlefield", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Han-Sol Park", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Rebecca L. Ursin", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Abhinaya Ganesan", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Oyinkansola Kusemiju", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Brittany Barnaba", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Curtisha Charles", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Michelle Prizzi", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Jaylynn R. Johnstone", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Christine Payton", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Weiwei Dai", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Joelle Fuchs", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Guido Massaccesi", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Derek T. Armstrong", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Jennifer L. Townsend", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Sara C. Keller", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Zoe O Demko", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Chen Hu", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Mei-Cheng Wang", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Lauren M. Sauer", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Heba H. Mostafa", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Jeanne C. Keruly", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Shruti H. Mehta", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Sabra L. Klein", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Andrea L. Cox", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Andrew Pekosz", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Christopher D. Heaney", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "David L. Thomas", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Paul W. Blair", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Yukari C. Manabe", + "author_inst": "The Johns Hopkins University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.01.21252243", "rel_title": "On the Environmental Determinants of COVID-19 Seasonality", @@ -875022,57 +879537,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.01.21252508", - "rel_title": "Experiences of COVID-19 Recovered Patients - A Qualitative Case Study from a Hotspot in Saudi Arabia", - "rel_date": "2021-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.01.21252508", - "rel_abs": "BackgroundCOVID-19 is highly contagious and can have fatal outcomes in the elderly and those with comorbidities. Social distancing is highly recommended by the World Health Organization to prevent the spread of the disease. However, it is difficult to maintain social distancing in highly populated areas where people live in close proximity. Such high-risk areas have the potential to become hotspots for the disease spread, should one person therein contract the disease. Nakkasah is one such area in the Makkah city of Saudi Arabia which has been a hotspot in this pandemic. This study aims to qualitatively explore the experiences of COVID-19 recovered patients residing in this area.\n\nMethodsWe employed semi-structured face-to-face interviews with people living in Nakkasah, above 18 years of age, and recovered from COVID-19. An interview guide was developed, validated, piloted, and minor changes were made. Two trained students conducted the interviews in the Arabic language in a semi-private area of the community center. The interviews were audio-recorded, with informed consent from interviewees, transcribed verbatim, and thematically analyzed later.\n\nResultsEleven eligible COVID-19 recovered people (two female and nine male) agreed to be interviewed, and their verbal informed consent was audio recorded. The mean interview time was 24 minutes. Thematic analysis generated 30 subthemes, which were categorized into seven overarching themes: information about COVID-19; life during COVID-19 illness; spreading of COVID-19; precautionary measures; interventions that helped in recovery; impact of COVID-19 on life; support received during COVID-19 illness.\n\nConclusionExperiences of people from the hotspot who had recovered from COVID-19 highlighted how life had been like in the hotspot under lockdown especially with having been afflicted with the infection, factors that facilitated their recovery, and the way their lives were and have been affected due to COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Abdulrahman Alhajjaji", - "author_inst": "College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia" - }, - { - "author_name": "Ahmad Kurdi", - "author_inst": "College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia" - }, - { - "author_name": "Sultan Faqeh", - "author_inst": "College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia" - }, - { - "author_name": "Safwan Alansari", - "author_inst": "College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia" - }, - { - "author_name": "Akrm Abdulaziz", - "author_inst": "College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia" - }, - { - "author_name": "Moayad Allihyani", - "author_inst": "College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia" - }, - { - "author_name": "Omar Almaghamsi", - "author_inst": "College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia" - }, - { - "author_name": "Ejaz Cheema", - "author_inst": "School of Pharmacy, University of Birmingham, Birmingham, UK" - }, - { - "author_name": "Majid Ali", - "author_inst": "Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.02.21252444", "rel_title": "An overview of the National COVID-19 Chest Imaging Database: data quality and cohort analysis", @@ -877155,6 +881619,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.23.21252328", + "rel_title": "SARS-CoV-2 antibodies detected in human breast milk post-vaccination", + "rel_date": "2021-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252328", + "rel_abs": "ImportanceThe SARS-CoV-2 pandemic has infected over a hundred million people worldwide, with almost 2.5 million deaths at the date of this publication. In the United States, Pfizer-BioNTech and Moderna vaccines were first administered to the public starting in December 2020, and no lactating women were included in the initial trials of safety/efficacy. Research on SARS-CoV-2 vaccination in lactating women and the potential transmission of passive immunity to the infant through breast milk is needed to guide patients, clinicians and policy makers during the worldwide effort to curb the spread of this virus.\n\nObjectiveTo determine whether SARS-CoV-2 specific immunoglobins are found in breast milk post-vaccination, and to characterize the time course and types of immunoglobulins present.\n\nDesignProspective cohort study\n\nSettingProvidence Portland Medical Center, Oregon, USA\n\nParticipantsSix lactating women who planned to receive both doses of the Pfizer-BioNTech or Moderna vaccine between December 2020 and January 2021. Breast milk samples were collected pre-vaccination and at 11 additional timepoints, with last sample at 14 days post 2nd dose of vaccine.\n\nExposureTwo doses of Pfizer-BioNTech or Moderna SARS-CoV-2 vaccine.\n\nMain Outcome(s) and Measure(s)Levels of SARS-CoV-2 specific IgA and IgG immunoglobulins in breast milk.\n\nResultsIn this cohort of 6 lactating women who received 2 doses of SARS-CoV-2 vaccine, we observed significantly elevated levels of SARS-CoV-2 specific IgG and IgA antibodies in breast milk beginning at Day 7 after the initial vaccine dose, with an IgG-dominant response.\n\nConclusions and RelevanceWe are the first to show that maternal vaccination results in SARS-CoV-2 specific immunoglobulins in breast milk that may be protective for infants.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jill K Baird", + "author_inst": "Legacy Medical Group, Portland OR USA" + }, + { + "author_name": "Shawn M Jensen", + "author_inst": "Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, USA" + }, + { + "author_name": "Walter J Urba", + "author_inst": "Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, USA" + }, + { + "author_name": "Bernard A Fox", + "author_inst": "Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, USA" + }, + { + "author_name": "Jason R Baird", + "author_inst": "Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, USA" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.26.21252555", "rel_title": "Introductions and evolutions of SARS-CoV-2 strains in Japan", @@ -877404,29 +881903,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.02.28.21252625", - "rel_title": "Seasonal patterns COVID-19 and Flu Like Illnesses comparable", - "rel_date": "2021-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.28.21252625", - "rel_abs": "BackgroundDuring the first wave of COVID-19 it was hypothesized that COVID-19 is subject to multi-wave seasonality, similar to Influenza-Like Illnesses since time immemorial. One year into the pandemic, we aimed to test the seasonality hypothesis for COVID-19.\n\nMethodsWe calculated the average annual time-series for Influenza-Like Illnesses based on incidence data from 2016 till 2019 in the Netherlands, and compared these with two COVID-19 time-series during 2020/2021 for the Netherlands. We plotted the time-series on a standardized logarithmic infection scale. Finally, we calculated correlation coefficients and used univariate regression analysis to estimate the strength of the association between the time-series of COVID-19 and Influenza-Like Illnesses.\n\nResultsThe time-series for COVID-19 and Influenza-Like Illnesses were strongly and highly significantly correlated. The COVID-19 peaks were all during flu season, and lows were all in the opposing period. Finally, COVID-19 meets the multi-wave characteristics of earlier flu-like pandemics, namely a short first wave at the tail-end of a flu season, and a longer and more intense second wave during the subsequent flu season.\n\nConclusionsWe conclude that seasonal patterns of COVID-19 incidence and Influenza-Like Illnesses incidence are highly similar, in a country in the temperate climate zone, such as the Netherlands. Further, the COVID-19 pandemic satisfies the criteria of earlier respiratory pandemics, namely a first wave that is short-lived at the tail-end of flu season, and a second wave that is longer and more severe.\n\nThis seems to imply that the same factors that are driving the seasonality of Influenza-Like Illnesses are causing COVID-19 seasonality as well, such as solar radiation (UV), temperature, relative humidity, and subsequently seasonal allergens and allergies.\n\nHIGHLIGHTSO_LITime-series analysis shows that COVID-19 and historic of Influenza-Like illnesses have highly similar seasonal patterns in the Netherlands.\nC_LIO_LICOVID-19 satisfies the criteria of earlier flu-like pandemics, namely a short cycle at the end of flu season, and a longer, more intense cycle during the subsequent flu season.\nC_LIO_LIThe implication is that the seasonal factors driving flu season, are also responsible for COVID-19 seasonality.\nC_LIO_LIWe developed and applied a new method to determine seasonality, encompassing comparative time-series analysis, a standardized logarithmic infection scale, and qualitative seasonality criteria.\nC_LI", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Martijn J Hoogeveen", - "author_inst": "Open University Netherlands" - }, - { - "author_name": "Ellen K Hoogeveen", - "author_inst": "Jeroen Bosch Ziekenhuis" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.26.21251720", "rel_title": "Unmasking the Current Scenario of Indian Biomedical Devices Industry: Ventilators being the Heart of the Discussion", @@ -879161,6 +883637,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.01.21252598", + "rel_title": "Investigation of ventilation conditions associated with CO2 concentration changes in ultrasonographic exam room from the perspective of COVID-19 infection control", + "rel_date": "2021-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.01.21252598", + "rel_abs": "ObjectivesVentilation is an important factor in preventing COVID-19 infection. To clarify the state of ventilation in ultrasonic exam rooms, as an index of ventilation rate, the carbon dioxide (CO2) concentration in our exam rooms was measured.\n\nMethodsWe measured the CO2 concentration in each exam room before the examination and 0-15 minutes after end of the exam.\n\nThe subjects were 70 cases (abdomen: 24, breast: 16, neck: 16, and musculoskeletal: 14). In infant cases, one parent accompanied the patient during the examination.\n\nResultsThe highest CO2 concentration was 2261 ppm, observed after the breast examination. In all cases, the CO2 concentration in the exam room was highest immediately after the examination or two minutes after. Almost all cases had recovered to within 120% of the pre-examination CO2 concentrations within 15 minutes after the examination. The average CO2 concentration after ultrasonography was significantly higher for breast examinations than others.\n\nConclusionsEven in a hospital with modern ventilation equipment, the CO2 concentration in the ultrasound room was high after the exam and it takes 15 minutes to recover to the pre-exam state. Care must be taken to ensure adequate ventilation in ultrasonographic facilities.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Roka Namoto Matsubayashi", + "author_inst": "National Hospital Organization Kyushu Medical Center" + }, + { + "author_name": "Shino Harada", + "author_inst": "National Hospital Organization Kyushu Medical Center" + }, + { + "author_name": "Mitsuhiro Tominaga", + "author_inst": "National Hospital Organization Kyushu Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.03.01.21252330", "rel_title": "Does Telemedicine Reduce health disparities? Longitudinal Evidence during the COVID-19 Pandemic in the US", @@ -879274,57 +883777,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.02.21252203", - "rel_title": "Performance evaluation of the Roche Elecsys Anti-SARS-CoV-2 S immunoassay", - "rel_date": "2021-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252203", - "rel_abs": "BackgroundThe Elecsys(R) Anti-SARS-CoV-2 S immunoassay (Roche Diagnostics International Ltd, Rotkreuz, Switzerland) has been developed for the in vitro quantitative detection of antibodies to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein. We evaluated the performance of this assay using samples from seven sites in Germany, Austria, and Switzerland.\n\nMethodsAnonymized frozen, residual serum, or plasma samples from blood donation centers or routine diagnostic testing were used for this study. For specificity and sensitivity analyses, presumed negative samples collected before October 2019 and SARS-CoV-2 PCR-confirmed single or sequential samples were tested, respectively. The performance of the Elecsys Anti-SARS-CoV-2 S immunoassay was also compared with other commercial immunoassays.\n\nResultsThe overall specificity (n=7880 pre-pandemic samples) and sensitivity (n=240 PCR-positive samples [[≥]14 days post-PCR]) for the Elecsys Anti-SARS-CoV-2 S immunoassay were 99.95% (95% confidence interval [CI]: 99.87-99.99) and 97.92% (95% CI: 95.21- 99.32), respectively. Compared with seven other immunoassays, the Elecsys Anti-SARS-CoV-2 S assay had comparable or greater specificity and sensitivity. The Elecsys Anti-SARS-CoV-2 S immunoassay had significantly higher specificity compared with the LIAISON(R) SARS-CoV-2 S1/S2 IgG, ADVIA Centaur(R) SARS-CoV-2 Total, ARCHITECT SARS-CoV-2 IgG, iFlash-SARS-CoV-2 IgM, and EUROIMMUN Anti-SARS-CoV-2 IgG and IgA assays, and significantly higher sensitivity ([≥]14 days post-PCR) compared with the ARCHITECT SARS-CoV-2 IgG, iFlash-SARS-CoV-2 IgG and IgM, and EUROIMMUN Anti-SARS-CoV-2 IgG assays.\n\nConclusionThe Elecsys Anti-SARS-CoV-2 S assay demonstrated a robust and favorable performance across samples from multiple European sites, with a very high specificity and sensitivity for the detection of anti-S antibodies.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Elena Riester", - "author_inst": "Labor Augsburg MVZ GmbH, Augsburg, Germany" - }, - { - "author_name": "Peter Findeisen", - "author_inst": "MVZ Labor Limbach, Heidelberg, Germany" - }, - { - "author_name": "J. Kolja Hegel", - "author_inst": "Labor Berlin, Charite Vivantes Services GmbH, Berlin, Germany" - }, - { - "author_name": "Michael Kabesch", - "author_inst": "University Children's Hospital Regensburg (KUNO) at the Hospital St. Hedwig of the Order of St. John and the University Hospital, University of Regensburg, Germ" - }, - { - "author_name": "Andreas Ambrosch", - "author_inst": "Institute for Laboratory Medicine, Microbiology and Hygiene, Barmherzige Bruder Hospital, Regensburg, Germany" - }, - { - "author_name": "Christopher M Rank", - "author_inst": "Roche Diagnostics GmbH, Penzberg, Germany" - }, - { - "author_name": "Florina Langen", - "author_inst": "Roche Diagnostics GmbH, Penzberg, Germany" - }, - { - "author_name": "Tina Laengin", - "author_inst": "Roche Diagnostics GmbH, Penzberg, Germany" - }, - { - "author_name": "Christoph Niederhauser", - "author_inst": "Interregionale Blood Transfusion Swiss Red Cross, Bern, Switzerland" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.02.433608", "rel_title": "Perturbation of ACE2 structural ensembles by SARS-CoV-2 spike protein binding", @@ -880875,6 +885327,137 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.03.01.433314", + "rel_title": "Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains", + "rel_date": "2021-03-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.01.433314", + "rel_abs": "We examined the immunogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant B.1.1.7 that arose in the United Kingdom and spread globally. Antibodies elicited by B.1.1.7 infection exhibited significantly reduced recognition and neutralisation of parental strains or of the South Africa B.1.351 variant, than of the infecting variant. The drop in cross-reactivity was more pronounced following B.1.1.7 than parental strain infection, indicating asymmetric heterotypic immunity induced by SARS-CoV-2 variants.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Nikhil Faulkner", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Kevin Ng", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Mary Wu", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Ruth Harvey", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Saira Hussain", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Maria Greco", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "William Bolland", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Scott Warchal", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Marios Margaritis", + "author_inst": "UCL" + }, + { + "author_name": "Stavroula Paraskevopoulou", + "author_inst": "UCL" + }, + { + "author_name": "Judith Heaney", + "author_inst": "UCL" + }, + { + "author_name": "Hannah Rickman", + "author_inst": "UCL" + }, + { + "author_name": "Catherine Houlihan", + "author_inst": "UCL" + }, + { + "author_name": "Moria Spyer", + "author_inst": "UCL" + }, + { + "author_name": "Daniel Frampton", + "author_inst": "UCL" + }, + { + "author_name": "Matthew Byott", + "author_inst": "UCL" + }, + { + "author_name": "Tulio de Oliveira", + "author_inst": "University of KwaZulu-Natal,SA" + }, + { + "author_name": "Alex Sigal", + "author_inst": "University of KwaZulu-Natal,SA" + }, + { + "author_name": "Svend Kjaer", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Charles Swanton", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Sonia Gandhi", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Rupert Beale", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Steve Gamblin", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "John Mccauley", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Rodney Daniels", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Michael Howell", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "David Bauer", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Eleni Nastouli", + "author_inst": "UCL" + }, + { + "author_name": "George Kassiotis", + "author_inst": "The Francis Crick Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.27.433180", "rel_title": "Negligible impact of SARS-CoV-2 variants on CD4+ and CD8+ T cell reactivity in COVID-19 exposed donors and vaccinees.", @@ -881096,25 +885679,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.01.433428", - "rel_title": "A Comparison of Performance for Different SARS-Cov-2 Sequencing Protocols", - "rel_date": "2021-03-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.01.433428", - "rel_abs": "SARS-Cov-2 genome sequencing has been identified as a fundamental tool for fighting the COVID-19 pandemic. It is used, for example, for identifying new variants of the virus and for elaborating phylogenetic trees that help to trace the spread of the virus. In the present study we provide a comprehensive comparison between the quality of the assemblies obtained from different sequencing protocols. We demonstrate how some protocols actively promoted by different high-level administrations are inefficient and how less-used alternative protocols show a significant increased performance. This increase of performance could lead to cheaper sequencing protocols and therefore to a more convenient escalation of the sequencing efforts around the world.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Juanjo Bermudez", - "author_inst": "Contignant Technologies SL" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2021.02.28.433266", "rel_title": "Day-night and seasonal variation of human gene expression across tissues", @@ -882449,6 +887013,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.25.21252451", + "rel_title": "Muscle Strength Explains the Protective Effect of Physical Activity against COVID-19 Hospitalization among Adults aged 50 Years and Older", + "rel_date": "2021-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.25.21252451", + "rel_abs": "ObjectivesPhysical activity has been proposed as a protective factor for COVID-19 hospitalization. However, the mechanisms underlying this association are unclear. Here, we examined the association between physical activity and COVID-19 hospitalization and whether this relationship was explained by other risk factors for severe COVID-19.\n\nMethodWe used data from adults aged 50 years and older from the Survey of Health, Ageing and Retirement in Europe. The outcome was self-reported hospitalization due to COVID-19 measured before August 2020. The main exposure was usual physical activity, self-reported between 2004 and 2017. Data were analyzed using logistic regression models.\n\nResultsAmong the 3139 participants included in the study (69.3 {+/-} 8.5 years, 1763 women), 266 were tested positive for COVID-19 and 66 were hospitalized. Results showed that individuals who engaged in physical activity more than once a week had lower odds of COVID-19 hospitalization than individuals who hardly ever or never engaged in physical activity (odds ratios = 0.41, 95% confidence interval = 0.22-0.74, p = .004). This association between physical activity and COVID-19 hospitalization was explained by muscle strength, but not by other risk factors.\n\nConclusionThese findings suggest that, after 50 years of age, engaging in physical activity more than once a week is associated with lower odds of COVID-19 hospitalization. The protective effect of physical activity on COVID-19 hospitalization is explained by muscle strength.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Silvio Maltagliati", + "author_inst": "Universite Grenoble Alpes" + }, + { + "author_name": "Stefan Sieber", + "author_inst": "University of Geneva" + }, + { + "author_name": "Philippe Sarrazin", + "author_inst": "Universite Grenoble Alpes" + }, + { + "author_name": "Stephane Cullati", + "author_inst": "University of Fribourg" + }, + { + "author_name": "Aina Chalabaev", + "author_inst": "Universite Grenoble Alpes" + }, + { + "author_name": "Gregoire P Millet", + "author_inst": "University of Lausanne" + }, + { + "author_name": "Matthieu P Boisgontier", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Boris Cheval", + "author_inst": "University of Geneva" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "sports medicine" + }, { "rel_doi": "10.1101/2021.02.26.21252552", "rel_title": "The Charitable Feeding System helps Food Insecure Participants maintain Fruit and Vegetable intake during COVID-19.", @@ -882570,65 +887181,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.25.21252493", - "rel_title": "SARS-CoV-2 Total and Subgenomic RNA Viral Load in Hospitalized Patients", - "rel_date": "2021-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.25.21252493", - "rel_abs": "Understanding viral load in patients infected with SARS-CoV-2 is critical to epidemiology and infection control. Previous studies have demonstrated that SARS-CoV-2 RNA can be detected for many weeks after symptom onset. The clinical significance of this finding is unclear and, in most patients, likely does not represent active infection. There are, however, patients who shed infectious virus for weeks. Detection of subgenomic RNA transcripts expressed by SARS-CoV-2 has been proposed to represent productive infection and may be a tractable marker for monitoring infectivity. Here, we use RT-PCR to quantify total and subgenomic nucleocapsid (N) and envelope (E) transcripts in 190 SARS-CoV-2 positive samples collected on hospital admission. We relate these findings to duration of symptoms. We find that all transcripts decline at the same rate; however, subgenomic E becomes undetectable before other transcripts. In Kaplan-Meier analysis the median duration of symptoms to a negative test is 14 days for sgE and 25 days for sgN. There is a linear decline in subgenomic RNA compared to total RNA suggesting subgenomic transcript copy number is highly dependent on copy number of total transcripts. The mean difference between total N and subgenomic N is 16-fold (4.0 cycles) and the mean difference between total E and sub-genomic E is 137-fold (7.1 cycles). This relationship is constant over duration of symptoms allowing prediction of subgenomic copy number from total copy number. Although Subgenomic E is undetectable at a time that may more closely reflect the duration of infectivity, its utility in determining active infection may be no more useful than a copy number threshold determined for total transcripts.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Derek E. Dimcheff", - "author_inst": "University of Michigan" - }, - { - "author_name": "Andrew L. Valesano", - "author_inst": "University of Michigan" - }, - { - "author_name": "Kalee E. Rumfelt", - "author_inst": "University of Michigan" - }, - { - "author_name": "William J. Fitzsimmons", - "author_inst": "University of Michigan" - }, - { - "author_name": "Christopher Blair", - "author_inst": "University of Michigan" - }, - { - "author_name": "Carmen Mirabelli", - "author_inst": "University of Michigan" - }, - { - "author_name": "Joshua G. Petrie", - "author_inst": "University of Michigan" - }, - { - "author_name": "Emily T. Martin", - "author_inst": "University of Michigan" - }, - { - "author_name": "Chandan Bhambhani", - "author_inst": "University of Michigan" - }, - { - "author_name": "Muneesh Tewari", - "author_inst": "University of Michigan" - }, - { - "author_name": "Adam S. Lauring", - "author_inst": "University of Michigan" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.26.21252482", "rel_title": "Evaluation of a SARS-CoV-2 Vaccine NVX-CoV2373 in Younger and Older Adults", @@ -883935,6 +888487,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.23.21252319", + "rel_title": "Control of COVID-19 transmission on an urban university campus during a second wave of the pandemic", + "rel_date": "2021-02-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252319", + "rel_abs": "ImportanceThe COVID-19 pandemic had a wide-ranging impact on educational institutions across the United States. Given potential financial challenges and adverse psychosocial effects of campus closure, as done in the spring of 2020 in response to the first wave, many institutions of higher education developed strategies to allow campuses to reopen and operate in the fall despite the ongoing threat of COVID-19. Many however opted to have limited campus re-opening in order to minimize potential risk of spread of SARS-CoV-2.\n\nObjectiveTo analyze how Boston University (BU) fully reopened its campus in the fall of 2020 and controlled COVID-19 transmission despite worsening transmission in the city of Boston.\n\nDesignMulti-faceted intervention case study.\n\nSettingLarge urban university campus.\n\nInterventionsThe BU response included a high-throughput SARS-CoV-2 PCR testing facility with capacity to delivery results in less than 24 hours; routine asymptomatic screening for COVID-19; daily health attestations; compliance monitoring and feedback; robust contact tracing, quarantine and isolation in on campus facilities; face mask use; enhanced hand hygiene; social distancing recommendations; de-densification of classrooms and public places; and enhancement of all building air systems.\n\nMain Outcomes and MeasuresBetween August and December 2020, BU conducted >500,000 COVID-19 tests and identified 719 individuals with COVID-19: 627 (87.2%) students, 11 (1.5%) faculty, and 212 (25.5%) staff. Overall, about 1.8% of the BU community tested positive. Infections among faculty and staff were mostly acquired off campus, while undergraduate infections were more likely acquired in non-classroom campus settings. Of 837 close contacts traced, 86 (10.3%) tested positive for COVID-19. BU contact tracers identified a source of transmission for 51.5% of cases with 55.7% identifying a source outside of BU. Among infected faculty and staff with a known source of infection, the majority reported a transmission source outside of BU (100% for faculty and 79.8% for staff).\n\nConclusions and RelevanceBU was successful in containing COVID-19 transmission on campus while minimizing off campus acquisition of COVID-19 from the greater Boston area. A coordinated strategy of testing, contact tracing, isolation and quarantine, with robust management and oversight, can control COVID-19 transmission, even in an urban university setting.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Davidson H Hamer", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Laura White", + "author_inst": "Boston University" + }, + { + "author_name": "Helen E Jenkins", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "christopher J gill", + "author_inst": "boston university school of public health" + }, + { + "author_name": "Hannah N. Landsberg", + "author_inst": "Boston University" + }, + { + "author_name": "Catherine Klapperich", + "author_inst": "Boston University" + }, + { + "author_name": "Katia Bulekova", + "author_inst": "Boston University" + }, + { + "author_name": "Judy Platt", + "author_inst": "Boston University" + }, + { + "author_name": "Linette Decarie", + "author_inst": "Boston University" + }, + { + "author_name": "Wayne Gilmore", + "author_inst": "Boston University" + }, + { + "author_name": "Megan Pilkington", + "author_inst": "Boston University" + }, + { + "author_name": "Trevor L. McDowell", + "author_inst": "Boston University" + }, + { + "author_name": "Mark A. Fari", + "author_inst": "Boston University" + }, + { + "author_name": "Douglas M. Densmore", + "author_inst": "Boston University" + }, + { + "author_name": "Lena Landaverde", + "author_inst": "Boston University" + }, + { + "author_name": "Wenrui Li", + "author_inst": "Boston University" + }, + { + "author_name": "Tom Rose", + "author_inst": "Boston University" + }, + { + "author_name": "Stephen P. Burgay", + "author_inst": "Boston University" + }, + { + "author_name": "Candice Miller", + "author_inst": "Boston University" + }, + { + "author_name": "Lynn Doucette-Stamm", + "author_inst": "Boston University" + }, + { + "author_name": "Kelly Lockard", + "author_inst": "Boston University" + }, + { + "author_name": "Kenneth Elmore", + "author_inst": "Boston University" + }, + { + "author_name": "Tracy Schroeder", + "author_inst": "Boston University" + }, + { + "author_name": "Ann M. Zaia", + "author_inst": "Boston University" + }, + { + "author_name": "Eric D. Kolaczyk", + "author_inst": "Boston University" + }, + { + "author_name": "Gloria Waters", + "author_inst": "Boston University" + }, + { + "author_name": "Robert A. Brown", + "author_inst": "Boston University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.23.21252299", "rel_title": "The Public Health Impact of Delaying a Second Dose of the BNT162b2 or mRNA-1273 COVID-19 Vaccine", @@ -884220,97 +888895,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.02.24.21252368", - "rel_title": "Longitudinal protection following natural SARS-CoV-2 infection and early vaccine responses: insights from a cohort of community based dental health care professionals", - "rel_date": "2021-02-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.24.21252368", - "rel_abs": "BackgroundThe threshold of protection for anti-SARS-CoV-2 spike glycoprotein antibodies and their longevity are not known. Interpretation of serological results in with respect to international reference material can inform this essential question.\n\nMethods1,507 West Midlands dental care professionals were recruited into this study in June 2020. Baseline seroprevalence of antibodies directed against the SARS-CoV-2 spike glycoprotein was determined and the cohort was followed longitudinally for 6 months until January/February 2021 through the second wave of the COVID-19 pandemic in the United Kingdom, and commencement of vaccination.\n\nResultsBaseline seroprevalence was 16.3% in this cohort, compared to estimates in the general population of between 6-7%. Seropositivity was retained in over 70% of participants at 3 and 6-month follow up and conferred a 74% reduced risk of infection. During follow-up, no PCR-proven infections occurred in individuals with a baseline anti-SARS-CoV-2 IgG level greater than 147.6 IU/ml with respect to the World Health Organization international standard 20-136. Post-vaccination, antibody responses were more rapid and of higher magnitude in individuals with who were seropositive at baseline.\n\nConclusionNatural infection leads to a serological response that remains detectable in over 70% of individuals 6 months after initial sampling and 9 months from the peak of the first wave of the pandemic. This response is associated with protection from future infection. Even if serological responses wane, a single dose of the Pfizer-BioNTech vaccine is associated with an antibody response indicative of immunological memory.\n\nFundingThe Association of Clinical Biochemistry and Laboratory Medicine and The Institute for Global Innovation (IGI) of the University of Birmingham.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Adrian M Shields", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Sian E Faustini", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Caroline A Kristunas", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Alex M Cook", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Claire Backhouse", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Lynsey A Dunbar", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Daniel Ebanks", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Beena Emmanuel", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Eddie J Crouch", - "author_inst": "Birmingham Local Dental Committee" - }, - { - "author_name": "Annika T Kroeger", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Josefine Hirschfeld", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Praveen Sharma", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Raza Jaffery", - "author_inst": "Birmingham Community Healthcare Trust" - }, - { - "author_name": "Sylwia Nowak", - "author_inst": "Birmingham Community Healthcare Trust" - }, - { - "author_name": "Samantha Gee", - "author_inst": "Birmingham Community Healthcare Trust" - }, - { - "author_name": "Mark T Drayson", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Alex G Richter", - "author_inst": "University of Birminghan" - }, - { - "author_name": "Thomas Dietrich", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Iain L.C. Chapple", - "author_inst": "University of Birmingham" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.02.24.21252304", "rel_title": "Epidemiological Philosophy of Pandemics", @@ -886061,6 +890645,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.23.21252294", + "rel_title": "Evaluation of COVID-19 as a risk factor for maternal-fetal and neonatal complications: protocol of a systematic review and meta-analysis of cohort and case-control studies.", + "rel_date": "2021-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252294", + "rel_abs": "BackgroundCOVID-19 in pregnant women has been suggested to impair maternal-fetal and neonatal outcomes. We then designed the present systematic review with meta-analysis to evaluate the repercussion of such disease over maternal fetal and neonatal mortality, need for intensive care, way of delivery, premature delivery, birth weight, Apgar score, presence of intrauterine growth restriction (IGR), and presence of amniotic fluid change.\n\nMethodsWe will conduct a computerized search through MEDLINE/PubMed, LILACS/BIREME, Web of science, Biorxiv, Medrxiv, and Embase on July 23, 2020. We will include cohort and case-control studies fully reported comparing pregnant women with COVID-19 with those not affected by the disease for maternal fetal and neonatal mortality, need for intensive care, way of delivery, premature delivery occurrence, birth weight, Apgar scores, presence of intrauterine growth restriction, and presence of amniotic fluid change. Three doubles of reviewers will perform in duplicate and independently all steps on screening, risk of bias judgments, and data extraction with ability to discuss disagreements with supervising authors. Pooled effects will be estimated by both fixed and random-effects models and presented according to qualitative and quantitative heterogeneity assessment. Sensitivity analyses will be performed as well as a priori subgroup, meta-regression and multiple meta-regression analyses. Well also evaluate the risk of selective publication by assessing funnel plot asymmetry and the quality of the evidence by the application of the GRADE recommendations.\n\nDiscussionThis systematic review with meta-analysis aims to assess the repercussion of COVID-19 in pregnant women over maternal-fetal and neonatal outcomes and to help clinicians and health systems improve such population outcomes throughout the current pandemic.\n\nSystematic review registrationThis review protocol was also submitted to PROSPERO registration on February 9, 2021.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Priscila Bezerra", + "author_inst": "Instituto de Medicina Integral professor Fernando Figueira" + }, + { + "author_name": "Fernanda Gabriella de Siqueira Barros Nogueira Sr.", + "author_inst": "Instituto de Medicina Integral Prof. Fernando Figueira (IMIP)" + }, + { + "author_name": "Alan Chaves dos Santos", + "author_inst": "Instituto de medicina integral professor Fernando Figueira" + }, + { + "author_name": "Anna Katharina Souza Lima", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "David Emanuel Ribeiro", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "Elias Almeida Silva Barbosa", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "Suellen Casado dos Santos", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "Clistenes Cristian de Carvalho", + "author_inst": "Instituto de Medicina Integral Professor Fernando Figueira" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2021.02.23.21251915", "rel_title": "Clinical evaluation of the molecular-based BD SARS-CoV-2/Flu for the BD MAX\u2122 System", @@ -886154,33 +890785,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.02.24.432807", - "rel_title": "Modeling SARS-CoV-2 nsp1-5'-UTR complex via the extended ensemble simulations", - "rel_date": "2021-02-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.24.432807", - "rel_abs": "Nonstructural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a 180-residue protein that blocks translation of host mRNAs in SARS-CoV-2-infected cells. Although it is known that SARS-CoV-2s own RNA evades nsp1s host translation shutoff, the molecular mechanism underlying the evasion was poorly understood. We performed an extended ensemble molecular dynamics simulation to investigate the mechanism of the viral RNA evasion. Simulation results showed that the stem loop structure of the SARS-CoV-2 RNA 5-untranslated region (SL1) is recognized by both nsp1s globular region and intrinsically disordered region. The recognition presumably enables selective translation of viral RNAs. Cluster analysis of the binding mode and detailed analysis of the binding poses revealed several residues involved in the SL1 recognition mechanism. The simulation results imply that the nsp1 C-terminal helices are lifted from the 40S ribosome upon the binding of SL1 to nsp1, unblocking translation of the viral RNA.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Shun Sakuraba", - "author_inst": "National Institutes for Quantum and Radiological Science and Technology (QST)" - }, - { - "author_name": "Xie Qilin", - "author_inst": "Ritsumeikan University" - }, - { - "author_name": "Kota Kasahara", - "author_inst": "Ritsumeikan University" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.02.25.432861", "rel_title": "Antiviral Resistance against Viral Mutation: Praxis and Policy for SARS CoV-2", @@ -888071,6 +892675,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.22.21252254", + "rel_title": "Associations Between Google Search Trends for Symptoms and COVID-19 Confirmed and Death Cases in the United States", + "rel_date": "2021-02-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21252254", + "rel_abs": "We utilize functional data analysis techniques to investigate patterns of COVID-19 positivity and mortality in the US and their associations with Google search trends for COVID-19 related symptoms. Specifically, we represent state-level time series data for COVID-19 and Google search trends for symptoms as smoothed functional curves. Given these functional data, we explore the modes of variation in the data using functional principal component analysis (FPCA). We also apply functional clustering analysis to identify patterns of COVID-19 confirmed case and death trajectories across the US. Moreover, we quantify the associations between Google COVID-19 search trends for symptoms and COVID-19 confirmed case and death trajectories using dynamic correlation. Finally, we examine the dynamics of correlations for the top nine Google search trends of symptoms commonly associated with COVID-19 confirmed case and death trajectories. Our results reveal and characterize distinct patterns for COVID-19 spread and mortality across the US. The dynamics of these correlations suggest the feasibility of using Google queries to forecast COVID-19 cases and mortality for up to three weeks in advance. Our results and analysis framework set the stage for the development of predictive models for forecasting COVID-19 confirmed cases and deaths using historical data and Google search trends for nine symptoms associated with both outcomes.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Mostafa Abbas", + "author_inst": "Geisinger" + }, + { + "author_name": "Thomas B. Morland", + "author_inst": "Geisinger" + }, + { + "author_name": "Eric S. Hall", + "author_inst": "Geisinger" + }, + { + "author_name": "Yasser El-Manzalawy", + "author_inst": "Geisinger" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.23.21252230", "rel_title": "Prior COVID-19 Infection and Antibody Response to Single Versus Double Dose mRNA SARS-CoV-2 Vaccination", @@ -888192,41 +892827,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.24.432734", - "rel_title": "Targeting of the NLRP3 Inflammasome for early COVID-19", - "rel_date": "2021-02-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.24.432734", - "rel_abs": "Following entry and replication of Severe Acute Respiratory Syndrome-coronavirus-2 (SARS-CoV-2) into ACE2 expressing cells, the infected cells undergo lysis releasing more virus but also cell contents. In the lung, constitutive cytokines such as IL-1 are released together with other cell contents. A cascade of inflammatory cytokines ensues, including chemokines and IL-1{beta}, triggering both local as well as systemic inflammation. This cascade of inflammatory cytokines in patients with COVID-19 is termed \"Cytokine Release Syndrome\" (CRS), and is associated with poor outcomes and death. Many studies reveal that blocking IL-1 activities in COVID-19 patients reduces disease severity and deaths. Here we report highly significant circulating levels of IL-1{beta}, IL-1 Receptor antagonist, IL-6, TNF, IL-10 and soluble urokinase plasminogen activator receptor in COVID-19 patients with mild or no symptoms. We also report that in circulating myeloid cells from the same patients, there is increased expression of the NOD-, LRR- and pyrin domain-containing 3 (NLRP3) early in the infection. We observed increased NLRP3 gene expression in myeloid cells correlated with IL-1{beta} gene expression and also with elevated circulating IL-1{beta} levels. We conclude that early in SARS-CoV-2 infection, NLRP3 activation takes place and initiates the CRS. Thus, NLRP3 is a target to reduce the organ damage of inflammatory cytokines of the CRS.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Carlo Marchetti", - "author_inst": "University of Colorado" - }, - { - "author_name": "Kara Mould", - "author_inst": "National Jewish Health, Medicine, Denver, Colorado, United States" - }, - { - "author_name": "Isak W. Tengesdal", - "author_inst": "Department of Medicine, University of Colorado Denver, Aurora, CO and Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), " - }, - { - "author_name": "William J. Janssen", - "author_inst": "National Jewish Health, Medicine, Denver, Colorado, United States" - }, - { - "author_name": "Charles A. Dinarello", - "author_inst": "Department of Medicine, University of Colorado Denver, Aurora, CO and Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), " - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.24.432576", "rel_title": "Increased transmission of SARS-CoV-2 lineage B.1.1.7 (VOC 2020212/01) is not accounted for by a replicative advantage in primary airway cells or antibody escape", @@ -889993,6 +894593,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.19.21252073", + "rel_title": "Health-related quality of life of adult COVID-19 patients following one-month illness experience since diagnosis: findings of a cross-sectional study in Bangladesh", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.19.21252073", + "rel_abs": "BackgroundThe pandemic coronavirus disease 2019 (COVID-19) stances an incredible impact on the quality of life of the patients. The disease not only denigrates the physical health of the patients but also affects their mental health. This cross-sectional study aimed to assess the health-related quality of life (HRQOL) of patients.\n\nMethodsThe study was conducted at the National Institute of Preventive and Social Medicine (NIPSOM), Dhaka, Bangladesh during the period from June to November 2020. The study enrolled 1204 adult (>18 years) COVID-19 patients diagnosed by real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay and completed the one-month duration of illness. The patients were interviewed with the CDC HRQOL-14 questionnaire to assess their HRQOL. Data were collected by telephone-interview and reviewing medical records using a semi-structured questionnaire and checklist respectively. Informed consent was obtained from each patient before data collection.\n\nResultsThe majority of the COVID-19 patients were males (72.3%), urban residents (50.2%), and diverse service holders (49.6%). More than one-third (35.5%) of patients had comorbidity including hypertension (55.6%), diabetes mellitus (55.6%), ischaemic heart disease (16.4%), chronic lung (12.4%), kidney (2.8%), and liver (4.2%) diseases. The mean{+/-}SD duration of physical illness was 9.83({+/-}7.09) days, and it was 7.97({+/-}8.12) days for mental illness. During the one-month disease course, the general health condition was excellent/very good/good in 70.1% of the patients while it was fair/poor in 29.8% of the patients. Older age, sex, and marital status were significantly associated with at least one dimension of HRQOL. Patients having symptoms of COVID-19 and comorbidity had significantly poorer HRQOL.\n\nConclusionCOVID-19 pretenses a significant impact on the HRQOL of the patients including physical and mental illness during the clinical course. Our findings suggest more pragmatic preventive, promotive, and curative measures considering illness experiences of the COVID-19 patients to restore their quality of life.\n\nHighlightsSince COVID-19 was identified first in china in 2019, it has been transmitted globally and caused a significant impact on human health. A few studies have been carried out on HRQOL of COVID-19 patients and struggled with an accurate estimation of the severity of their physical and mental illness. Most of the studies recognized the poor quality of life of COVID-19 patients after the one-month disease course. Our study provides new insights on the HRQOL of the COVID-19 patients using the CDC HRQOL-14 questionnaire. We measured the HRQOL following one-month illness experience of the patients using three modules: the healthy days core; the activity limitations; and the healthy days symptoms. The study adds information regarding general health conditions including both the physical and mental health of COVID-19 patients. The study also complements information regarding the activity limitations of the patients. The study findings could contribute to designing an efficient clinical algorithm to alleviate the illness sufferings of the COVID-19 patients using a more pragmatic approach. The study conserves decisive policy implications to concoct effective interventions for improving the HRQOL of COVID-19 patients in the country and elsewhere in other countries world-wide.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Md. Ziaul Islam", + "author_inst": "National Institute of Preventive and Social Medicine (NIPSOM)" + }, + { + "author_name": "Baizid Khoorshid Riaz", + "author_inst": "National Institute of Preventive and Social Medicine" + }, + { + "author_name": "Syeda Sumaiya Efa", + "author_inst": "Diabetic Association of Bangladesh" + }, + { + "author_name": "Sharmin Farjana", + "author_inst": "Shaheed Suhrawardy Medical College Hospital" + }, + { + "author_name": "Fahad Mahmood", + "author_inst": "National Institute of Preventive and Social Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.20.21251855", "rel_title": "Transmission of SARS-CoV-2 Considering Shared Chairs in Outpatient Dialysis: A Real-World Case-Control Study", @@ -890122,41 +894757,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2021.02.19.21252118", - "rel_title": "Phased implementation of COVID-19 vaccination: rapid assessment of policy adoption, reach and effectiveness to protect the most vulnerable in the US", - "rel_date": "2021-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.19.21252118", - "rel_abs": "ObjectivesThe US and rest of the world have suffered from the COVID-19 pandemic for over a year. The high transmissibility and severity of this virus have provoked governments to adopt a variety of mitigation strategies. Some of these previous measures, such as social distancing and mask mandates, were effective in reducing the case growth rate yet became economically and administratively difficult to enforce as the pandemic continued. In late December 2020, COVID-19 vaccines were first approved in the US and states began a phased implementation of COVID-19 vaccination. However, there is limited quantitative evidence regarding the effectiveness of the phased COVID-19 vaccination. This study aims to provide a rapid assessment of the adoption, reach, and effectiveness of the phased implementation of COVID-19 vaccination.\n\nMethodsWe utilize an event-study analysis to evaluate the effect of vaccination on the state-level, daily COVID-19 case growth rate.\n\nResultsThrough this analysis, we assert that vaccination is effective in reducing the spread of COVID-19 shortly after the first shots were given. Specifically, the case growth rate declined by 0.124, 0.347, 0.345, 0.464, 0.490, and 0.756 percentage points corresponding to the 1-5, 6-10, 11-15, 16-20, 21-25, and 26 or more day periods after the initial shots.\n\nConclusionsThe findings could be insightful for policymakers as they work to optimize vaccine distribution in later phases, and also for the public as the COVID-19 related health risk is a contentious issue.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yun Li", - "author_inst": "george mason university" - }, - { - "author_name": "Moming Li", - "author_inst": "University of California at San Francisco" - }, - { - "author_name": "Megan Rice", - "author_inst": "Carnegie Mellon University" - }, - { - "author_name": "Yanfang Su", - "author_inst": "Washington University" - }, - { - "author_name": "Chaowei Yang", - "author_inst": "George Mason University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.02.19.21252095", "rel_title": "Analysis of key factors of a SARS-CoV-2 vaccination program: A mathematical modeling approach", @@ -891939,6 +896539,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.19.21252106", + "rel_title": "Impact of environmental temperature on Covid-19 spread: Model and analysis of measurements recorded during the second pandemic in Cyprus", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.19.21252106", + "rel_abs": "The paper investigates the effect of the environmental temperature on the spread of COVID-19. We study the daily numbers of the cases infected and deaths caused by Covid-19 during the second wave of the pandemic within 2020, and how they were affected by the daily average-high temperature for the districts of the Republic of Cyprus. Among the findings of the paper, we show that (i) the average ratio of the PCR to rapid positive tests is [~]2.57{+/-}0.25, as expected from the tests responses, indicating that PCR overestimates positivity by [~]2.5 times; (ii) the average age of deaths caused by Covid-19 increases with rate about a year of age per week; (iii) the probability of a person infected by Covid-19 to develop severe symptoms leading to death is strongly depended on the persons age, while the probability of having a death on the age of [~]67 or younger is less than 1/1000; (iv) the number of infected cases and deaths declined dramatically when the environmental temperature reaches and/or climbs above the critical temperature of TC=30.1{+/-}2.4 C0; (v) the observed negative correlation between the exponential growth rate of the infected cases and the environmental temperature can be described within the framework of chemical kinetics, with at least two competing reactions, the connection of the coronavirus towards the receptor and the dissolution of the coronavirus; the estimated activation energy difference corresponding to the competing chemical reactions, 0.212{+/-}0.25 eV, matches the known experimental value; and (vi) the infected cases will decline to zero, when the environmental temperature climbs above the critical temperature within the summery days of 2021, which is expected for the Republic of Cyprus by the 16th of May, 2021.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "George Livadiotis", + "author_inst": "Southwest Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.22.21252208", "rel_title": "Vaccination efforts in Brazil: scenarios and perspectives under a mathematical modeling approach", @@ -892060,49 +896679,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.22.21252205", - "rel_title": "A rapid review of equity considerations in large-scale testing campaigns during infectious disease epidemics", - "rel_date": "2021-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21252205", - "rel_abs": "ContextLarge-scale testing is an intervention that is instrumental for infectious disease control and a central tool for the COVID-19 pandemic. Our rapid review aimed to identify if and how equity has been considered in large-scale testing initiatives.\n\nMethodsWe searched Web of Science and PubMed in November 2020 and followed PRISMA recommendations for scoping reviews. Articles were analyzed using descriptive and thematic analysis.\n\nResultsOur search resulted in 291 studies of which 41 were included for data extraction after full article screening. Most of the included articles (83%) reported on HIV-related screening programs, while the remaining programs focused on other sexually transmitted infections (n=3) or COVID-19 (n=4). None of the studies presented a formal definition of (in)equity in testing, however, 23 articles did indirectly include elements of equity in the program or intervention design, largely through the justification of their target population.\n\nConclusionThe studies included in our rapid review did not explicitly consider equity in their design or evaluation. It is imperative that equity is incorporated into the design of infectious disease testing programs and serves as an important reminder of how equity considerations are needed for SARS-CoV-2 testing and vaccination programs.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Katarina Ost", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Louise Duquesne", - "author_inst": "University de Montreal" - }, - { - "author_name": "Claudia Duguay", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Lola Traverson", - "author_inst": "CEPED, Institute for Research on Sustainable Development, IRD-Universite de Paris, ERL INSERM SAGESUD" - }, - { - "author_name": "Isadora Mathevet", - "author_inst": "Centre population et Developpement CEPED" - }, - { - "author_name": "Valery Ridde", - "author_inst": "CEPED, Institute for Research on Sustainable Development, IRD-Universite de Paris, ERL INSERM SAGESUDD," - }, - { - "author_name": "Kate Zinszer", - "author_inst": "Universite de Montreal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.23.432474", "rel_title": "SARS-CoV-2 causes brain inflammation and induces Lewy body formation in macaques", @@ -893765,6 +898341,153 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.02.20.432046", + "rel_title": "Reduced binding and neutralization of infection- and vaccine-induced antibodies to the B.1.351 (South African) SARS-CoV-2 variant", + "rel_date": "2021-02-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.20.432046", + "rel_abs": "The emergence of SARS-CoV-2 variants with mutations in the spike protein is raising concerns about the efficacy of infection- or vaccine-induced antibodies to neutralize these variants. We compared antibody binding and live virus neutralization of sera from naturally infected and spike mRNA vaccinated individuals against a circulating SARS-CoV-2 B.1 variant and the emerging B.1.351 variant. In acutely-infected (5-19 days post-symptom onset), convalescent COVID-19 individuals (through 8 months post-symptom onset) and mRNA-1273 vaccinated individuals (day 14 post-second dose), we observed an average 4.3-fold reduction in antibody titers to the B.1.351-derived receptor binding domain of the spike protein and an average 3.5-fold reduction in neutralizing antibody titers to the SARS-CoV-2 B.1.351 variant as compared to the B.1 variant (spike D614G). However, most acute and convalescent sera from infected and all vaccinated individuals neutralize the SARS-CoV-2 B.1.351 variant, suggesting that protective immunity is retained against COVID-19.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Venkata Viswanadh Edara", + "author_inst": "Emory University" + }, + { + "author_name": "Carson Norwood", + "author_inst": "Emory University" + }, + { + "author_name": "Katharine Floyd", + "author_inst": "Emory University" + }, + { + "author_name": "Lilin Lai", + "author_inst": "Emory University" + }, + { + "author_name": "Meredith E Davis-Gardner", + "author_inst": "Emory University" + }, + { + "author_name": "William H Hudson", + "author_inst": "Emory University" + }, + { + "author_name": "Grace Mantus", + "author_inst": "Emory University" + }, + { + "author_name": "Lindsay E Nyhoff", + "author_inst": "Emory University" + }, + { + "author_name": "Max W Adelman", + "author_inst": "Emory University" + }, + { + "author_name": "Rebecca Fineman", + "author_inst": "Emory University" + }, + { + "author_name": "Shivan Patel", + "author_inst": "Emory University" + }, + { + "author_name": "Rebecca Byram", + "author_inst": "Emory University" + }, + { + "author_name": "Dumingu Nipuni Gomes", + "author_inst": "Emory University" + }, + { + "author_name": "Garett Michael", + "author_inst": "Emory University" + }, + { + "author_name": "Hayatu Abdullahi", + "author_inst": "Emory University" + }, + { + "author_name": "Nour Beydoun", + "author_inst": "Emory University" + }, + { + "author_name": "Bernadine Panganiban", + "author_inst": "Emory University" + }, + { + "author_name": "Nina McNair", + "author_inst": "Emory University" + }, + { + "author_name": "Kieffer Hellmeister", + "author_inst": "Emory University" + }, + { + "author_name": "Jamila Pitts", + "author_inst": "Emory University" + }, + { + "author_name": "Joy Winters", + "author_inst": "Emory University" + }, + { + "author_name": "Jennifer Kleinhenz", + "author_inst": "Emory University" + }, + { + "author_name": "Jacob Usher", + "author_inst": "Emory University" + }, + { + "author_name": "Anne Piantadosi", + "author_inst": "Emory University" + }, + { + "author_name": "Jesse J Waggoner", + "author_inst": "Emory University" + }, + { + "author_name": "Ahmed Babiker", + "author_inst": "Emory University" + }, + { + "author_name": "David S Stephens", + "author_inst": "Emory University" + }, + { + "author_name": "Evan J Anderson", + "author_inst": "Emory University" + }, + { + "author_name": "Srilatha Edupuganti", + "author_inst": "Emory University" + }, + { + "author_name": "Nadine Rouphael", + "author_inst": "Emory University" + }, + { + "author_name": "Rafi Ahmed", + "author_inst": "Emory University" + }, + { + "author_name": "Jens Wrammert", + "author_inst": "Emory University" + }, + { + "author_name": "Mehul S Suthar", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.20.432110", "rel_title": "A novel glucocorticoid and androgen receptor modulator reduces viral entry and innate immune inflammatory responses in the Syrian Hamster model of SARS-CoV-2", @@ -893898,41 +898621,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.02.18.21251992", - "rel_title": "Demographic benchmarks for equitable coverage of the COVID-19 vaccination program among priority populations", - "rel_date": "2021-02-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21251992", - "rel_abs": "We report the demographic distribution of non-institutionalized populations in the US who are prioritized for COVID-19 vaccination by ethnicity, age and sex and region. The composition of non-institutionalized priority populations was estimated using a nationally representative sample of 25,417 adults interviewed in the National Health Interview Survey (NHIS) in 2018. A relatively large fraction of individuals prioritized for the earliest distribution of the vaccine are women, non-Hispanic Black, and young to middle aged adults. Overall, the study provides a platform to track equity in vaccine coverage and to better tailor health communication strategies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Kushagra Vashist", - "author_inst": "Department of Epidemiology, Rollins School of Public Health, Emory University" - }, - { - "author_name": "Tabia Akintobi", - "author_inst": "Morehouse School of Medicine" - }, - { - "author_name": "Robert A. Bednarczyk", - "author_inst": "Department of Epidemiology, Rollins School of Public Health, Emory University, Hubert Department of Global Health, Rollins School of Public Health, Emory Univer" - }, - { - "author_name": "K.M Venkat Narayan", - "author_inst": "Department of Epidemiology, Rollins School of Public Health, Emory University, Hubert Department of Global Health, Rollins School of Public Health, Emory Univer" - }, - { - "author_name": "Shivani A. Patel", - "author_inst": "Department of Epidemiology, Rollins School of Public Health, Emory University, Hubert Department of Global Health, Rollins School of Public Health, Emory Univer" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.18.21252016", "rel_title": "Diagnostic accuracy of RT-PCR for detection of SARS-CoV-2 compared to a composite reference standard in hospitalized patients", @@ -895407,6 +900095,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.16.21251838", + "rel_title": "Profile of SARS-CoV-2-specific CD4 T cell response: Relationship with disease severity and impact of HIV-1 and active Mycobacterium tuberculosis co-infection", + "rel_date": "2021-02-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251838", + "rel_abs": "T cells are involved in control of COVID-19, but limited knowledge is available on the relationship between antigen-specific T cell response and disease severity. Here, we assessed the magnitude, function and phenotype of SARS-CoV-2-specific CD4 T cells in 95 hospitalized COVID-19 patients (38 of them being HIV-1 and/or tuberculosis (TB) co-infected) and 38 non-COVID-19 patients, using flow cytometry. We showed that SARS-CoV-2-specific CD4 T cell attributes, rather than magnitude, associates with disease severity, with severe disease being characterized by poor polyfunctional potential, reduced proliferation capacity and enhanced HLA-DR expression. Moreover, HIV-1 and TB co-infection skewed the SARS-CoV-2 T cell response. HIV-1 mediated CD4 T cell depletion associated with suboptimal T cell and humoral immune responses to SARS-CoV-2; and a decrease in the polyfunctional capacity of SARS-CoV-2-specific CD4 T cells was observed in COVID-19 patients with active TB. Our results also revealed that COVID-19 patients displayed reduced frequency of Mtb-specific CD4 T cells, with possible implications for TB disease progression. There results corroborate the important role of SARS-CoV-2-specific T cells in COVID-19 pathogenesis and support the concept of altered T cell functions in patients with severe disease.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Catherine Riou", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Elsa du Bruyn", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Cari Stek", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Remy Daroowala", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Rene T Goliath", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Fatima Abrahams", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Qonita Said-Hartley", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Brian W Allowed", + "author_inst": "Stellenbosch University and Tygerberg Hospital" + }, + { + "author_name": "Marvin Hsiao", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Katalin A Wilkinson", + "author_inst": "University of Cape Town and The Francis Crick Institute" + }, + { + "author_name": "Cecilia S Lindestam Arlehamn", + "author_inst": "La Jolla Institute for Immunology" + }, + { + "author_name": "Alessandro Sette", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Sean Wasserman", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Robert J Wilkinson", + "author_inst": "University of Cape Town, Imperial College London and The Francis Crick Institute" + }, + { + "author_name": "- the HIATUS consortium", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.18.21251939", "rel_title": "Applicability of Neighborhood and Building Scale Wastewater-Based Genomic Epidemiology to Track the SARS-CoV-2 Pandemic and other Pathogens.", @@ -895504,73 +900267,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.02.18.21251368", - "rel_title": "Early Identification of SARS-CoV-2 Emergence in the DoD via Retrospective Analysis of 2019-2020 Upper Respiratory Illness Samples", - "rel_date": "2021-02-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21251368", - "rel_abs": "The first case of non-travel related SARS-COV-2 was detected late February 2020 in California, however the delay of diagnostic testing and initial stringent testing criteria made it difficult to identify those who could have acquired it through community spread. There was speculation by many that the virus may have been circulating at least a month earlier [1], and environmental sampling has suggested that versions of this virus were found many months before the first human samples were identified [2]. Here we performed a retrospective study from residual samples collected from a global DoD Respiratory Surveillance Program to establish a tentative timeline by which this virus was circulating in our DoD population. We performed RT-PCR for SARS-COV-2 and compared to the dates of these cases to the first cases identified in respective states and counties using the Johns Hopkins COVID tracker website. Twenty-four positive samples were identified out of approximately 7,000 tested. Although we found some early cases in certain regions, we did not see circulation before late February in samples collected both in the US and outside the USA.\n\nSUMMARYO_ST_ABSWhat is already known about this topic?C_ST_ABSWe know that the first reported case of SARS-COV-2 was mid-January; however, there has been conjecture that the virus was found in the community before this date.\n\nWhat is added by this report?Here we took samples collection from a global respiratory surveillance program and evaluated for the presence of SARS-COV-2 RNA. The first case we found in the surveillance program was approximately 30-60 days before the first case was identified on military installations via diagnostic testing, however was not earlier than the mid-January reported case in California.\n\nWhat are the implications for public health practice?The implementation of new and emerging pathogen detection assays into already established surveillance programs could detect early community spread and possibly reduce spread of pathogen among vulnerable populations.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Richard R Chapleau", - "author_inst": "US Air Force School of Aerospace Medicine" - }, - { - "author_name": "Monica Christian", - "author_inst": "US Air Force School of Aerospace Medicine" - }, - { - "author_name": "Benjamin Connors", - "author_inst": "US Air Force School of Aerospace Medicine" - }, - { - "author_name": "Christa Premo", - "author_inst": "US Air Force School of Aerospace Medicine" - }, - { - "author_name": "Tim Chao", - "author_inst": "US Air Force School of Aerospace Medicine" - }, - { - "author_name": "Juan Rodriguez", - "author_inst": "US Air Force School of Aerospace Medicine" - }, - { - "author_name": "Shana Huntsberger", - "author_inst": "US Air Force School of Aerospace Medicine" - }, - { - "author_name": "Jennifer Meyer", - "author_inst": "US Air Force School of Aerospace Medicine" - }, - { - "author_name": "Amanda Javorina", - "author_inst": "US Air Force School of Aerospace Medicine" - }, - { - "author_name": "Kenney Reynolds", - "author_inst": "US Air Force School of Aerospace Medicine" - }, - { - "author_name": "David S Riddle", - "author_inst": "US Air Force School of Aerospace Medicine" - }, - { - "author_name": "Mark W Lisanby", - "author_inst": "US Air Force School of Aerospace Medicine" - }, - { - "author_name": "Clarise R Starr", - "author_inst": "US Air Force School of Aerospace Medicine" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.28.21249723", "rel_title": "Obesity and COVID-19 Mortality: A Cross-Country Analysis", @@ -896785,6 +901481,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.16.21251625", + "rel_title": "Healthcare-associated COVID-19 in England: a national data linkage study", + "rel_date": "2021-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251625", + "rel_abs": "ObjectivesNosocomial transmission was an important aspect of SARS-CoV-1 and MERS-CoV outbreaks. Healthcare-associated SARS-CoV-2 infection has been reported in single and multi-site hospital-based studies in England, but not nationally.\n\nMethodsAdmission records for all hospitals in England were linked to SARS-CoV-2 national test data for the period 01/03/2020 to 31/08/2020. Case definitions were: community-onset community-acquired (CO.CA), first positive test (FPT) <14 days pre-admission, up to day 2 of admission; hospital-onset indeterminate healthcare-associated (HO.iHA), FPT on day 3-7; hospital-onset probable healthcare-associated (HO.pHA), FPT on day 8-14; hospital-onset definite healthcare-associated (HO.HA), FPT from day 15 of admission until discharge; community-onset possible healthcare-associated (CO.pHA), FPT [≤]14 days post-discharge.\n\nResultsOne-third (34.4%, 100,859/293,204) of all laboratory-confirmed COVID-19 cases were linked to a hospital record. HO.pHA and HO.HA cases represented 5.3% (15,564/293,204) of all laboratory-confirmed cases and 15.4% (15,564/100,859) of laboratory-confirmed cases among hospital patients. CO.CA and CO.pHA cases represented 86.5% (253,582/293,204) and 5.1% (14,913/293,204) of all laboratory-confirmed cases, respectively.\n\nConclusionsUp to 1 in 6 SARS-CoV-2 infections among hospitalised patients with COVID-19 in England during the first 6 months of the pandemic could be attributed to nosocomial transmission, but these represent less than 1% of the estimated 3 million COVID-19 cases in this period.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Alex Bhattacharya", + "author_inst": "Public Health England" + }, + { + "author_name": "Simon M Collin", + "author_inst": "Public Health England" + }, + { + "author_name": "James Stimson", + "author_inst": "Public Health England" + }, + { + "author_name": "Simon Thelwall", + "author_inst": "Public Health England" + }, + { + "author_name": "Olisaeloka Nsonwu", + "author_inst": "Public Health England" + }, + { + "author_name": "Sarah Gerver", + "author_inst": "Public Health England" + }, + { + "author_name": "Julie Robotham", + "author_inst": "Public Health England" + }, + { + "author_name": "Mark Wilcox", + "author_inst": "University of Leeds" + }, + { + "author_name": "Susan Hopkins", + "author_inst": "Public Health England" + }, + { + "author_name": "Russell Hope", + "author_inst": "Public Health England" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.16.21251844", "rel_title": "An exploratory study on the correlation of population SARS-CoV-2 cycle threshold values to local disease dynamics", @@ -897014,49 +901765,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.16.21251641", - "rel_title": "Size and duration of COVID-19 clusters go along with a high SARS-CoV-2 viral load : a spatio-temporal investigation in Vaud state, Switzerland", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251641", - "rel_abs": "To understand the geographical and temporal spread of SARS-CoV-2 during the first wave of infection documented in the canton of Vaud, Switzerland, we analysed clusters of positive cases using the precise place of residence of 33651 individuals tested (RT-PCR) between January 10 and June 30, 2020. We identified both space-time (SaTScan) and transmission (MST-DBSCAN) clusters; we estimated their duration, their transmission behavior (emergence, growth, reduction, etc.) and relative risk. For each cluster, we computed the within number of individuals, their median age and viral load.\n\nAmong 1684 space-time clusters identified, 457 (27.1%) were significant (p [≤] 0.05), i.e. harboring a higher relative risk of infection, as compared to other regions. They lasted a median of 11 days (IQR 7-13) and included a median of 12 individuals per cluster (IQR 5-20). The majority of significant clusters (n=260; 56.9 %) had at least one person with an extremely high viral load (above 1 billion copies/ml). Those clusters were considerably larger (median of 17 infected individuals, p < 0.001) than clusters with subjects showing a viral load lower than 1 million copies/ml (median of 3 infected individuals). The highest viral loads were found in clusters with the lowest average age, while clusters with the highest average age had low to middle viral load. Interestingly, in 20 significant clusters the viral load of three first cases were all below 100000 copies/ml suggesting that subjects with less than 100000 copies/ml may still have been contagious. Noteworthy, the dynamics of transmission clusters made it possible to identify three diffusion zones, which mainly differentiated rural from urban areas, the latter being more prone to last and spread in a new nearby clusters.\n\nThe use of geographic information is key for public health decision makers to mitigate the spread of the virus. This study suggests that early localization of clusters help implementing targeted protective measures limiting the spread of the SARS-CoV-2 virus.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ana\u00efs Ladoy", - "author_inst": "Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Lausanne, Switzerland; Group of Geographic Information Research and Analysis in Population Health (GIRAPH), Swi" - }, - { - "author_name": "Onya Opota", - "author_inst": "Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland" - }, - { - "author_name": "Pierre-Nicolas Carron", - "author_inst": "Department of Emergency Medicine, Lausanne University Hospital, Rue du Bugnon 46, CH-1011, Lausanne, Switzerland" - }, - { - "author_name": "Idris Guessous", - "author_inst": "Division and Department of Primary Care Medicine, Geneva University Hospitals, Geneva, Switzerland; Group of Geographic Information Research and Analysis in Pop" - }, - { - "author_name": "S\u00e9verine Vuilleumier", - "author_inst": "La Source School of Nursing, University of Applied Sciences and Arts Western Switzerland (HES-SO), Lausanne, Switzerland" - }, - { - "author_name": "St\u00e9phane Joost", - "author_inst": "Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne (EPFL), Lausanne, Switzerland; Group of Geographic Information Research and Analysis in Population Health (GIRAPH), Swi" - }, - { - "author_name": "Gilbert Greub", - "author_inst": "Institute of Microbiology, University Hospital Centre and University of Lausanne, Switzerland; Infectious Diseases Service, University Hospital Centre, Lausanne" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.16.21251673", "rel_title": "Circulatory Cytokines and Chemokines Profile in Human Coronaviruses: A systematic review and meta-analysis", @@ -898423,6 +903131,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.17.21251758", + "rel_title": "Prediction of Mortality in hospitalized COVID-19 patients in a statewide health network", + "rel_date": "2021-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.17.21251758", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSImportanceC_ST_ABSA predictive model to automatically identify the earliest determinants of both hospital discharge and mortality in hospitalized COVID-19 patients could be of great assistance to caregivers if the predictive information is generated and made available in the immediate hours following admission.\n\nObjectiveTo identify the most important predictors of hospital discharge and mortality from measurements at admission for hospitalized COVID-19 patients.\n\nDesignObservational cohort study.\n\nSettingElectronic records from hospitalized patients.\n\nParticipantsPatients admitted between March 3rd and August 24th with COVID-19 in Johns Hopkins Health System hospitals.\n\nExposures216 phenotypic variables collected within 48 hours of admission.\n\nMain OutcomesWe used age-stratified (<60 and >=60 years) random survival forests with competing risks to identify the most important predictors of death and discharge. Fine-Gray competing risk regression (FGR) models were then constructed based on the most important RSF-derived covariates.\n\nResultsOf 2212 patients, 1913 were discharged (age 57{+/-}19, time-to-discharge 9{+/-}11 days) while 279 died (age 75{+/-}14, time to death 14{+/-}15 days). Patients >= 60 years were nearly 10 times as likely to die within 60 days of admission as those <60. As the pandemic evolved, the rate of hospital discharge increased in both older and younger patients. Incident death and hospital discharge were accurately predicted by measures of respiratory distress, inflammation, infection, renal function, red cell turn over and cardiac stress. FGR models for each of hospital discharge and mortality as outcomes based on these variables performed well in the older (AUC 0.80-0.85 at 60-days) and younger populations (AUC >0.90 at 60-days).\n\nConclusions and RelevanceWe identified markers collected within 2 days of admission that predict hospital discharge and mortality in COVID-19 patients and provide prediction models that may be used to guide patient care. Our proposed model suggests that hospital discharge and mortality can be forecasted with high accuracy based on 8-10 variables at this stage of the COVID-19 pandemic. Our findings also point to several specific pathways that could be the focus of future investigations directed at reducing mortality and expediting hospital discharge among COVID-19 patients. Probability of hospital discharge increased over the course of the pandemic.\n\nKO_SCPLOWEYC_SCPLOW PO_SCPLOWOINTSC_SCPLOWO_ST_ABSQuestionC_ST_ABSCan we predict the likelihood of hospital discharge as well as mortality from data obtained in the first 48 hours from admission in hospitalized COVID-19 patients?\n\nFindingsModels based on extensive phenotyping mined directly from electronic medical records followed by variable selection, accounted for the competing events of hospital death versus discharge, predicted both death and discharge with area under the receiver operating characteristic curves of >0.80.\n\nMeaningHospital discharge and mortality can be forecasted with high accuracy based on just 8-10 variables, and the probability of hospital discharge increased over the course of the pandemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Bharath Ambale Venkatesh", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Thiago Quinaglia", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Mahsima Shabani", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Jaclyn Sesso", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Karan Kapoor", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Matthew Matheson", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Colin O Wu", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Christopher Cox", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Joao A Lima", + "author_inst": "Johns Hopkins Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.16.21251849", "rel_title": "Convalescent plasma for preventing critical illness in COVID-19: A phase 2 trial and immune profile", @@ -898648,45 +903407,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.02.18.21251809", - "rel_title": "The unexpected dynamics of COVID-19 in Manaus, Brazil: Herd immunity versus interventions", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21251809", - "rel_abs": "In late March 2020, SARS-CoV-2 arrived in Manaus, Brazil, and rapidly developed into a large-scale epidemic that collapsed the local health system, and resulted in extreme death rates. Several key studies reported that [~]76% of residents of Manaus were infected (attack rate AR[~=]76%) by October 2020, suggesting protective herd immunity had been reached. Despite this, in November an unexpected second wave of COVID-19 struck again, and proved to be larger than the first creating a catastrophe for the unprepared population. It has been suggested that this could only be possible if the second wave was driven by reinfections. Here we use novel methods to model the epidemic from mortality data, evaluate the impact of interventions, in order to provide an alternative explanation as to why the second wave appeared. The method fits a \"flexible\" reproductive number R0(t) that changes over the epidemic, and found AR[~=]30-34% by October 2020, for the first wave, which is far less than required for herd immunity, yet in-line with recent seroprevalence estimates. The two-strain model provides an accurate fit to observed epidemic datasets, and finds AR[~=]70% by March 2021. Using genomic data, the model estimates transmissibility of the new P.1 virus lineage, as 1.9 times as transmissible as the non-P1. The model thus provides a reasonable explanation for the two-wave dynamics in Manaus, without the need to rely on reinfections which until now have only been found in small numbers in recent surveillance efforts.\n\nSignificanceThis paper explores the concept of herd immunity and approaches for assessing attack rate during the explosive outbreak of COVID-19 in the city of Manaus, Brazil. The event has been repeatedly used to exemplify the epidemiological dynamics of the disease and the phenomenon of herd immunity, as claimed to be achieved by the end of the first wave in October 2020. A novel modelling approach reconstructs these events, specifically in the presence of interventions. The analysis finds herd immunity was far from being attained, and thus a second wave was readily possible, as tragically occurred in reality. Based on genomic data, the multi-strain model gives insights on the new highly transmissible variant of concern P.1 and role of reinfection.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Daihai He", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Yael Artzy-Randrup", - "author_inst": "University of Amsterdam, Amsterdam, Netherlands" - }, - { - "author_name": "Salihu S Musa", - "author_inst": "Hong Kong Polytechnic University" - }, - { - "author_name": "Tiago Graf", - "author_inst": "Instituto Goncalo Moniz" - }, - { - "author_name": "Felipe Naveca", - "author_inst": "Instituto Leonidas e Maria Deane" - }, - { - "author_name": "Lewi Stone", - "author_inst": "RMIT University, Melbourne, Australia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.17.21251722", "rel_title": "The epidemiological characteristics of the primary health care based COVID-19 swabbed persons in Qatar, March- October 2020", @@ -900153,6 +904873,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.15.21249420", + "rel_title": "COVID-19 Associated Stroke--A Single Centre Experience", + "rel_date": "2021-02-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21249420", + "rel_abs": "Background and PurposeVarious neurological complications have been reported in association with COVID-19. We report our experience of COVID-19 with stroke at a single center over a period of eight months spanning 1 March to 31 October 2020.\n\nMethodsWe recruited all patients admitted to Internal Medicine with an acute stroke, who also tested positive for COVID-19 on RTPCR. We included all stroke cases in our analysis for prediction of in-hospital mortality, and separately analyzed arterial infarcts for vascular territory of ischemic strokes.\n\nResultsThere were 62 stroke cases among 3923 COVID-19 admissions (incidence 1.6%). Data was available for 58 patients {mean age 52.6 years; age range 17-91; F/M=20/38; 24% (14/58) aged [≤]40; 51% (30/58) hypertensive; 36% (21/58) diabetic; 41% (24/58) with O2 saturation <95% at admission; 32/58 (55.17 %) in-hospital mortality}. Among 58 strokes, there were 44 arterial infarcts, seven bleeds, three arterial infarcts with associated cerebral venous sinus thrombosis, two combined infarct and bleed, and two of indeterminate type. Among the total 49 infarcts, Carotid territory was the commonest affected (36/49; 73.5%), followed by vertebrobasilar (7/49; 14.3%) and both (6/49; 12.2%). Concordant arterial block was seen in 61% (19 of 31 infarcts with angiography done). Early stroke (within 48 hours of respiratory symptoms) was seen in 82.7% (48/58) patients. Patients with poor saturation at admission were older (58 vs 49 years) and had more comorbidities and higher mortality (79% vs 38%). Mortality was similar in young strokes and older patients, although the latter required more intense respiratory support. Logistic regression analysis showed that low GCS and requirement for increasing intensity of respiratory support predicted in-hospital mortality.\n\nConclusionsWe had a 1.6% incidence of COVID-19 related stroke of which the majority were carotid territory infarcts. In-hospital mortality was 55.17%, predicted by low GCS at admission.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Uma Sundar", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Niteen Karnik", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Amita Mukhopadhyay", + "author_inst": "Dr Chandramma Dayananda Sagar Institute of Medical Education and Research, Kanakapura 562112, Ramanagara District, Karnataka, India" + }, + { + "author_name": "Pramod Darole", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Shaonak Kolte", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Ashank Bansal", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Yojana Gokhale", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Dnaneshwar Asole", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Anagha Joshi", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Sangeeta Pednekar", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Swati Chavan", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Trupti Trivedi", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Namita Padwal", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Lalana Kalekar", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Charulata Londhe", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Rupal Padhiyar", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Dharmendra Pandey", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Dhirendra Yadav", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Sonal Honrao", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Prerana Bhavsar", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Priyanshu Shah", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Satish Gosavi", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Aniket Wadal", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Awesh Shingare", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Mayuri Trivedi", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Gauri Pathak Oak", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.13.21251670", "rel_title": "Excess Mortality in Suicide caused by COVID-19 in Japan", @@ -900330,169 +905169,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.15.21251511", - "rel_title": "Mapping of SARS-CoV-2 Brain Invasion and Histopathology in COVID-19 Disease", - "rel_date": "2021-02-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251511", - "rel_abs": "The coronavirus SARS-CoV-2 (SCV2) causes acute respiratory distress, termed COVID-19 disease, with substantial morbidity and mortality. As SCV2 is related to previously-studied coronaviruses that have been shown to have the capability for brain invasion, it seems likely that SCV2 may be able to do so as well. To date, although there have been many clinical and autopsy-based reports that describe a broad range of SCV2-associated neurological conditions, it is unclear what fraction of these have been due to direct CNS invasion versus indirect effects caused by systemic reactions to critical illness. Still critically lacking is a comprehensive tissue-based survey of the CNS presence and specific neuropathology of SCV2 in humans. We conducted an extensive neuroanatomical survey of RT-PCR-detected SCV2 in 16 brain regions from 20 subjects who died of COVID-19 disease. Targeted areas were those with cranial nerve nuclei, including the olfactory bulb, medullary dorsal motor nucleus of the vagus nerve and the pontine trigeminal nerve nuclei, as well as areas possibly exposed to hematogenous entry, including the choroid plexus, leptomeninges, median eminence of the hypothalamus and area postrema of the medulla. Subjects ranged in age from 38 to 97 (mean 77) with 9 females and 11 males. Most subjects had typical age-related neuropathological findings. Two subjects had severe neuropathology, one with a large acute cerebral infarction and one with hemorrhagic encephalitis, that was unequivocally related to their COVID-19 disease while most of the 18 other subjects had non-specific histopathology including focal {beta}-amyloid precursor protein white matter immunoreactivity and sparse perivascular mononuclear cell cuffing. Four subjects (20%) had SCV2 RNA in one or more brain regions including the olfactory bulb, amygdala, entorhinal area, temporal and frontal neocortex, dorsal medulla and leptomeninges. The subject with encephalitis was SCV2-positive in a histopathologically-affected area, the entorhinal cortex, while the subject with the large acute cerebral infarct was SCV2-negative in all brain regions. Like other human coronaviruses, SCV2 can inflict acute neuropathology in susceptible patients. Much remains to be understood, including what viral and host factors influence SCV2 brain invasion and whether it is cleared from the brain subsequent to the acute illness.", - "rel_num_authors": 37, - "rel_authors": [ - { - "author_name": "Geidy E Serrano", - "author_inst": "Banner Health" - }, - { - "author_name": "Jessica E. Walker", - "author_inst": "Banner Health" - }, - { - "author_name": "Richard Arce", - "author_inst": "Banner Health" - }, - { - "author_name": "Michael J Glass", - "author_inst": "Banner" - }, - { - "author_name": "Daisy Vargas", - "author_inst": "Banner Health" - }, - { - "author_name": "Lucia Sue", - "author_inst": "Banner Health" - }, - { - "author_name": "Anthony J Intorcia", - "author_inst": "Banner Health" - }, - { - "author_name": "Courtney M. Nelson", - "author_inst": "Banner Health" - }, - { - "author_name": "Javon Oliver", - "author_inst": "Banner Health" - }, - { - "author_name": "Jaclyn Papa", - "author_inst": "Banner Health" - }, - { - "author_name": "Aryck Russell", - "author_inst": "Banner Health" - }, - { - "author_name": "Katsuko E. Suszczewicz", - "author_inst": "Banner Health" - }, - { - "author_name": "Claryssa Borja", - "author_inst": "Banner Health" - }, - { - "author_name": "Christine Belden", - "author_inst": "Banner Health" - }, - { - "author_name": "Danielle Goldfarb", - "author_inst": "Banner Health" - }, - { - "author_name": "David Shprecher", - "author_inst": "Banner Health" - }, - { - "author_name": "Alireza Atri", - "author_inst": "Banner Health" - }, - { - "author_name": "Charles H. Adler", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Holly A Shill", - "author_inst": "Barrow Neurological Institute" - }, - { - "author_name": "Erika Driver-Dunckley", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Shyamal H. Mehta", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Benjamin Readhead", - "author_inst": "Arizona State University" - }, - { - "author_name": "Matthew J Huentelman", - "author_inst": "Translational Genomics Research Institute" - }, - { - "author_name": "Joseph L. Peters", - "author_inst": "Banner Health" - }, - { - "author_name": "Christian Bimi", - "author_inst": "Banner Health" - }, - { - "author_name": "Joseph P. Mizgerd", - "author_inst": "Boston University" - }, - { - "author_name": "Eric M. Reiman", - "author_inst": "Banner Health" - }, - { - "author_name": "Thomas J. Montine", - "author_inst": "Stanford University" - }, - { - "author_name": "Marc Desforges", - "author_inst": "Centre Hospitalier Universitaire Sainte-Justine" - }, - { - "author_name": "James L. Zehnder", - "author_inst": "Stanford University" - }, - { - "author_name": "Malaya K. Sahoo", - "author_inst": "Stanford University" - }, - { - "author_name": "Haiyu Zhang", - "author_inst": "Stanford University" - }, - { - "author_name": "Daniel Solis", - "author_inst": "Stanford University" - }, - { - "author_name": "Benjamin A. Pinsky", - "author_inst": "Stanford University" - }, - { - "author_name": "Michael Deture", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Dennis W. Dickson", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Thomas G. Beach", - "author_inst": "Banner Health" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.15.21251623", "rel_title": "FDA-authorized COVID-19 vaccines are effective per real-world evidence synthesized across a multi-state health system", @@ -901931,6 +906607,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.15.21251781", + "rel_title": "Epidemiological dynamics of the incidence of COVID-19 in children and the relationship with the opening of schools in Catalonia (Spain)", + "rel_date": "2021-02-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251781", + "rel_abs": "Here we analyse the epidemiological trend of the incidence of COVID-19 in children in Catalonia (Spain) during the first 20 weeks of the 2020-2021 school year. This study demonstrates that while schools were open the incidence rate among children remained significantly lower than in general population, despite a greater diagnostic effort in children. These results suggest that schools have not played a significant role in the SARS-CoV-2 dissemination in Catalonia.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Aida Perramon", + "author_inst": "Universitat Pompeu Fabra, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Antoni Soriano-Arandes", + "author_inst": "Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain" + }, + { + "author_name": "David Pino", + "author_inst": "Department of Physics, Universitat Politecnica de Catalunya (UPC BarcelonaTech), Barcelona, Catalonia, Spain" + }, + { + "author_name": "Uxue Lazcano", + "author_inst": "Agencia de Qualitat i Avaluacio Sanitaries de Catalunya (AQuAS), Barcelona, Catalonia, Spain" + }, + { + "author_name": "Cristina Andres", + "author_inst": "Respiratory Viruses Unit, Department of Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Marti Catala", + "author_inst": "Comparative Medicine and Bioimage Centre of Catalonia (CMCiB), Fundacio Institut d'Investigacio en Ciencies de la Salut Germans Trias i Pujol (IGTP), Badalona, " + }, + { + "author_name": "Anna Gatell", + "author_inst": "Equip Pediatria Territorial Alt Penedes-Garraf, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Mireia Carulla", + "author_inst": "ABS Pla d'Urgell (Mollerussa), Lleida, Catalonia, Spain" + }, + { + "author_name": "Dolors Canadell", + "author_inst": "CAP Barbera del Valles, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Gemma Ricos", + "author_inst": "CAP Drassanes, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Maria Teresa Riera-Bosch", + "author_inst": "EAP Vic Nord, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Silvia Burgaya", + "author_inst": "EAP Manlleu, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Olga Salvado", + "author_inst": "CAP Llibertat Reus, Tarragona, Catalonia, Spain" + }, + { + "author_name": "Javier Cantero", + "author_inst": "Corporacio del Maresme i la Selva, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Monica Vila", + "author_inst": "EAP Horta, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Miriam Poblet", + "author_inst": "Equip Territorial Pediatric Sabadell Nord, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Almudena Sanchez", + "author_inst": "CAP Les Hortes, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Anna Maria Ristol", + "author_inst": "CAP Can Serra Hospitalet de Llobregat, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Pepe Serrano", + "author_inst": "Equip Pediatria Territorial Alt Penedes-Garraf, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Andres Anton", + "author_inst": "Respiratory Viruses Unit, Department of Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Clara Prats", + "author_inst": "Department of Physics, Universitat Politecnica de Catalunya (UPC BarcelonaTech), Barcelona, Catalonia, Spain" + }, + { + "author_name": "Pere Soler-Palacin", + "author_inst": "Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.15.21251788", "rel_title": "COVID-19 European Regional Tracker", @@ -902040,45 +906819,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.17.431566", - "rel_title": "E484K mutation in SARS-CoV-2 RBD enhances binding affinity with hACE2 but reduces interactions with neutralizing antibodies and nanobodies: Binding free energy calculation studies", - "rel_date": "2021-02-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.17.431566", - "rel_abs": "The pandemic of the COVID-19 disease caused by SARS-CoV-2 has led to more than 100 million infections and over 2 million deaths worldwide. The progress in the developments of effective vaccines and neutralizing antibody therapeutics brings hopes to eliminate the threat of COVID-19. However, SARS-CoV-2 continues to mutate, and several new variants have been emerged. Among the various naturally-occurring mutations, the E484K mutation shared by both the 501Y.V2 and 501Y.V3 variants attracted serious concerns, which may potentially enhance the receptor binding affinity and reduce the immune response. In the present study, the molecular mechanism behind the impacts of E484K mutation on the binding affinity of the receptor-binding domain (RBD) with the receptor human angiotensin-converting enzyme 2 (hACE2) was investigated by using the molecular dynamics (MD) simulations combined with the molecular mechanics-generalized Born surface area (MMGBSA) method. Our results indicate that the E484K mutation results in more favorable electrostatic interactions compensating the burial of the charged and polar groups upon the binding of RBD with hACE2, which significantly improves the RBD-hACE2 binding affinity. Besides that, the E484K mutation also causes the conformational rearrangements of the loop region containing the mutant residue, which leads to more tight binding interface of RBD with hACE2 and formation of some new hydrogen bonds. The more tight binding interface and the new hydrogen bonds formation also contribute to the improved binding affinity of RBD to the receptor hACE2. In addition, six neutralizing antibodies and nanobodies complexed with RBD were selected to explore the effects of E484K mutation on the recognition of these antibodies to RBD. The simulation results show that the E484K mutation significantly reduces the binding affinities to RBD for most of the studied neutralizing antibodies, and the decrease in the binding affinities is mainly owing to the unfavorable electrostatic interactions caused by the mutation. Our studies revealed that the E484K mutation may improve the binding affinity between RBD and the receptor hACE2, implying more transmissibility of the E484K-containing variants, and weaken the binding affinities between RBD and the studied neutralizing antibodies, indicating reduced effectiveness of these antibodies. Our results provide valuable information for the effective vaccine development and antibody drugs design.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Wei Bu Wang", - "author_inst": "Yanshan University" - }, - { - "author_name": "Yu Liang", - "author_inst": "National Vaccine and Serum Institute" - }, - { - "author_name": "Yu Qin Jin", - "author_inst": "National Vaccine and Serum Institute" - }, - { - "author_name": "Jing Zhang", - "author_inst": "National Vaccine and Serum Institute" - }, - { - "author_name": "Ji Guo Su", - "author_inst": "Yanshan University" - }, - { - "author_name": "Qi Ming Li", - "author_inst": "National Vaccine and Serum Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.02.17.431554", "rel_title": "Association of CXCR6 with COVID-19 severity: Delineating the host genetic factors in transcriptomic regulation", @@ -903736,6 +908476,137 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.02.15.431291", + "rel_title": "Favourable antibody responses to human coronaviruses in children and adolescents with autoimmune rheumatic diseases", + "rel_date": "2021-02-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.15.431291", + "rel_abs": "Differences in humoral immunity to coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), between children and adults remain unexplained and the impact of underlying immune dysfunction or suppression unknown. Here, we examined the antibody immune competence of children and adolescents with prevalent inflammatory rheumatic diseases, juvenile idiopathic arthritis (JIA), juvenile dermatomyositis (JDM) and juvenile systemic lupus erythematosus (JSLE), against the seasonal human coronavirus (HCoV)-OC43 that frequently infects this age group. Despite immune dysfunction and immunosuppressive treatment, JIA, JDM and JSLE patients mounted comparable or stronger responses than healthier peers, dominated by IgG antibodies to HCoV-OC43 spike, and harboured IgG antibodies that cross-reacted with SARS-CoV-2 spike. In contrast, responses to HCoV-OC43 and SARS-CoV-2 nucleoproteins exhibited delayed age-dependent class-switching and were not elevated in JIA, JDM and JSLE patients, arguing against increased exposure. Consequently, autoimmune rheumatic diseases and their treatment were associated with a favourable ratio of spike to nucleoprotein antibodies.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Claire Deakin", + "author_inst": "UCL" + }, + { + "author_name": "Georgina Cornish", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Kevin Ng", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Nikhil Faulkner", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "William Bolland", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Veera Panova", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Joshua Hope", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Annachiara Rosa", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Ruth Harvey", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Saira Hussain", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Chris Earl", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Bethany Jebson", + "author_inst": "UCL" + }, + { + "author_name": "Merry Wilkinson", + "author_inst": "UCL" + }, + { + "author_name": "Lucy Marshall", + "author_inst": "UCL" + }, + { + "author_name": "Lizzy Rosser", + "author_inst": "UCL" + }, + { + "author_name": "Ania Radziszewska", + "author_inst": "UCL" + }, + { + "author_name": "Hannah Peckham", + "author_inst": "UCL" + }, + { + "author_name": "Judith Heaney", + "author_inst": "UCL" + }, + { + "author_name": "Hannah Rickman", + "author_inst": "UCL" + }, + { + "author_name": "Stavroula Paraskevopoulou", + "author_inst": "UCL" + }, + { + "author_name": "Catherine Houlihan", + "author_inst": "UCL" + }, + { + "author_name": "Moria Spyer", + "author_inst": "UCL" + }, + { + "author_name": "Steve Gamblin", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "John Mccauley", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Eleni Nastouli", + "author_inst": "UCL" + }, + { + "author_name": "Peter Cherepanov", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Coziana Ciurtin", + "author_inst": "UCL" + }, + { + "author_name": "Lucy Wedderburn", + "author_inst": "UCL" + }, + { + "author_name": "George Kassiotis", + "author_inst": "The Francis Crick Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.15.430863", "rel_title": "Live attenuated SARS-CoV-2 vaccine candidate: Protective immunity without serious lung lesions in Syrian hamsters", @@ -903897,61 +908768,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.02.15.431198", - "rel_title": "Single-Domain SARS-CoV-2 S1 and RBD Antibodies Isolated from Immunized Llama Effectively Bind Targets of the Wuhan, UK, and South African Strains in vitro", - "rel_date": "2021-02-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.15.431198", - "rel_abs": "The spreading of SARS-CoV-2 variants has become a major challenge of the current fight against the pandemic. Of particular concerns are the strains that have arisen from the United Kingdom (UK) and South Africa. The UK variant spreads rapidly and is projected to overtake the original strain in the US as early as in March 2021, while the South African variant appears to evade some effects of the current vaccines. Potential false-negative diagnosis using currently available antigen kits that may not recognize these variants could cause another wave of community infection. Therefore, it is imperative that antibodies used in the detection kits are validated for binding against these variants. Here we report that the nanoantibodies (nAbs in our terminology, also referred to as VHH fragments, single domain antibodies, nanobodies) that we have developed for rapid antigen detection test bind the receptor binding domain (RBD) of the S1 protein from the original COVID-SARS-2 virus as well as those from the UK and South African variants. This finding validates our antibodies used in our assay for the detection of these major variant strains.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Divora Yamane", - "author_inst": "Allele Biotechnology and Pharmaceuticals, Inc." - }, - { - "author_name": "Ivan Lu", - "author_inst": "Allele Biotechnology and Pharmaceuticals, Inc." - }, - { - "author_name": "Winson Tiahjono", - "author_inst": "Allele Biotechnology and Pharmaceuticals, Inc." - }, - { - "author_name": "Lauren Rubidoux", - "author_inst": "Allele Biotechnology and Pharmaceuticals, Inc." - }, - { - "author_name": "Abbas Hussain", - "author_inst": "Allele Biotechnology and Pharmaceuticals, Inc." - }, - { - "author_name": "John C Cancilla", - "author_inst": "Scintillon Institute" - }, - { - "author_name": "Erika Duggan", - "author_inst": "Scintillon Institute" - }, - { - "author_name": "Nathan C Shaner", - "author_inst": "Allele Biotechnology and Pharmaceuticals, Inc." - }, - { - "author_name": "Nobuki Nakanishi", - "author_inst": "Allele Biotechnology and Pharmaceuticals, Inc., Scintillon Institute" - }, - { - "author_name": "Jiwu Wang", - "author_inst": "Allele Biotechnology and Pharmaceuticals, Inc., Scintillon Institute" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.16.431318", "rel_title": "The Host Interactome of Spike Expands the Tropism of SARS-CoV-2", @@ -905381,6 +910197,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.02.12.431032", + "rel_title": "Pulsed broad-spectrum UV light effectively inactivates SARS-CoV-2 on multiple surfaces", + "rel_date": "2021-02-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.12.431032", + "rel_abs": "The ongoing SARS-CoV-2 pandemic has resulted in an increased need for technologies capable of efficiently disinfecting public spaces as well as personal protective equipment. UV light disinfection is a well-established method for inactivating respiratory viruses. Here, we have determined that broad-spectrum, pulsed UV light is effective at inactivating SARS-CoV-2 on multiple surfaces. For hard, non-porous surfaces we observed that SARS-CoV-2 was inactivated to undetectable levels on plastic and glass with a UV dose of 34.9 mJ/cm2 and stainless steel with a dose of 52.5 mJ/cm2. We also observed that broad-spectrum, pulsed UV light is effective at reducing SARS-CoV-2 on N95 respirator material to undetectable levels with a dose of 103 mJ/cm2. We included UV dosimeter cards that provide a colorimetric readout of UV dose and demonstrated their utility as a means to confirm desired levels of exposure were reached. Together, the results present here demonstrate that broad-spectrum, pulsed UV light is an effective technology for the inactivation of SARS-CoV-2 on multiple surfaces.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Alexander S Jureka", + "author_inst": "Georgia State University" + }, + { + "author_name": "Caroline G Williams", + "author_inst": "Georgia State University" + }, + { + "author_name": "Christopher F Basler", + "author_inst": "Georgia State University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.12.431026", "rel_title": "Jumper Enables Discontinuous Transcript Assembly in Coronaviruses", @@ -905502,49 +910345,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.02.11.21251584", - "rel_title": "Recent and forecast post-COVID trends in hospital activity in England amongst 0 to 24 year olds: analyses using routine hospital administrative data", - "rel_date": "2021-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.11.21251584", - "rel_abs": "BackgroundIncreasing hospital use in the past decade has placed considerable strain on children and young peoples (CYP) health services in England. Greater integration of healthcare may reduce these increases. We projected CYP healthcare activity out to 2040 and examined the potential impact of integrated care systems on projected activity.\n\nMethodsWe used routine administrative data (Hospital Episode Statistics (HES)) on emergency department (ED) attendances, emergency admissions and outpatient (OP) attendances for England by age-group for 0-24 year olds from 2007 to 2017. Bayesian projections of future activity used projected population and ethnicity and future child poverty rates. Cause data were used to identify ambulatory-care-sensitive-conditions (ACSC).\n\nFindingsED attendances, emergency admissions and OP attendances increased in all age groups from 2007 to 2017. ED and OP attendances increased 60-80% amongst children under 10 years. ACSC and neonatal causes drove the majority of increases in emergency admissions. Activity was projected to increase by 2040 by 50-145% for ED attendances, 20-125% for OP attendances and 4-58% for total admissions. Scenarios of increasing or decreasing child poverty resulted in small changes to forecast activity. Scenarios in which 50% of ACSC were seen outside hospital in integrated care reduced estimated activity in 2040 by 21.2-25.9% for admissions and 23.5-30.1% for ED attendances across poverty scenarios amongst infants.\n\nInterpretationThe rapid increases in CYP healthcare activity seen in the past decade may continue for the next decade given projected changes in population and child poverty, unless some of the drivers of increased activity are addressed. Contrary to these pessimistic scenarios, our findings suggest that development of integrated care for CYP at scale in England has the potential to dramatically reduce or even reverse these forecast increases\n\nFundingNil funding obtained.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThere has been marked increases in hospital use (inpatient, outpatient and emergency department (ED)) by children and young people (CYP). Search of the PubMed database using the search terms: (((((\"child\"[MeSH Major Topic]) OR (\"adolescent\"[MeSH Major Topic])) OR (\"infant\"[MeSH Major Topic]))) AND ((healthcare use[Text Word])) OR (emergency admission[Text Word])) AND (united kingdom[Text Word]). Drivers of increased activity include population growth and sociodemographic factors, help-seeking behaviour, growth in medical knowledge and capability, and by factors within the health system. Additional factors in child health include increased survival of premature neonates and those with congenital conditions and rising parental expectations of modern medicine. Previous studies have shown that ambulatory-care-sensitive-conditions (ACSC) are responsible for much of the increase in CYP emergency activity in England and Scotland.\n\nAdded value of this studyThis is the first study to use existing data to project possible future scenarios for CYP healthcare activity out to 2030 and 2040 in any country. Our future scenarios are based upon authoritative projections for population, ethnic diversity and child poverty in England and allow us to estimate the potential impact of integrated care scenarios in which ACSC are treated outside hospital. We show that future projected CYP activity is very high if mitigations such as integrated care are not instituted in England.\n\nImplications of all the available evidenceHealthcare activity has grown dramatically over the last decade in CYP, largely due to ACSC and the consequences of premature delivery. Projections to 2040 suggest that similar increases are likely over the next 2 decades without action to reduce child poverty and implementation of integrated care at scale in the NHS.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Joseph L Ward", - "author_inst": "UCL Great Ormond St. Institute of Child Health" - }, - { - "author_name": "Dougal Hargreaves", - "author_inst": "School of Public Health, Imperial College London" - }, - { - "author_name": "Marie Rogers", - "author_inst": "Royal College of Paediatrics and Child Health" - }, - { - "author_name": "Alison Firth", - "author_inst": "Royal College of Paediatrics and Child Health" - }, - { - "author_name": "Steve Turner", - "author_inst": "Child Health, University of Aberdeen, Aberdeen and the Royal Aberdeen Childrens Hospital, NHS Grampian, Aberdeen." - }, - { - "author_name": "Russell M. Viner", - "author_inst": "UCL Great Ormond St. Institute of Child Health" - }, - { - "author_name": "- Royal College of Paediatrics and Child Health Paediatrics 2040 Data Working Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.02.11.21251591", "rel_title": "Noncommunicable Diseases, Sociodemographic Vulnerability, and the Risk of Mortality in Hospitalized Children and Adolescents with COVID-19 in Brazil: A Syndemic in Play", @@ -906931,6 +911731,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.02.10.21251478", + "rel_title": "CATALYST trial protocol: A multicentre, open-label, phase II, multi-arm trial for an early and accelerated evaluation of the potential treatments for COVID-19 in hospitalised adults", + "rel_date": "2021-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251478", + "rel_abs": "IntroductionSevere SARS-CoV-2 infection is associated with a dysregulated immune response. Inflammatory monocytes and macrophages are crucial, promoting injurious, pro-inflammatory sequelae. Immunomodulation is, therefore, an attractive therapeutic strategy and we sought to test licensed and novel candidate drugs.\n\nMethods and analysisThe CATALYST trial is a multi-arm, open-label, multi-centre, phase II platform trial designed to identify candidate novel treatments to improve outcomes of patients hospitalised with COVID-19 compared with usual care. Treatments with evidence of biomarker improvements will be put forward for larger-scale testing by current national phase III platform trials. Hospitalised patients >16 years with a clinical picture strongly suggestive of SARS-CoV-2 pneumonia (confirmed by chest X-ray or CT scan, with or without a positive reverse transcription polymerase chain reaction (RT-PCR) assay) and a C-Reactive Protein (CRP) [≥]40 mg/L are eligible. The primary outcome measure is CRP, measured serially from admission to day 14, hospital discharge or death. Secondary outcomes include the WHO Clinical Progression Improvement Scale as a principal efficacy assessment.\n\nEthics and disseminationThe protocol was approved by the East Midlands - Nottingham 2 Research Ethics Committee (20/EM/0115) and given Urgent Public Health status; initial approval was received on 05-May-2020, current protocol version (v6.0) approval on 12-Oct-2020. The MHRA also approved all protocol versions. The results of this trial will be disseminated through national and international presentations and peer-reviewed publications.\n\nTrial registration numberEudraCT Number: 2020-001684-89\n\nISRCTN Number: 40580903\n\nStrengths and limitations of this trialO_LICATALYST will provide a rapid readout on the safety and proof-of-concept of candidate novel treatments\nC_LIO_LICATALYST will enable phase III trial resources to be focussed and allocated for agents with a high likelihood of success\nC_LIO_LICATALYST uses Bayesian multi-level models to allow for nesting of repeated measures data, with factors for each individual patient and treatment arm, and allowing for non-linear responses\nC_LIO_LICATALYST is not designed to provide a definitive signal on clinical outcomes\nC_LI", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Tonny Veenith", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Benjamin A Fisher", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Daniel Slade", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Anna Rowe", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Rowena Sharpe", + "author_inst": "University of Birmingham" + }, + { + "author_name": "David R Thickett", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Tony Whitehouse", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Matthew Rowland", + "author_inst": "University of Oxford" + }, + { + "author_name": "James Scriven", + "author_inst": "University Hospitals Birmingham NHS Trust" + }, + { + "author_name": "Dhruv Parekh", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Sarah J Bowden", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Joshua S Savage", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Duncan Richards", + "author_inst": "University of Oxford" + }, + { + "author_name": "Julian Bion", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Pamela Kearns", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Simon Gates", + "author_inst": "University of Birmingham" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.02.11.21251581", "rel_title": "A genetically-informed study disentangling the relationships between tobacco smoking, cannabis use, alcohol consumption, substance use disorders and respiratory infections, including COVID-19", @@ -907060,101 +911939,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2021.02.11.21251553", - "rel_title": "Performance characteristics of five antigen-detecting rapid diagnostic test (Ag-RDT) for SARS-CoV-2 asymptomatic infection: a head-to-head benchmark comparison", - "rel_date": "2021-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.11.21251553", - "rel_abs": "Background Mass testing for early identification and isolation of infectious COVID-19 individuals, irrespective of concurrent symptoms, is an efficacious strategy to reduce disease transmission. Antigen-detecting rapid diagnostic tests (Ag-RDT) appear as a potentially suitable tool for mass testing on account of their ease-of-use, fast turnaround time, and low cost. However, benchmark comparisons are scarce, particularly in the context of unexposed asymptomatic individuals.\r\n\r\nMethods We used nasopharyngeal specimens from unexposed asymptomatic individuals to assess five Ag-RDTs: PanBio\u2122 COVID-19 Ag Rapid test (Abbott), CLINITEST\u00ae Rapid COVID-19 Antigen Test (Siemens), SARS-CoV-2 Rapid Antigen Test (Roche Diagnostics), SARS-CoV-2 Antigen Rapid Test Kit (Lepu Medical), and COVID-19 Coronavirus Rapid Antigen Test Cassette (Surescreen). Samples were collected between December 2020-January 2021 during the third wave of the epidemic in Spain.\r\n\r\nFindings The analysis included 101 specimens with confirmed positive PCR results and 185 with negative PCR. For the overall sample, the performance parameters of Ag-RDTs were as follows: Abbott assay, sensitivity 38\u00b76% (95% CI 29\u00b71\u201348\u00b78) and specificity 99\u00b75% (97\u2013100%); Siemens, sensitivity 51\u00b75% (41\u00b73\u201361\u00b76) and specificity 98\u00b74% (95\u00b73\u201399\u00b76); Roche, sensitivity 43\u00b76% (33\u00b77\u201353\u00b78) and specificity 96\u00b72% (92\u00b74\u201398\u00b75); Lepu, sensitivity 45\u00b75% (35\u00b76\u201355\u00b78) and specificity 89\u00b72% (83\u00b78\u201393\u00b73%); Surescreen, sensitivity 28\u00b78% (20\u00b72\u201338\u00b76) and specificity 97\u00b78% (94\u00b75\u201399\u00b74%). For specimens with cycle threshold (Ct) <30 in RT-qPCR, all Ag-RDT achieved a sensitivity of at least 70%, with Siemens, Roche, and Lepu assays showing sensitivities higher than 80%. In models according to population prevalence, all Ag-RDTs will have a NPV >99% and a PPV<50% at 1% prevalence.\r\n\r\nInterpretation Two commercial, widely available assays can be used for SARS-CoV-2 antigen testing to achieve sensitivity in specimens with a Ct<30 and specificity of at least 80% and 96%, respectively. Estimated negative and positive predictive values suggests the suitability of Ag-RDTs for mass screenings of SARS-CoV-2 infection in the general population.\r\n\r\nFunding Blueberry diagnostics, Fundaci\u00f3 Institut d\u2019Investigaci\u00f3 en Ci\u00e8ncies de la Salut Germans Trias i Pujol, and #YoMeCorono.org crowdfunding campaign.\r\n\r\nEvidence before this study In December 2020, we searched on PubMed for articles containing the terms \u201cantigen\u201d, \u201ctest\u201d (or Ag-RDT), and \u201cSARS-CoV-2\u201d or \u201cCOVID-19\u201d either in the title or the abstract. Our search yielded 79 entries corresponding to articles written in English. Of them, 33 were articles presenting the diagnostic performance of qualitative lateral-flow antigen-detecting rapid diagnostic tests (Ag-RDT). Four of these articles reported the results of head-to-head comparisons of various Ag-RDTs; in all cases, the number of tests was lower than the recommended for retrospective assessments of diagnostic performance (i.e., minimum of 100 PCR positive and 100 PCR negative). Furthermore, all head-to-head comparisons found in the literature included specimens obtained among individuals with varying disease status (none of which asymptomatic), thus limiting the adequacy of the estimates for an asymptomatic screening strategy.\r\n\r\nAdded value of this study We compared for the first time head-to-head five Ag-RDT using a powered set of fresh respiratory specimens PCR-confirmed positive or negative, collected from unexposed asymptomatic individuals during screening campaigns for early detection of SARS-CoV-2 infection. The sample size was large enough to draw robust conclusions. Our analysis identified four Ag-RDTs (i.e., assays marketed by Abbott, Siemens, Roche, and Surescreen) with specificity higher than 96%. Despite the low sensitivity for the overall sample (range 29% to 51%), the corresponding values for the subset of samples with Ct <30 were higher than 80% for Siemens, Roche, and Lepu assays. The estimated NPV for a screening performed in an area with 1% prevalence would be >99% for all tests, while the PPV would be <50%.\r\n\r\nImplications of all the available evidence Current data on the diagnostic performance of Ag-RDTs is heterogeneous and precludes benchmark assessments. Furthermore, the screening of asymptomatic populations is currently not considered among the intended uses of Ag-RDT, mostly because of lack of evidence on test performance in samples from unexposed asymptomatic individuals. Our findings add to the current evidence in two ways: first, we provide benchmarking data on Ag-RDTs, assessed head-to-head in a single set of respiratory specimens; second, we provide data on the diagnostic performance of Ag-RDTs in unexposed asymptomatic individuals. Our findings support the idea that Ag-RDTs can be used for mass screening in low prevalence settings and accurately rule out a highly infectious case in such setting.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Barbara Baro", - "author_inst": "ISGlobal" - }, - { - "author_name": "Pau Rodo", - "author_inst": "Fight AIDS and Infectious Diseases Foundation" - }, - { - "author_name": "Dan Ouchi", - "author_inst": "Fight AIDS and Infectious Diseases Foundation" - }, - { - "author_name": "Antoni E Bordoy", - "author_inst": "Hospital Universitari Germans Trias i Pujol" - }, - { - "author_name": "Emilio N Saya Amaro", - "author_inst": "Hospital Universitari Germans Trias i Pujol" - }, - { - "author_name": "Sergi V Salsench", - "author_inst": "Hospital Universitari Germans Trias i Pujol" - }, - { - "author_name": "Sonia Molinos", - "author_inst": "Hospital Universitari Germans Trias i Pujol" - }, - { - "author_name": "Andrea Alemany", - "author_inst": "Fight AIDS and Infectious Diseases Foundation, Hospital Universitari Germans Trias i Pujol,14Faculty of Medicine and Health Sciences, University of Barcelona" - }, - { - "author_name": "Maria Ubals", - "author_inst": "Fight AIDS and Infectious Diseases Foundation, Hospital Universitari Germans Trias i Pujol,Faculty of Medicine and Health Sciences, University of Barcelona" - }, - { - "author_name": "Marc Corbacho-Monne", - "author_inst": "Fight AIDS and Infectious Diseases Foundation, Hospital Universitari Germans Trias i Pujol, Faculty of Medicine and Health Sciences, University of Barcelona" - }, - { - "author_name": "Pere Millat", - "author_inst": "ISGlobal" - }, - { - "author_name": "Michael Marks", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Bonaventura Clotet", - "author_inst": "Fight AIDS and Infectious Diseases Foundation, Hospital Universitari Germans Trias i Pujol, IrsiCaixa AIDS Research Institute, Germans Trias i Pujol Research In" - }, - { - "author_name": "Nuria Prat", - "author_inst": "Gerencia Territorial Metropolitana Nord, Institut Catala de la Salut" - }, - { - "author_name": "Jordi Ara", - "author_inst": "Hospital Universitari Germans Trias i Pujol, Gerencia Territorial Metropolitana Nord, Institut Catala de la Salut" - }, - { - "author_name": "Marti Vall-Mayans", - "author_inst": "Fight AIDS and Infectious Diseases Foundation, Hospital Universitari Germans Trias i Pujol" - }, - { - "author_name": "Camila Gonzalez-Beiras", - "author_inst": "Fight AIDS and Infectious Diseases Foundation" - }, - { - "author_name": "Quique Bassat", - "author_inst": "ISGlobal, Centro de Investigacao em Saude de Manhica (CISM),ICREA, Pediatrics Department, Hospital Sant Joan de Deu (University of Barcelona), CIBERESP" - }, - { - "author_name": "Ignacio Blanco", - "author_inst": "Hospital Germans Trias" - }, - { - "author_name": "Oriol Mitja", - "author_inst": "Fundacion de Lucha contra el Sida y las enfermedades infecciosas, Hospital Universitari Germans Trias i Pujol,Lihir Medical Centre - InternationalSOS" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.10.21251477", "rel_title": "Associations between measures of social distancing and SARS-CoV-2 seropositivity: a nationwide population-based study in the Netherlands", @@ -908669,6 +913453,232 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.10.21251247", + "rel_title": "Safety and efficacy of the ChAdOx1 nCoV-19 (AZD1222) Covid-19 vaccine against the B.1.351 variant in South Africa", + "rel_date": "2021-02-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251247", + "rel_num_authors": 53, + "rel_authors": [ + { + "author_name": "Shabir Ahmed Madhi", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Vicky Lynne Baillie", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Clare Louise Cutland", + "author_inst": "Wits- Alive: African Leadership in Vaccinology Expertise, University of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Merryn Voysey", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" + }, + { + "author_name": "Anthonet L Koen", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Lee Fairlie", + "author_inst": "Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johanesburg, South Africa" + }, + { + "author_name": "Sherman D Padayachee", + "author_inst": "Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Keertan Dheda", + "author_inst": "Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute University of Cape Town, South Africa" + }, + { + "author_name": "Shaun L Barnabas", + "author_inst": "Family Centre for Research with Ubuntu, Department of Paediatrics, University of Stellenbosch, Cape Town, South Africa" + }, + { + "author_name": "Qasim Ebrahim Bhorat", + "author_inst": "Soweto Clinical Trials Centre" + }, + { + "author_name": "Carmen Briner", + "author_inst": "Perinatal HIV Research Unit, Faculty of Health Science, University of the Witwatersrand, South Africa" + }, + { + "author_name": "Gaurav Kwatra", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Khatija Ahmed", + "author_inst": "Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Parvinder Aley", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" + }, + { + "author_name": "Sutika Bhikha", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Jinal N Bhiman", + "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa." + }, + { + "author_name": "As'ad Ebrahim Bhorat", + "author_inst": "Soweto Clinical Trials Centre, Soweto, South Africa" + }, + { + "author_name": "Jeanine du plessis", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Aliasgar Esmail", + "author_inst": "Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute University of Cape Town, South Africa" + }, + { + "author_name": "Marisa Groenewald", + "author_inst": "Family Centre for Research with Ubuntu, Department of Paediatrics, University of Stellenbosch, Cape Town, South Africa" + }, + { + "author_name": "Elizea Horne", + "author_inst": "Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johanesburg, South Africa" + }, + { + "author_name": "Shi-Hsia Hwa", + "author_inst": "Africa Health Research Institute, Durban 4001, South Africa." + }, + { + "author_name": "Aylin Jose", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Teresa Lambe", + "author_inst": "Jenner Institute, Nuffield Department of Medicine, University of Oxford, UK" + }, + { + "author_name": "Matt Laubscher", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Mookho Malahleha", + "author_inst": "Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Masebole Masenya", + "author_inst": "Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johanesburg, South Africa" + }, + { + "author_name": "Mduduzi Masilela", + "author_inst": "Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Shakeel McKenzie", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Kgaogelo Molapo", + "author_inst": "Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Andrew Moultrie", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Suzette Oelofse", + "author_inst": "Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute University of Cape Town, South Africa" + }, + { + "author_name": "Faeezah Patel", + "author_inst": "Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johanesburg, South Africa" + }, + { + "author_name": "Sureshnee Pillay", + "author_inst": "KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban South Africa" + }, + { + "author_name": "Sarah Rhead", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" + }, + { + "author_name": "Hylton Rodel", + "author_inst": "Africa Health Research Institute, Durban 4001, South Africa." + }, + { + "author_name": "Lindie Rossouw", + "author_inst": "Family Centre for Research with Ubuntu, Department of Paediatrics, University of Stellenbosch, Cape Town, South Africa" + }, + { + "author_name": "Carol Taoushanis", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Houryiah Tegally", + "author_inst": "KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban South Africa" + }, + { + "author_name": "Asha Thombrayil", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Samuel van Eck", + "author_inst": "Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johanesburg, South Africa" + }, + { + "author_name": "Constantinos Wibmer", + "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa." + }, + { + "author_name": "Nicholas M Durham", + "author_inst": "Astra Zeneca Biopharmaceuticals, Cambridge, UK" + }, + { + "author_name": "Elizabeth J Kelly", + "author_inst": "Astra Zeneca Biopharmaceuticals, Cambridge, UK" + }, + { + "author_name": "Tonya Villafana", + "author_inst": "Astra Zeneca Biopharmaceuticals, Cambridge, UK" + }, + { + "author_name": "Sarah Gilbert", + "author_inst": "Jenner Institute, Nuffield Department of Medicine, University of Oxford, UK" + }, + { + "author_name": "Andrew J Pollard", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" + }, + { + "author_name": "Tulio de Oliveira", + "author_inst": "KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban South Africa" + }, + { + "author_name": "Penny L Moore", + "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa." + }, + { + "author_name": "Alex Sigal", + "author_inst": "Africa Health Research Institute, Durban 4001, South Africa." + }, + { + "author_name": "Alane Izu", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "- Network for Genomic Surveillance in South Africa (NGS-SA)", + "author_inst": "" + }, + { + "author_name": "- Wits VIDA COVID vaccine trial group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.10.21251392", "rel_title": "COVID-19 and Influenza: Vaccination Before and During the Pandemic among the Lebanese Adult Population", @@ -908787,56 +913797,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.10.21251480", - "rel_title": "Symptom reporting in over 1 million people: community detection of COVID-19", - "rel_date": "2021-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251480", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Joshua Elliott", - "author_inst": "Imperial College London" - }, - { - "author_name": "Matthew Whitaker", - "author_inst": "Imperial College London" - }, - { - "author_name": "Barbara Bodinier", - "author_inst": "Imperial College London" - }, - { - "author_name": "Steven Riley", - "author_inst": "Imperial College London" - }, - { - "author_name": "Helen Ward", - "author_inst": "Imperial College London" - }, - { - "author_name": "Graham Cooke", - "author_inst": "Imperial College" - }, - { - "author_name": "Ara Darzi", - "author_inst": "Imperial College London" - }, - { - "author_name": "Marc Chadeau-Hyam", - "author_inst": "Imperial College London" - }, - { - "author_name": "Paul Elliott", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.10.21251500", "rel_title": "A robust phenomenological approach to investigate COVID-19 data for France", @@ -910479,6 +915439,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.02.08.21250309", + "rel_title": "Hospitalizations for emergency-sensitive conditions in Germany during the Covid-19 pandemic - Insights from the German-wide Helios hospital network", + "rel_date": "2021-02-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21250309", + "rel_abs": "BackgroundWhile there are numerous reports that describe emergency care during the early Covid-19 pandemic, there is scarcity of data for later stages. This study analyzes hospitalization rates for 37 emergency-sensitive conditions in the largest German-wide hospital network during different pandemic phases.\n\nMethodsUsing claims data of 80 hospitals, consecutive cases between January 1 and November 17, 2020 were analyzed and compared to a corresponding period in 2019. Incidence-rate ratios (IRR) comparing the both periods were calculated using Poisson regression to model the number of hospitalizations per day.\n\nResultsThere was a hospitalization deficit between March 12 and June 13, 2020 (coinciding with the 1st pandemic wave) with 32,807 hospitalizations as opposed to 39,379 in 2019 (IRR 0.83, 95% CI 0.82 - 0.85, P<0.01). During the following period (June 14 to November 17, 2020, including the start of 2nd wave), hospitalizations were reduced from 63,799 in 2019 to 59,910 in 2020, but this reduction was not that pronounced (IRR 0.94, 95% CI 0.93 - 0.95, P<0.01). There was an increase in hospitalizations for acute myocardial infarction, aortic aneurism/dissection and pulmonary embolism after the 1st wave during which hospitalizations had been reduced for those conditions. In contrast, hospitalizations for sepsis, pneumonia, obstructive pulmonary disease, and intracranial injuries were reduced during the entire pandemic.\n\nConclusionsThere was an overall reduction of hospitalizations for emergency-sensitive conditions in Germany during the Covid-19 pandemic with heterogeneous effects on different disease categories. The increase of hospitalizations for acute myocardial infarction, aortic aneurism/dissection and pulmonary embolism is an alarming signal that requires attention and further studies.\n\nKEY MESSAGESO_ST_ABSWhat is already known on this subjectC_ST_ABSO_LIThere has been a reduction in emergency room visits and hospital admissions for several emergent medical and surgical conditions during the early Covid-19 pandemic (1st wave).\nC_LI\n\nWhat this study addsO_LIUsing claims data of 80 German-wide Helios hospitals, we found an overall reduction of hospitalizations for emergency-sensitive conditions in Germany during the Covid-19 pandemic until mid November 2020 with heterogeneous effects on different disease categories. While hospitalizations for sepsis, pneumonia, obstructive pulmonary disease, and intracranial injuries were reduced during the entire pandemic. There was an alarming increase of hospitalizations for acute myocardial infarction, aortic aneurism/dissection and pulmonary embolism after the 1st wave.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "ANDREAS BOLLMANN", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Sven Hohenstein", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Vincent Pellissier", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Sebastian Koenig", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Laura Ueberham", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Gerhard Hindricks", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Andreas Meier-Hellmann", + "author_inst": "Helios Hospitals" + }, + { + "author_name": "Ralf Kuhlen", + "author_inst": "Helios Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2021.02.10.430668", "rel_title": "Data-driven analysis of COVID-19 reveals specific severity patterns distinct from the temporal immune response", @@ -910864,77 +915871,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.08.21251344", - "rel_title": "Novel SARS-CoV-2 spike variant identified through viral genome sequencing of the pediatric Washington D.C. COVID-19 outbreak", - "rel_date": "2021-02-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21251344", - "rel_abs": "The SARS-CoV-2 virus has emerged as a global pandemic, severely impacting everyday life. Significant resources have been dedicated towards profiling the viral genome in the adult population. We present an analysis of viral genomes acquired from pediatric patients presenting to Childrens National Hospital in Washington D.C, including 24 with primary SARS CoV2 infection and 3 with Multisystem Inflammatory Syndrome in Children (MIS-C) undergoing treatment at our facility. Viral genome analysis using next generation sequencing indicated that approximately 81% of the analyzed strains were of the GH clade, 7% of the cases belonged to the GR clade, and 12% of the cases belonged to S, V, or G clades. One sample, acquired from a neonatal patient, presented with the highest viral RNA load of all patients evaluated at our center. Viral sequencing of this sample identified a SARS-CoV-2 spike variant, S:N679S. Analysis of data deposited in the GISAID global database of viral sequences shows the S:N679S variant is present in eight other sequenced samples within the US mid-Atlantic region. The similarity of the regional sequences suggests transmission and persistence of the SARS-CoV-2 variant within the Capitol region, raising the importance of increasing the frequency of SARS-CoV-2 genomic surveillance.\n\nIMPORTANCEA variant in the SARS-CoV-2 spike protein was identified in a febrile neonate who was hospitalized with COVID-19. This patient exhibited the highest viral RNA load of any COVID-19 patient tested at our center. Viral sequencing identified a spike protein variant, S:N679S, which is proximal to the cleavage site at residue 681. The SARS-CoV-2 surface spike is a protein trimer (three subunits) which serves as the key target for antibody therapies and vaccine development. Study of viral sequences from the GISAID database revealed eight related sequences from the US mid-Atlantic region. The identification of this variant in a very young patient, its critical location in the spike polyprotein, and the evidence that it has been detected in other patients in our region underscores the need for increased viral sequencing to monitor variant prevalence and emergence, which may have a direct impact on recommended public health measures and vaccination strategies.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jonathan Edward LoTempio Jr.", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Erik Antonio Billings", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Kyah Draper", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Christal Ralph", - "author_inst": "Children's National Hopsital" - }, - { - "author_name": "Madhi Moshgriz", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Nhat Duong", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Jennifer Dien Bard", - "author_inst": "Children's Hospital Los Angeles" - }, - { - "author_name": "Xiaowu Gai", - "author_inst": "Children's Hospital Los Angeles" - }, - { - "author_name": "David Wessel", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Roberta L DeBiasi", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Joseph M Campos", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Eric Vilain", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Meghan Delaney", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Drew G Michael", - "author_inst": "Children's National Hospital" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.02.08.21251001", "rel_title": "Expression of ACE2 receptor, soluble ACE2, Angiotensin I, Angiotensin II and Angiotensin (1-7), is modulated in COVID-19 patients.", @@ -912793,6 +917729,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.02.07.21251311", + "rel_title": "Poor antigen-specific responses to the second BNT162b2 mRNA vaccine dose in SARS-CoV-2-experienced individuals", + "rel_date": "2021-02-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251311", + "rel_abs": "The use of COVID-19 vaccines will play the major role in helping to end the pandemic that has killed millions worldwide. COVID-19 vaccines have resulted in robust humoral responses and protective efficacy in human trials, but efficacy trials excluded individuals with a prior diagnosis of COVID-19. As a result, little is known about how immune responses induced by mRNA vaccines differ in individuals who recovered from COVID-19. Here, we evaluated longitudinal immune responses to two-dose BNT162b2 mRNA vaccination in 15 adults who recovered from COVID-19, compared to 21 adults who did not have prior COVID-19 diagnosis. Consistent with prior studies of mRNA vaccines, we observed robust cytotoxic CD8+ T cell responses in both cohorts following the second dose. Furthermore, SARS-CoV-2-naive individuals had progressive increases in humoral and antigen-specific antibody-secreting cell (ASC) responses following each dose of vaccine, whereas SARS-CoV-2-experienced individuals demonstrated strong humoral and antigen-specific ASC responses to the first dose but muted responses to the second dose of the vaccine at the time points studied. Together, these data highlight the relevance of immunological history for understanding vaccine immune responses and may have significant implications for personalizing mRNA vaccination regimens used to prevent COVID-19, including booster shots.\n\nOne Sentence SummaryPrior history of COVID-19 affects adaptive immune responses to mRNA vaccination.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Marie Ines Samanovic-Golden", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Amber R Cornelius", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Sophie L Gray-Gaillard", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Joseph Richard Allen", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Trishala Karmacharya", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Jimmy P Wilson", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Sara Wesley Hyman", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Michael Tuen", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Sergei B Koralov", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Mark J Mulligan", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Ramin Sedaghat Herati", + "author_inst": "NYU School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.07.21251309", "rel_title": "The effect of respiratory activity, ventilatory therapy and facemasks on total aerosol emissions", @@ -912910,25 +917905,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.07.21251291", - "rel_title": "Rapid Impact Analysis of B 1.1.7 Variant on the Spread of SARS-CoV-2 in North Carolina", - "rel_date": "2021-02-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251291", - "rel_abs": "BackgroundSeveral cases of the B1.1.7 variant of the SARS-CoV-2 virus were identified in North Carolina first on January 23, 2021 in Mecklenburg County and later in Guilford County on January 28, 2021.[1,2] This variant has been associated with higher levels of transmissibility.[3-6] This study examines the potential impact of increased transmissibility as the B1.1.7 variant becomes more predominant given current vaccine distribution plans and existing non-pharmaceutical interventions (NPIs).\n\nMethodWe explored the anticipated impact on the effective reproduction number for North Carolina and Guilford County given the date of import of B1.1.7. The approximate growth rate in proportion of B1.1.7 observed in the United Kingdom was fit and used to establish the estimate share of B1.1.7 circulating in North Carolina. Using the nowcasted reproduction numbers, a stochastic discrete compartmental model was fit with the current vaccination rates and B1.1.7 transmissibility to estimate the impact on the effective reproduction number.\n\nResultsWe found that the effective reproduction number for North Carolina and Guilford County may exceed one, indicating a return to accelerating spread of infection in April as the proportion of B1.1.7 increases. The effective reproduction number will likely decrease into March, then increase as the proportion of B1.1.7 increases in circulation in the population.\n\nConclusionsExisting non-pharmaceutical interventions will need to remain in effect through the spring. Given the current vaccination rate and these interventions, it is likely that there will be an increase in SARS-CoV-2 infections. The impact of the variant will likely be heterogeneous across North Carolina given the reproduction number and volume of susceptible persons in each county at the time of introduction of the variant. Age-based vaccinations will likely reduce the overall impact on hospitalizations. This analysis underlines the need for population level genetic surveillance to confirm the proportion of variants circulating.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Michael E DeWitt Jr.", - "author_inst": "Cone Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.07.21251262", "rel_title": "L18F substrain of SARS-CoV-2 VOC-202012/01 is rapidly spreading in England", @@ -914403,6 +919379,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.04.21251131", + "rel_title": "Using Machine Learning to Predict Mortality for COVID-19 Patients on Day Zero in the ICU", + "rel_date": "2021-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251131", + "rel_abs": "RationaleGiven the expanding number of COVID-19 cases and the potential for upcoming waves of infection, there is an urgent need for early prediction of the severity of the disease in intensive care unit (ICU) patients to optimize treatment strategies.\n\nObjectivesEarly prediction of mortality using machine learning based on typical laboratory results and clinical data registered on the day of ICU admission.\n\nMethodsWe studied retrospectively 263 COVID-19 ICU patients. To find parameters with the highest predictive values, Kolmogorov-Smirnov and Pearson chi-squared tests were used. Logistic regression and random forest (RF) algorithms were utilized to build classification models. The impact of each marker on the RF model predictions was studied by implementing the local interpretable model-agnostic explanation technique (LIME-SP).\n\nResultsAmong 66 documented parameters, 15 factors with the highest predictive values were identified as follows: gender, age, blood urea nitrogen (BUN), creatinine, international normalized ratio (INR), albumin, mean corpuscular volume, white blood cell count, segmented neutrophil count, lymphocyte count, red cell distribution width (RDW), and mean cell hemoglobin along with a history of neurological, cardiovascular, and respiratory disorders. Our RF model can predict patients outcomes with a sensitivity of 70% and a specificity of 75%.\n\nConclusionsThe most decisive variables in our model were increased levels of BUN, lowered albumin levels, increased creatinine, INR, and RDW along with gender and age. Complete blood count parameters were also crucial for some patients. Considering the importance of early triage decisions, this model can be a useful tool in COVID-19 ICU decision-making.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Elham Jamshidi", + "author_inst": "Division of Pulmonary Medicine, Department of Medicine, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland." + }, + { + "author_name": "Amirhossein Asgary", + "author_inst": "Department of Biotechnology, College of Sciences, University of Tehran, Tehran, Iran." + }, + { + "author_name": "Nader Tavakoli", + "author_inst": "Trauma and Injury Research Center, Iran University of Medical Sciences, Tehran, Iran." + }, + { + "author_name": "Alireza Zali", + "author_inst": "Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehra" + }, + { + "author_name": "Hadi Esmaily", + "author_inst": "Department of Clinical Pharmacy, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran." + }, + { + "author_name": "Seyed Hamid Jamaldini", + "author_inst": "Department of Genetic, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran" + }, + { + "author_name": "Amir Daaee", + "author_inst": "School of Mechanical Engineering, Sharif University of Technology, Tehran, Iran" + }, + { + "author_name": "Amirhesam Babajani", + "author_inst": "Department of Pharmacology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Mohammad Ali Sendani Kashi", + "author_inst": "Master of Business Administration (MBA)-University of Tehran, Tehran, Iran." + }, + { + "author_name": "Masoud Jamshidi", + "author_inst": "Department of Exercise Physiology, Tehran University, Iran." + }, + { + "author_name": "Sahand Rahi", + "author_inst": "Laboratory of the Physics of Biological Systems, Institute of Physics, Ecole polytechnique federale de Lausanne (EPFL), Lausanne, Switzerland" + }, + { + "author_name": "Nahal Mansouri", + "author_inst": "Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole polytechnique federale de Lausanne (EPFL), Lausanne, Switzerland" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.04.21251170", "rel_title": "Symptoms of COVID-19 infection and magnitude of antibody response in a large community-based study", @@ -914612,33 +919651,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dermatology" }, - { - "rel_doi": "10.1101/2021.02.04.21251176", - "rel_title": "Assessment of Vaccination and Underreporting on COVID-19 Infections in Turkey Based On Effective Reproduction Number", - "rel_date": "2021-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251176", - "rel_abs": "In this paper, we introduce a SEIR type COVID-19 model where the infected class is further divided into subclasses with individuals in intensive care (ICUs) and ventilation units. The model is validated with the symptomatic COVID-19 cases, deaths, and the number of patients in ICUs and ventilation units as reported by Republic of Turkey, Ministry of Health for the period March 11, 2020 through May 30, 2020 when the nationwide lockdown is in order. COVID-19 interventions in Turkey are incorporated into the model to detect the future trend of the outbreak accurately. We tested the effect of underreporting and we found that the peaks of the disease differ significantly depending on the rate of underreporting, however, the timing of the peaks remains constant.\n\nThe lockdown is lifted on June 1, and the model is modified to include a time dependent transmission rate which is linked to the effective reproduction number [R]t through basic reproduction number [R]0. The modified model captures the changing dynamics and peaks of the outbreak successfully. With the onset of vaccination on 13 January 2021, we augment the model with the vaccination class to investigate the impact of vaccination rate and efficacy. We observe that vaccination rate is a more critical parameter than the vaccine efficacy to eliminate the disease successfully.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Tugba Akman Yildiz", - "author_inst": "University of Turkish Aeronautical Association" - }, - { - "author_name": "Emek Kose", - "author_inst": "St. Mary's College of Maryland" - }, - { - "author_name": "Necibe Tuncer", - "author_inst": "Florida Atlantic University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.04.21251165", "rel_title": "COVID-19 prevention behaviour over time in Australia: Patterns and long-term predictors from April to July 2020", @@ -916381,6 +921393,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.06.21251099", + "rel_title": "COVID-19 increases age- and sex-controlled 21-day fatality rates for patients with melanoma, hematologic malignancies, uterine cancer, or kidney cancer", + "rel_date": "2021-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.06.21251099", + "rel_abs": "IntroductionPrior research has reported an increased risk of fatality for cancer patients, but most studies investigated the risk by comparing cancer patients to non-cancer patients among COVID-19 infections. Only a few studies have compared the impact of a COVID-19 infection to non-infection with matched cancer patients and types.\n\nMethods & MaterialsWe conducted survival analyses of 4,606 cancer patients with COVID-19 test results from March 16 to October 11, 2020 in UK Biobank and estimated the overall hazard ratio of fatality with and without COVID-19 infection. We also examined the hazard ratios of thirteen specific cancer types with at least 100 patients.\n\nResultsCOVID-19 resulted in an overall hazard ratio of 7.76 (95% CI: [5.78, 10.40], p<10-10) by studying the survival rate of 4,606 cancer patients for 21-days after the tests. The hazard ratio was shown to vary among cancer type, with over a 10-fold increase in fatality rate (false discovery rate[≤]0.02) for melanoma, hematologic malignancies, uterine cancer, and kidney cancer using a stratified analysis on each of the cancer types. Although COVID-19 imposed a higher risk for localized cancers compared to distant metastasis ones, those of distant metastasis yielded higher fatality rates due to their multiplicative effects.\n\nConclusionThe results highlight the importance of timely care for localized and hematological cancer patients and the necessity to vaccinate uninfected patients as soon as possible, particularly for the cancer types influenced most by COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Haiquan Li", + "author_inst": "Department of Biosystems Engineering, University of Arizona" + }, + { + "author_name": "Edwin Alexander Baldwin", + "author_inst": "Department of Biosystems Engineering, University of Arizona" + }, + { + "author_name": "Xiang Zhang", + "author_inst": "Department of Biosystems Engineering, University of Arizona" + }, + { + "author_name": "Colleen Kenost", + "author_inst": "Department of Biomedical Informatics, University of Utah" + }, + { + "author_name": "Wenting Luo", + "author_inst": "Statistics and Data Science GIDP, Biosystems Analytics & Technology Program, University of Arizona" + }, + { + "author_name": "Elizabeth A Calhoun", + "author_inst": "Department of Population Health, University of Kansas Medical Center" + }, + { + "author_name": "Lingling An", + "author_inst": "Department of Biosystems Engineering, University of Arizona" + }, + { + "author_name": "Charles L Bennett", + "author_inst": "Department of Clinical Pharmacy and Outcomes Sciences, University of South Carolina" + }, + { + "author_name": "Yves A Lussier", + "author_inst": "Department of Biomedical Informatics, University of Utah" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2021.02.05.21251085", "rel_title": "Molecular Mechanism of Parosmia", @@ -916470,89 +921533,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.07.21251062", - "rel_title": "Performance of three SARS-CoV-2 immunoassays, three rapid lateral flow tests and a novel bead-based affinity surrogate test for the detection of SARS-CoV-2 antibodies in human serum", - "rel_date": "2021-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251062", - "rel_abs": "For the control of immunity in COVID-19 survivors and vaccinated subjects there is an urgent need for reliable and rapid serological assays.\n\nBased on samples from 63 COVID-19 survivors up to seven months after symptom onset, and on 50 serum samples taken before the beginning of the pandemic, we compared the performance of three commercial immunoassays for the detection of SARS-CoV-2 IgA and IgG antibodies (Euroimmun SARS-COV-2 IgA/IgG, Mikrogen recomWell SARS-CoV-2 IgA/IgG, and SERION ELISA agile SARS-CoV-2 IgA/IgG) and three rapid lateral flow (immunochromatographic) tests (Abbott Panbio COVID-19 IgG/IgM, NADAL COVID-19 IgG/IgM, and Cleartest Corona 2019-nCOV IgG/IgM) with a plaque-reduction neutralization test (PRNT50) representing the gold standard. In addition, we report and validate a novel, non-commercial flow cytometry bead-based surrogate test.\n\n57 out of 63 PCR-confirmed COVID-19 patients (90 %) showed neutralizing antibodies. The sensitivity of the seven assays ranged from 7.0 % to 98.3 %, the specificity from 86.0 % to 100.00 %. Only one commercial immunoassay showed a sensitivity and specificity of greater than 98 %. These data indicate abundant interassay variability.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Manuel Krone", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Julia G\u00fctling", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Johannes Wagener", - "author_inst": "Department of Clinical Microbiology, Trinity College Dublin, St James's Hospital Campus, Dublin, Ireland" - }, - { - "author_name": "Thi\u00ean-Tr\u00ed L\u00e2m", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Christoph Schoen", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Ulrich Vogel", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "August Stich", - "author_inst": "Department of Tropical Medicine and Epidemic Control, Medical Mission Institute, Wuerzburg, Germany" - }, - { - "author_name": "Florian Wedekink", - "author_inst": "Department of Gynecology, Section for Experimental Tumor Immunology, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "J\u00f6rg Wischhusen", - "author_inst": "Department of Gynecology, Section for Experimental Tumor Immunology, University Hospital Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Thomas Kerkau", - "author_inst": "Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Niklas Beyersdorf", - "author_inst": "Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Silvana Klingler", - "author_inst": "Institute of Systems Immunology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Simone Backes", - "author_inst": "Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Lars D\u00f6lken", - "author_inst": "Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Georg Gasteiger", - "author_inst": "Institute of Systems Immunology, University of Wuerzburg, Wuerzburg, Germany" - }, - { - "author_name": "Oliver Kurzai", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany'Oliver Kurzai' " - }, - { - "author_name": "Alexandra Schubert-Unkmeir", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Josef-Schneider-Str.2, Build. E1, 97078 Wuerzburg, Germany" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.06.21251283", "rel_title": "Decreased SARS-CoV-2 viral load following vaccination", @@ -918175,6 +923155,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.04.21251111", + "rel_title": "SARS-CoV-2 Worldwide Replication Drives Rapid Rise and Selection of Mutations across the Viral Genome: A Time-Course StudyPotential Challenge for Vaccines and Therapies", + "rel_date": "2021-02-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251111", + "rel_abs": "Scientists and the public were alarmed at the first large viral variant of SARS-CoV2 reported in December 2020. We have followed the time course of emerging viral mutants and variants during the SARS-CoV-2 pandemic in ten countries on four continents. We examined complete SARS-CoV-2 nucleotide sequences in GISAID, (Global Initiative of Sharing All Influenza Data) with sampling dates extending until January 20, 2021. These sequences originated from ten different countries: United Kingdom, South Africa, Brazil, USA, India, Russia, France, Spain, Germany, and China. Among the novel mutations, some previously reported mutations waned and some of them increased in prevalence over time. VUI2012/01 (B.1.1.7) and 501Y.V2 (B.1.351), the so-called UK and South Africa variants, respectively, and two variants from Brazil, 484K.V2, now called P.1 and P.2, increased in prevalence. Despite lockdowns, worldwide active replication in genetically and socio-economically diverse populations facilitated selection of new mutations. The data on mutant and variant SARS-CoV-2 strains provided here comprise a global resource for easy access to the myriad mutations and variants detected to date globally. Rapidly evolving new variant and mutant strains might give rise to escape variants, capable of limiting the efficacy of vaccines, therapies, and diagnostic tests.\n\nSignificance and New Aspects of Study - SynopsisO_LIWe examine the time course of emerging mutations in the SARS-CoV-2 genome that have rapidly been selected in the worlds populations through the beginning of 2021. A study of the prevalence of viral mutations in the GISAID database in ten different countries - United Kingdom, South Africa, Brazil, US, India, Russia, France, Spain, Germany, and China - revealed widespread mutations along the genome.\nC_LIO_LIWe previously identified about 10 hotspot mutations in the SARS-CoV-2 genome that became prevalent in many of the countries studied1. Since the beginning of February, many new mutations arose in the ten countries (and worldwide). The preponderance of variants and mutations correlated with the increased spread of Covid-19.\nC_LIO_LIThere was a temporal progression from about 10 predominant mutants shared by several countries up to the end of May 2020, followed by a consistent and rapid increase in the number of new mutations between June and December along with the emergence of variants of concern, first reported in December 2020.\nC_LIO_LIWe examine the relative frequencies of mutations, along with variants of interest, in 10 countries up until January 20, 2021. Investigations on the pathogenic properties of individual SARS-CoV-2 mutations will be urgently needed to understand the kaleidoscopic patterns of worldwide Covid-19 outbreaks and symptoms. Monitoring the frequency and speed of mutant selection have direct relevance to diagnostic testing, vaccines and therapeutics.\nC_LIO_LIAs an explanation for efficient viral mutagenesis, we hypothesize that the viral spike protein - as documented - facilitates viral entry via the cells ACE receptor2. This in turn interacts with the APOBEC polypeptide, an m-RNA editing function. The actually observed frequent C to U (T) transitions and other base exchanges are thus effected. Hence, as one of the earliest steps upon viral entry, active mutagenesis commences, since SARS-CoV-2 exploits one of the cells defenses against viral infections.\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Stefanie Weber", + "author_inst": "University of Cologne/Erlangen University" + }, + { + "author_name": "Christina C.M. Ramirez", + "author_inst": "UCLA School of Public Health, Los Angeles" + }, + { + "author_name": "Barbara Weiser", + "author_inst": "University of California, Davis," + }, + { + "author_name": "Harold Burger", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Walter Doerfler", + "author_inst": "Friedrich-Alexander University Erlangen" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.04.21250932", "rel_title": "The systemic inflammatory response and clinicopathological characteristics in patients admitted to hospital with COVID-19 infection: Comparison of 2 consecutive cohorts", @@ -918448,77 +923463,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.06.430041", - "rel_title": "Subgenomic RNAs as molecular indicators of asymptomatic SARS-CoV-2 infection", - "rel_date": "2021-02-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.06.430041", - "rel_abs": "In coronaviridae such as SARS-CoV-2, subgenomic RNAs (sgRNA) are replicative intermediates, therefore, their abundance and structures could infer viral replication activity and severity of host infection. Here, we systematically characterized the sgRNA expression and their structural variation in 81 clinical specimens collected from symptomatic and asymptomatic individuals with a goal of assessing viral genomic signatures of disease severity. We demonstrated the highly coordinated and consistent expression of sgRNAs from individuals with robust infections that results in symptoms, and found their expression is significantly repressed in the asymptomatic infections, indicating that the ratio of sgRNAs to genomic RNA (sgRNA/gRNA) is highly correlated with the severity of the disease. Using long read sequencing technologies to characterize full-length sgRNA structures, we also observed widespread deletions in viral RNAs, and identified unique sets of deletions preferentially found primarily in symptomatic individuals, with many likely to confer changes in SARS-CoV-2 virulence and host responses. Furthermore, based on the sgRNA structures, the frequently occurred structural variants in SARS-CoV-2 genomes serves as a mechanism to further induce SARS-CoV-2 proteome complexity. Taken together, our results show that differential sgRNA expression and structural mutational burden both appear to be correlated with the clinical severity of SARS-CoV-2 infection. Longitudinally monitoring sgRNA expression and structural diversity could further guide treatment responses, testing strategies, and vaccine development.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Chee Hong Wong", - "author_inst": "The Jackson Laboratory" - }, - { - "author_name": "Chew Yee Ngan", - "author_inst": "The Jackson Laboratory" - }, - { - "author_name": "Rachel L. Goldfeder", - "author_inst": "The Jackson Laboratory" - }, - { - "author_name": "Jennifer Idol", - "author_inst": "The Jackson Laboratory" - }, - { - "author_name": "Chris Kuhlberg", - "author_inst": "The Jackson Laboratory" - }, - { - "author_name": "Rahul Maurya", - "author_inst": "The Jackson Laboratory" - }, - { - "author_name": "Kevin Kelly", - "author_inst": "The Jackson Laboratory" - }, - { - "author_name": "Gregory Omerza", - "author_inst": "The Jackson Laboratory" - }, - { - "author_name": "Nicholas Renzette", - "author_inst": "The Jackson Laboratory" - }, - { - "author_name": "Francine De Abreu", - "author_inst": "The Jackson Laboratory" - }, - { - "author_name": "Lei Li", - "author_inst": "The Jackson Laboratory" - }, - { - "author_name": "Frederick A. Browne", - "author_inst": "Griffin Hospital" - }, - { - "author_name": "Edison T. Liu", - "author_inst": "The Jackson Laboratory" - }, - { - "author_name": "Chia-Lin Wei", - "author_inst": "The Jackson Laboratory" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.02.02.21250836", "rel_title": "Exponential increase in neutralizing and spike specific antibodies following vaccination of COVID-19 convalescent plasma donors", @@ -920013,6 +924957,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.02.02.21251043", + "rel_title": "COVID-19 infection and subsequent thromboembolism: A self-controlled case series analysis of a population cohort", + "rel_date": "2021-02-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21251043", + "rel_abs": "ObjectiveAn unexpectedly large number of people infected with Covid-19 had experienced a thrombotic event. This study aims to assess the associations between Covid-19 infection and thromboembolism including myocardial infarction (MI), ischaemic stroke, deep-vein thrombosis (DVT), and pulmonary embolism (PE).\n\nPatients and MethodsA self-controlled case-series study was conducted covering the whole of Scotlands general population. The study population comprised individuals with confirmed (positive test) Covid-19 and at least one thromboembolic event between March 2018 and October 2020. Their incidence rates during the risk interval (5 days before to 56 days after the positive test) and the control interval (the remaining periods) were compared intra-personally.\n\nResultsAcross Scotland, 1,449 individuals tested positive for Covid-19 and experienced a thromboembolic event. The risk of thromboembolism was significantly elevated over the whole risk period but highest in the 7 days following the positive test (IRR 12.01, 95% CI 9.91-14.56) in all included individuals. The association was also present in individuals not originally hospitalised for Covid-19 (IRR 4.07, 95% CI 2.83-5.85). Risk of MI, stroke, PE and DVT were all significantly higher in the week following a positive test. The risk of PE and DVT was particularly high and remained significantly elevated even 56 days following the test.\n\nConclusionConfirmed Covid-19 infection was associated with early elevations in risk with MI, ischaemic stroke, and substantially stronger and prolonged elevations with DVT and PE both in hospital and community settings. Clinicians should consider thromboembolism, especially PE, among people with Covid-19 in the community.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Frederick Ho", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Kenneth Man", + "author_inst": "UCL" + }, + { + "author_name": "Mark Toshner", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Colin Church", + "author_inst": "NHS Greater Glasgow and Clyde" + }, + { + "author_name": "Carlos Celis-Morales", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Ian Wong", + "author_inst": "UCL" + }, + { + "author_name": "Colin Berry", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Naveed Sattar", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Jill Pell", + "author_inst": "University of Glasgow" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2021.02.03.21251011", "rel_title": "GPS-estimated foot traffic data and venue selection for COVID-19 serosurveillance studies", @@ -920222,57 +925217,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.03.21251004", - "rel_title": "Ethnic differences in COVID-19 mortality during the first two waves of the Coronavirus Pandemic: a nationwide cohort study of 29 million adults in England", - "rel_date": "2021-02-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.03.21251004", - "rel_abs": "BackgroundEthnic minorities have experienced disproportionate COVID-19 mortality rates in the UK and many other countries. We compared the differences in the risk of COVID-19 related death between ethnic groups in the first and second waves the of COVID-19 pandemic in England. We also investigated whether the factors explaining differences in COVID-19 death between ethnic groups changed between the two waves.\n\nMethodsUsing data from the Office for National Statistics Public Health Data Asset on individuals aged 30-100 years living in private households, we conducted an observational cohort study to examine differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and second wave (from 1st September to 28th December 2020). We estimated age-standardised mortality rates (ASMR) in the two waves stratified by ethnic groups and sex. We also estimated hazard ratios (HRs) for ethnic-minority groups compared with the White British population, adjusted for geographical factors, socio-demographic characteristics, and pre-pandemic health conditions.\n\nResultsThe study population included over 28.9 million individuals aged 30-100 years living in private households. In the first wave, all ethnic minority groups had a higher risk of COVID-19 related death compared to the White British population. In the second wave, the risk of COVID-19 death remained elevated for people from Pakistani (ASMR: 339.9 [95% CI: 303.7 - 376.2] and 166.8 [141.7 - 191.9] deaths per 100,000 population in men and women) and Bangladeshi (318.7 [247.4 - 390.1] and 127.1 [91.1 - 171.3] in men and women)background but not for people from Black ethnic groups. Adjustment for geographical factors explained a large proportion of the differences in COVID-19 mortality in the first wave but not in the second wave. Despite an attenuation of the elevated risk of COVID-19 mortality after adjusting for sociodemographic characteristics and health status, the risk was substantially higher in people from Bangladeshi and Pakistani background in both the first and the second waves.\n\nConclusionBetween the first and second waves of the pandemic, the reduction in the difference in COVID-19 mortality between people from Black ethnic background and people from the White British group shows that ethnic inequalities in COVID-19 mortality can be addressed. The continued higher rate of mortality in people from Bangladeshi and Pakistani background is alarming and requires focused public health campaign and policy changes.\n\n*VN and NI contributed equally to this paper\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSA recent systematic review by Pan and colleagues demonstrated that people of ethnic minority background in the UK and the USA have been disproportionately affected by the Coronavirus (COVID-19) pandemic, compared to White populations. While several studies have investigated whether adjusting for socio-demographic and economic factors and medical history reduces the estimated difference in risk of mortality and hospitalisation, the reasons for the differences in the risk of experiencing harms from COVID-19 are still being explored during the course of the pandemic. Studies so far have analysed the ethnic differences in COVID-19 mortality in the first wave of the pandemic. The evidence on the temporal trend of ethnic inequalities in COVID-19 mortality, especially those from the second wave of the pandemic, is scarce.\n\nAdded value of this studyUsing data from the Office for National Statistics (ONS) Public Health Data Asset on 29 million adults aged 30-100 years living in private households in England, we conducted an observational cohort study to examine the differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and second wave (from 1st September to 28th December 2020). We find that in the first wave all ethnic minority groups were at elevated risk of COVID-19 related death compared to the White British population. In the second wave, the differences in the risk of COVID-19 related death attenuated for Black African and Black Caribbean groups, remained substantially higher in people from Bangladeshi background, and worsened in people from Pakistani background. We also find that some of the factors explaining these differences in mortality have changed in the two waves.\n\nImplications of all the available evidenceThe risk of COVID-19 mortality during the first wave of the pandemic was elevated in people from ethnic minority background. An appreciable reduction in the difference in COVID-19 mortality in the second wave of the pandemic between people from Black ethnic background and people from the White British group is reassuring, but the continued higher rate of mortality in people from Bangladeshi and Pakistani background is alarming and requires focused public health campaign and policy response. Focusing on treating underlying conditions, although important, may not be enough in reducing the inequalities in COVID-19 mortality. Focused public health policy as well as community mobilisation and participatory public health campaign involving community leaders may help reduce the existing and widening inequalities in COVID-19 mortality.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Vahe Nafilyan", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Nazrul Islam", - "author_inst": "Nuffield Department of Population Health, Big Data Institute, University of Oxford" - }, - { - "author_name": "Rohini Mathur", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Daniel Ayoubkhani", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Amitava Banerjee", - "author_inst": "University College London" - }, - { - "author_name": "Myer Glickman", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Ben Humberstone", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Ian DIamond", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "Diabetes Research Centre, University of Leicester" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.03.21250992", "rel_title": "Using a household structured branching process to analyse contact tracing in the SARS-CoV-2 pandemic", @@ -922863,6 +927807,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.02.03.429646", + "rel_title": "Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens", + "rel_date": "2021-02-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.03.429646", + "rel_abs": "The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last twenty years. Enzootic and epizootic coronaviruses of diverse lineages also pose a significant threat to livestock, as most recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and swine acute diarrhea-associated coronavirus (SADS-CoV). Unique to RNA viruses, coronaviruses encode a proofreading exonuclease (ExoN) that lowers point mutation rates to increase the viability of large RNA virus genomes, which comes with the cost of limiting virus adaptation via point mutation. This limitation can be overcome by high rates of recombination that facilitate rapid increases in genetic diversification. To compare dynamics of recombination between related sequences, we developed an open-source computational workflow (IDPlot) to measure nucleotide identity, locate recombination breakpoints, and infer phylogenetic relationships. We analyzed recombination dynamics among three groups of coronaviruses with noteworthy impacts on human health and agriculture: SARSr-CoV, Betacoronavirus-1, and SADSr-CoV. We found that all three groups undergo recombination with highly diverged viruses from sparsely sampled or undescribed lineages, which can disrupt the inference of phylogenetic relationships. In most cases, no parental origin of recombinant regions could be found in genetic databases, suggesting that much coronavirus diversity remains unknown. These patterns of recombination expand the genetic pool that may contribute to future zoonotic events. Our results also illustrate the limitations of current sampling approaches for anticipating zoonotic threats to human and animal health.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Stephen A. Goldstein", + "author_inst": "University of Utah" + }, + { + "author_name": "Joe Brown", + "author_inst": "University of Utah" + }, + { + "author_name": "Brent S Pedersen", + "author_inst": "University of Utah" + }, + { + "author_name": "Aaron R. Quinlan", + "author_inst": "University of Utah" + }, + { + "author_name": "Nels C. Elde", + "author_inst": "University of Utah" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2021.02.04.429819", "rel_title": "Codon arrangement modulates MHC-I peptides presentation: implications for a SARS-CoV-2 peptide-based vaccine", @@ -923016,45 +927995,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.02.01.21250853", - "rel_title": "IN-HOSPITAL CONTINUATION WITH ANGIOTENSIN RECEPTOR BLOCKERS IS ASSOCIATED WITH A LOWER MORTALITY RATE THAN CONTINUATION WITH ANGIOTENSIN CONVERTING ENZYME INHIBITORS IN COVID-19 PATIENTS A RETROSPECTIVE COHORT STUDY", - "rel_date": "2021-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250853", - "rel_abs": "BackgroundSeveral studies have reported a reduced risk of death associated with the inpatient use of angiotensin receptor blockers (ARBs) and angiotensin converting enzyme inhibitors (ACEIs) in COVID-19 patients, but have been criticized for incurring in several types of bias. Also, most studies have pooled ACEIs and ARBs as if they were a unique group, overlooking their pharmacological differences. We aimed to assess whether the in-hospital continuation of ARBs and ACEIs, in regular users of these drugs, was associated with a reduced risk of death as compared to their discontinuation and also to compare head-to-head ARBs with ACEIs.\n\nMethodsAdult patients with a PCR-confirmed diagnosis of COVID-19 requiring admission during March, 2020 were consecutively selected from 7 hospitals in Madrid, Spain. Among them, we identified outpatient users of ACEIs/ARBs and divided them in two cohorts depending on treatment discontinuation/continuation at admission. Then, they were followed-up until discharge or in-hospital death. An intention-to-treat survival analysis was carried out and hazard ratios (HRs) and their 95%CI were computed through a Cox regression model adjusted for propensity scores of discontinuation and controlled by potential mediators.\n\nResultsOut of 625 ACEI/ARB users, 340(54.4%) discontinued treatment. The in-hospital mortality rates were 27.6% and 27.7% in discontinuation and continuation cohorts, respectively (HR=1.01; 95%CI:0.70-1.46). No difference in mortality was observed between ARB and ACEI discontinuation (28.6% vs. 27.1%, respectively), while a significantly lower mortality rate was found among patients who continued with ARBs (20.8%,N=125) as compared to those who continued with ACEIs (33.1%,N=136; p=0.03). The head-to-head comparison (ARB vs. ACEI continuation) yielded an adjusted HR of 0.52 (95%CI:0.29-0.93), being especially notorious among males (HR=0.34; 95%CI:0.12-0.93), subjects older than 74 years (HR=0.46; 95%CI:0.25-0.85), and patients with obesity (HR=0.22; 95%CI:0.05-0.94), diabetes (HR=0.36; 95%CI:0.13-0.97) and heart failure (HR=0.12; 95%CI:0.03-0.97).\n\nConclusionsAmong regular users of ARBs admitted for COVID-19, the in-hospital continuation with them was associated with an improved survival, while this was not observed with ACEIs. Regular users of ARBs should continue with this treatment if admitted for COVID-19, unless medically contraindicated. In admitted ACEI users, a switching to ARBs should be considered, especially among high-risk patients.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC=\"FIGDIR/small/21250853v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (41K):\norg.highwire.dtl.DTLVardef@1984ec8org.highwire.dtl.DTLVardef@5c67c2org.highwire.dtl.DTLVardef@9ffbfforg.highwire.dtl.DTLVardef@1594277_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Francisco Jose De Abajo", - "author_inst": "University of Alcala and University Hospital Principe de Asturias" - }, - { - "author_name": "Antonio Rodriguez-Miguel", - "author_inst": "University of Alcala and University Hospital Principe de Asturias" - }, - { - "author_name": "Sara Rodriguez-Martin", - "author_inst": "University of Alcala and University Hospital Principe de Asturias" - }, - { - "author_name": "Victoria Lerma", - "author_inst": "University Hospital Principe de Asturias" - }, - { - "author_name": "Alberto Garcia-Lledo", - "author_inst": "University of Alcala and University Hospital Principe de Asturias" - }, - { - "author_name": "- MED-ACE2-COVID19 Study Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2021.01.31.21250863", "rel_title": "Stay Home and Stay Active? The impact of stay-at-home restrictions on physical activity routines in the UK during the COVID-19 pandemic", @@ -924741,6 +929681,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.02.21250825", + "rel_title": "Evaluation of Depression, Anxiety and Sleep Quality in the Brazilian Population During Social Isolation Due to the New Coronavirus (SARS-CoV-2) pandemic: the DEGAS-CoV Study", + "rel_date": "2021-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250825", + "rel_abs": "IntroductionThe new coronavirus infection (COVID-19) has caused distress and repercussions in mental and physical health of individuals. Depression, anxiety and worsening of sleep quality have been reported in several recent articles that surveyed populations all over the globe. Our work meant to access, through a cross-sectional study, these disorders in the Brazilian population, through the application of an online questionnaire conducted on the second trimester of 2020.\n\nMaterials and MethodsWe applied an online questionnaire, filled with questions regarding social, economic, financial, educational and health status, as well as questions from the Hospital Anxiety and Depression Scale (HAD), and from the Pittsburgh Sleep Quality Index (PSQI).\n\nResultsWe collected 2,695 valid answers, from April 24th to May 31st, 2020. Age ranged from 18 to 79 years, mean of 31.3. Women were 76.3%, men 23.7%. Symptoms of Anxiety were found in 56.5%, of depression in 46.1%, and of bad sleep in 49.2%. Some groups were more prone than others to one or more of those conditions, such as: younger people, women, mestizos, Northeasterners, people with lesser years of education, of lower income or whose income dropped significantly during the pandemic, caregivers, students, sedentary or people practicing less physical activity, people who followed more hours of news of COVID-19 and those less engaged in social and instrumental activities.\n\nConclusionanxiety, depression and bad sleep quality were significantly high in our survey. Mental and sleep health is heterogeneously affected among individuals, depending on social, economic, financial, educational and health status.\n\nO_TEXTBOXHIGHLIGHTS\n\n- An online survey (DEGAS-CoV) was conducted between April 30th and May 31st, 2020, with people living in Brazil, aged 18 or more. The study obtained 2,695 valid answers.\n- Rates of possible anxiety, possible depression and bad sleep quality were 56.5%, 46.1% and 49.2%, respectively. Rates are similar to another Brazilian survey, with 45,161 participants, conducted in a similar time window.\n- Were more prone to mental and/or sleep conditions: younger participants, women, mestizos, unemployed, students, people with less years of education, people with lower income or with considerable drops of income during the virus outbreak, caregivers, people who followed more news of COVID-19, people less engaged in social and instrumental activities, smokers, sedentary or those who practiced less physical activity, and people who had symptoms suspected (confirmed or not) of SARS-CoV-2 infection.\n- Alcohol drinkers were slightly less likely to be possibly depressed. That finding needs more clarification and may be due to confounders.\n\n\nC_TEXTBOX", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Paulo Afonso Mei", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Amanda Sasse", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Ana Lara Navarrete Fernandez", + "author_inst": "Pontificia Universidade Catolica de Goias" + }, + { + "author_name": "Barbara Neiva Perri", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Breno Alexander Bispo", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Giselly Brito Santana", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Gabriela Sakita Munhos", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Giovanni Giuliani Verghetti", + "author_inst": "Universidade Sao Leopoldo Mandic Araras" + }, + { + "author_name": "Guilherme Barbosa de Almeida Oliveira Martins", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Jennifer Pereira da Rocha", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Jessyca Rosa Lopes Mendonca", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Julia Patel Lebl", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Valdemiro Da Rolt Jr", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Lais Grabner Ruivo", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Laura Loeb", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Marielly Isepon", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Marina Joseane Pachecco", + "author_inst": "Universidade Sao Leopoldo Mandic Araras" + }, + { + "author_name": "Cintia Zonta Baptista", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Fabio Soares Nespoli", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Paloma Ricciardi de Castro", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Paola Ricciardi de Castro", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Rafaela Dotta Brustolin", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Taysa Maria Pimentel Goncalves Gomes Silva", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Victoria Gomes Andreata", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Amilton Santos Jr", + "author_inst": "Universidade Estadual de Campinas" + }, + { + "author_name": "Tania Marchiori de Oliveira Cardoso", + "author_inst": "Universidade Estadual de Campinas" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.02.01.21250943", "rel_title": "Seroprevalence of SARS-CoV-2 during pregnancy and associated outcomes: results from an ongoing prospective cohort study, New York City", @@ -925022,45 +930081,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.02.02.21250796", - "rel_title": "Scientists' opinion, attitudes, and consensus towards immunity passports", - "rel_date": "2021-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250796", - "rel_abs": "ObjectivesWe measured attitudes towards \"immunity passports\" in the context of COVID-19 of a large sample of scientists. Consensus of scientists opinions on a different aspect of immunity passports was assessed.\n\nMethodsWe designed and implemented a survey to capture what scientists from around the world and different scientific background think about immunity certification. The survey was sent to the corresponding authors of scholarly articles published in the last five years in the top 20-ranked journals in each of the 27 subject areas between May and June 2020. Responses from 12,738 scientists were captured, and their distribution was tabulated by participants in health science and other fields. Consensus of responses was calculated using a variant of Shannon Entropy, made suitable for the ordinal response variables.\n\nResultsHalf of the scientists surveyed, regardless of academic background agree that a potential immunity passport program will be good for public health (50.2%) and the economy (54.4%), with 19.1% and 15.4% of participants disagree, respectively. A significant proportion of scientists raised concerns about immunity certification over fairness to others (36.5%) and social inequality (45.5%). There is little consensus in the different aspects of immunity passport among scientists. Overall, scientists with health background hold a more conservative view towards immunity certification.\n\nConclusionsOur findings suggest a lack of general agreement regarding the potential health and economic benefits, societal costs, and ethical issues of an immunity certification program within the scientific community. Given the relevant and important implications of immunity passport due to the increasing vaccine availability and efficacy, more attention should be given to the discussion of the design and implementation of immunity certification program.\n\nStrengths and limitations of this studyO_LIFirst cross-disciplinary survey with a large and international sample size that enables mapping of scientists opinions and attitudes towards COVID-19 immunity certificates.\nC_LIO_LIFrom the survey responses, we measured, reported, and compared the levels of consensus of scientists between health-related and non-health-related discipline.\nC_LIO_LIResponse rate and sample representativeness are moderate.\nC_LI", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ivan Aranzales", - "author_inst": "Queensland University of Technology" - }, - { - "author_name": "Ho Fai Chan", - "author_inst": "Queensland University of Technology" - }, - { - "author_name": "Reiner Eichenberger", - "author_inst": "University of Fribourg" - }, - { - "author_name": "Rainer Hegselmann", - "author_inst": "Frankfurt School of Finance & Management" - }, - { - "author_name": "David Stadelmann", - "author_inst": "University of Bayreuth" - }, - { - "author_name": "Benno Torgler", - "author_inst": "Queensland University of Technology" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.02.02.21250758", "rel_title": "Timing of Convalescent plasma administration and 28-day mortality for COVID-19 pneumonia.", @@ -926639,6 +931659,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.02.02.429431", + "rel_title": "Potential global impact of the N501Y mutation on MHC-II presentation and immune escape", + "rel_date": "2021-02-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.02.429431", + "rel_abs": "The B.1.1.7 SARS-CoV-2 variant, characterized by the N501Y mutation, is rapidly emerging, raising concerns about its effectiveness on natural as well as vaccine-induced adaptive viral immunity at the population level. Since CD4 T cell responses are of critical importance to the antibody response, we examined the global effects of N501Y mutation on MHC-II presentation compared to the N501 wildtype and found poorer presentation across the majority of MHC-II alleles. This suggests that the N501Y mutation may not only diminish binding of antibodies to the RBD but also interfere with their production by weakening the cooperation between T and B cells, facilitating immune escape.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Andrea Castro", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Hannah Carter", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Maurizio Zanetti", + "author_inst": "University of California, San Diego" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.02.03.429355", "rel_title": "Impact of the B.1.1.7 variant on neutralizing monoclonal antibodies recognizing diverse epitopes on SARS-CoV-2 Spike", @@ -927012,57 +932059,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.02.03.429510", - "rel_title": "Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2", - "rel_date": "2021-02-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.03.429510", - "rel_abs": "Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness as well as DFT properties. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, the proposed kinase inhibitors and a few of the predicted nucleotidyl transferase inhibitors significantly inhibited the aforementioned enzymatic activity. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Abhisek Dwivedy", - "author_inst": "National Institute of Immunology, New Delhi, India" - }, - { - "author_name": "Richard Mariadasse", - "author_inst": "Department of Bioinformatics, Alagappa University, Tamil Nadu, India" - }, - { - "author_name": "Mohammed Ahmad", - "author_inst": "National Institute of Immunology, New Delhi, India" - }, - { - "author_name": "Sayan Chakraborty", - "author_inst": "National Institute of Immunology, New Delhi, India" - }, - { - "author_name": "Deepsikha Kar", - "author_inst": "National Institute of Immunology, New Delhi, India" - }, - { - "author_name": "Satish Tiwari", - "author_inst": "National Institute of Immunology, New Delhi, India" - }, - { - "author_name": "Tanmay Majumdar", - "author_inst": "National Institute of Immunology, New Delhi, India" - }, - { - "author_name": "Jeyaraman Jeyakanthan", - "author_inst": "Department of Bioinformatics, Alagappa University, Tamil Nadu, India" - }, - { - "author_name": "Bichitra Biswal", - "author_inst": "National Institute of Immunology" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.02.03.429495", "rel_title": "Molecular dynamics simulation study of effects of key mutations in SARS-CoV-2 on protein structures", @@ -928553,6 +933549,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.31.429023", + "rel_title": "Mn2+ coordinates Cap-0-RNA to align substrates for efficient 2'-O-methyl transfer by SARS-CoV-2 nsp16", + "rel_date": "2021-02-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.31.429023", + "rel_abs": "Capping viral messenger RNAs is essential for efficient translation and prevents their detection by host innate immune responses. For SARS-CoV-2, RNA capping includes 2'-O-methylation of the first ribonucleotide by methyltransferase nsp16 in complex with activator nsp10. The reaction requires substrates, a short RNA and SAM, and is catalyzed by divalent cations, with preference for Mn2+. Crystal structures of nsp16-nsp10 with capped RNAs revealed a critical role of metal ions in stabilizing interactions between ribonucleotides and nsp16, resulting in precise alignment of the substrates for methyl transfer. An aspartate residue that is highly conserved among coronaviruses alters the backbone conformation of the capped RNA in the binding groove. This aspartate is absent in mammalian methyltransferases and is a promising site for designing coronavirus-specific inhibitors.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "George Minasov", + "author_inst": "Northwestern University, Feinberg School of Medicine" + }, + { + "author_name": "Monica Rosas-Lemus", + "author_inst": "Northwestern University, Feinberg School of Medicine" + }, + { + "author_name": "Ludmilla Shuvalova", + "author_inst": "Northwestern University, Feinberg School of Medicine" + }, + { + "author_name": "Nicole L. Inniss", + "author_inst": "Northwestern University, Feinberg School of Medicine" + }, + { + "author_name": "Joseph S. Brunzelle", + "author_inst": "Northwestern Synchrotron Research Center" + }, + { + "author_name": "Courtney M. Daczkowski", + "author_inst": "Purdue University" + }, + { + "author_name": "Paul Hoover", + "author_inst": "Northwestern University, Feinberg School of Medicine" + }, + { + "author_name": "Andrew D Mesecar", + "author_inst": "Purdue University" + }, + { + "author_name": "Karla J Satchell", + "author_inst": "Northwestern University Feinberg School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.31.429001", "rel_title": "Identification of anti-severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) oxysterol derivatives in vitro", @@ -928798,25 +933845,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.01.31.429010", - "rel_title": "Environmentally-induced mdig is a major contributor to the severity of COVID-19 through fostering expression of SARS-CoV-2 receptor NRPs and glycan metabolism", - "rel_date": "2021-02-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.31.429010", - "rel_abs": "The novel {beta}-coronavirus, SARS-CoV-2, the causative agent of coronavirus disease 2019 (COVID-19), has infected more than 101 million people and resulted in 2.2 million death worldwide. Recent epidemiological studies suggested that some environmental factors, such as air pollution, might be the important contributors to the mortality of COVID-19. However, how environmental exposure enhances the severity of COVID-19 remains to be fully understood. In the present report, we provide evidence showing that mdig, a previously reported environmentally-induced oncogene that antagonizes repressive trimethylation of histone proteins, is a master regulator for SARS-CoV-2 receptors neuropilin-1 (NRP1) and NRP2, cathepsins, glycan metabolism and inflammation, key determinants for viral infection and cytokine storm of the patients. Depletion of mdig in bronchial epithelial cells by CRISPR-Cas-9 gene editing resulted in a decreased expression of NRP1, NRP2, cathepsins, and genes involved in protein glycosylation and inflammation, largely due to a substantial enrichment of lysine 9 and/or lysine 27 trimethylation of histone H3 (H3K9me3/H3K27me3) on these genes as determined by ChIP-seq. These data, accordingly, suggest that mdig is a key mediator for the severity of COVID-19 in response to environmental exposure and targeting mdig may be one of the effective strategies in ameliorating the symptom and reducing the mortality of COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Fei Chen", - "author_inst": "Wayne State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.01.31.428824", "rel_title": "Identification of a conserved neutralizing epitope present on spike proteins from highly pathogenic coronaviruses", @@ -930291,6 +935319,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.29.21250407", + "rel_title": "12-lead Electrocardiogram in Hospitalized COVID 19 Patients", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250407", + "rel_abs": "COVID-19 pandemic resulted in considerable morbidity and mortality. We analyzed 345 Electrocardiograms of 100 COVID-19 patients admitted to our tertiary care center in Detroit, during the initial month of Covid-19. Findings were correlated with mortality, cardiac injury and inflammatory markers. Our cohort included 61% males and 77% African Americans. The median age and BMI were 66 years (57-74) and 31 kg/m2 (26.1-39), respectively. We observed atrial arrhythmias in 29% of the patients (17% new onset), First degree heart block in 12%, ST-T segment changes in 17%, S1Q3T3 pattern in 19%, premature ventricular complexes in 23%, premature atrial complexes in 13%, Q waves in 27%, T wave inversion in 42% of the cases. While presence of premature atrial complexes or left atrial abnormality correlated with mortality (P = 0.02 & 0.03, respectively), other findings did not show significant correlation in this small cohort of patients.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Mohamed Shokr", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Omar Chehab", + "author_inst": "Department of Internal Medicine, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Mustafa Ajam", + "author_inst": "Department of Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, OR, USA" + }, + { + "author_name": "Manmohan Singh", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Said Ashraf", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "John Dawdy", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Mohit Pahuja", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Vivek Reddy", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Ahmed Subahi", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "M. Chadi Alraies", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Luis Afonso", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Randy Lieberman", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2021.01.28.21250129", "rel_title": "Application of a 27-protein candidate cardiovascular surrogate endpoint to track risk ascendancy and resolution in COVID-19.", @@ -930496,41 +935587,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.01.30.21250083", - "rel_title": "Increasing but inadequate intention to receive Covid-19 vaccination over the first 50 days of impact of the more infectious variant and roll-out of vaccination in UK: indicators for public health messaging", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.30.21250083", - "rel_abs": "ObjectivesTo inform critical public health messaging by determining how changes in Covid-19 vaccine hesitancy, attitudes to the priorities for administration, the emergence of new variants and availability of vaccines may affect the trajectory and achievement of herd immunity.\n\nMethods>9,000 respondents in an ongoing cross-sectional participatory longitudinal epidemiology study (LoC-19, n=18,581) completed a questionnaire within their personal electronic health record in the week reporting first effective Covid-19 vaccines, and then again after widespread publicity of the increased transmissibility of a new variant (November 13th and December 31st 2020 respectively). Questions covered willingness to receive Covid-19 vaccination and attitudes to prioritisation. Descriptive statistics, unadjusted and adjusted odds ratios (ORs) and natural language processing of free-text responses are reported, and how changes over the first 50 days of both vaccination roll-out and new-variant impact modelling of anticipated transmission rates and the likelihood and time to herd immunity.\n\nFindingsCompared with the week reporting the first efficacious vaccine there was a 15% increase in acceptance of Covid-19 vaccination, attributable in one third to the impact of the new variant, with 75% of respondents \"shielding\" - staying at home and not leaving unless essential - regardless of health status or tier rules. 12.5% of respondents plan to change their behaviour two weeks after completing vaccination compared with 45% intending to do so only when cases have reduced to a low level. Despite the increase from 71% to 86% over this critical 50-day period, modelling of planned uptake of vaccination remains below that required for rapid effective herd immunity - now estimated to be 90 percent in the presence of a new variant escalating R0 to levels requiring further lockdowns. To inform the public messaging essential therefore to improve uptake, age and female gender were, respectively, strongly positively and negatively associated with wanting a vaccine. 22.7% disagreed with the prioritisation list, though 70.3% were against being able to expedite vaccination through payment. Teachers (988, 12.6%) and Black, Asian and Minority Ethnic (BAME) (837, 10.7%) groups were most cited by respondents for prioritisation.\n\nInterpretationIn this sample, the growing impact of personal choice among the increasingly informed public highlights a decrease in Covid-19 vaccine hesitancy over time, with news of a new variant motivating increased willingness for vaccination but at levels below what may be required for effective herd immunity. We identify public preferences for next-in-line priorities, headed by teachers and BAME groups, consideration of which will help build trust and community engagement critical for maximising compliance with not only the vaccination programme but also all other public health measures.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Patrik Bachtiger", - "author_inst": "Imperial College London" - }, - { - "author_name": "Alexander Adamson", - "author_inst": "Imperial College London" - }, - { - "author_name": "William A Maclean", - "author_inst": "Imperial College London" - }, - { - "author_name": "Jennifer K Quint", - "author_inst": "Imperial College London" - }, - { - "author_name": "Nicholas S Peters", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.29.21250789", "rel_title": "Relative humidity predicts day-to-day variations in COVID-19 cases in the city of Buenos Aires", @@ -931965,6 +937021,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.29.21250793", + "rel_title": "COVID-19 spread and Weather in U.S. states: a cross-correlative study on summer-autumn 2020.", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250793", + "rel_abs": "An effect of weather on sars-cov-2 transmission is regularly proposed as a putative cause of unexplained fluctuations of covid-19 new cases, but clear data supporting this hypothesis remains to be presented. Here I measured longitudinal time-series correlations between outdoor temperature, humidity and covid-19 reproduction number (Rt) in the 50 U.S. states (+DC). In order to mitigate the confounding influence of varying social restriction measures, the analysis spans a 5-month period during summer and autumn 2020 when restrictions were comparatively lower and more stable. I used a cross-covariance approach to account for a variable delay between infection and case report. For a delay near 11 days, most U.S. states exhibited a negative correlation between outdoor temperature and Rt, as well as between absolute humidity and Rt (mean r = -0.35). In 21 states, the correlation was strong (r < -0.5). Individual state data are presented, and associations between cold and/or dry weather episodes and short-term new case surges are proposed. After identifying potential confounding factors, I discuss 3 possible causal mechanisms that could explain a correlation between outdoor weather and indoor disease transmission: behavioral adaptations to cold weather, respiratory tract temperature, and the importing of outdoor absolute humidity to indoor spaces.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Emmanuel de Margerie", + "author_inst": "CNRS" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.30.21250830", "rel_title": "Estimated SARS-CoV-2 Seroprevalence in Healthy Children and Those with Chronic Illnesses in The Washington Metropolitan Area as of October 2020", @@ -932086,61 +937161,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.31.21250859", - "rel_title": "Prognosis and hematological findings in patients with COVID-19 in an Amazonian population of Peru", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.31.21250859", - "rel_abs": "ObjectiveThis study examined the laboratory results of COVID-19 patients from a hospital in the Peruvian Amazon and their clinical prognosis.\n\nMethodsAn analytical cross-sectional study was carried out whose purpose was to identify the laboratory tests of patients with COVID-19 and mortality in a hospital in Ucayali, Peru during the period from March 13 to May 9, 2020, selecting a total of 127 with Covid-19. Mean and the standard deviation was described for age, leukocytes, neutrophils, platelets, RDW-SD; median and interquartile range for the variables lymphocyte, RN / L, fibrinogen, CRP, D-dimer, DHL, hematocrit, monocytes, eosinophils.\n\nResultsNo differences were observed in this population regarding death and sex (OR: 1.31; 95% CI 0.92 to 1.87), however, it was observed that, for each one-year increase, the probability of death increased by 4% (PR: 1.04, 95% CI 1.03 to 1.05). The IRR (Incidence Risk Ratio) analysis for the numerical variables showed results strongly associated with hematological values such as Leukocytes (scaled by 2500 units) (IRR: 1.08, 95% CI 1.03 to 1.13), neutrophils (scaled by 2500 units) (IRR: 1.08; 95% CI 1.03 to 1.13), on the contrary, it is observed that the increase of 1000 units in lymphocytes, the probability of dying decreased by 48% (IRR: 0.52; 95% CI 0.38 to 071).\n\nConclusionParameters such as leukocytes and neutrophils were statistically much higher in patients who died.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Sebastian Iglesias-Osores", - "author_inst": "Universidad Nacional Pedro Ruiz Gallo" - }, - { - "author_name": "Arturo Rafael-Heredia", - "author_inst": "Universidad Nacional de Ucayali" - }, - { - "author_name": "Eric Ricardo Rojas-Tello", - "author_inst": "Hospital II Essalud Pucallpa" - }, - { - "author_name": "Washington A. Ortiz-Uribe", - "author_inst": "Universidad Nacional de Ucayali" - }, - { - "author_name": "Walter Leveau-Bartra", - "author_inst": "Universidad Nacional de Ucayali" - }, - { - "author_name": "Orison Armando Leveau-Bartra", - "author_inst": "Universidad Nacional de Ucayali" - }, - { - "author_name": "Miguel Alcantara-Mimbela", - "author_inst": "Universidad Nacional Pedro Ruiz Gallo" - }, - { - "author_name": "Lizbeth M. Cordova-Rojas", - "author_inst": "Universidad Nacional de Jaen" - }, - { - "author_name": "Elmer Lopez-Lopez", - "author_inst": "Universidad Senor de Sipan" - }, - { - "author_name": "Virgilio E. Failoc-Rojas", - "author_inst": "Universidad San Ignacio de Loyola" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2021.01.31.21250870", "rel_title": "Immuno-fibrotic drivers of impaired lung function in post-COVID-19 syndrome", @@ -933783,6 +938803,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.28.21250700", + "rel_title": "Surveillance-to-Diagnostic Testing Program for Asymptomatic SARS-CoV-2 Infections on a Large, Urban Campus - Georgia Institute of Technology, Fall 2020", + "rel_date": "2021-01-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.28.21250700", + "rel_abs": "A SARS-CoV-2 testing program combining pooled saliva sample surveillance leading to diagnosis and intervention surveyed over 112,000 samples from 18,029 students, staff and faculty, as part of integrative efforts to mitigate transmission at the Georgia Institute of Technology in Fall 2020. Cumulatively, 1,508 individuals were confirmed diagnostically. The surveillance strategy, including focused intensification of testing given case clusters, was effective in disrupting transmission following rapid case increases upon entry in August 2020, and again in November 2020. Owing to broad adoption by the campus community, the program protected higher risk staff while allowing some normalization of research activities.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Greg C Gibson", + "author_inst": "Georgia Tech" + }, + { + "author_name": "Joshua S Weitz", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Michael P. Shannon", + "author_inst": "Georgia Tech Research Institute" + }, + { + "author_name": "Benjamin Holton", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Anton Bryksin", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Brian Liu", + "author_inst": "Georgia Tech Research Institute" + }, + { + "author_name": "Sandra Bramblett", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Julianne Williamson", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Michael Farrell", + "author_inst": "Georgia Tech Research Institute" + }, + { + "author_name": "Alexander Ortiz", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Chaouki T. Abdallah", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Andr\u00e9s Garc\u00eda", + "author_inst": "Georgia Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.29.428890", "rel_title": "Recombinant production of a functional SARS-CoV-2 spike receptor binding domain in the green algae Chlamydomonas reinhardtii", @@ -934008,85 +939091,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.01.25.21249942", - "rel_title": "Development and external validation of prognostic models for COVID-19 to support risk stratification in secondary care", - "rel_date": "2021-01-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.25.21249942", - "rel_abs": "ObjectivesExisting UK prognostic models for patients admitted to hospital with COVID-19 are limited by reliance on comorbidities, which are under-recorded in secondary care, and lack of imaging data among the candidate predictors. Our aims were to develop and externally validate novel prognostic models for adverse outcomes (death, intensive therapy unit (ITU) admission) in UK secondary care; and externally validate the existing 4C score.\n\nDesignCandidate predictors included demographic variables, symptoms, physiological measures, imaging, laboratory tests. Final models used logistic regression with stepwise selection.\n\nSettingModel development was performed in data from University Hospitals Birmingham (UHB). External validation was performed in the CovidCollab dataset.\n\nParticipantsPatients with COVID-19 admitted to UHB January-August 2020 were included.\n\nMain outcome measuresDeath and ITU admission within 28 days of admission.\n\nResults1040 patients with COVID-19 were included in the derivation cohort; 288 (28%) died and 183 (18%) were admitted to ITU within 28 days of admission. Area under the receiver operating curve (AUROC) for mortality was 0.791 (95%CI 0.761-0.822) in UHB and 0.767 (95%CI 0.754-0.780) in CovidCollab; AUROC for ITU admission was 0.906 (95%CI 0.883-0.929) in UHB and 0.811 (95%CI 0.795-0.828) in CovidCollab. Models showed good calibration. Addition of comorbidities to candidate predictors did not improve model performance. AUROC for the 4C score in the UHB dataset was 0.754 (95%CI 0.721-0.786).\n\nConclusionsThe novel prognostic models showed good discrimination and calibration in derivation and external validation datasets, and outperformed the existing 4C score. The models can be integrated into electronic medical records systems to calculate each individual patients probability of death or ITU admission at the time of hospital admission. Implementation of the models and clinical utility should be evaluated.\n\nArticle SummaryO_ST_ABSStrengths and limitations of this studyC_ST_ABSO_LIWe developed novel prognostic models predicting mortality and ITU admission within 28 days of admission for patients hospitalised with COVID-19, using a large routinely collected dataset gathered at admission with a wide range of possible predictors (demographic variables, symptoms, physiological measures, imaging, laboratory test results).\nC_LIO_LIThese novel models showed good discrimination and calibration in both derivation and external validation cohorts, and outperformed the existing ISARIC model and 4C score in the derivation dataset. We found that addition of comorbidities to the set of candidate predictors included in model derivation did not improve model performance.\nC_LIO_LIIf integrated into hospital electronic medical records systems, the model algorithms will provide a predicted probability of mortality or ITU admission for each patient based on their individual data at, or close to, the time of admission, which will support clinicians decision making with regard to appropriate patient care pathways and triage. This information might also assist clinicians in explaining complex prognostic assessments and decisions to patients and their relatives.\nC_LIO_LIA limitation of the study was that in the external validation cohort we were unable to examine all of the predictors included in the original full UHB model due to only a reduced set of candidate predictors being available in CovidCollab. Nevertheless, the reduced model performed well and the results suggest it may be applicable in a wide range of datasets where only a reduced set of predictor variables is available.\nC_LIO_LIFurthermore, it was not possible to carry out stratified analysis by ethnicity as the UHB dataset contained too few patients in most of the strata, and no ethnicity data was available in the CovidCollab dataset.\nC_LI", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Nicola J Adderley", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Thomas Taverner", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Malcolm Price", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Christopher Sainsbury", - "author_inst": "University of Birmingham" - }, - { - "author_name": "David Greenwood", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Joht Singh Chandan", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Yemisi Takwoingi", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Rashan Haniffa", - "author_inst": "University of Oxford" - }, - { - "author_name": "Isaac Hosier", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Carly Welch", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Dhruv Parekh", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Suzy Gallier", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Krishna M Gokhale", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Alastair K Denniston", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Elizabeth Sapey", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Krishnarajah Nirantharakumar", - "author_inst": "University of Birmingham" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.25.21250189", "rel_title": "Longitudinal analyses reveal age-specific immune correlates of COVID-19 severity", @@ -935593,6 +940597,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.26.21250349", + "rel_title": "HLA-A*11:01:01:01, HLA*C*12:02:02:01-HLA-B*52:01:02:02, age and sex are associated with severity of Japanese COVID-19 with respiratory failure", + "rel_date": "2021-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250349", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing coronavirus disease 2019 (COVID-19) was announced as an outbreak by the World Health Organization (WHO) in January 2020 and as a pandemic in March 2020. The majority of infected individuals have experienced no or only mild symptoms, ranging from fully asymptomatic cases to mild pneumonic disease. However, a minority of infected individuals develop severe respiratory symptoms. The objective of this study was to identify susceptible HLA alleles and clinical markers for the early identification of severe COVID-19 among hospitalized COVID-19 patients. A total of 137 patients with mild COVID-19 (mCOVID-19) and 53 patients with severe COVID-19 (sCOVID-19) were recruited from the Center Hospital of the National Center for Global Health and Medicine (NCGM), Tokyo, Japan for the period of February-August 2020. High-resolution sequencing-based typing for eight HLA genes was performed using next-generation sequencing. In the HLA association studies, HLA-A*11:01:01:01 [Pc = 0.013, OR = 2.26 (1.27-3.91)] and HLA-C*12:02:02:01-HLA-B*52:01:01:02 [Pc = 0.020, OR = 2.25 (1.24-3.92)] were found to be significantly associated with the severity of COVID-19. After multivariate analysis controlling for other confounding factors and comorbidities, HLA-A*11:01:01:01 [P = 3.34E-03, OR = 3.41 (1.50-7.73)], age at diagnosis [P = 1.29E-02, OR = 1.04 (1.01-1.07)] and sex at birth [P = 8.88E-03, OR = 2.92 (1.31-6.54)] remained significant. Early identification of potential sCOVID-19 could help clinicians prioritize medical utility and significantly decrease mortality from COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Seik-Soon Khor", + "author_inst": "Genome Medical Science Project, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Yosuke Omae", + "author_inst": "Genome Medical Science Project, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Nao Nishida", + "author_inst": "Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan" + }, + { + "author_name": "Masaya Sugiyama", + "author_inst": "Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan" + }, + { + "author_name": "Noriko Kinoshita", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Tetsuya Suzuki", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Michiyo Suzuki", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Satoshi Suzuki", + "author_inst": "Biobank, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Shinyu Izumi", + "author_inst": "Department of Respiratory Medicine, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Masayuki Hojo", + "author_inst": "Department of Respiratory Medicine, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Masashi Mizokami", + "author_inst": "Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan" + }, + { + "author_name": "Katsushi Tokunaga", + "author_inst": "Genome Medical Science Project, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.27.21250048", "rel_title": "A Rapid and Low-Cost protocol for the detection of B.1.1.7 lineage of SARS-CoV-2 by using SYBR Green-Based RT-qPCR", @@ -935690,49 +940761,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.27.20240309", - "rel_title": "Beyond the new normal: assessing the feasibility of vaccine-based elimination of SARS-CoV-2", - "rel_date": "2021-01-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.20240309", - "rel_abs": "As the COVID-19 pandemic drags into its second year, there is hope on the horizon, in the form of SARS-CoV-2 vaccines which promise disease elimination and a return to pre-pandemic normalcy. In this study we critically examine the basis for that hope, using an epidemiological modeling framework to establish the link between vaccine characteristics and effectiveness in bringing an end to this unprecedented public health crisis. Our findings suggest that vaccines that do not prevent infection will allow extensive endemic SARS-CoV-2 spread upon a return to pre-pandemic social and economic conditions. Vaccines that only reduce symptomatic COVID-19 or mortality will fail to mitigate serious COVID-19 mortality risks, particularly in the over-65 population, likely resulting in hundreds of thousands of US deaths on a yearly basis. Our modeling points to the possibility of complete SARS-CoV-2 elimination with high population-level compliance and a vaccine that is highly effective at reducing SARS-CoV-2 infection. Notably, vaccine-mediated reduction of transmission is critical for elimination, and in order for partially-effective vaccines to play a positive role in SARS-CoV-2 elimination, other stackable (complementary) interventions must be deployed simultaneously.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Madison Stoddard", - "author_inst": "Fractal Therapeutics" - }, - { - "author_name": "Sharanya Sarkar", - "author_inst": "Department of Microbiology and Immunology, Dartmouth College" - }, - { - "author_name": "Ryan P. Nolan", - "author_inst": "Halozyme Therapeutics" - }, - { - "author_name": "Douglas E White", - "author_inst": "Unaffiliated" - }, - { - "author_name": "Laura White", - "author_inst": "Boston University" - }, - { - "author_name": "Natasha S Hochberg", - "author_inst": "Department of Epidemiology, Boston University School of Public Health" - }, - { - "author_name": "Arijit Chakravarty", - "author_inst": "Fractal Therapeutics" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.27.21250619", "rel_title": "Evaluation of COVID-19 vaccination strategies with a delayed second dose", @@ -937227,6 +942255,153 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2021.01.27.428516", + "rel_title": "SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral Spike vaccines", + "rel_date": "2021-01-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.27.428516", + "rel_abs": "The SARS-CoV-2 Spike glycoprotein mediates virus entry and is a major target for neutralizing antibodies. All current vaccines are based on the ancestral Spike with the goal of generating a protective neutralizing antibody response. Several novel SARS-CoV-2 variants with multiple Spike mutations have emerged, and their rapid spread and potential for immune escape have raised concerns. One of these variants, first identified in the United Kingdom, B.1.1.7 (also called VUI202012/01), contains eight Spike mutations with potential to impact antibody therapy, vaccine efficacy and risk of reinfection. Here we employed a lentivirus-based pseudovirus assay to show that variant B.1.1.7 remains sensitive to neutralization, albeit at moderately reduced levels (~2-fold), by serum samples from convalescent individuals and recipients of two different vaccines based on ancestral Spike: mRNA-1273 (Moderna), and protein nanoparticle NVX-CoV2373 (Novavax). Some monoclonal antibodies to the receptor binding domain (RBD) of Spike were less effective against the variant while others were largely unaffected. These findings indicate that B.1.1.7 is not a neutralization escape variant that would be a major concern for current vaccines, or for an increased risk of reinfection.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Haili Tang", + "author_inst": "Duke University" + }, + { + "author_name": "Charlene McDana", + "author_inst": "Duke University" + }, + { + "author_name": "Xiaoying Shen", + "author_inst": "Duke University" + }, + { + "author_name": "Kshitij Wagh", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Haili Tang", + "author_inst": "Duke University" + }, + { + "author_name": "Will Fischer", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Charlene McDana", + "author_inst": "Duke University" + }, + { + "author_name": "James Theiler", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Kshitij Wagh", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Hyejin Yoon", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Will Fischer", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Dapeng Li", + "author_inst": "Duke University" + }, + { + "author_name": "James Theiler", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Barton F Haynes", + "author_inst": "Duke University" + }, + { + "author_name": "Hyejin Yoon", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "S. Gnanakaran", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Dapeng Li", + "author_inst": "Duke University" + }, + { + "author_name": "Nicholas W Hengartner", + "author_inst": "Los Alamos Nationa Lab" + }, + { + "author_name": "Barton F Haynes", + "author_inst": "Duke University" + }, + { + "author_name": "Rolando Pajon", + "author_inst": "Moderna Inc" + }, + { + "author_name": "S. Gnanakaran", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Gale Smith", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Nicholas W Hengartner", + "author_inst": "Los Alamos Nationa Lab" + }, + { + "author_name": "Filip Dubovsky", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Rolando Pajon", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Gregory M Glenn", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Gale Smith", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Bette Korber", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Filip Dubovsky", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "David Montefiori", + "author_inst": "Duke University" + }, + { + "author_name": "Gregory M Glenn", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Bette Korber", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "David Montefiori", + "author_inst": "Duke University" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.27.428534", "rel_title": "Unbiased interrogation of memory B cells from convalescent COVID-19 patients reveals a broad antiviral humoral response targeting SARS-CoV-2 antigens beyond the spike protein", @@ -937432,29 +942607,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.01.28.428521", - "rel_title": "Modeling mutational effects on biochemical phenotypes using convolutional neural networks: application to SARS-CoV-2", - "rel_date": "2021-01-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.28.428521", - "rel_abs": "Biochemical phenotypes are major indexes for protein structure and function characterization. They are determined, at least in part, by the intrinsic physicochemical properties of amino acids and may be reflected in the protein three-dimensional structure. Modeling mutational effects on biochemical phenotypes is a critical step for understanding protein function and disease mechanism as well as enabling drug discovery. Deep Mutational Scanning (DMS) experiments have been performed on SARS-CoV-2s spike receptor binding domain and the human ACE2 zinc-binding peptidase domain - both central players in viral infection and evolution and antibody evasion - quantifying how mutations impact binding affinity and protein expression. Here, we modeled biochemical phenotypes from massively parallel assays, using convolutional neural networks trained on protein sequence mutations in the virus and human host. We found that neural networks are significantly predictive of binding affinity, protein expression, and antibody escape, learning complex interactions and higher-order features that are difficult to capture with conventional methods from structural biology. Integrating the intrinsic physicochemical properties of amino acids, including hydrophobicity, solvent-accessible surface area, and long-range non-bonded energy per atom, significantly improved prediction (empirical p<0.01) though there was such a strong dependence on the sequence data alone to yield reasonably good prediction. We observed concordance of the DMS data and our neural network predictions with an independent study on intermolecular interactions from molecular dynamics (multiple 500 ns or 1 s all-atom) simulations of the spike protein-ACE2 interface, with critical implications for the use of deep learning to dissect molecular mechanisms. The mutation- or genetically-determined component of a biochemical phenotype estimated from the neural networks has improved causal inference properties relative to the original phenotype and can facilitate crucial insights into disease pathophysiology and therapeutic design.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Bo Wang", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Eric R Gamazon", - "author_inst": "Vanderbilt University Medical Centter and Clare Hall, University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.01.28.428642", "rel_title": "Coronavirus associated molecular mimicry common to SARS-CoV-2 peptide", @@ -939005,6 +944157,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.01.26.428208", + "rel_title": "Do examinations prepare students for higher education? A lesson from the Covid-19 lockdown.", + "rel_date": "2021-01-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.26.428208", + "rel_abs": "The COVID-19 pandemic caused severe disruption to education in the UK in 2020, with most of the school teaching moving online and national school examinations being cancelled. This was particularly disruptive for those taking end of school examinations in preparation for higher education. Biological science courses require students to absorb a lot of new vocabulary and concepts, with examinations traditionally focusing on content recall rather than reasoning. Students who had entered university in September 2019 were compared with those arriving in September 2020 with respect to their knowledge of bioscience vocabulary and understanding of key concepts. Results showed no significant difference between those who had gone through the examination process in 2019 relative to those who had not, in 2020. This suggests the cramming of information for examinations has no detectable effect on the knowledge and understanding of biology that students take with them to university.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Harriet L Jones", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Valentina Zini", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Jon R Green", + "author_inst": "University of Birmingham" + }, + { + "author_name": "John R Prendergast", + "author_inst": "JRP Information Services" + }, + { + "author_name": "Jon Scott", + "author_inst": "University of Leicester" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2021.01.21.21250249", "rel_title": "Evaluation of six commercial SARS-CoV-2 Enzyme-Linked Immunosorbent assays for clinical testing and serosurveillance.", @@ -939294,69 +944481,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.20.21250173", - "rel_title": "The usefulness of a quantitative olfactory test for the detection of COVID-19.", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.20.21250173", - "rel_abs": "BackgroundDuring the COVID-19 pandemic, olfactory dysfunction (anosmia or hyposmia) has been reported by many patients and recognized as a prevalent and early symptom of infection. This finding has been associated with viral-induced olfactory neuron dysfunction rather than the nasal congestion typically found in cold- or flu-like states. In literature, the prevalence of anosmia varies from 15% to 85%, and the studies, in general, were based on the subjective evaluation of patients self-reports of loss of smell (yes or no question). In the present study, we quantitatively evaluated olfactory dysfunction and the prevalence of fever in symptomatic patients suspected of having COVID-19 using a scratch-and-sniff olfactory test and infrared temperature testing with RT-PCR as the gold-standard comparator method to diagnose COVID-19 infection.\n\nMethodsOutpatients had their forehead temperature checked with an infrared non-contact thermometer (temperature guns). After that, they received two olfactory smell identification test (SIT) cards (u-Smell-it; CT, USA) that each had 5 scent windows and were asked to scratch with a pencil and sniff each of the 10 small circles containing the microencapsulated fragrances and mark the best option on a response card. Nasopharyngeal swabs were then collected for Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) to determine if the patients were positive or negative for COVID-19 infection. We considered the number of hits (correct answers) [≤] 5 as positive for loss of smell (LOS) in the olfactory test; [≥] 6 hits was considered negative for LOS (i.e. normal olfactory function). All data were analyzed using Excel and Matlab software.\n\nResultsIn the present study, 165 patients were eligible for the olfactory test and nasopharyngeal swab collection RT-PCR. Five patients were excluded because of inconclusive PCR results (n=2) and missing data (n=3). A total of 160 patients completed all the protocols. The RT-PCR positivity rate for COVID-19 was 27.5% (n=44), and PCR+ patients scored significantly worse in the olfactory test (5.5{+/-}3.5) compared to RT-PCR-patients (8.2{+/-}1.8, p<0.001). 0/44 PCR+ patients presented with a fever ([≥]37.8{degrees}C). In contrast an olfactory SIT had a specificity of 94.8% (95% CI, 89.1 - 98.1), sensitivity of 47.7% (95% CI, 32.7 - 63.3), accuracy of 0.82 (95% CI, 0.75 - 0.87), positive predictive value of 77.8% (95% CI, 59.6 - 88.8), negative predictive value of 82.7% (85% CI, 78.7 - 86.7), and odds ratio of 16.7.\n\nConclusionOur results suggest that temperature checking failed to detect COVID-19 infection, while an olfactory test may be useful to help identify COVID-19 infection in symptomatic patients.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Marcos Adriano Lessa", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Stella M R Cotta-Pereira", - "author_inst": "Oswaldo Cruz Foudation" - }, - { - "author_name": "Frederico A Ferreira", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Terezinha Marta Pereira Pinto Castineira", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Rafael de Mello Galiez", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Debora Souza Faffe", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Isabela de Carvalho Leitao", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Diana Mariani", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Erica Ramos dos Santos Nascimento", - "author_inst": "Federal University of Rio de Janeiro" - }, - { - "author_name": "Flavia Soares Lessa", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Isabela Brasil Succi", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Carlos Eduardo Pedreira", - "author_inst": "Federal University of Rio de Janeiro" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.20.21250143", "rel_title": "Comparison study of commercial COVID-19 RT-PCR kits propose an approach to evaluate their performances", @@ -940747,6 +945871,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.25.21250082", + "rel_title": "SARS-CoV-2 RNA screening in routine pathology specimens", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.25.21250082", + "rel_abs": "Virus detection methods are important to cope with the SARS-CoV-2 pandemics. Apart from the lung, SARS-CoV-2 was detected in multiple organs in severe cases. Less is known on organ tropism in patients developing mild or no symptoms, and some of such patients might be missed in symptom-indicated swab testing.\n\nHere we tested and validated several approaches and selected the most reliable RT-PCR protocol for the detection of SARS-CoV-2 RNA in patients routine diagnostic formalin-fixed and paraffin-embedded (FFPE) specimens available in pathology, to assess a) organ tropism in samples from COVID-19-positive patients, b) unrecognized cases in selected tissues from negative or not-tested patients during a pandemic peak, and c) retrospectively, pre-pandemic lung samples.\n\nWe identified SARS-CoV-2 RNA in four samples from confirmed COVID-19 patients, in two gastric biopsies, one colon resection, and one pleural effusion specimen, while all other specimens, particularly from patients with mild COVID-19 disease course, were negative. In the pandemic peak cohort, we identified one previously unrecognized COVID-19 case in tonsillectomy samples. All pre-pandemic lung samples were negative.\n\nIn conclusion, SARS-CoV-2 RNA detection in FFPE pathology specimens can potentially improve surveillance of COVID-19, allow retrospective studies, and advance our understanding of SARS-CoV-2 organ tropism and effects.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Saskia E von Stillfried", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Sophia Villwock", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Roman D Buelow", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Sonja Djudjaj", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Eva M Buhl", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Angela Maurer", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Nadina Ortiz-Bruechle", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Peter Celec", + "author_inst": "Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia; Institute of Pathophysiology, Faculty of Medicine, Comenius" + }, + { + "author_name": "Barbara M Klinkhammer", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Dickson WL Wong", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Claudio Cacchi", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Till Braunschweig", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Ruth Knuechel", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Edgar Dahl", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Peter Boor", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany and Departments of Nephrology and Immunology, RWTH Aachen University Hospital, Aachen, " + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.21.21249906", "rel_title": "Genomic Epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil", @@ -940936,45 +946135,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.22.20249050", - "rel_title": "A High-throughput Microsphere-based Immunoassay of Anti-SARS-CoV-2 IgM Testing for COVID-19 Diagnostics", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.22.20249050", - "rel_abs": "The pandemic of novel coronavirus disease COVID-19 is rapidly expanding across the world. A positive result of antibody tests suggests that the individual has potentially been exposed to SARS-CoV-2, thus allowing to identify asymptomatic infections and determine the seroprevalence in a given population. The aim of this study was to evaluate the performances of a newly developed high throughput immunoassay for anti-SARS-CoV-2 IgM antibody detection on the Luminex MAGPIX platform. Clinical agreement studies were performed in 42 COVID-19 patient serum samples and 162 negative donor serum/plasma samples. Positive percent agreement (PPA) was 42.86% (95% CI: 9.90% to 81.59%), 71.43% (95% CI: 29.04% to 96.33%), and 28.57% (95% CI: 13.22% to 48.67%) for samples collected on 0-7 days, 8-14 days, and 2-8 weeks from symptom onset, respectively. Negative Percent Agreement (NPA) was 97.53% (95% CI: 93.80% to 99.32%). There was no cross-reactivity with the SARS-CoV-2 IgG antibody Hemoglobin (200 mg/dL), bilirubin (2 mg/dL), triglyceride (250 mg/dL) and EDTA (10 mM) showed no significant interfering effect on this assay. In conclusion, an anti-SARS-CoV-2 IgM antibody assay with high sensitivity and specificity has been developed. With the high throughput, this assay will speed up the anti-SARS-CoV-2 IgM testing.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Dayu Zhang", - "author_inst": "DiaCarta" - }, - { - "author_name": "Tianyang Xu", - "author_inst": "DiaCarta" - }, - { - "author_name": "Eric Chu", - "author_inst": "DiaCarta" - }, - { - "author_name": "Aiguo Zhang", - "author_inst": "DiaCarta" - }, - { - "author_name": "Jinwei Du", - "author_inst": "DiaCarta" - }, - { - "author_name": "Michael Sha", - "author_inst": "Diacarta Inc" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.24.21250384", "rel_title": "Assessment of The Relationship of REMS and MEWS Scores with Prognosis in Patients Diagnosed with Covid-19 Admitted to the Emergency Department", @@ -942673,6 +947833,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.26.21250507", + "rel_title": "Estimation of the SARS-CoV-2 infection fatality rate in Germany", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250507", + "rel_abs": "Assessing the infection fatality rate (IFR) of SARS-CoV-2 is one of the most controversial issues during the pandemic. Due to asymptomatic or mild courses of COVID-19, many infections remain undetected. Reported case fatality rates - COVID-19-associated deaths divided by number of detected infections - are therefore poor estimates of the IFR. Endogenous changes of the population at risk of a SARS-CoV-2 infection, changing test practices and an improved understanding of the pathogenesis of COVID-19 further exacerbate the estimation of the IFR. Here, we propose a strategy to estimate the IFR of SARS-CoV-2 in Germany that combines official data on reported cases and fatalities supplied by the Robert Koch Institute (RKI) with data from seroepidemiological studies in two infection hotspots, the Austrian town Ischgl and the German municipality Gangelt, respectively. For this purpose, we use the law of total probability to derive an approximate formula for the IFR that is based on a set of assumptions regarding data quality and test specificity and sensitivity. The resulting estimate of the IFR in Germany of 0.83% (95% CI: [0.69%; 0.98%]) that is based on a combination of the RKI and Ischgl data is notably higher than the IFR estimate reported in the Gangelt study (0.36% [0.29%; 0.45%]). It is closer to the consolidated estimate based on a meta-analysis (0.68% [0.53%; 0.82%]), where the difference can be explained by Germanys disadvantageous age structure. As a result of virus mutations, vaccination strategies, and improved therapy, a re-estimation of the IFR will eventually be mandated; the proposed method is able to account for such developments.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Thomas Dimpfl", + "author_inst": "University of T\u00fcbingen, Department of Statistics and Econometrics" + }, + { + "author_name": "Jantje S\u00f6nksen", + "author_inst": "University of T\u00fcbingen, Department of Statistics and Econometrics" + }, + { + "author_name": "Ingo Bechmann", + "author_inst": "University of Leipzig, Institute of Anatomy" + }, + { + "author_name": "Joachim Grammig", + "author_inst": "University of T\u00fcbingen, Department of Statistics and Econometrics" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.25.21250505", "rel_title": "Community structured model for vaccine strategies to control COVID19 spread: a mathematical study", @@ -942854,57 +948045,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.26.21249335", - "rel_title": "Elevated HScore is Associated with Poor Clinical Outcomes in COVID-19, Even in the Absence of Secondary Hemophagocytic Lymphohistiocytosis.", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21249335", - "rel_abs": "IntroductionPatients with Coronavirus Disease 2019 (COVID-19) frequently experience a hyperinflammatory syndrome, that leads to unfavorable outcomes. This condition resembles Secondary Hemophagocytic Lymphohistiocytosis (sHLH) described in neoplastic, rheumatic and other infectious diseases. However, it has not been prospectively studied on these patients. A scoring system (HScore) has been validated for sHLH, and recently proposed to evaluate hyperinflammation in COVID-19.\n\nMethods143 patients aged [≥]18 years admitted because of COVID-19 were enrolled in a prospective, single-center, cohort study. HScore was calculated within the 72 hours since admission. The incidence of sHLH during hospitalization was evaluated. Additionally, the relationship between HScore [≥]130 points and either the requirement of mechanical ventilation or 60-days mortality was explored.\n\nResultsThe median age of enrolled patients was 57 (21-100), and 63.6% were male. The median HScore was 96 (33-169). One patient was diagnosed with sHLH (incidence 0,7%), due to a HScore of 169. After adjusting for age, sex, comorbidities and obesity, HScore [≥]130 was independently associated with the composite clinical outcome (HR 2.13, p=0.022).\n\nConclusionsHLH is not frequent among COVID-19 patients. HScore can efficiently predict the risk for poor outcomes.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Rafael Benavente", - "author_inst": "University of Chile" - }, - { - "author_name": "Camila Pe\u00f1a M.D.", - "author_inst": "Hospital del Salvador" - }, - { - "author_name": "Allyson Cid M.D.", - "author_inst": "Hospital del Salvador" - }, - { - "author_name": "Nicol\u00e1s Cabello M.D.", - "author_inst": "Hospital del Salvador" - }, - { - "author_name": "Pablo Bustamante M.D.", - "author_inst": "Hospital del Salvador" - }, - { - "author_name": "Marco \u00c1lvarez M.D.", - "author_inst": "Hospital del Salvador" - }, - { - "author_name": "Elizabeth Henr\u00edquez M.D.", - "author_inst": "Hospital del Salvador" - }, - { - "author_name": "Andr\u00e9s Soto M.D.", - "author_inst": "Hospital del Salvador" - }, - { - "author_name": "\u00c9rika Rubilar M.D.", - "author_inst": "Hospital del Salvador" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2021.01.25.21249684", "rel_title": "Home-based management of COVID-19 by identification of low-risk features", @@ -944391,6 +949531,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.21.21249176", + "rel_title": "Distinct Autoimmune Antibody Signatures Between Hospitalized Acute COVID-19 Patients, SARS-CoV-2 Convalescent Individuals, and Unexposed Pre-Pandemic Controls", + "rel_date": "2021-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21249176", + "rel_abs": "Increasing evidence suggests that autoimmunity may play a role in the pathophysiology of SARS-CoV-2 infection during both the acute and long COVID phases of disease. However, an assessment of autoimmune antibodies in convalescent SARS-CoV-2 patients has not yet been reported.\n\nMethodologyWe compared the levels of 18 different IgG autoantibodies (AABs) between four groups: (1) unexposed pre-pandemic subjects from the general population (n = 29); (2) individuals hospitalized with acute moderate-severe COVID-19 (n = 20); (3) convalescent SARS-COV-2-infected subjects with asymptomatic to mild viral symptoms during the acute phase with samples obtained between 1.8 and 7.3 months after infection (n = 9); and (4) unexposed pre-pandemic subjects with systemic lupus erythematous (SLE) (n = 6). Total IgG and IgA levels were also measured from subjects in groups 1-3 to assess non-specific pan-B cell activation.\n\nResultsAs expected, in multivariate analysis, AABs were detected at much higher odds in SLE subjects (5 of 6, 83%) compared to non-SLE pre-pandemic controls (11 of 29, 38%) [odds ratio (OR) 19.4,95% CI, 2.0 - 557.0, p = 0.03]. AAB detection (percentage of subjects with one or more autoantibodies) was higher in SARS-CoV-2 infected convalescent subjects (7 of 9, 78%) [OR 17.4, 95% CI, 2.0 - 287.4, p = 0.02] and subjects with acute COVID-19 (12 of 20, 60%) compared with non-SLE pre-pandemic controls, but was not statistically significant among the latter [OR 1.8,95% CI, 0.6 - 8.1, p = 0.23]. Within the convalescent subject group, AABs were detected in 5/5 with reported persistent symptoms and 2/4 without continued symptoms (p = 0.17). The multivariate computational algorithm Partial Least Squares Determinant Analysis (PLSDA) was used to determine if distinct AAB signatures distinguish subject groups 1-3. Of the 18 autoantibodies measured, anti-Beta 2-Glycoprotein, anti-Proteinase 3-ANCA, anti-Mi-2 and anti-PM/Scl-100 defined the convalescent group; anti-Proteinase 3-ANCA, anti-Mi-2, anti-Jo-1 and anti-RNP/SM defined acute COVID-19 subjects; and anti-Proteinase 3-ANCA, anti-Mi-2, anti-Jo-1, anti-Beta 2-Glycoprotein distinguished unexposed controls. The AABs defining SARS-COV-2 infected from pre-pandemic subjects are widely associated with myopathies, vasculitis, and antiphospholipid syndromes, conditions with some similarities to COVID-19. Compared to pre-pandemic non-SLE controls, subjects with acute COVID-19 had higher total IgG concentration (p-value=0.006) but convalescent subjects did not (p-value=0.08); no differences in total IgA levels were found between groups.\n\nConclusionsOur findings support existing studies suggesting induction of immune responses to self-epitopes during acute, severe COVID-19 with evidence of general B cell hyperactivation. Also, the preponderance of AAB positivity among convalescent individuals up to seven months after infection indicates potential initiation or proliferation, and then persistence of self-reactive immunity without severe initial disease. These results underscore the importance of further investigation of autoimmunity during SARS-CoV-2 infection and its role in the onset and persistence of post-acute sequelae of COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Nahid Bhadelia", + "author_inst": "Department of Medicine, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories (NEIDL), Boston University" + }, + { + "author_name": "Anna Belkina", + "author_inst": "Flow Cytometry Core Facility and Department of Pathology and Laboratory Medicine, Boston University School of Medicine" + }, + { + "author_name": "Alex Olson", + "author_inst": "Department of Medicine, Boston University School of Medicine" + }, + { + "author_name": "Thomas Winter", + "author_inst": "Research Occupational Health Program, Boston University" + }, + { + "author_name": "Patricia Urick", + "author_inst": "Research Occupational Health Program, Boston University" + }, + { + "author_name": "Nina Lin", + "author_inst": "Department of Medicine, Boston University School of Medicine" + }, + { + "author_name": "Ian Rifkin", + "author_inst": "Renal Section, Department of Medicine, Boston University School of Medicine and Renal Section, Department of Medicine, VA Boston Healthcare System" + }, + { + "author_name": "Yachana Kataria", + "author_inst": "Department of Pathology and Laboratory Medicine, Boston University School of Medicine" + }, + { + "author_name": "Rachel Yuen", + "author_inst": "Department of Microbiology; Boston University School of Medicine" + }, + { + "author_name": "Manish Sagar", + "author_inst": "Department of Medicine, Boston University School of Medicine" + }, + { + "author_name": "Jennifer Cappione", + "author_inst": "Department of Microbiology; Boston University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.22.21249716", "rel_title": "An interactive COVID-19 virus Mutation Tracker (CovMT) with a particular focus on critical mutations in the Receptor Binding Domain (RBD) region of the Spike protein", @@ -944680,57 +949879,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.20.20243782", - "rel_title": "COVID-19 Diagnostic Testing For All - Using Non-Dilutive Saliva Sample Collection, Stabilization and Ambient Transport Devices", - "rel_date": "2021-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.20.20243782", - "rel_abs": "COVID-19 testing is not accessible for millions during this pandemic despite our best efforts. Without greatly expanded testing of asymptomatic individuals, contact tracing and subsequent isolation of spreaders remains as a means for control. In an effort to increase RT-PCR assay testing for the presence of the novel beta-coronavirus SARS-CoV-2 as well as improve sample collection safety, GenTegra LLC has introduced two products for saliva collection and viral RNA stabilization: GTR-STM (GenTegra Saliva Transport Medium) and GTR-STMdk (GenTegra Saliva Transport Medium Direct to PCR). Both products contain a proprietary formulation based on GenTegras novel \"Active Chemical Protection\" (ACP) technology that gives non-dilutive, error-free saliva sample collection using RNA stabilization chemicals already dried in the collection tube.\n\nGTR-STM can be used for safer saliva-based sample collection at home (or at a test site). Following saliva collection, the sample-containing GTR-STM can be kept at ambient temperature during shipment to an authorized CLIA lab for analysis. SARS-CoV-2 viral RNA in GTR-STM is stable for over a month at ambient temperature, easily surviving the longest transit times from home to lab. GTR-STM enhances patient comfort, convenience, compliance and reduces infectious virus exposure to essential medical and lab professionals.\n\nAlternatively, the GTR-STMdk direct-into-PCR product can be used to improve lab throughput and reduce reagent costs for saliva sample collection and testing at any lab site with access to refrigeration. GTR-STMdk reduces lab process time by 25% and reagent costs by 30% compared to other approaches. Since GTR-STMdk retains SARS-CoV-2 viral RNA stability for three days at ambient temperature, it is optimized for lab test site rather than at home saliva collection. SARS-COV-2 viral RNA levels as low as 0.4 genome equivalents/uL are detected in saliva samples using GTR-STMdk. The increased sensitivity of SARS-CoV-2 detection can expand COVID-19 testing to include asymptomatic individuals using pooled saliva.\n\nOne Sentence SummaryGTR-STM and Direct-into-PCR GTR-STMdk offer substantive improvements in SARS-CoV-2 viral RNA stability, safety, and RT-PCR process efficiency for COVID-19 testing by using a non-dilutive saliva sample collection system for individuals at home or onsite respectively.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Yuan Jin Carrington", - "author_inst": "GenTegra, LLC" - }, - { - "author_name": "Justin Orlino", - "author_inst": "GenTegra, LLC" - }, - { - "author_name": "Alejandro Romero", - "author_inst": "GenTegra, LLC" - }, - { - "author_name": "Jessica Rochelle Gustin", - "author_inst": "GenTegra, LLC" - }, - { - "author_name": "Mahssa Rezaei", - "author_inst": "GenTegra, LLC" - }, - { - "author_name": "Elizabeth Green", - "author_inst": "GenTegra, LLC" - }, - { - "author_name": "Summer Linn Rose", - "author_inst": "GenTegra, LLC" - }, - { - "author_name": "Ramani A. Aiyer", - "author_inst": "GenTegra, LLC" - }, - { - "author_name": "Shanavaz Nasarabadi", - "author_inst": "GenTegra, LLC" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.22.21249811", "rel_title": "High-altitude is associated with better short-term survival in critically ill COVID-19 patients admitted to the ICU", @@ -946365,6 +951513,133 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.01.25.428136", + "rel_title": "mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge", + "rel_date": "2021-01-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.25.428136", + "rel_abs": "The mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase 3 results. Human studies, however, cannot provide the controlled response to infection and complex immunological insight that are only possible with preclinical studies. Hamsters are the only model that reliably exhibit more severe SARS-CoV-2 disease similar to hospitalized patients, making them pertinent for vaccine evaluation. We demonstrate that prime or prime-boost administration of mRNA-1273 in hamsters elicited robust neutralizing antibodies, ameliorated weight loss, suppressed SARS-CoV-2 replication in the airways, and better protected against disease at the highest prime-boost dose. Unlike in mice and non-human primates, mRNA-1273- mediated immunity was non-sterilizing and coincided with an anamnestic response. Single-cell RNA sequencing of lung tissue permitted high resolution analysis which is not possible in vaccinated humans. mRNA-1273 prevented inflammatory cell infiltration and the reduction of lymphocyte proportions, but enabled antiviral responses conducive to lung homeostasis. Surprisingly, infection triggered transcriptome programs in some types of immune cells from vaccinated hamsters that were shared, albeit attenuated, with mock-vaccinated hamsters. Our results support the use of mRNA-1273 in a two-dose schedule and provides insight into the potential responses within the lungs of vaccinated humans who are exposed to SARS-CoV-2.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Michelle Meyer", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Yuan Wang", + "author_inst": "Princeton University" + }, + { + "author_name": "Darin Edwards", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Gregory R Smith", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Aliza B Rubenstein", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Palaniappan Ramanathan", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Chad E Mire", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Colette Pietzsch", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Xi Chen", + "author_inst": "Flatiron Institute, Simons Foundation" + }, + { + "author_name": "Yongchao Ge", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Wan Sze Cheng", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Carole Henry", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Angela Woods", + "author_inst": "Moderna Inc" + }, + { + "author_name": "LingZhi Ma", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Guillaume B. E. Stewart-Jones", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Kevin W Bock", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Minai Mahnaz", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Bianca M Nagata", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Sivakumar Periasamy", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Pei-Yong Shi", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Barney S Graham", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Ian N Moore", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Irene Ramos", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Olga G. Troyanskaya", + "author_inst": "Princeton University" + }, + { + "author_name": "Elena Zaslavsky", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Andrea Carfi", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Stuart C Sealfon", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alexander Bukreyev", + "author_inst": "University of Texas Medical Branch at Galveston" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.25.428122", "rel_title": "Profiling transcription factor sub-networks in type I interferon signaling and in response to SARS-CoV-2 infection", @@ -946526,81 +951801,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.01.25.428125", - "rel_title": "The CXCR6/CXCL16 axis links inflamm-aging to disease severity in COVID-19 patients", - "rel_date": "2021-01-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.25.428125", - "rel_abs": "Advancing age and chronic health conditions, significant risk factors for severe COVID-19, are associated with a pro-inflammatory state, termed inflamm-aging. CXCR6+ T cells are known to traffic to the lung and have been reported to increase with age. The ligand of CXCR6, CXCL16, is constitutively expressed in the lung and upregulated during inflammatory responses and the CXCR6/CXCL16 axis is associated with severe lung disease and pneumonia. Genome-wide association studies have also recently identified 3p21.31, encompassing the CXCR6 gene, as a susceptibility locus for severe COVID-19. We assessed numbers T cells expressing the chemokine receptor CXCR6 and plasma levels of CXCL16, in control and COVID-19 patients. Results demonstrated that circulating CD8+CXCR6+ T cells were significantly elevated with advancing age, yet virtually absent in patients with severe COVID-19. Peripheral levels of CXCL16 were significantly upregulated in severe COVID-19 patients compared to either mild COVID-19 patients or SARS-CoV-2 negative controls. This study supports a significant role of the CXCR6/CXCL16 axis in the immunopathogenesis of severe COVID-19.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Daniel J Payne", - "author_inst": "Leeds Teaching Hospitals NHS Trust" - }, - { - "author_name": "Surita Dalal", - "author_inst": "Leeds Teaching Hospitals NHS Trust" - }, - { - "author_name": "Richard Leach", - "author_inst": "Leeds Teaching Hospitals NHS Trust" - }, - { - "author_name": "Richard Parker", - "author_inst": "Leeds Teaching Hospitals NHS Trust" - }, - { - "author_name": "Stephen Griffin", - "author_inst": "Faculty of Medicine and Health, University of Leeds" - }, - { - "author_name": "Clive S McKimmie", - "author_inst": "Faculty of Medicine and Health, University of Leeds" - }, - { - "author_name": "Graham P Cook", - "author_inst": "Faculty of Medicine and Health, University of Leeds" - }, - { - "author_name": "Stephen J Richards", - "author_inst": "Faculty of Medicine and Health, University of Leeds" - }, - { - "author_name": "Peter Hillmen", - "author_inst": "Leeds Teaching Hospitals NHS Trust" - }, - { - "author_name": "Tal Munir", - "author_inst": "Leeds Teaching Hospitals NHS Trust" - }, - { - "author_name": "Kathryn Riley", - "author_inst": "Leeds Teaching Hospitals NHS Trust" - }, - { - "author_name": "Claire McKinley", - "author_inst": "Faculty of Medicine and Health, University of Leeds" - }, - { - "author_name": "Sandra Place", - "author_inst": "Leeds Teaching Hospitals NHS Trust" - }, - { - "author_name": "Richard L Baretto", - "author_inst": "Birmingham Heartlands Hospital" - }, - { - "author_name": "Darren J Newton", - "author_inst": "Faculty of Medicine and Health, University of Leeds" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.01.16.21249939", "rel_title": "Tool for estimating the probability of having COVID-19 with one or more negative RT-PCR results", @@ -947867,6 +953067,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.22.21250289", + "rel_title": "Development and validation of a predictive model for critical illness in adult patients requiring hospitalization for COVID-19", + "rel_date": "2021-01-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.22.21250289", + "rel_abs": "BackgroundIdentifying factors that can predict severe disease in patients needing hospitalization for COVID-19 is crucial for early recognition of patients at greatest risk.\n\nObjective1) Identify factors predicting intensive care unit (ICU) transfer and (2) develop a simple calculator for clinicians managing patients hospitalized with COVID-19.\n\nMethodsA total of 2,685 patients with laboratory-confirmed COVID-19 admitted to a large metropolitan health system in Georgia, USA between March and July 2020 were included in the study. Seventy-five percent of patients were included in the training dataset (admitted March 1 to July 10). Through multivariable logistic regression, we developed a prediction model (probability score) for ICU transfer. Then, we validated the model by estimating its performance accuracy (area under the curve [AUC]) using data from the remaining 25% of patients (admitted July 11 to July 31).\n\nResultsWe included 2,014 and 671 patients in the training and validation datasets, respectively. Diabetes mellitus, coronary artery disease, chronic kidney disease, serum C-reactive protein, and serum lactate dehydrogenase were identified as significant risk factors for ICU transfer, and a prediction model was developed. The AUC was 0.752 for the training dataset and 0.769 for the validation dataset. We developed a free, web-based calculator to facilitate use of the prediction model (https://icucovid19.shinyapps.io/ICUCOVID19/).\n\nConclusionOur validated, simple, and accessible prediction model and web-based calculator for ICU transfer may be useful in assisting healthcare providers in identifying hospitalized patients with COVID-19, who are at high risk for clinical deterioration.\n\nTriage of such patients for early aggressive treatment can impact clinical outcomes for this potentially deadly disease.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Neha Paranjape", + "author_inst": "Wellstar Medical Group" + }, + { + "author_name": "Lauren Staples", + "author_inst": "Kennesaw State University" + }, + { + "author_name": "Christina Stradwick", + "author_inst": "Kennesaw State University" + }, + { + "author_name": "Herman Ray", + "author_inst": "Kennesaw State University" + }, + { + "author_name": "Ian Saldanha", + "author_inst": "Brown University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.01.21.21250261", "rel_title": "Using body temperature and variables commonly available in the EHR to predict acute infection: A proof-of-concept study showing improved pretest probability estimates for acute COVID-19 infection among discharged emergency department patients", @@ -947984,29 +953219,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.21.21250237", - "rel_title": "Agent-Based Simulation of Covid-19 Vaccination Policies in CovidSIMVL", - "rel_date": "2021-01-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21250237", - "rel_abs": "An agent-based infectious disease modeling tool (CovidSIMVL) is employed in this paper to explore outcomes associated with MRNA two-dose vaccination regimens set out in Emergency Use Authorization (EUA) documents submitted by Pfizer and Moderna to the US Department of Health & Human Services. As well, the paper explores outcomes associated with a third \"Hybrid\" policy that reflects ranges of expected levels of protection according to Pfizer and Moderna EUAs, but entails a 35 day separation between first and second dose, which exceeds the 21 days set out in Pfizer documentation or the 28 days in Moderna documentation.\n\nFour CovidSIMVL parameters are varied in the course of 75 simulated clinical trials. Two relate directly to the vaccines and their impacts (duration between doses; degree of expected protection conferred by different vaccines following first or second dose). Two relate to the simulation contexts to which the vaccines are applied (degree of infectivity; duration of infectivity). The simulated trials demonstrate expected effects for timing of second dose, and for degree of protection associated with first and second dose of Pfizer and Moderna vaccines, and the effects are consistent with an assumed value of 75% for degree of protection after first and second doses for the Hybrid vaccine. However, the simulated trials suggest a more complex interaction between expected level of protection following first dose, timing of second dose and degree of infectivity. These results suggest that policy options should not be considered independent of the transmission dynamics that are manifested in the contexts in which the policies could be applied.\n\nCovidSIMVL embodies stochasticity in the mechanisms that govern viral transmission, and it treats the basic reproduction number (R0)as an emergent characteristic of transmission dynamics, not as a pre-set value that determines those dynamics. As such, results reported in this paper reflect outcomes that could happen, but do not necessarily reflect what is more or less likely to happen, given different configurations of parameters. The discussion section goes into some measure of detail regarding next steps that could be pursued to enhance the potential for agent-based models such as CovidSIMVL to inform exploration of possible vaccination policies, and to project outcomes that are possible or likely in local contexts, where stochasticity and heterogeneity of transmission must be featured in models that are intended to reflect local realism.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ernie Chang", - "author_inst": "Contractor" - }, - { - "author_name": "Kenneth Andrew Moselle", - "author_inst": "Island Health (Vancouver Island Health Authority)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.22.21250283", "rel_title": "Negative Excess Mortality in Pneumonia Death caused by COVID-19 in Japan", @@ -949545,6 +954757,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.01.15.21249893", + "rel_title": "COVID-19 propagation by diffusion - a two-dimensional approach for Germany", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.15.21249893", + "rel_abs": "Diffusion comes anytime and everywhere. If there is a gradient or a potential difference of a quantity a diffusion process happens and this ends if an equilibrium is reached only. The concentration of a species maybe such quantity, or the voltage. An electric currant will be driven by a voltage difference for example.\n\nIn this COVID-19 pandemic one observes both regions with low incidence and other ones with high incidence. The local different people density could be a reason for that. In populous areas like big cities or congested urban areas higher COVID-19 incidences could be observed than in rural regions.\n\nThe aim of this paper consists in the application of a diffusion concept to describe one possible issue of the the COVID-19 propagation.\n\nThis will be discussed for the German situation based on the quite different incidence data for the different federal states of Germany.\n\nWith this ansatz some phenomenoms of the actual development of the pandemic could be confirmed. The model gives a possibility to investigate certain scenarios like border-crossings or local spreading events and their influence on the COVID-19 propagation as well.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Guenter K.F. Baerwolff", + "author_inst": "Technical University Berlin" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.15.20249089", "rel_title": "Physician Perceptions of Catching COVID-19", @@ -949662,41 +954893,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.17.21249990", - "rel_title": "Population-based seroprevalence of SARS-CoV-2 antibodies in a high-altitude setting in Peru", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.17.21249990", - "rel_abs": "BackgroundLittle evidence exists about the prevalence of COVID-19 infection at high altitude. We aimed to estimate the population-based seroprevalence of COVID-19 in Cusco at the end of the first wave.\n\nMethodsA population-based survey was conducted in September 2020 in three settings in Cusco: (1) Cusco city at 3300 meters above the sea level (m.a.s.l.), (2) the periphery of Cusco (Santiago, San Jeronimo, San Sebastian, and Wanchaq) at 3300 m.a.s.l., and (3) Quillabamba city, located at 1050 m.a.s.l. People aged [≥]18 years within a family unit were included. The diagnosis of COVID-19 infection was based on identifying total antibodies (IgM and IgG) anti-SARS-CoV-2 in serum using the Elecsys Anti-SARS-CoV-2 chemiluminescence test.\n\nFindingsWe enrolled 1924 participants from 712 families. Of the total, 637 participants were COVID-19 seropositive. Seroprevalence was 38{middle dot}8% (95%CI: 33{middle dot}4%-44{middle dot}9%) in Cusco city, 34{middle dot}9% (95%CI: 30{middle dot}4%-40{middle dot}1%) in the periphery of Cusco, and 20{middle dot}3% (95%CI: 16{middle dot}2%-25{middle dot}6%) in Quillabamba. In 141 families (19{middle dot}8%; 95%CI: 17{middle dot}0%-22{middle dot}8%) the whole members were positive to the test. Living with more than three persons in the same house, a positive COVID-19 case at home, and a member who died in the last five months were factors associated with COVID-19 positivity. The smell/taste alteration was the symptom most associated with seropositivity (aOR= 14{middle dot}27, 95% CI: 8{middle dot}24-24{middle dot}70); whereas always wearing a face shield (aOR= 0{middle dot}62; 95% CI: 0{middle dot}46-0{middle dot}84) or a facial mask (aOR= 0{middle dot}65, 95% CI: 0{middle dot}47-0{middle dot}88) reduced that probability.\n\nInterpretationSeroprevalence of COVID-19 in Cusco was high, with significant differences between settings. Wearing masks and face shields were associated with lower rate of infection; however, efforts must be made to sustain them over time since there is still a high proportion of susceptible people.\n\nFundingFondo Nacional de Desarrollo Cientifico, Tecnologico y de Innovacion Tecnologica (FONDECYT - Peru) and Universidad Andina del Cusco.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "CHARLES HUAMANI", - "author_inst": "UNIVERSIDAD ANDINA DEL CUSCO" - }, - { - "author_name": "Lucio Velasquez", - "author_inst": "UNIVERSIDAD ANDINA DEL CUSCO" - }, - { - "author_name": "Sonia Montes", - "author_inst": "Hospital Nacional Adolfo Guevara Velasco, EsSalud, Cusco" - }, - { - "author_name": "Ana Mayanga Herrera", - "author_inst": "Universidad Cientifica del Sur, Lima" - }, - { - "author_name": "Antonio Bernabe-Ortiz", - "author_inst": "Universidad Cientifica del Sur, Lima" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.16.21249924", "rel_title": "Sword of Damocles or choosing well. Population genetics sheds light into the future of the COVID-19 pandemic and SARS-CoV-2 new mutant strains.", @@ -950951,6 +956147,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.18.21250012", + "rel_title": "Studying the course of Covid-19 by a recursive delay approach", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.18.21250012", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWIn an earlier paper we proposed a recursive model for epidemics; in the present paper we generalize this model to include the asymptomatic or unrecorded symptomatic people, which we call dark people (dark sector). We call this the SEPARd-model. A delay differential equation version of the model is added; it allows a better comparison to other models. We carry this out by a comparison with the classical SIR model and indicate why we believe that the SEPARd model may work better for Covid-19 than other approaches.\n\nIn the second part of the paper we explain how to deal with the data provided by the JHU, in particular we explain how to derive central model parameters from the data. Other parameters, like the size of the dark sector, are less accessible and have to be estimated more roughly, at best by results of representative serological studies which are accessible, however, only for a few countries. We start our country studies with Switzerland where such data are available. Then we apply the model to a collection of other countries, three European ones (Germany, France, Sweden), the three most stricken countries from three other continents (USA, Brazil, India). Finally we show that even the aggregated world data can be well represented by our approach.\n\nAt the end of the paper we discuss the use of the model. Perhaps the most striking application is that it allows a quantitative analysis of the influence of the time until people are sent to quarantine or hospital. This suggests that imposing means to shorten this time is a powerful tool to flatten the curves.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Erhard Scholz", + "author_inst": "University of Wuppertal" + }, + { + "author_name": "Matthias Kreck", + "author_inst": "University of Bonn" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.18.21249998", "rel_title": "The Association between Early Country-level Testing Capacity and Later COVID-19 Mortality Outcomes", @@ -951056,61 +956275,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.18.21250032", - "rel_title": "Remote care for mental health: qualitative study with service users, carers and staff during the COVID-19 pandemic", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.18.21250032", - "rel_abs": "ObjectivesTo explore the experiences of service users, carers and staff seeking or providing secondary mental health services during the COVID-19 pandemic.\n\nDesignQualitative interview study, co-designed with mental health service users and carers.\n\nMethodsWe conducted semi-structured, telephone or online interviews with a purposively constructed sample; a peer researcher with lived experience conducted and analysed interviews with service users. Analysis was based on the constant comparison method.\n\nSettingNHS secondary mental health services in England between June and August 2020.\n\nParticipantsOf 65 participants, 20 had either accessed or needed to access English secondary mental healthcare during the pandemic; 10 were carers of people with mental health difficulties; 35 were members of staff working in NHS secondary mental health services during the pandemic.\n\nResultsExperiences of remote care were mixed. Some service users valued the convenience of remote methods in the context of maintaining contact with familiar clinicians. Most participants commented that a lack of non-verbal cues and the loss of a therapeutic safe space challenged therapeutic relationship building, assessments, and identification of deteriorating mental wellbeing. Some carers felt excluded from remote meetings and concerned that assessments were incomplete without their input. Like service users, remote methods posed challenges for clinicians who reported uncertainty about technical options and a lack of training. All groups expressed concern about intersectionality exacerbating inequalities and the exclusion of some service user groups if alternatives to remote care are lost.\n\nConclusionsWhilst remote mental healthcare is likely to become increasingly widespread in secondary mental health services, our findings highlight the continued importance of a tailored, personal approach to decisions about remote mental healthcare. Further research should focus on which types of consultations best suit face-to-face interaction, and for whom and why, and which can be provided remotely and by which medium.\n\nARTICLE SUMMARYO_ST_ABSStrengths and limitations of this studyC_ST_ABSO_LIStrengths include its qualitative approach in speaking to a large sample of participants with varied mental health difficulties, carers, and a diverse range of mental healthcare staff.\nC_LIO_LIIts novelty lies in a deep exploration of the views and experiences of remote mental healthcare during a pandemic.\nC_LIO_LIThe methods are strengthened by the involvement of experts-by-experience and the use of peer research methods.\nC_LIO_LIWe did not adopt a narrative method; the interviews were one-off conversations so we could not explore change as the pandemic progressed and people may have become accustomed to remote care.\nC_LIO_LIThe study used remote methods to comply with UK lockdown regulations; this will have excluded some groups without the ability to engage remotely.\nC_LI", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Elisa Liberati", - "author_inst": "THIS Institute (The Healthcare Improvement Studies Institute), Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK" - }, - { - "author_name": "Natalie Richards", - "author_inst": "THIS Institute (The Healthcare Improvement Studies Institute), Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK" - }, - { - "author_name": "Jennie Parker", - "author_inst": "McPin Foundation, London, SE1 4YR, UK" - }, - { - "author_name": "Janet Willars", - "author_inst": "Department of Health Sciences, University of Leicester, Leicester, UK" - }, - { - "author_name": "David Scott", - "author_inst": "Population Health and Genomics, University of Dundee, Dundee, UK" - }, - { - "author_name": "Nicola Boydell", - "author_inst": "Centre for Biomedicine Self and Society, Usher Institute, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Vanessa Pinfold", - "author_inst": "McPin Foundation, London, SE1 4YR, UK" - }, - { - "author_name": "Graham Martin", - "author_inst": "THIS Institute (The Healthcare Improvement Studies Institute), Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK" - }, - { - "author_name": "Mary Dixon-Woods", - "author_inst": "THIS Institute (The Healthcare Improvement Studies Institute), Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK" - }, - { - "author_name": "Peter B Jones", - "author_inst": "Department of Psychiatry, University of Cambridge; Cambridgeshire & Peterborough NHS Foundation Trust, Cambridge, CB2 0SZ, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.01.17.21249947", "rel_title": "Sleeping under the waves: a longitudinal study across the contagion peaks of COVID-19 pandemic in Italy", @@ -952877,6 +958041,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.01.19.426622", + "rel_title": "Evaluation of the effects of SARS-CoV-2 genetic mutations on diagnostic RT-PCR assays", + "rel_date": "2021-01-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.19.426622", + "rel_abs": "Several mutant strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging. Mismatch(es) in primer/probe binding regions would decrease the detection sensitivity of the PCR test, thereby affecting the results of clinical testing. In this study, we conducted an in silico survey on SARS-CoV-2 sequence variability within the binding regions of primer/probe published by the Japan National Institute of Infectious Diseases (NIID) and Centers for Disease Control and Prevention (CDC). In silico analysis revealed the presence of mutations in the primer/probe binding regions. We performed RT-PCR assays using synthetic RNAs containing the mutations and showed that some mutations significantly decreased the detection sensitivity of the RT-PCR assays.\n\nOur results highlight the importance of genomic monitoring of SARS-CoV-2 and evaluating the effects of mismatches on PCR testing sensitivity.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Takeru Nakabayashi", + "author_inst": "H.U. Group Research Institute G.K." + }, + { + "author_name": "Yuki Kawasaki", + "author_inst": "H.U. Group Research Institute G.K." + }, + { + "author_name": "Koichiro Murashima", + "author_inst": "H.U. Group Research Institute G.K." + }, + { + "author_name": "Kazuya Omi", + "author_inst": "H.U. Group Research Institute G.K." + }, + { + "author_name": "Satoshi Yuhara", + "author_inst": "H.U. Group Research Institute G.K." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.01.20.427105", "rel_title": "Use Of Canine Olfactory Detection For COVID-19 Testing Study On U.A.E. Trained Detection Dog Sensitivity", @@ -953030,45 +958229,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2021.01.19.21250128", - "rel_title": "Sleep in Frontline Healthcare Workers on Social Media During the COVID-19 Pandemic", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.21250128", - "rel_abs": "ImportanceDuring the pandemic, healthcare workers on social media are sharing their challenges, including sleep disturbances.\n\nObjectiveTo assess sleep using validated measures among frontline healthcare workers on social media\n\nDesignA self-selection survey was distributed on Facebook, Twitter, and Instagram for 16 days (August 31-September 15, 2020) targeting healthcare workers (HCW) who were clinically active during the pandemic. Study participants completed the Pittsburgh Sleep Quality Index (PSQI), Insomnia Severity Index (ISI), and reported demographic/career information. Poor sleep quality was defined as PSQI>5. Moderate-to-severe insomnia was defined as an ISI>14. The mini-Z was used to measure burnout. Multivariate logistic regression tested associations between demographics, career characteristics, and sleep outcomes.\n\nSettingOnline self-selection survey on social media\n\nParticipants963 surveys were completed. Participants were predominantly White (92.8%), female (73.4%), aged 30-49 (71.9%), and physicians (64.4%). Mean sleep duration was 6.1 (SD 1.2) hours. Nearly 90% reported poor sleep (PSQI). One third (33.0%) reported moderate or severe insomnia. Many (60%) experienced sleep disruptions due to device usage or had bad dreams at least once per week (45%). Over 50% reported burnout. In multivariable logistic regressions, non-physician (OR 2.4; CI: 1.7, 3.4), caring for COVID-19 patients (OR 1.8; CI 1.2, 2.8), Hispanic ethnicity (OR 2.2; CI: 1.4, 3.5), being female (OR 1.6; CI 1.1, 2.4), and having a sleep disorder (OR 4.3; CI 2.7,6.9) were associated with increased odds of insomnia. In open-ended comments (n=310), poor sleep mapped to four categories: children and family, work demands, personal health, and pandemic-related sleep disturbances.\n\nConclusionDuring the COVID-19 pandemic, 90% of frontline healthcare workers surveyed on social media reported poor sleep, over one-third reported insomnia, and over half reported burnout. Many also reported sleep disruptions due to device usage and nightmares. Sleep interventions for frontline healthcare workers are urgently needed.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSHow are frontline healthcare workers on social media sleeping during the pandemic?\n\nFindingsDuring the COVID-19 pandemic, 90% of frontline healthcare workers on social media are reporting poor sleep, and one third are reporting insomnia. Those who report sleep disturbances were more likely to report burnout.\n\nMeaningInterventions aimed at improving the sleep of frontline healthcare workers are warranted.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Nancy H Stewart", - "author_inst": "University of Kansas Medical Center" - }, - { - "author_name": "Anya L Koza", - "author_inst": "Kansas City University" - }, - { - "author_name": "Serena Dhaon", - "author_inst": "University of Illinois" - }, - { - "author_name": "Christiana Shoushtari", - "author_inst": "Advocate Lutheran General Hospital" - }, - { - "author_name": "Maylyn Martinez", - "author_inst": "The University of Chicago" - }, - { - "author_name": "Vineet M Arora", - "author_inst": "The University of Chicago" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.01.19.21250124", "rel_title": "Deficient hand washing facilities in public toilets in the time of the COVID-19 pandemic: A survey in one high-income country", @@ -954699,6 +959859,65 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.01.19.427282", + "rel_title": "SARS-CoV-2 infection of circulating immune cells is not responsible for virus dissemination in severe COVID-19 patients", + "rel_date": "2021-01-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.19.427282", + "rel_abs": "In late 2019 a novel coronavirus (SARS-CoV-2) emerged, and has since caused a global pandemic. Understanding the pathogenesis of COVID-19 disease is necessary to inform development of therapeutics, and management of infected patients. Using scRNAseq of blood drawn from SARS-CoV-2 patients, we asked whether SARS-CoV-2 may exploit immune cells as a Trojan Horse to disseminate and access multiple organ systems. Our data suggests that circulating cells are not actively infected with SARS-CoV-2, and do not appear to be a source of viral dissemination.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Nicole L Rosin", + "author_inst": "University of Calgary" + }, + { + "author_name": "Arzina Jaffer", + "author_inst": "University of Calgary" + }, + { + "author_name": "Sarthak Sinha", + "author_inst": "University of Calgary" + }, + { + "author_name": "Rory P Mulloy", + "author_inst": "University of Calgary" + }, + { + "author_name": "Carolyn Robinson", + "author_inst": "University of Calgary" + }, + { + "author_name": "Elodie Labit", + "author_inst": "University of Calgary" + }, + { + "author_name": "Luiz G Almeida", + "author_inst": "University of Calgary" + }, + { + "author_name": "Antoine Dufour", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jennifer A Corcoran", + "author_inst": "University of Calgary" + }, + { + "author_name": "Bryan Yipp", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jeff Biernaskie", + "author_inst": "University of Calgary" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.19.427250", "rel_title": "COVID-19 Knowledge, Attitudes, and Practices of United Arab Emirates Medical and Health Sciences Students: A Cross Sectional Study", @@ -954832,29 +960051,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.16.426965", - "rel_title": "Fluorescent Glycan Fingerprinting of SARS2 Spike Proteins", - "rel_date": "2021-01-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.16.426965", - "rel_abs": "Glycosylation is the most common post-translational modification and has myriad biological functions. However, glycan analysis and research has always been a challenge. Here, we would like to present new techniques of glycan fingerprinting based on enzymatic fluorescent labeling and gel electrophoresis. The method is illustrated on SARS-2 spike (S) glycoproteins. SARS-2, a novel coronavirus and the causative agent of COVID-19 pandemic, has devastated the world since the end of 2019. To obtain the N-glycan fingerprint of a S protein, glycans released from the protein are first labeled through enzymatic incorporation of fluorophore-conjugated sialic acid or fucose, and then separated on acrylamide gel through electrophoresis, and finally visualized with a fluorescent imager. To identify the labeled glycans of a fingerprint, glycan standards and glycan ladders that are enzymatically generated are run alongside the samples as references. By comparing the mobility of a labeled glycan to that of a glycan standard, the identity of glycans maybe determined. Due to lack of enzyme for broad O-glycans releasing, O-glycans on the RBD protein are labeled with fluorescent sialic acid and digested with trypsin to obtain labeled glycan peptides that are then separated on gel. Glycan fingerprinting could serve as a quick way for global assessment of the glycosylation of a glycoprotein.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Zhengliang L Wu", - "author_inst": "R&D systems/Bio-techne" - }, - { - "author_name": "James M Ertelt", - "author_inst": "R&D Systems/Bio-techne" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.01.16.425365", "rel_title": "SARS-CoV-2 RECoVERY: a multi-platform open-source bioinformatic pipeline for the automatic construction and analysis of SARS-CoV-2 genomes from NGS sequencing data", @@ -957192,6 +962388,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.14.21249637", + "rel_title": "SARS-CoV-2 infection control implementation based on sources of infection showing directions for three age groups in Japan", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249637", + "rel_abs": "BackgroundSome aspects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in children and adults remain unclear. This report describes different SARS-CoV-2 transmission patterns by age group in Japan.\n\nMethods and findingsThis retrospective observational case series study analyzed transmission patterns of real-time polymerase chain reaction (RT-PCR)-confirmed SARS-CoV-2 infections found by local health authorities and commercial laboratories during January 14 through July 31, 2020 in Japan. After ascertaining the infection source for every symptomatic case as clusters at households, daycare facilities, schools, hospitals and workplaces etc., their associated transmission patterns were analyzed. Identified cases were divided into three groups: underage, < 20; adults, 20-59; and elderly people 60 years old and older. The reproductive number (R)s of respective transmission directions found for the respective age groups were compared.\n\nOf 26,986 total cases, 23,746 unknown cases were found, leaving 3,240 ascertained sources of infection (12.0%) comprising 125 (3.9%) underage, 2350 (72.5%) adult, and 765 (23.6%) elderly people. The respective Rs of underage infection sources directed to underage, adult, and elderly people were estimated respectively as 0.0415 (95% CI, 0.0138-0.0691), 1.11 (95% CI, 0.9171-1.3226), and 0.2811 (95% CI, 0.2074-0.3687). The respective Rs of adult infection source directed to underage, adult, and elderly people were estimated respectively as 0.0140 (95% CI, 0.0120-0.0162), 0.5392 (95% CI, 0.5236-0.5550), and 0.1135 (95% CI, 0.1074-0.1197). The respective Rs of elderly infection source directed to underage, adult, and elderly people were estimated as 0.065 (95% CI, 0.0039-0.0091), 0.3264 (95% CI, 0.3059-0.3474), and 0.3991 (95% CI, 0.3757-0.4229).\n\nConclusionsThe main sources of SARS-CoV-2 infection were adults and elderly people. The R of underage people directed to adults was greater than 1 because of close familial contact but they were unlikely to become carriers transmitting SARS-CoV-2 because they accounted for a minority for transmissions. Apparently, SARS-CoV-2 was transmitted among adults and elderly people, suggesting that infection control of SARS-CoV-2 should be managed specifically by generation.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Atsuko Hata", + "author_inst": "Kitano hospital, The Tazuke Kofukai Medical Research Institute" + }, + { + "author_name": "Junko Kurita", + "author_inst": "Tokiwa University, Ibaraki, Japan" + }, + { + "author_name": "Eri Muso", + "author_inst": "Kyoto Kacho University" + }, + { + "author_name": "Toshiro Katayama", + "author_inst": "Morinomiya University of Medical Sciences" + }, + { + "author_name": "Takahide Hata", + "author_inst": "Kitano hospital, The Tazuke Kofukai Medical Research Institute" + }, + { + "author_name": "Yasushi Ohkusa", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.01.15.21249863", "rel_title": "How to best test suspected cases of COVID-19: an analysis of the diagnostic performance of RT-PCR and alternative molecular methods for the detection of SARS-CoV-2", @@ -957457,77 +962692,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.15.21249879", - "rel_title": "Anticipating the curve: can online symptom-based data reflect COVID-19 case activity in Ontario, Canada?", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.15.21249879", - "rel_abs": "BackgroundLimitations in laboratory diagnostic capacity and reporting delays have hampered efforts to mitigate and control the ongoing COVID-19 pandemic globally. Syndromic surveillance of COVID-19 is an important public health tool that can help detect outbreaks, mobilize a rapid response, and thereby reduce morbidity and mortality. The primary objective of this study was to determine whether syndromic surveillance through self-reported COVID-19 symptoms could be a timely proxy for laboratory-confirmed case trends in the Canadian province of Ontario.\n\nMethodsWe retrospectively analyzed self-reported symptoms data collected using an online tool - Outbreaks Near Me (ONM) - from April 20th to Oct 11th, 2020 in Ontario, Canada. We estimated the correlation coefficient between the weekly proportion of respondents reporting a COVID-like illness (CLI) to both the weekly number of PCR-confirmed COVID-19 cases and the percent positivity in the same period for the same week and with a one-week lag.\n\nResultsThere were 314,686 responses from 188,783 unique respondents to the ONM symptom survey. Respondents were more likely to be female and be in the 40-59 age demographic compared to the Ontario general population. There was a strong positive correlation between the weekly number of reported cases in Ontario and the percent of respondents reporting CLI each week (r = 0.89, p <0.01) and with a one-week lag (r = 0.89, p <0.01).\n\nInterpretationWe demonstrate a strong positive and significant correlation (r = 0.89, p <0.01) between percent of self-reported COVID-like illness and the subsequent weeks COVID-19 cases reported, highlighting that a rise in CLI may precede official statistics by at least 1 week. This demonstrates the utility of syndromic surveillance in predicting near-future disease activity. Digital surveillance systems are low-cost tools that may help measure the burden of COVID-19 in a community if there is under-detection of cases through conventional laboratory diagnostic testing. This additional information can be used to guide a healthcare response and policy decisions.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Arjuna S Maharaj", - "author_inst": "University of Toronto" - }, - { - "author_name": "Jennifer Parker", - "author_inst": "University of Toronto" - }, - { - "author_name": "Jessica P Hopkins", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Effie Gournis", - "author_inst": "Dalla Lana School of Public Health, University of Toronto" - }, - { - "author_name": "Isaac Bogoch", - "author_inst": "University of Toronto" - }, - { - "author_name": "Benjamin Rader", - "author_inst": "Boston University" - }, - { - "author_name": "Christina M Astley", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Noah M Ivers", - "author_inst": "University of Toronto" - }, - { - "author_name": "Jared B Hawkins", - "author_inst": "Boston University" - }, - { - "author_name": "Liza Lee", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Ashleigh Tuite", - "author_inst": "University of Toronto" - }, - { - "author_name": "David N Fisman", - "author_inst": "University of Toronto" - }, - { - "author_name": "John S Brownstein", - "author_inst": "Boston University" - }, - { - "author_name": "Lauren Lapointe-Shaw", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.13.21249540", "rel_title": "A Vital Sign-based Prediction Algorithm for Differentiating COVID-19 Versus Seasonal Influenza in Hospitalized Patients", @@ -959122,6 +964286,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.12.21249603", + "rel_title": "Isolation of SARS-CoV-2 from the air in a car driven by a COVID patient with mild illness", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.12.21249603", + "rel_abs": "We used a Sioutas personal cascade impactor sampler (PCIS) to screen for SARS-CoV-2 in a car driven by a COVID-19 patient. SARS-CoV-2 was detectable at all PCIS stages by PCR and was cultured from the section of the sampler collecting particles in the 0.25 to 0.50 {square}m size range.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "John A Lednicky", + "author_inst": "University of Florida" + }, + { + "author_name": "Michael Lauzardo", + "author_inst": "University of Florida" + }, + { + "author_name": "Md. Mabubul Alam", + "author_inst": "Univesrity of Florida" + }, + { + "author_name": "Maha Elbadry", + "author_inst": "Univesrity of Florida" + }, + { + "author_name": "Caroline Stephenson", + "author_inst": "Univesrity of Florida" + }, + { + "author_name": "Julia C. Gibson", + "author_inst": "University of Florida" + }, + { + "author_name": "John Glenn Morris Jr.", + "author_inst": "University of Florida" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.10.20248871", "rel_title": "Emergence of multiple SARS-CoV-2 mutations in an immunocompromised host", @@ -959427,29 +964634,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.11.20248882", - "rel_title": "Modelling the effect of lockdown", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.11.20248882", - "rel_abs": "1This note models the effect of the lockdown during the first wave of COVID-19. We use SEIR type of model with a certain time lag between infection and becoming infectious. Firstly we compare the timing of the change of the coefficient of infection, growth rate of confirmed cases corresponds to the change of mobility index, and secondly we assume the change of the coefficient of infection, activity index {beta} (analogous to R0) and fit the parameter to reproduce the actual number of confirmed cases. Finally, we assume that the activity index {beta} is proportional to the square of the mobility and fit the parameters. The curves in various cuontries fits reasonably well in any cases, but estimating {beta} from various parameters (including temperature) remains as an important task.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Hideto Kamei", - "author_inst": "-" - }, - { - "author_name": "Akihiro Sato", - "author_inst": "Yokohama City University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.12.21249495", "rel_title": "Mitigation of COVID-19 using social distancing of the elderly in Brazil: The vertical quarantine effects in hospitalizations and deaths", @@ -961104,6 +966288,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.12.20248588", + "rel_title": "Bacterial superinfection pneumonia in SARS-CoV-2 respiratory failure", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.12.20248588", + "rel_abs": "BackgroundSevere community-acquired pneumonia secondary to SARS-CoV-2 is a leading cause of death. Current guidelines recommend patients with SARS-CoV-2 pneumonia receive empirical antibiotic therapy for suspected bacterial superinfection, but little evidence supports these recommendations.\n\nMethodsWe obtained bronchoscopic bronchoalveolar lavage (BAL) samples from patients with SARS-CoV-2 pneumonia requiring mechanical ventilation. We analyzed BAL samples with multiplex PCR and quantitative culture to determine the prevalence of superinfecting pathogens at the time of intubation and identify episodes of ventilator-associated pneumonia (VAP) over the course of mechanical ventilation. We compared antibiotic use with guideline-recommended care.\n\nResultsThe 179 ventilated patients with severe SARS-CoV-2 pneumonia discharged from our hospital by June 30, 2020 were analyzed. 162 (90.5%) patients had at least one BAL procedure; 133 (74.3%) within 48 hours after intubation and 112 (62.6%) had at least one subsequent BAL during their hospitalization. A superinfecting pathogen was identified within 48 hours of intubation in 28/133 (21%) patients, most commonly methicillin-sensitive Staphylococcus aureus or Streptococcus species (21/28, 75%). BAL-based treatment reduced antibiotic use compared with guideline-recommended care. 72 patients (44.4%) developed at least one VAP episode. Only 15/72 (20.8%) of initial VAPs were attributable to multidrug-resistant pathogens. The incidence rate of VAP was 45.2/1000 ventilator days.\n\nConclusionsWith use of sensitive diagnostic tools, bacterial superinfection at the time of intubation is infrequent in patients with severe SARS-CoV-2 pneumonia. Treatment based on current guidelines would result in substantial antibiotic overuse. The incidence rate of VAP in ventilated patients with SARS-CoV-2 pneumonia are higher than historically reported.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Chiagozie O. Pickens", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Catherine A. Gao", + "author_inst": "Northwestern" + }, + { + "author_name": "Michael J. Cuttica", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Sean B. Smith", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Lorenzo Pesce", + "author_inst": "Department of Pharmacology, Northwestern University Department of Pharmacology School of Medicine" + }, + { + "author_name": "Rogan Grant", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Mengjia Kang", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Luisa Morales-Nebreda", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Avni A. Bavishi", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Jason Arnold", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Anna Pawlowski", + "author_inst": "Clinical Translational Sciences Institute, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Chao Qi", + "author_inst": "Department of Pathology, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "GR Scott Budinger", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Benjamin D. Singer", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Richard G. Wunderink", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "- NU COVID Investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.01.14.21249831", "rel_title": "Increased peripheral blood neutrophil activation phenotypes and NETosis in critically ill COVID-19 patients", @@ -961333,49 +966596,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.01.12.21249697", - "rel_title": "Mortality of Diabetes-related Acute Metabolic Emergencies in COVID-19 patients: a systematic review and meta-analysis", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.12.21249697", - "rel_abs": "PurposeLittle is known on the mortality rate in COVID-19 related acute metabolic emergencies, namely diabetic ketoacidosis (DKA), hyperglycaemic hyperosmolar state (HHS), combined DKA/HHS, and euglycaemic diabetic ketoacidosis (EDKA).\n\nMethodsA systematic literature review was conducted using EMBASE, PubMed/Medline, and Google Scholar from January 1, 2020 to January 9, 2021 to identify all case report series, cross-sectional studies, and meta-analyses of case reports describing mortality rate in DKA, HHS, and EDKA, in COVID-19 patients. The Joanna Briggs Institute critical appraisal checklist for case reports was used for quality assessment.\n\nResultsFrom 313 identified publications, 4 fulfilled the inclusion criteria and analyzed qualitatively and quantitatively. A systematic review and meta-analysis with subgroup analyses examined mortality rate in a total of 152 COVID-19 patients who had developed DKA, HHS, combined DKA/HHS, or EDKA. Combined mortality rate and confidence intervals (CI) were estimated using random effects model. The study was registered to PROSPERO database (ID: 230737).\n\nResultsCombined mortality rate was found to be 27.1% [95% CI: 11.2-46.9%]. Heterogeneity was considerable (I2=83%; 95% CI: 56-93%), corrected to 67% according to Von Hippel adjustment for small meta-analyses. Funnel plot presented no apparent asymmetry; Eggers and Beggs test yielded in P=0.44 and P=0.50, respectively. Sensitivity analysis failed to explain heterogeneity.\n\nConclusionCOVID-19 related acute metabolic emergencies (DKA, HHS, and EDKA) are characterized by considerable mortality; thus, clinicians should be aware of timely detection and immediate treatment commencing.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Vasileios Periklis Papadopoulos", - "author_inst": "Xanthi General Hospital" - }, - { - "author_name": "Peny Avramidou", - "author_inst": "Xanthi General Hospital" - }, - { - "author_name": "Stefania-Aspasia Bakola", - "author_inst": "Xanthi General Hospital" - }, - { - "author_name": "Dimitra-Georgia Zikoudi", - "author_inst": "Xanthi General Hospital" - }, - { - "author_name": "Ntilara Touzlatzi", - "author_inst": "Xanthi General Hospital" - }, - { - "author_name": "Marios-Vasileios Koutroulos", - "author_inst": "Xanthi General Hospital" - }, - { - "author_name": "Dimitrios K Filippou", - "author_inst": "Medical School, National and Kapodistrian University of Athens" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2021.01.13.21249507", "rel_title": "Epidemiology of the early COVID-19 epidemic in Orange County, California: comparison of predictors of test positivity, mortality, and seropositivity", @@ -963018,6 +968238,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.11.21249630", + "rel_title": "Determining the optimal COVID-19 policy response using agent-based modelling linked to health and cost modelling: Case study for Victoria, Australia", + "rel_date": "2021-01-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.11.21249630", + "rel_abs": "ImportanceDetermining the best policy on social restrictions and lockdowns for the COVID-19 pandemic is challenging.\n\nObjectiveTo determine the optimal policy response ranging from aggressive and moderate elimination, tight suppression (aiming for 1 to 5 cases per million per day) and loose suppression (5 to 25 cases per million per day).\n\nDesignTwo simulation models in series: an agent-based model to estimate daily SARS-CoV-2 infection rates and time in four stages of social restrictions; a proportional multistate lifetable model to estimate long-run health impacts (health adjusted life years (HALYs) arising from SARS-CoV-2) and costs (health systems, and health system plus GDP).\n\nThe net monetary benefit (NMB) of each policy option at varying willingness to pay (WTP) per HALY was calculated: NMB = HALYs x WTP - cost. The optimal policy response was that with the highest NMB.\n\nSetting and participantsThe State of Victoria, Australia, using simulation modeling of all residents.\n\nMain Outcome and MeasuresSARS-CoV-2 infection rates, time under various stages of restrictions, HALYs, health expenditure and GDP losses.\n\nResultsAggressive elimination resulted in the highest percentage of days with the lowest level of restrictions (median 31.7%, 90% simulation interval 6.6% to 64.4%). However, days in hard lockdown were similar across all four strategies (medians 27.5% to 36.1%).\n\nHALY losses (compared to a no-COVID-19 scenario) were similar for aggressive elimination (286, 219 to 389) and moderate elimination (314, 228 to 413), and nearly eight and 40-times higher for tight and loose suppression. The median GDP loss was least for moderate elimination ($US41.7 billion, $29.0 to $63.6 billion), but there was substantial overlap in simulation intervals between the four strategies.\n\nFrom a health system perspective aggressive elimination was optimal in 64% of simulations above a willingness to pay of $15,000 per HALY, followed by moderate elimination in 35% of simulations.\n\nModerate elimination was optimal from a partial societal perspective in half the simulations followed by aggressive elimination in a quarter.\n\nShortening the pandemic duration to 6 months saw loose suppression become preferable under a partial societal perspective.\n\nConclusions and RelevanceElimination strategies were preferable over a 1-year pandemic duration.\n\nFundingAnonymous philanthropic donation to the University of Melbourne.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSTo determine the optimal of four policy responses to COVID-19 in the State of Victoria, Australia (aggressive and moderate elimination, tight suppression (aiming for 1 to 5 cases per million per day) and loose suppression (5 to 25 cases per million per day), based on estimated future health loss and costs from both a health system and partial societal perspective.\n\nFindingsFrom a health system perspective aggressive elimination was optimal in 64% of simulations above a willingness to pay of $15,000 per HALY, followed by moderate elimination in 35% of simulations. Moderate elimination was optimal from a partial societal perspective (i.e., including GDP losses) in half the simulations followed by aggressive elimination in a quarter.\n\nMeaningWhilst there is considerable uncertainty in outcomes for all the four policy options, the two elimination options are usually optimal from both a health system and a partial societal (health expenditure plus GDP cost) perspective.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Professor Tony Blakely", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Dr Jason Thompson", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Dr Laxman Bablani", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Patrick Andersen", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Dr Driss Ait Ouakrim", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Dr Natalie Carvalho", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Patrick Abraham", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Marie-Anne Boujaoude", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Ameera Katar", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Edifofon Akpan", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Nick Wilson", + "author_inst": "University of Otago, Wellington" + }, + { + "author_name": "Professor Mark Stevenson", + "author_inst": "University of Melbourne" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.11.21249564", "rel_title": "The 2020 SARS-CoV-2 epidemic in England: key epidemiological drivers and impact of interventions", @@ -963299,37 +968582,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.10.21249557", - "rel_title": "Vaccination in a two-group epidemic model", - "rel_date": "2021-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.10.21249557", - "rel_abs": "Epidemic progression depends on the structure of the population. We study a two-group epidemic model with the difference between the groups determined by the rate of disease transmission. The basic reproduction number, the maximal and the total number of infected individuals are characterized by the proportion between the groups. We consider different vaccination strategies and determine the outcome of the vaccination campaign depending on the distribution of vaccinated individuals between the groups.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Sebastian Anita", - "author_inst": "Faculty of Mathematics, \"Alexandru Ioan Cuza\" University of Iasi, Romania" - }, - { - "author_name": "Malay Banerjee", - "author_inst": "IIT Kanpur" - }, - { - "author_name": "Samiran Ghosh", - "author_inst": "IIT Kanpur, India" - }, - { - "author_name": "Vitaly Volpert", - "author_inst": "CNRS, University Lyon 1" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.11.21249565", "rel_title": "Lessons learnt from the use of compartmental models over the COVID-19 induced lockdown in France", @@ -964716,6 +969968,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.09.21249489", + "rel_title": "Impact of COVID-19 pandemic on use of Pediatric Emergency Health Services in a Tertiary Care Pediatric Hospital in North India", + "rel_date": "2021-01-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.09.21249489", + "rel_abs": "ObjectiveTo compare Pediatric Emergency attendance pre-COVID 19 to that during COVID 19 pandemic and to study changes in patient profiles attending Pediatric Emergency Department during COVID 19 pandemic.\n\nMethodsWe conducted a retrospective cross-sectional observational study and collected data from Medical Record Section during the COVID-19 pandemic from January to June 2020 and compared it with data from 2019 in similar months. Data collected was analyzed to find out the impact of COVID - 19 on use of pediatric emergency health services with respect to patient attendance, age and clinical profile before and during COVID-19 in a tertiary care hospital in New Delhi.\n\nResultsWe observed a 43% decline in PED visits which increased to 75% during the period of lock-down (p value = 0.005). There was a significant decrease in children of age group 1-5 years attending PED. Mortality rate during lockdown had gone up by nearly 3times than the average monthly mortality.\n\nConclusionsWhile children might not have been directly affected by the COVID-19 pandemic, but the fear of COVID 19 and measures taken to control the pandemic has affected the health seeking behavior of patients to an extent that indirectly caused more damage than anticipated.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ravitanaya Sodani", + "author_inst": "Lady Hardinge Medical College, New Delhi, India" + }, + { + "author_name": "Shalu Gupta", + "author_inst": "Lady Hardinge Medical College & Kalawati Saran Children's Hospital, New Delhi, India" + }, + { + "author_name": "Virendra Kumar", + "author_inst": "Lady Hardinge Medical College & Kalawati Saran Children's Hospital, New Delhi, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.01.06.20249030", "rel_title": "Convergence of Comorbidity and COVID-19 Infection to Fatality: An Investigation Based on Concurrent Health Status Evaluation among the Elderly Population in Kerala", @@ -964901,25 +970180,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.09.21249494", - "rel_title": "Assessments of heavy lift UAV quadcopter drone to support COVID 19 vaccine cold chain delivery for indigenous people in remote areasin South East Asia", - "rel_date": "2021-01-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.09.21249494", - "rel_abs": "Vaccine delivery is one important aspect need to be strengthened within health systems. One of the main challenges in COVID 19 vaccine delivery is how to cover indigenous population in remote and isolated forests in South East Asia. Another issue in COVID 19 cold chain delivery is requirement for a carrier that can maintain the suitable storage temperature. Related to this condition, COVID 19 vaccine should be delivered using heavy vaccine cooler box and this demand delivery system equipped with heavy lift capacity. In here, this study proposes and assess the potential used of heavy lift UAV quadcopter to expand the COVID 19 vaccine delivery to indigenous people living in village that impeded by rugged terrain. The landscape and terrain analysis show that access to the villages was dominated by 15%-45% slopes and the available access is only 1.5 m width trail. To transport 500 vials with 10 kg carrier along 2 km trail, it requires 2 persons to walk for 1 hour. By using drone, a straight line route with a length of 1.5 km can be developed. There were at least 3 drone types were available commercially to lift 10 kg load and several drones with payload capacity below 10 kg. For carrying 100 vials to village using drones, it is estimated the required delivery time was 1.23-1.38 minutes. Around 1.57-1.66 minute delivery times were required to transport 250 vials. For carrying the maximum and full loads of 500 vials or equals to 10 kg load, a drone requires in average of 3.13 minute delivery times. This required drone delivery time is significantly below the required time by walking that almost 1 hour. Drones were limited by flight operational times. Whereas all required delivery times for each drone assessed in this study were still below the drone operational time. The lowest drone operational time was 16 minutes and this is still higher than the time required for a drone to deliver the vaccine. Considering the effectiveness and anticipating vaccine vaccination, UAV quadcopter drone is a feasible option to support COVID 19 vaccine delivery to reach indigenous people in isolated areas.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Andrio Adwibowo", - "author_inst": "University of Indonesia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2021.01.09.21249498", "rel_title": "Risk factors for bacterial infections in patients with moderate to severe COVID-19: A case control study", @@ -966422,6 +971682,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.01.10.21249548", + "rel_title": "Atmospheric PM2.5 before and after Lockdown in relation to COVID-19 Evolution and daily Viral Counts: Could Viral Natural Selection have occurred due to changes in the Airborne Pollutant PM2.5 acting as a Vector for SARS-CoV-2?", + "rel_date": "2021-01-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.10.21249548", + "rel_abs": "BackgroundGenes coding for SARS-CoV-2 have been detected on the microscopic airborne pollutant particulate matter, which has been suggested as a vector for COVID-19 transmission. Lockdown in China has been shown to be associated with significant reduction in pollution including the particulate matter component which coincided with the appearance of a viral mutant (Clade G) which steadily displaced the original Clade D after lockdown. The reason why Clade G developed a fitness advantage is as yet unknown. This paper examines the possible role of airborne particulate matter PM2.5 as selective pressure determining viral Clade predominance and further shedding light on the mode of SARS-CoV-2 transmission.\n\nMethodsThe average levels of PM2.5 of a number of cities were obtained from the Air Quality Index (AQI), a real-time assessment of atmospheric pollution. The daily average PM2.5 levels were assessed between January 23rd and April 29th 2020 determined by the timeline when viral counts in Beijing and other cities were available. Daily viral counts of Clades D and G were available starting from the 12th February as determined by the scientific literature published in August 2020. The cities chosen were Beijing, Sheffield, Nottingham, Sydney and Cambridge because of their substantially elevated viral counts compared to other cities. Cities as opposed to vaster areas/nations were chosen as PM2.5 levels vary across regions and countries.\n\nResultsFor the time period assessed, the Beijing PM2.5 pattern initiated with highly elevated mean PM2.5 levels of 155.8{micro}g/m3 (SD+/-73.6) during high viral counts, followed by 82.1{micro}g/m3 (SD+/-44.9) (p<0.04) when the viral counts decreased. In all the other cities assessed, the pattern differed whereby the PM2.5 levels increased significantly over the preceding baseline contemporaneously with the viral count rise. The changes in these cities PM2.5 levels were on average 31.5{micro}g/m3 before viral counts rose and 56.35{micro}g/m3 contemporaneous with viral count rise. The average levels of PM2.5 in these cities started to decrease one week after lockdown to 46{micro}g/m3 when measured over 2 weeks post-lockdown.\n\nAs regards the viral counts from data retrieved from Beijing, the latter part of the bell-shaped curve and a subsequent smaller curve of the viral count was available for evaluation. The average viral count for Clade D in Beijing was 11.1(SD+/-13.5) followed by a mean viral count for Clade G was 13.8(SD+/-9.2). Conversely in all the other cities besides Beijing, the viral counts averaged 45.8 for Clade D and 161 for Clade G. The variation in viral counts between cities suggests the strong possibility of variation in the availability of sampling between cities.\n\nThe newer variant, Clade G demonstrated viral counts initially appearing in mid-February in Beijing to later displace Clade D as the dominant viral Clade. The appearance of Clade G coincided with the decreasing gradient of PM2.5 levels. A number of significant correlations were obtained between PM2.5 levels and the viral count in all the cities reviewed.\n\nConclusionCOVID-19 viral counts appear to increase concomitant with increasing PM2.5 levels. Viral counts of both Clades correlated differentially with PM2.5 levels in all the cities assessed. The significantly highly elevated PM2.5 levels in Beijing resulted in correlating mainly with Clade D, however Clade G began to appear with decreasing PM2.5 levels, suggesting the beginnings for the initial SARS-CoV-2 Clade evolution. Clade G, the newer variant was able to flourish at lower levels of PM2.5 than Clade D. Clade G may possibly have utilized other sources of particulate matter as a viral vector, such as that derived from tobacco smoking, whereby 66% of Chinese males are smokers and 70% of the Chinese non-smoking population are exposed to 2nd hand smoking.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Yves Muscat Baron", + "author_inst": "Medical School, University of Malta." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.10.21249151", "rel_title": "Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples", @@ -966647,77 +971926,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2021.01.11.426080", - "rel_title": "Immunological and cardio-vascular pathologies associated with SARS-CoV-2 infection in golden syrian hamster", - "rel_date": "2021-01-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.11.426080", - "rel_abs": "Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection in golden Syrian hamster (GSH) causes lung pathology and resembles human coronavirus disease (Covid-19). However, extra-pulmonary pathologies of SARS-CoV-2 infection that result in long Covid remains undefined in GSH. Here, using in silico modelling we show that hamster angiotensin-converting enzyme-2 (ACE-2) and neuropilin-1 (NRP-1) interaction with SARS-CoV-2 is similar to human. Intranasal SARS-CoV-2 infection in GSH resulted in early onset of lung pathologies marked by aggressive inflammatory response. Remarkably, late phase of SARS-CoV2 infection in GSH showed cardiovascular complications (CVC) characterized by ventricular hypertrophy, ventricular wall thickening, interstitial coronary fibrosis and altered lipidomics with elevated cholesterol, low-density lipoprotein and long chain fatty acid triglycerides. Moreover, serum metabolomics profile of infected GSH correlated with Covid19 patients. Together, we propose GSH as a suitable animal model to study immediate and long Covid19 pathologies that could be extended to therapeutics against Covid19 related CVC.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Zaigham Abbas Rizvi", - "author_inst": "Immuno-biology Lab, Infection and Immunology centre, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridaba" - }, - { - "author_name": "Rajdeep Dalal", - "author_inst": "Immuno-biology Lab, Infection and Immunology centre, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridaba" - }, - { - "author_name": "Srikanth Sadhu", - "author_inst": "Immuno-biology Lab, Infection and Immunology centre, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridaba" - }, - { - "author_name": "Yashwant Kumar", - "author_inst": "Translational Health Science and Technology Institute" - }, - { - "author_name": "Tripti Shrivastava", - "author_inst": "Infection and immunology centre, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway" - }, - { - "author_name": "Sonu Kumar Gupta", - "author_inst": "Translational Health Science and Technology Institute" - }, - { - "author_name": "Suruchi Aggarwal", - "author_inst": "Translational Health Science and Technology Institute" - }, - { - "author_name": "Manas Ranjan Tripathy", - "author_inst": "Immuno-biology Lab, Infection and Immunology centre, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridaba" - }, - { - "author_name": "Amit Kumar Yadav", - "author_inst": "THSTI" - }, - { - "author_name": "Guruprasad R Medigeshi", - "author_inst": "Translational Health Science and Technology Institute" - }, - { - "author_name": "Amit Kumar Pandey", - "author_inst": "Translational Health Science and Technology Institute" - }, - { - "author_name": "Sweety Samal", - "author_inst": "Infection and Immunology centre, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway" - }, - { - "author_name": "Shailendra Asthana", - "author_inst": "THSTI" - }, - { - "author_name": "Amit Awasthi", - "author_inst": "Translational Health Science and Technology Institute" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.01.09.426021", "rel_title": "Hypoxia reduces cell attachment of SARS-CoV-2 spike protein by modulating the expression of ACE2 and heparan sulfate", @@ -968728,6 +973936,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.08.20249041", + "rel_title": "The incremental value of computed tomography of COVID-19 pneumonia in predicting ICU admission", + "rel_date": "2021-01-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.08.20249041", + "rel_abs": "RationaleTriage is crucial for patients management and estimation of the required Intensive Care Unit (ICU) beds is fundamental for Health Systems during the COVID-19 pandemic.\n\nObjectiveTo assess whether chest Computed Tomography (CT) of COVID-19 pneumonia has an incremental role in predicting patients admission to ICU.\n\nMethodsWe performed volumetric and texture analysis of the areas of the affected lung in CT of 115 outpatients with COVID-19 infection presenting to the Emergency Room with dyspnea and unresponsive hypoxyemia. Admission blood laboratory including lymphocyte count, serum lactate dehydrogenase, D-dimer and C-Reactive Protein and the ratio between the arterial partial pressure of oxygen and inspired oxygen were collected. By calculating the areas under the receiver-operating characteristic curves (AUC), we compared the performance of blood laboratory-arterial gas analyses features alone and combined with the CT features in two hybrid models (Hybrid radiological and Hybrid radiomics)for predicting ICU admission. Following a machine learning approach, 63 patients were allocated to the training and 52 to the validation set.\n\nMeasurements and Main ResultsTwenty-nine (25%) of patients were admitted to ICU. The Hybrid radiological model comprising the lung %consolidation performed significantly (p=0.04) better in predicting ICU admission in the validation (AUC=0.82; 95%Confidence Interval 0.68-0.95) set than the blood laboratory-arterial gas analyses features alone (AUC=0.71; 95%Confidence Interval 0.56-0.86). A risk calculator for ICU admission was derived and is available at:https://github.com/cgplab/covidapp\n\nConclusionsThe volume of the consolidated lung in CT of patients with COVID-19 pneumonia has a mild but significant incremental value in predicting ICU admission.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Maurizio Bartolucci", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Matteo Benelli", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Margherita Betti", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Sara Bicchi", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Luca Fedeli", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Federico Giannelli", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Donatella Aquilini", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Alessio Baldini", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Guglielmo Consales", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Massimo Edoardo Di Natale", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Pamela Lotti", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Letizia Vannucchi", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Michele Trezzi", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Lorenzo Nicola Mazzoni", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Sandro Santini", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Roberto Carpi", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Daniela Matarrese", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Luca Bernardi", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Mario Mascalchi", + "author_inst": "University of Florence" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2021.01.06.21249325", "rel_title": "Pregnancy and neonatal outcomes of COVID-19, co-reporting of common outcomes from the PAN-COVID and AAP SONPM registry", @@ -968909,29 +974208,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.06.21249280", - "rel_title": "Mobilefuge: A low-cost, portable, open source, 3D-printed centrifuge that can be used for purification of saliva samples for SARS-CoV2 detection", - "rel_date": "2021-01-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.06.21249280", - "rel_abs": "One of the best ways to contain the spread of COVID-19 is frequent testing of as many people as possible and timely isolation of uninfected personnel from infected personnel. However, the cost of massive testing is affordable in many countries. The existing technologies might not be scalable to offer affordable testing for millions of people. To address this issue, novel testing methods based on Loop-Mediated Isothermal Amplification (LAMP) were proposed that are more sensitive, require less reagents and can work with saliva samples instead of more tedious nasal swabs. As a result, LAMP based protocols can make it possible to drive the cost down to one dollar per test. These LAMP based methods require a centrifuge device, mostly for separation of viral particles from reaction inhibitors in saliva samples. However, centrifuge is neither accessible nor affordable in many resource limited settings, especially during this pandemic situation when normal supply chains are heavily disrupted. To overcome these challenges, we invented a low-cost centrifuge that can be useful for carrying out low-cost LAMP based detection of SARS-Cov2 virus in saliva. The 3D printed centrifuge (Mobilefuge) is portable, robust, stable, safe, easy to build and operate. The Mobilefuge doesnt require soldering or programming skills and can be built without any specialised equipment, yet practical enough for high throughput use. More importantly, Mobilefuge can be powered from widely available USB ports, including mobile phones and associated power supplies. This allows the Mobilefuge to be used even in off-grid and resource limited settings. We believe that our invention will aid the efforts to contain the spread of COVID-19 by lowering the costs of testing equipment. Apart from the COVID-19 testing, the Mobilefuge can have applications in the field of biomedical research and diagnostics.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Mohini Bhupathi", - "author_inst": "Rossa Lodge, Rossa Avenue, Bishopstown, Cork, T12YWR0, Ireland." - }, - { - "author_name": "Ganga Chinna Rao Devarapu", - "author_inst": "Centre for Advanced Photonics and Process Analysis, Cork Institute of Technology, Cork, T12P928, Ireland." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.28.20248874", "rel_title": "Evaluation of vertical transmission of SARS-CoV-2 in utero: nine pregnant women and their newborns", @@ -970566,6 +975842,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.07.21249381", + "rel_title": "Comparing the age and sex trajectories of SARS-CoV-2 morbidity with other respiratory pathogens points to potential immune mechanisms.", + "rel_date": "2021-01-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.07.21249381", + "rel_abs": "Comparing age and sex differences in SARS-CoV-2 hospitalization and mortality with influenza and other health outcomes opens the way to generating hypotheses as to the underlying mechanisms, building on the extraordinary advances in immunology and physiology that have occurred over the last year. Notable departures in health outcomes starting around puberty suggest that burdens associated with influenza and other causes are reduced relative to the two emergent coronaviruses over much of adult life. Two possible hypotheses could explain this: protective adaptive immunity for influenza and other infections, or greater sensitivity to immunosenescence in the coronaviruses. Comparison of sex differences suggest an important role for adaptive immunity; but immunosenescence might also be relevant, if males experience faster immunosenescence. Involvement of the renin-angiotensin-system in SARS-CoV-2 infection might drive high sensitivity to disruptions of homeostasis. Overall, these results highlight the long tail of vulnerability in the age profile relevant to the emergent coronaviruses, which more transmissible variants have the potential to uncover at the younger end of the scale, and aging populations will expose at the other end of the scale.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "C. Jessica E. Metcalf", + "author_inst": "Princeton University" + }, + { + "author_name": "Juliette Paireau", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Megan ODriscoll", + "author_inst": "Department of Genetics, Cambridge University" + }, + { + "author_name": "Mathilde Pivette", + "author_inst": "Sante publique France, French national public health agency, Saint Maurice, France" + }, + { + "author_name": "Bruno Hubert", + "author_inst": "Sante publique France, French national public health agency, Saint Maurice, France" + }, + { + "author_name": "Isabelle Pontais", + "author_inst": "Sante publique France, French national public health agency, Saint Maurice, France" + }, + { + "author_name": "Derek Cummings", + "author_inst": "Department of Biology, University of Florida, Gainesville, USA" + }, + { + "author_name": "Simon Cauchemez", + "author_inst": "Institut Pasteur, Paris" + }, + { + "author_name": "Henrik Salje", + "author_inst": "Department of Biology, University of Florida, Gainesville, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.07.21249392", "rel_title": "Predicting severity of Covid-19 using standard laboratory parameters", @@ -970695,20 +976022,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.07.21249401", - "rel_title": "Timeliness of U.S. mortality data releases during the COVID-19 pandemic: delays are associated with electronic death registration system and elevated weekly mortality", - "rel_date": "2021-01-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.07.21249401", - "rel_abs": "All-cause mortality counts allow public health authorities to identify populations experiencing excess deaths from pandemics, natural disasters, and other emergencies. Delays in the completeness of mortality counts may contribute to misinformation because death counts take weeks to become accurate. We estimate the timeliness of all-cause mortality releases during the Covid-19 pandemic for the dates 3 April to 5 September 2020 by estimating the number of weekly data releases of the NCHS Fluview Mortality Surveillance System until mortality comes within 99% of the counts in the 19 March 19 2021 provisional mortality data release. States mortality counts take 5 weeks at median (interquartile range 4--7 weeks) to completion. The fastest states were Maine, New Hampshire, Vermont, New York, Utah, Idaho, and Hawaii. States that had not adopted the electronic death registration system (EDRS) were 4.8 weeks slower to achieve complete mortality counts, and each weekly death per 10^8 was associated with a 0.8 week delay. Emergency planning should improve the timeliness of mortality data by improving state vital statistics digital infrastructure.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.07.21249394", "rel_title": "A two-phase stochastic dynamic model for COVID-19 mid-term policy recommendations in Greece: a pathway towards mass vaccination", @@ -971955,6 +977268,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.05.21249247", + "rel_title": "SARS-CoV-2 seroprevalence in the urban population of Qatar: An analysis of antibody testing on a sample of 112,941 individuals", + "rel_date": "2021-01-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.05.21249247", + "rel_abs": "BackgroundQatar has experienced a large SARS-CoV-2 epidemic. Our first objective was to assess the proportion of the urban population that has been infected with SARS-CoV-2, by measuring the prevalence of detectable antibodies. Our second objective was to identify predictors for infection and for having higher antibody titers.\n\nMethodsResidual blood specimens from individuals receiving routine and other clinical care between May 12-September 9, 2020 were tested for anti-SARS-CoV-2 antibodies. Associations with seropositivity and higher antibody titers were identified through regression analyses. Probability weights were applied in deriving the epidemiological measures.\n\nResultsWe tested 112,941 individuals ([~]10% of Qatars urban population), of whom 51.6% were men and 66.0% were 20-49 years of age. Seropositivity was 13.3% (95% CI: 13.1-13.6%) and was significantly associated with sex, age, nationality, clinical-care type, and testing date. The proportion with higher antibody titers varied by age, nationality, clinical-care type, and testing date. There was a strong correlation between higher antibody titers and seroprevalence in each nationality, with a Pearson correlation coefficient of 0.85 (95% CI: 0.47-0.96), suggesting that higher antibody titers may indicate repeated exposure to the virus. The percentage of antibody-positive persons with prior PCR-confirmed diagnosis was 47.1% (95% CI: 46.1-48.2%), severity rate was 3.9% (95% CI: 3.7-4.2%), criticality rate was 1.3% (95% CI: 1.1-1.4%), and fatality rate was 0.3% (95% CI: 0.2-0.3%).\n\nConclusionsFewer than two in every 10 individuals in Qatars urban population had detectable antibodies against SARS-CoV-2 between May 12-September 9, 2020, suggesting that this population is still far from the herd immunity threshold and at risk from a subsequent epidemic wave.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Peter V. Coyle", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" + }, + { + "author_name": "Mohamed Ali Ben Hadj Kacem", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Naema Hassan Abdulla Al Molawi", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Reham Awni El Kahlout", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Imtiaz Gilliani", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Nourah Younes", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Zaina Al Kanaani", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Abdullatif Al Khal", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Einas Al Kuwari", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Hanan F. Abdul Rahim", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Gheyath K. Nasrallah", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Hadi M. Yassine", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Mohamed G. Al Kuwari", + "author_inst": "Primary Health Care Corporation, Doha, Qatar" + }, + { + "author_name": "Hamad Eid Al Romaihi", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Mohamed H. Al-Thani", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.04.21249235", "rel_title": "Machine Learning Forecast of Growth in COVID-19 Confirmed Infection Cases with Non-Pharmaceutical Interventions and Cultural Dimensions: Algorithm Development and Validation", @@ -972168,73 +977588,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.01.05.21249216", - "rel_title": "Prevalence and Factors associated with Mental health impact of COVID-19 Pandemic in Bangladesh: A survey-based cross-sectional study", - "rel_date": "2021-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.05.21249216", - "rel_abs": "BackgroundFeelings of isolation, insecurity, and instability triggered by COVID-19 could have a long-term impact on the mental health status of individuals. This study examined the prevalence and factors associated with the mental health symptoms of anxiety, depression, and stress during the COVID-19 pandemic in Bangladesh.\n\nMethodsFrom 1st - 30th April 2020, we used a validated self-administered questionnaire to conduct a cross-sectional study on 10,609 participants through an online survey platform. We assessed mental health status using the Depression, Anxiety, and Stress Scale (DASS-21). The total depression, anxiety, and stress subscale scores were divided into normal, mild, moderate, severe, and multinomial logistic regression was used to examine associated factors.\n\nResultsThe prevalence of depressive symptoms was 15%, 34%, and 15% for mild, moderate, and severe depressive symptoms, respectively. The prevalence of anxiety symptoms was 59% for severe anxiety symptoms, 14% for moderate anxiety symptoms, and 14% for mild anxiety symptoms while, the prevalence for stress levels were 16% for severe stress level, 22% for moderate stress level and 13% for mild stress level. Multivariate analyses revealed that the most consistent factors associated with mild, moderate, and severe of the three mental health subscales (depression, anxiety, and stress) were respondents who lived in Dhaka and Rangpur division, females, those who self-quarantine in the previous 7 days before the survey and those respondents who experienced chills, breathing difficulty, dizziness, and sore throat.\n\nConclusionOur results showed that about 64%, 87%, and 61% experienced depressive symptoms, anxiety symptoms, and levels of stress, respectively. In Bangladesh, there is a need for better mental health support for females especially those that lived in Dhaka and Rangpur division and experienced chills, breathing difficulty, dizziness, and sore throat during COVID-19 and other future pandemics.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Dr. Tanvir Abir", - "author_inst": "International University of Business, Agriculture and Technology, Dhaka-1230, Bangladesh" - }, - { - "author_name": "Dr. Nazmul Ahsan Kalimullah", - "author_inst": "Begum Rokeya University, Rangpur-5404, Bangladesh" - }, - { - "author_name": "Dr. L Osuagwu Uchechukwu", - "author_inst": "Western Sydney University, Australia" - }, - { - "author_name": "Dewan Muhammad Nur -A Yazdani", - "author_inst": "International University of Business, Agriculture and Technology, Dhaka-1230, Bangladesh" - }, - { - "author_name": "Taha Husain", - "author_inst": "Begum Rokeya University, Rangpur 5404, Bangladesh" - }, - { - "author_name": "Piwuna Christopher Goson", - "author_inst": "University of Jos, Nigeria" - }, - { - "author_name": "Palash Basak", - "author_inst": "University of Newcastle, Callaghan 2308, Australia" - }, - { - "author_name": "Md Adnan Rahman", - "author_inst": "International University of Business Agriculture and Technology (IUBAT), Dhaka-1230, Bangladesh" - }, - { - "author_name": "Dr. Abdullah Al Mamun", - "author_inst": "UCSI University, Kuala Lumpur 56000, Malaysia" - }, - { - "author_name": "Dr. P. Yukthamarani Permarupan", - "author_inst": "Universiti Malaysia Kelantan, Kota Bharu 16100, Malaysia" - }, - { - "author_name": "Md Yusuf Hossein Khan", - "author_inst": "International University of Business Agriculture and Technology (IUBAT), Dhaka-1230, Bangladesh" - }, - { - "author_name": "Dr. Abul Hasnat Milton", - "author_inst": "Research International, Dhaka, Bangladesh & Epidemiology Resource Centre, NSW, Australia" - }, - { - "author_name": "Dr. Kingsley Agho", - "author_inst": "Western Sydney University, Campbelltown, NSW 2560, Australia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2021.01.04.21249236", "rel_title": "Saliva viral load is a dynamic unifying correlate of COVID-19 severity and mortality", @@ -973725,6 +979078,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.06.425543", + "rel_title": "Heterogeneity versus the COVID-19 Pandemic", + "rel_date": "2021-01-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.06.425543", + "rel_abs": "In this paper, heterogeneity is formally defined, and its properties are explored. We define and distinguish observable versus non-observable heterogeneity. It is proposed that heterogeneity among the vulnerable is a significant factor in the contagion impact of COVID-19, as demonstrated with incidence rates on a Diamond Princess Cruise ship in February 2020. Given the nature of the disease, its heterogeneity and human social norms, pre-voyage and post-voyage quick testing procedures may become the new standard for cruise ship passengers and crew. The technological advances in testing available today would facilitate more humanistic treatment as compared to more archaic quarantine and isolation practices for all onboard ship. With quick testing, identification of those infected and thus not allowed to embark on a cruise or quarantining those disembarking and other mitigation strategies, the popular cruise adventure could be available safely again. Whatever the procedures implemented, the methodological purpose of this study should add valuable insight in the modeling of disease and specifically, the COVID-19 virus.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ramalingam Shanmugam", + "author_inst": "Texas State University" + }, + { + "author_name": "Gerald Ledlow", + "author_inst": "University of Texas Health Science Center at Tyler: The University of Texas Health Science Center at Tyler" + }, + { + "author_name": "Karan P. Singh", + "author_inst": "University of Texas Health Science Center Tyler" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2021.01.06.425544", "rel_title": "Complex Systems Analysis Informs on the Spread of COVID-19", @@ -973854,53 +979234,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.01.05.20248202", - "rel_title": "Coronavirus-19 and coagulopathy: A Systematic Review", - "rel_date": "2021-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.05.20248202", - "rel_abs": "BackgroundUnderstanding the association between Coronavirus Disease 2019 (COVID-19) and coagulopathy may assist clinical prognostication, and influence treatment and outcomes. We aimed to systematically describe the relationship between hemostatic laboratory parameters and important clinical outcomes among adults with COVID-19.\n\nMethodsA systematic review of randomized clinical trials, observational studies and case series published in PubMed (Medline), EMBASE, and CENTRAL from December 1, 2019 to March 25, 2020. Studies of adult patients with COVID-19 that reported at least one hemostatic laboratory parameter were included.\n\nResultsData were extracted from 57 studies (N=12,050 patients) that met inclusion criteria. The average age of patients was 52 years and 45% were women. Of the included studies, 92.7% (N=38/41 studies) reported an average platelet count [≥] 150 x 109/L, 68.2% (N=15/22 studies) reported an average prothrombin time (PT) between 11-14 s, 55% (N=11/20 studies) reported an average activated partial thromboplastin time (aPTT) between 25-35 s, and 34.4% (N=11/32 studies) reported a D-dimer concentration above the upper limit of normal (ULN). Eight studies (7 cohorts and 1 case series) reported hemostatic lab values for survivors versus non-survivors. Among non-survivors, D-dimer concentrations were reported in 4 studies and all reported an average above the ULN.\n\nInterpretationMost patients had a normal platelet count, elevated D-dimer, PT and aPTT values in the upper reference interval; D-dimer elevation appeared to correlate with poor outcomes. Further studies are needed to better correlate these hemostatic parameters with the risk of adverse outcomes such as thrombosis and bleeding.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Stephanie G Lee", - "author_inst": "St Michael's Hospital, University of Toronto" - }, - { - "author_name": "Michael Fralick", - "author_inst": "Sinai Health System, University of Toronto" - }, - { - "author_name": "Grace Tang", - "author_inst": "St Michael's Hospital, University of Toronto" - }, - { - "author_name": "Brandon Tse", - "author_inst": "St Michael's Hospital, University of Toronto" - }, - { - "author_name": "Lisa Baumann Kreuziger", - "author_inst": "Versiti Blood Research Institute, Medical College of Wisconsin" - }, - { - "author_name": "Mary Cushman", - "author_inst": "Larner College of Medicine at the University of Vermont" - }, - { - "author_name": "Peter Juni", - "author_inst": "St Michael's Hospital, University of Toronto" - }, - { - "author_name": "Michelle Sholzberg", - "author_inst": "St Michael's Hospital, University of Toronto" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2021.01.05.21249154", "rel_title": "Use of the FebriDx point-of-care assay as part of a triage algorithm for medical admissions with possible COVID-19", @@ -974963,6 +980296,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2021.01.04.21249195", + "rel_title": "The incidence, characteristics and outcomes of pregnant women hospitalized with symptomatic and asymptomatic SARS-CoV-2 infection in the UK from March to September 2020: a national cohort study using the UK Obstetric Surveillance System (UKOSS)", + "rel_date": "2021-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.04.21249195", + "rel_abs": "BackgroundEvidence on risk factors, incidence and impact of SARS-CoV-2 infection in pregnant mothers and their babies has rapidly expanded but there is a lack of population level data to inform accurate incidence rates and unbiased descriptions of characteristics and outcomes. The primary aim of this study was to describe the incidence, characteristics and outcomes of hospitalized pregnant women with symptomatic and asymptomatic SARS-CoV-2 in the UK compared to pregnant women without SARS-CoV-2 in order to inform future clinical guidance and management.\n\nMethods and FindingsWe conducted a national, prospective cohort study of all hospitalized pregnant women with confirmed SARS-CoV-2 from 1st March 2020 to 31st August 2020 using the UK Obstetric Surveillance System (UKOSS) across all 194 hospitals in the UK with a consultant-led maternity unit. Incidence was estimated using the latest national maternity data. Overall, 1148 hospitalized women had confirmed SARS-CoV-2 in pregnancy, 63% of which were symptomatic. Therefore, the estimated incidence of hospitalization with symptomatic SARS-CoV-2 was 2.0 per 1000 maternities (95% CI 1.9-2.2) and for asymptomatic SARS-CoV-2 was 1.2 per 1000 maternities (95% CI 1.1-1.4). Compared to pregnant women without SARS-CoV-2, women hospitalized with symptomatic SARS-CoV-2 were more likely to be overweight or obese (adjusted OR 1.86, 95% CI 1.39-2.48 and aOR 2.07, 95% CI 1.53-2.29 respectively), to be of Black, Asian or Other minority ethnic group (aOR 6.24, 95% CI 3.93-9.90, aOR 4.36, 95% CI 3.19-5.95 and aOR 12.95, 95% CI 4.93-34.01 respectively), and to have a relevant medical comorbidity (aOR 1.83, 95% CI 1.32-2.54). Compared to pregnant women without SARS-CoV-2, hospitalized pregnant women with symptomatic SARS-CoV-2 were more likely to be admitted to intensive care (aOR 57.67, 95% CI 7.80-426.70) but the absolute risk of poor outcomes was low. Cesarean births and neonatal unit admission were increased regardless of symptom status (symptomatic aOR 2.60, 95% CI 1.97-3.42 and aOR 3.08, 95% CI 1.99-4.77 respectively; asymptomatic aOR 2.02, 95% CI 1.52-2.70 and aOR 1.84, 95% 1.12-3.03 respectively). Iatrogenic preterm births were more common in women with symptomatic SARS-CoV-2 (aOR 11.43, 95% CI 5.07-25.75). The risks of stillbirth or neonatal death were not significantly increased, regardless of symptom status but numbers were small. The limitations of this study include the restriction to women hospitalized with SARS-CoV-2, who may by nature of their admission have been at greater risk of adverse outcome.\n\nConclusionsWe have identified factors that increase the risk of symptomatic and asymptomatic SARS-CoV-2 in pregnancy. The increased risks of cesarean and iatrogenic preterm birth provide clear evidence of the indirect impact of SARS-CoV-2 on mothers and maternity care in high income settings. Clinicians can be reassured that the majority of women do not experience severe complications of SARS-CoV-2 in pregnancy and women with mild disease can be discharged to continue their pregnancy safely.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Nicola Vousden", + "author_inst": "University of Oxford" + }, + { + "author_name": "Kathryn Bunch", + "author_inst": "University of Oxford" + }, + { + "author_name": "Edward Morris", + "author_inst": "Royal College of Obstetricians and Gynaecologists" + }, + { + "author_name": "Nigel Simpson", + "author_inst": "University of Leeds" + }, + { + "author_name": "Christopher Gale", + "author_inst": "Imperial College London" + }, + { + "author_name": "Patrick O'Brien", + "author_inst": "University College London" + }, + { + "author_name": "Maria Quigley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peter Brocklehurst", + "author_inst": "University College London" + }, + { + "author_name": "Jennifer J Kurinczuk", + "author_inst": "University of Oxford" + }, + { + "author_name": "Marian Knight", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2021.01.04.425336", "rel_title": "SARS-CoV-2 susceptibility of cell lines and substrates commonly used in diagnosis and isolation of influenza and other viruses", @@ -975208,41 +980596,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.01.03.424883", - "rel_title": "Rejuveinix Mitigates Sepsis-Associated Oxidative Stress in the Brain of Mice: Clinical Impact Potential in COVID-19 and Nervous System Disorders", - "rel_date": "2021-01-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.03.424883", - "rel_abs": "Here, we demonstrate that our anti-sepsis and COVID-19 drug candidate Rejuveinix (RJX) substantially improves the survival outcome in the LPS-GalN animal model of sepsis and multi-organ failure. One hundred (100) percent (%) of untreated control mice remained alive throughout the experiment. By comparison, 100% of LPS-GalN injected mice died at a median of 4.6 hours. In contrast to the invariably fatal treatment outcome of vehicle-treated control mice, 40% of mice treated with RJX (n=25) remained alive with a 2.4-fold longer median time survival time of 10.9 hours (Log-rank X2=20.60, P<0.0001). Notably, RJX increased the tissue levels of antioxidant enzymes SOD, CAT, and GSH-Px, and reduced oxidative stress in the brain. These findings demonstrate the clinical impact potential of RJX as a neuroprotective COVID-19 and sepsis drug candidate.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Fatih Uckun", - "author_inst": "Reven Pharmaceuticals (Reven LLC)" - }, - { - "author_name": "Mehmet Tuzcu", - "author_inst": "Firat University" - }, - { - "author_name": "Marcus Gitterle", - "author_inst": "Christus Health System" - }, - { - "author_name": "Michael Volk", - "author_inst": "Reven Pharmaceuticals (Reven LLC)" - }, - { - "author_name": "Kazim Sahin", - "author_inst": "Firat University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2021.01.04.424792", "rel_title": "Hydroxyzine inhibits SARS-CoV-2 Spike protein binding to ACE2 in a qualitative in vitro assay", @@ -976625,6 +981978,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.30.20248890", + "rel_title": "Detection of SARS-CoV-2 in the air from hospitals and closed rooms occupied by COVID-19 patients", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.30.20248890", + "rel_abs": "To understand air transmission characteristics of SARS-CoV-2 and risks for health care personnel and visitors to hospitals, we analyzed air samples collected from various enclosures in hospitals at Hyderabad and Mohali and performed closed room experiments with COVID-19 positive individuals. We collected 64 air samples from COVID and non-COVID areas of various hospitals and 17 samples from closed rooms occupied by COVID patients. 4 samples from COVID care areas were positive for SARS-CoV-2 with no obvious predilection towards ICU/non-ICU areas in the hospital samples. In the closed room experiments, where one or more COVID-19 patients spent a short duration of time, one sample - collected immediately after the departure of three symptomatic patients from the room - was positive. Our results indicate that the chance of picking up SARS-CoV-2 in the air is directly related to a number of COVID positive cases in the room, their symptomatic status, and the duration of exposure and that the demarcation of hospital areas into COVID and non-COVID areas is a successful strategy to prevent cross infections. In neutral environmental conditions, the virus does not seem to spread farther away from the patients, especially if they are asymptomatic, giving an objective evidence for the effectiveness of physical distancing in curbing the spread of the epidemic.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Shivranjani Moharir", + "author_inst": "CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India" + }, + { + "author_name": "Sharat Sharath Chandra", + "author_inst": "CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India" + }, + { + "author_name": "Arushi Goel", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Bhuwaneshwar Thakur", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Gurpreet Singh Bhalla", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Dinesh Kumar", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Digvijay Singh Naruka", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Ashwani Kumar", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Amit Tuli", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Swathi Suravaram", + "author_inst": "ESI Hospital and Medical College, Hyderabad, India" + }, + { + "author_name": "Thrilok Chander Bingi", + "author_inst": "COVID-19 nodal centre, Hyderabad, India" + }, + { + "author_name": "M Srinivas", + "author_inst": "ESI Hospital and Medical College, Hyderabad, India" + }, + { + "author_name": "Rajarao Mesipogu", + "author_inst": "COVID-19 nodal centre, Hyderabad, India" + }, + { + "author_name": "Krishna Reddy", + "author_inst": "Durgabai Deshmukh Hospital, Hyderabad, India" + }, + { + "author_name": "Sanjeev Khosla", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Karthik Bharadwaj Tallapaka", + "author_inst": "CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India" + }, + { + "author_name": "Rakesh K Mishra", + "author_inst": "CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.23.20248803", "rel_title": "Clinical diagnosis of COVID-19: a prompt, feasible, and sensitive diagnostic tool for COVID-19 based on a 1,757-patient cohort (The AndroCoV Clinical Scoring for COVID-19 diagnosis).", @@ -976754,41 +982190,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.30.20249033", - "rel_title": "Imprecise assessment of mask use may obscure associations with SARS-CoV-2 positivity", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.30.20249033", - "rel_abs": "Masks are effective measures to prevent the transmission of SARS-CoV-2, however, lack of a national mandate coupled with poor adherence has led to suboptimal levels of transmission reduction. Although data has suggested that mask adherence is high, few studies have captured details on how mask wearing changes with activities and how these behaviors are associated with SARS-CoV-2 positivity. We recruited an online sample of 3,058 respondents from three US states (MD, FL, IL; n[~]1000/state) between September 16 - October 15, 2020. The median age of the sample was 47; 53% were female, 56% were white and 22% were working outside the home. Seventy three percent of the sample reported always wearing a mask indoors and outdoors based on local guidelines, however, 78% of participants who reported always wearing a mask reported taking their mask off when outside the home. While overall masking according to guidelines was not significantly associated with SARS-CoV-2 positivity, sometimes, often or always removing a mask during activities were significantly associated with SARS-CoV-2 positivity (adjusted odds ratio for always vs never removing mask: 9.92; 95% CI: 1.16 - 85.1). These findings suggest that masks were most effective when worn without removal reflecting the need for consistent use.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sophie Berube", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Steven Clipman", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Shruti H Mehta", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Sunil Solomon", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Amy Wesolowski", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.30.20249023", "rel_title": "COVID Outcome Prediction in the Emergency Department (COPE)", @@ -977927,6 +983328,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.31.20249088", + "rel_title": "Stages of COVID-19 pandemic and paths to herd immunity by vaccination: dynamical model comparing Austria, Luxembourg and Sweden", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.31.20249088", + "rel_abs": "BackgroundWorldwide more than 72 million people have been infected and 1.6 million died with SARS-CoV-2 by 15th December 2020. Non-pharmaceutical interventions which decrease social interaction have been implemented to reduce the spread of SARS-CoV-2 and to mitigate stress on healthcare systems and prevent deaths. The pandemic has been tackled with disparate strategies by distinct countries resulting in different epidemic dynamics. However, with vaccines now becoming available, the current urgent open question is how the interplay between vaccination strategies and social interaction will shape the pandemic in the next months.\n\nMethodsTo address this question, we developed an extended Susceptible-Exposed-Infectious-Removed (SEIR) model including social interaction, undetected cases and the progression of patients trough hospitals, intensive care units (ICUs) and death. We calibrated our model to data of Luxem-bourg, Austria and Sweden, until 15th December 2020. We incorporated the effect of vaccination to investigate under which conditions herd immunity would be achievable in 2021.\n\nResultsThe model reveals that Sweden has the highest fraction of undetected cases, Luxembourg displays the highest fraction of infected population, and all three countries are far from herd immunity as of December 2020. The model quantifies the level of social interactions, and allows to assess the level which would keep Reff (t) below 1. In December 2020, this level is around 1/3 of what it was before the pandemic for all the three countries. The model allows to estimate the vaccination rate needed for herd immunity and shows that 2700 vaccinations/day are needed in Luxembourg to reach it by mid of April and 45,000 for Austria and Sweden. The model estimates that vaccinating the whole countrys population within 1 year could lead to herd immunity by July in Luxembourg and by August in Austria and Sweden.\n\nConclusionThe model allows to shed light on the dynamics of the epidemics in different waves and countries. Our results emphasize that vaccination will help considerably but not immediately and therefore social measures will remain important for several months before they can be fully alleviated.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Francoise Kemp", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Daniele Proverbio", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Atte Aalto", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Laurent Mombaerts", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Aymeric Fouquier d Herouel", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Andreas Husch", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Christophe Ley", + "author_inst": "University of Ghent" + }, + { + "author_name": "Jorge Goncalves", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Alexander Skupin", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Stefano Magni", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.30.20249066", "rel_title": "Need of care in interpreting Google Trends-based COVID-19 infodemiological study results: potential risk of false-positivity", @@ -978060,57 +983516,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.02.21249137", - "rel_title": "Knowledge, attitude and practice toward COVID-19 among healthcare workers in public health facilities, Eastern Ethiopia", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.02.21249137", - "rel_abs": "On 13 March 2020, Ethiopia reported the first confirmed case of COVID-19 in Addis Ababa. COVID-19 is likely to overwhelm an already fragile health-care delivery system and reduce the availability of services for endemic health concerns such as malaria and diarrheal diseases.\n\nCross sectional study was conducted on heath care workers in three public health facilities in Somali region to assess knowledge, attitude and practice towards COVID-19. T-test and ANOVA were used to analyze the relationship between the dependent, and independent variables. Spearmans correlation was used to assess the relationship between mean knowledge and attitude scores.\n\nA vast majority of the participants were male (n = 293, 67.5%), with a mean age of 27.6 (SD: 5.3) years. The mean knowledge score was 13.7 (SD: 2.6) and the mean attitude score 10.5 (SD: 4.1). Only 45.2 % (n = 196) of the participants had a good attitude toward COVID-19. There was a negative correlation between knowledge scores, attitude scores (r=-0.295, P<0.001) and practice (r=-0.298, P<0.001).\n\nThe overall level of knowledge was good. However, the attitude and practice were relatively low. We recommend strategies for enhancing the capacity of healthcare workers to develop positive attitude and practice.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Alinoor Mohamed Farah", - "author_inst": "Jigjiga University" - }, - { - "author_name": "Tahir Yousuf Nour", - "author_inst": "Jigjiga University" - }, - { - "author_name": "Muse Obsiye Ibrahim", - "author_inst": "Jigjiga University" - }, - { - "author_name": "Mowlid Aqil Adan", - "author_inst": "Jigjiga University" - }, - { - "author_name": "Omar Moeline Ali", - "author_inst": "Jigjiga University" - }, - { - "author_name": "Muktar Arab Hussein", - "author_inst": "Jigjiga University" - }, - { - "author_name": "Abdullahi Bedel Budul", - "author_inst": "Jigjiga University" - }, - { - "author_name": "Muktar Omer", - "author_inst": "Jigjiga University" - }, - { - "author_name": "Fentabil Getnet", - "author_inst": "Jigjiga University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.02.21249146", "rel_title": "Do school closures reduce community transmission of COVID-19? A systematic review of observational studies", @@ -979465,6 +984870,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.26.20248878", + "rel_title": "Direct detection of SARS-CoV-2 RNA using high-contrast pH-sensitive dyes", + "rel_date": "2021-01-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.26.20248878", + "rel_abs": "The worldwide COVID-19 pandemic has had devastating effects on health, healthcare infrastructure, social structure, and economics. One of the limiting factors in containing the spread of this virus has been the lack of widespread availability of fast, inexpensive, and reliable methods for testing of individuals. Frequent screening for infected and often asymptomatic people is a cornerstone of pandemic management plans. Here, we introduce two pH sensitive LAMPshade dyes as novel readouts in an isothermal RT-LAMP amplification assay for SARS-CoV-2 RNA. The resulting JaneliaLAMP (jLAMP) assay is robust, simple, inexpensive, has low technical requirements and we describe its use and performance in direct testing of contrived and clinical samples without RNA extraction.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Timothy A Brown", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Katherine S. Schaefer", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Arthur Tsang", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Hyun Ah Yi", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Jonathan B. Grimm", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Andrew L. Lemire", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Fadi M. Jradi", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Charles Kim", + "author_inst": "Sensei Biotherapeutics" + }, + { + "author_name": "Kevin McGowan", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Kimberly Ritola", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Derek T Armstrong", + "author_inst": "Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Heba H. Mostafa", + "author_inst": "Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Wyatt Korff", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Ronald D. Vale", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Luke D Lavis", + "author_inst": "HHMI Janelia Research Campus" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.31.424987", "rel_title": "Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses", @@ -979922,61 +985402,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.12.31.424961", - "rel_title": "Comprehensive analysis of the host-virus interactome of SARS-CoV-2", - "rel_date": "2021-01-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.31.424961", - "rel_abs": "Host-virus protein-protein interaction is the key component of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lifecycle. We conducted a comprehensive interactome study between the virus and host cells using tandem affinity purification and proximity labeling strategies and identified 437 human proteins as the high-confidence interacting proteins. Functional characterization and further validation of these interactions elucidated how distinct SARS-CoV-2 viral proteins participate in its lifecycle, and discovered potential drug targets to the treatment of COVID-19. The interactomes of two key SARS-CoV-2 encoded viral proteins, NSP1 and N protein, were compared with the interactomes of their counterparts in other human coronaviruses. These comparisons not only revealed common host pathways these viruses manipulate for their survival, but also showed divergent protein-protein interactions that may explain differences in disease pathology. This comprehensive interactome of coronavirus disease-2019 provides valuable resources for understanding and treating this disease.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Zhen Chen", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Chao Wang", - "author_inst": "MD anderson Cancer Center" - }, - { - "author_name": "Xu Feng", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Litong Nie", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Mengfan Tang", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Huimin Zhang", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Yun Xiong", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Samuel K Swisher", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Mrinal Srivastava", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Junjie Chen", - "author_inst": "The University of Texas MD Anderson Cancer Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.12.30.424906", "rel_title": "Unbuttoning the impact of N501Y mutant RBD on viral entry mechanism: A computational insight", @@ -981135,6 +986560,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.12.29.424728", + "rel_title": "In vitro Targeting of Transcription Factors to Control the Cytokine Release Syndrome in COVID-19", + "rel_date": "2020-12-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.29.424728", + "rel_abs": "Treatment of the cytokine release syndrome (CRS) has become an important part of rescuing hospitalized COVID-19 patients. Here, we systematically explored the transcriptional regulators of inflammatory cytokines involved in the COVID-19 CRS to identify candidate transcription factors (TFs) for therapeutic targeting using approved drugs. We integrated a resource of TF-cytokine gene interactions with single-cell RNA-seq expression data from bronchoalveolar lavage fluid cells of COVID-19 patients. We found 581 significantly correlated interactions, between 95 TFs and 16 cytokines upregulated in the COVID-19 patients, that may contribute to pathogenesis of the disease. Among these, we identified 19 TFs that are targets of FDA approved drugs. We investigated the potential therapeutic effect of 10 drugs and 25 drug combinations on inflammatory cytokine production in peripheral blood mononuclear cells, which revealed two drugs that inhibited cytokine production and numerous combinations that show synergistic efficacy in downregulating cytokine production. Further studies of these candidate repurposable drugs could lead to a therapeutic regimen to treat the CRS in COVID-19 patients.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Clarissa S Santoso", + "author_inst": "Boston University" + }, + { + "author_name": "Zhaorong Li", + "author_inst": "Boston University" + }, + { + "author_name": "Jaice T Rottenberg", + "author_inst": "Boston University" + }, + { + "author_name": "Xing Liu", + "author_inst": "Boston University" + }, + { + "author_name": "Vivian X Shen", + "author_inst": "Boston University" + }, + { + "author_name": "Juan I Fuxman Bass", + "author_inst": "Boston University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.30.424801", "rel_title": "Pharmacophore-based peptide biologics neutralize SARS-CoV-2 S1 and deter S1-ACE2 interaction in vitro", @@ -981244,113 +986708,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.12.30.424862", - "rel_title": "Screening a library of FDA-approved and bioactive compounds for antiviral activity against SARS-CoV-2", - "rel_date": "2020-12-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.30.424862", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has emerged as a major global health threat. The COVID-19 pandemic has resulted in over 80 million cases and 1.7 million deaths to date while the number of cases continues to rise. With limited therapeutic options, the identification of safe and effective therapeutics is urgently needed. The repurposing of known clinical compounds holds the potential for rapid identification of drugs effective against SARS-CoV-2. Here we utilized a library of FDA-approved and well-studied preclinical and clinical compounds to screen for antivirals against SARS-CoV-2 in human pulmonary epithelial cells. We identified 13 compounds that exhibit potent antiviral activity across multiple orthogonal assays. Hits include known antivirals, compounds with anti-inflammatory activity, and compounds targeting host pathways such as kinases and proteases critical for SARS-CoV-2 replication. We identified seven compounds not previously reported to have activity against SARS-CoV-2, including B02, a human RAD51 inhibitor. We further demonstrated that B02 exhibits synergy with remdesivir, the only antiviral approved by the FDA to treat COVID-19, highlighting the potential for combination therapy. Taken together, our comparative compound screening strategy highlights the potential of drug repurposing screens to identify novel starting points for development of effective antiviral mono- or combination therapies to treat COVID-19.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Scott B Biering", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Erik Van Dis", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Eddie Wehri", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Livia H Yamashiro", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Xammy Nguyenla", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Claire Dugast-Darzacq", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Thomas GW Graham", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Julien R Stroumza", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Guillaume R Golovkine", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Allison W Roberts", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Daniel M Fines", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Jessica N Spradlin", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Carl C Ward", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Teena Bajaj", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Dustin Dovala", - "author_inst": "Novartis Institutes for BioMedical Research" - }, - { - "author_name": "Ursula S Gahmen", - "author_inst": "Gladstone Institute" - }, - { - "author_name": "Ruchika Bajaj", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Douglas M Fox", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Melanie Ott", - "author_inst": "Gladstone Institute" - }, - { - "author_name": "Niren Murthy", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Daniel Nomura", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Julia Schaletzky", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Sarah A Stanley", - "author_inst": "University of California, Berkeley" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.30.424641", "rel_title": "Characterization of cell-cell communication in COVID-19 patients", @@ -982808,6 +988165,169 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2020.12.28.424622", + "rel_title": "Landscapes and dynamic diversifications of B-cell receptor repertoires in COVID-19 patients", + "rel_date": "2020-12-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.28.424622", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the pandemic of coronavirus disease 2019 (COVID-19). Great international efforts have been put into the development of prophylactic vaccines and neutralizing antibodies. However, the knowledge about the B cell immune response induced by the SARS-CoV-2 virus is still limited. Here, we report a comprehensive characterization of the dynamics of immunoglobin heavy chain (IGH) repertoire in COVID-19 patients. By using next-generation sequencing technology, we examined the temporal changes in the landscape of the patients immunological status, and found dramatic changes in the IGH within the patients immune system after the onset of COVID-19 symptoms. Although different patients have distinct immune responses to SARS-CoV-2 infection, by employing clonotype overlap, lineage expansion and clonotype network analyses, we observed a higher clonotype overlap and substantial lineage expansion of B cell clones during 2-3 weeks of illness, which is of great importance to B-cell immune responses. Meanwhile, for preferences of V gene usage during SARS-CoV-2 infection, IGHV3-74 and IGHV4-34 and IGHV4-39 in COVID-19 patients were more abundant than that of healthy controls. Overall, we present an immunological resource for SARS-CoV-2 that could promote both therapeutic development as well as mechanistic research.", + "rel_num_authors": 37, + "rel_authors": [ + { + "author_name": "Haitao Xiang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Yingze Zhao", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Xinyang Li", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Peipei Liu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Longlong Wang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Meiniang Wang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Lei Tian", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Haixi Sun", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Wei Zhang", + "author_inst": "Department of Computer Science, City University of Hong Kong" + }, + { + "author_name": "Ziqian Xu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Beiwei Ye", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Xiaoju Yuan", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Pengyan Wang", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Ning Zhang", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Yuhuan Gong", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Chengrong Bian", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Zhaohai Wang", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Linxiang Yu", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Jin Yan", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Fanping Meng", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Changqing Bai", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Xiaoshan Wang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Xiaopan Liu", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Kai Gao", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Liang Wu", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Longqi F. Liu", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Ying Gu", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Yuhai J. Bi", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Yi Shi", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Shaogeng Zhang", + "author_inst": "The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Chen Zhu", + "author_inst": "The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Xun Xu", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Guizhen Wu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "George Gao", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Naibo Yang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "William Liu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Penghui Yang", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.29.424682", "rel_title": "ACE2 peptide fragment interacts with several sites on the SARS-CoV-2 spike protein S1", @@ -982985,33 +988505,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.12.29.424698", - "rel_title": "An Ultrasensitive Biosensor for Quantifying the Interaction of SARS-CoV-2 and Its Receptor ACE2 in Cells and in vitro", - "rel_date": "2020-12-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.29.424698", - "rel_abs": "The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is currently spreading and mutating with increasing speed worldwide. Therefore, there is an urgent need for a simple, sensitive, and high-throughput (HTP) assay to quantify virus-host interaction in order to quickly evaluate infectious ability of mutant virus and develop or validate virus-inhibiting drugs. Here we have developed an ultrasensitive bioluminescent biosensor to evaluate virus-cell interaction by quantifying the interaction between SARS-CoV-2 receptor binding domain (RBD) and its cellular receptor angiotensin-converting enzyme 2 (ACE2) both in living cells and in vitro. We have successfully used this novel biosensor to analyze SARS-CoV-2 RBD mutants, and evaluated candidate small molecules (SMs), antibodies, and peptides that may block RBD:ACE2 interaction. This simple, rapid and HTP biosensor tool will significantly expedite detection of viral mutants and anti-COVID-19 drug discovery processes.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Lidong Liu", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Yee Wah So", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Yutian Wang", - "author_inst": "University of British Columbia" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.12.25.20248427", "rel_title": "Maori and Pacific People in New Zealand have higher risk of hospitalisation for COVID-19", @@ -984545,6 +990038,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.23.20248444", + "rel_title": "Association between Use of Qingfei Paidu Tang and Mortality in Hospitalized Patients with COVID-19: A national retrospective registry study", + "rel_date": "2020-12-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248444", + "rel_abs": "BackgroundQingfei Paidu Tang (QPT), a formula of traditional Chinese medicine, which was suggested to be able to ease symptoms in patients with Coronavirus Disease 2019 (COVID-19), has been recommended by clinical guidelines and widely used to treat COVID-19 in China. However, whether it decreases mortality remains unknown.\n\nPurposeWe aimed to explore the association between QPT use and in-hospital mortality among patients hospitalized for COVID-19.\n\nStudy designA retrospective study based on a real-world database was conducted.\n\nMethodsWe identified patients consecutively hospitalized with COVID-19 in 15 hospitals from a national retrospective registry in China, from January through May 2020. Data on patients characteristics, treatments, and outcomes were extracted from the electronic medical records. The association of QPT use with mortality was evaluated using Cox proportional hazards models based on propensity score analysis.\n\nResultsOf the 8939 patients included, 28.7% received QPT. The crude mortality was 1.2% (95% confidence interval [CI] 0.8% to 1.7%) among the patients receiving QPT and 4.8% (95% CI 4.3% to 5.3%) among those not receiving QPT. After adjustment for patient characteristics and concomitant treatments, QPT use was associated with a relative reduction of 50% in in-hospital mortality (hazard ratio, 0.50; 95% CI, 0.37 to 0.66 P <0.001). This association was consistent across subgroups by sex and age. Meanwhile, the incidence of acute liver injury (8.9% [95% CI, 7.8% to 10.1%]vs. 9.9% [95% CI, 9.2% to 10.7%]; odds ratio, 0.96 [95% CI, 0.81% to 1.14%], P =0.658) and acute kidney injury (1.6% [95% CI, 1.2% to 2.2%] vs. 3.0% [95% CI, 2.6% to 3.5%]; odds ratio, 0.85 [95% CI, 0.62 to 1.17], P =0.318) was comparable between patients receiving QPT and those not receiving QPT. The major study limitations included that the study was an observational study based on real-world data rather than a randomized control trial, and the quality of data could be affected by the accuracy and completeness of medical records.\n\nConclusionsQPT was associated with a substantially lower risk of in-hospital mortality, without extra risk of acute liver injury or acute kidney injury among patients hospitalized with COVID-19.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Lihua Zhang", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Xin Zheng", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Xueke Bai", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Qing Wang", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Bowang Chen", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Haibo Wang", + "author_inst": "Clinical Trial Unit, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou Province,PRC" + }, + { + "author_name": "Jiapeng Lu", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Shuang Hu", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Xiaoyan Zhang", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Haibo Zhang", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Jiamin Liu", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Ying Shi", + "author_inst": "China Standard Medical Information Research Center, Shenzhen,PRC" + }, + { + "author_name": "Zhiye Zhou", + "author_inst": "China Standard Medical Information Research Center, Shenzhen,PRC" + }, + { + "author_name": "Lanxia Gan", + "author_inst": "China Standard Medical Information Research Center, Shenzhen,PRC" + }, + { + "author_name": "Xi Li", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Jing Li", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.23.20248784", "rel_title": "The importance of continued non-pharmaceutical interventions during the upcoming SARS-COV-2 vaccination campaign", @@ -984718,37 +990290,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.23.20248798", - "rel_title": "Support and follow-up needs of patients discharged from Intensive Care after severe COVID-19: a mixed-methods study of the views of UK general practitioners and intensive care staff during the pandemic's first wave", - "rel_date": "2020-12-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248798", - "rel_abs": "BackgroundAfter discharge from an intensive care unit(ICU), over 50% of patients face significant physical, mental and cognitive problems. The COVID-19 pandemic has resulted in a large cohort of these patients who will need follow-up services that can address their support needs.\n\nObjectivesTo identify follow-up services planned for COVID-19 patients discharged from ICU, and to explore the views of ICU staff and General Practitioners(GPs) regarding these patients future needs and care coordination.\n\nDesignSequential mixed-methods UK study. We explored usual follow-up practice after ICU discharge and changes in follow-up during the pandemic through a survey of ICU staff, and GP awareness of follow-up and support needs of patients discharged from ICU through a survey of GPs. Through these surveys, we identified participants for semi-structured interviews with both groups.\n\nResultsWe obtained 170 survey responses and conducted 23 interviews. Over 60% of GPs were unaware of the follow-up services generally provided by their local hospitals, and whether or not these were functioning during the pandemic. Eighty percent of ICUs reported some form of follow-up services, with 25% of these suspending provision during the peak of the pandemic, and over half modifying their provision (usually to provide the service remotely). Complex funding streams, poor communication between primary and secondary care, and lack of clarity about who was responsible for referrals and follow-up were the most common problems identified. Discharge documentation was described as poor and lacking key information. Both groups mentioned difficulties accessing services in the community.\n\nConclusionsThe pandemic has highlighted long-standing issues of continuity of care and complex funding streams for post-ICU follow-up care. The large cohort of ICU patients admitted due to COVID-19 highlights the need for improved follow-up services and communication between specialists and GPs, not only for COVID-19 patients, but for all those discharged from ICU.\n\nArticle SummaryO_ST_ABSStrengths and limitations of this studyC_ST_ABSO_LIThis is the first study exploring NHS staff views of post-ICU follow-up services to support patients recovering from severe COVID-19.\nC_LIO_LIResponses to our survey had good geographic spread but were limited in number and relied on volunteers.\nC_LIO_LIGP interviews were small in number, but our findings align with those of larger studies conducted before the pandemic.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ana Cristina Castro-Avila", - "author_inst": "University of York" - }, - { - "author_name": "Laura Jefferson", - "author_inst": "University of York" - }, - { - "author_name": "Veronica Dale", - "author_inst": "University of York" - }, - { - "author_name": "Karen Bloor", - "author_inst": "University of York" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.12.24.424332", "rel_title": "Genetic epidemiology of variants associated with immune escape from global SARS-CoV-2 genomes", @@ -986243,6 +991784,77 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.12.23.424254", + "rel_title": "Cell-type apoptosis in lung during SARS-CoV-2 infection", + "rel_date": "2020-12-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.23.424254", + "rel_abs": "The SARS-CoV-2 pandemic has inspired renewed interest in understanding the fundamental pathology of acute respiratory distress syndrome (ARDS) following infection because fatal COVID-19 cases are commonly linked to respiratory failure due to ARDS. The pathologic alteration known as diffuse alveolar damage in endothelial and epithelial cells is a critical feature of acute lung injury in ARDS. However, the pathogenesis of ARDS following SRAS-CoV-2 infection remains largely unknown.\n\nIn the present study, we examined apoptosis in post-mortem lung sections from COVID-19 patients and lung tissues from a non-human primate model of SARS-CoV-2 infection, in a cell-type manner, including type 1 and 2 alveolar cells and vascular endothelial cells (ECs), macrophages, and T cells. Multiple-target immunofluorescence (IF) assays and western blotting suggest both intrinsic and extrinsic apoptotic pathways are activated during SARS-CoV-2 infection. Furthermore, we observed that SARS-CoV-2 fails to induce apoptosis in human bronchial epithelial cells (i.e., BEAS2B cells) and primary human umbilical vein endothelial cells (HUVECs), which are refractory to SARS-CoV-2 infection. However, infection of co-cultured Vero cells and HUVECs or Vero cells and BEAS2B cells with SARS-CoV-2 induced apoptosis in both Vero cells and HUVECs/BEAS2B cells, but did not alter the permissiveness of HUVECs or BEAS2B cells to the virus. Post-exposure treatment of the co-culture of Vero cells and HUVECs with an EPAC1-specific activator ameliorated apoptosis in HUVECs. These findings may help to delineate a novel insight into the pathogenesis of ARDS following SARS-CoV-2 infection.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Yakun Liu", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Tania M. Garron", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Qing Chang", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Zhengchen Su", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Changcheng Zhou", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Eric C. Gong", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Junying Zheng", + "author_inst": "The University of Texas Medical Branch" + }, + { + "author_name": "Whitney Yin", + "author_inst": "University of Texas Medical Branch, Galveston" + }, + { + "author_name": "Thomas Ksiazek", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Trevor Brasel", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Yang Jin", + "author_inst": "Boston University Medical Campus" + }, + { + "author_name": "Paul Boor", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Jason Edward Comer", + "author_inst": "UTMB" + }, + { + "author_name": "Bin Gong", + "author_inst": "University of Texas Medical Branch" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.12.23.424189", "rel_title": "Berberine and obatoclax inhibit SARS-CoV-2 replication in primary human nasal epithelial cells in vitro", @@ -986468,89 +992080,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.12.22.20248501", - "rel_title": "Prevalence of bacterial pathogens and potential role in COVID-19 severity in patients admitted to intensive care units in Brazil", - "rel_date": "2020-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20248501", - "rel_abs": "Secondary bacterial and fungal infections are associated with respiratory viral infections and invasive mechanical ventilation. In Coronavirus disease 2019 (COVID-19), lung injury by SARS-CoV-2 and impaired immune response can provide a favorable environment for microorganism growth and colonization in hospitalized individuals. Recent studies suggest that secondary bacterial pneumonia is a risk factor associated with COVID-19. In Brazil, knowledge about microbiota present in COVID-19 patients is incipient. This work describes the microbiota of 21 COVID-19 patients admitted to intensive care units from two Brazilian centers. We identified respiratory, nosocomial and bacterial pathogens as prevalent microorganisms. Other bacterial opportunistic and commensal species are also represented. Virulence factors of these pathogenic species, metabolic pathways used to evade and modulate immunological processes and the interconnection between bacterial presence and virulence in COVID-19 progression are discussed.\n\nArticle Summary LineWe identified respiratory, nosocomial and bacterial pathogens as prevalent microorganisms in 21 Brazilian COVID-19 patients admitted to Intensive Care Units. Pathogen virulence factors and immune response evasion metabolic pathways are correlated to COVID-19 severity.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Fabiola Marques Carvalho", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Leandro Nascimento Lemos", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Luciane Prioli Ciapina", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Rennan Garcias Moreira", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Alexandra Gerber", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Ana Paula Guimaraes", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - }, - { - "author_name": "Tatiani Fereguetti", - "author_inst": "Hospital Eduardo de Menezes" - }, - { - "author_name": "Virginia Antunes de Andrade Zambelli", - "author_inst": "Hospital Eduardo de Menezes" - }, - { - "author_name": "Renata Avila", - "author_inst": "Hospital Eduardo de Menezes" - }, - { - "author_name": "Tailah Bernardo de Almeida", - "author_inst": "Instituto de Estudos do mar Almirante Paulo Moreira" - }, - { - "author_name": "Jheimson Silva Lima", - "author_inst": "Hospital Naval Marcilio Dias" - }, - { - "author_name": "Shana Priscila Coutinho Barroso", - "author_inst": "Hospital Naval Marcilio Dias" - }, - { - "author_name": "Mauro Martins Teixeira", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Renan Pedra Souza", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Cynthia Chester Cardoso", - "author_inst": "Universidade Federal do Rio de Janeiro" - }, - { - "author_name": "Renato Santana Aguiar", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Ana Tereza Ribeiro Vasconcelos", - "author_inst": "Laboratorio Nacional de Computacao Cientifica" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.12.22.20248695", "rel_title": "THE SEARCH FOR AN ASSOCIATION OF HLA ALLELES AND COVID-19 RELATED MORTALITY IN THE RUSSIAN POPULATION", @@ -987969,6 +993498,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.23.20248790", + "rel_title": "A Systematic Review of the Incubation Period of SARS-CoV-2: The Effects of Age, Biological Sex, and Location on Incubation Period", + "rel_date": "2020-12-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248790", + "rel_abs": "A systematic review of the incubation period of COVID-19 was compiled and analyzed from 21 quantitative studies. We investigated the incubation period of COVID-19 with regard to age, biological sex, location, and severity of the disease. Based on the data extracted, we report an overall mean and median incubation period for SARS-CoV-2 of 5.894 days and 5.598 days, respectively. The incubation period did not statistically vary for biological sex or age, but some studies suggest a longer incubation period in the young and elderly. Cases of COVID-19 in Wuhan and Hubei Province of China may have a shorter incubation period for COVID-19 but the shorter incubation period may be due to an increase in viral load. In studying coronavirus strains such as SARS and MERS, researchers have discovered an inverse relationship between incubation period length and virus severity. Taking into consideration that SARS-CoV-2 is part of the beta-coronavirus family, as well as the study mentioned above, we suggest that people who experience more severe disease due to SARS-CoV-2 may have a shorter incubation period.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Caitlin Daley", + "author_inst": "Wheaton College" + }, + { + "author_name": "Megan Fydenkevez", + "author_inst": "Wheaton College" + }, + { + "author_name": "Shari Ackerman-Morris", + "author_inst": "Wheaton College" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.22.20248736", "rel_title": "REAL-TIME MECHANISTIC BAYESIAN FORECASTS OF COVID-19 MORTALITY", @@ -988082,101 +993638,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.23.20248761", - "rel_title": "Forecasting intensive care unit demand during the COVID-19 pandemic: A spatial age-structured microsimulation model", - "rel_date": "2020-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248761", - "rel_abs": "BackgroundThe COVID-19 pandemic poses the risk of overburdening health care systems, and in particular intensive care units (ICUs). Non-pharmaceutical interventions (NPIs), ranging from wearing masks to (partial) lockdowns have been implemented as mitigation measures around the globe. However, especially severe NPIs are used with great caution due to their negative effects on the economy, social life and mental well-being. Thus, understanding the impact of the pandemic on ICU demand under alternative scenarios reflecting different levels of NPIs is vital for political decision-making on NPIs.\n\nObjectiveThe aim is to support political decision-making by forecasting COVID-19-related ICU demand under alternative scenarios of COVID-19 progression reflecting different levels of NPIs. Substantial sub-national variation in COVID-19-related ICU demand requires a spatially disaggregated approach. This should not only take sub-national variation in ICU-relevant disease dynamics into account, but also variation in the population at risk including COVID-19-relevant risk characteristics (e.g. age), and factors mitigating the pandemic. The forecast provides indications for policy makers and health care stakeholders as to whether mitigation measures have to be maintained or even strengthened to prevent ICU demand from exceeding supply, or whether there is leeway to relax them.\n\nMethodsWe implement a spatial age-structured microsimulation model of the COVID-19 pandemic by extending the Susceptible-Exposed-Infectious-Recovered (SEIR) framework. The model accounts for regional variation in population age structure and in spatial diffusion pathways. In a first step, we calibrate the model by applying a genetic optimization algorithm against hospital data on ICU patients with COVID-19. In a second step, we forecast COVID-19-related ICU demand under alternative scenarios of COVID 19 progression reflecting different levels of NPIs. We apply the model to Germany and provide state-level forecasts over a 2-month period, which can be updated daily based on latest data on the progression of the pandemic.\n\nResultsTo illustrate the merits of our model, we present here \"forecasts\" of ICU demand for different stages of the pandemic during 2020. Our forecasts for a quiet summer phase with low infection rates identified quite some variation in potential for relaxing NPIs across the federal states. By contrast, our forecasts during a phase of quickly rising infection numbers in autumn (second wave) suggested that all federal states should implement additional NPIs. However, the identified needs for additional NPIs varied again across federal states. In addition, our model suggests that during large infection waves ICU demand would quickly exceed supply, if there were no NPIs in place to contain the virus.\n\nConclusionOur results provide evidence for substantial spatial variation in (1) the effect of the pandemic on ICU demand, and (2) the potential and need for NPI adjustments at different stages of the pandemic. Forecasts with our spatial age-structured microsimulation model allow to take this spatial variation into account. The model is programmed in R and can be applied to other countries, provided that reliable data on the number of ICU patients infected with COVID-19 are available at sub-national level.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Sebastian Kluesener", - "author_inst": "Federal Institute for Population Research, Wiesbaden, Germany" - }, - { - "author_name": "Ralf Schneider", - "author_inst": "High Performance Computing Center, Stuttgart, Germany" - }, - { - "author_name": "Matthias Rosenbaum-Feldbruegge", - "author_inst": "Federal Institute for Population Research, Wiesbaden, Germany" - }, - { - "author_name": "Christian Dudel", - "author_inst": "Max Planck Institute for Demographic Research, Rostock, Germany" - }, - { - "author_name": "Elke Loichinger", - "author_inst": "Federal Institute for Population Research, Wiesbaden, Germany" - }, - { - "author_name": "Nikola Sander", - "author_inst": "Federal Institute for Population Research, Wiesbaden, Germany" - }, - { - "author_name": "Andreas Backhaus", - "author_inst": "Federal Institute for Population Research, Wiesbaden, Germany" - }, - { - "author_name": "Emanuele Del Fava", - "author_inst": "Max Planck Institute for Demographic Research, Rostock, Germany" - }, - { - "author_name": "Janina Esins", - "author_inst": "Robert Koch-Institut, Berlin, Germany" - }, - { - "author_name": "Martina Fischer", - "author_inst": "Robert Koch-Institut, Berlin, Germany" - }, - { - "author_name": "Linus Grabenhenrich", - "author_inst": "Robert Koch-Institut, Berlin, Germany" - }, - { - "author_name": "Pavel Grigoriev", - "author_inst": "Federal Institute for Population Research, Wiesbaden, Germany" - }, - { - "author_name": "Andre Grow", - "author_inst": "Max Planck Institute for Demographic Research, Rostock, Germany" - }, - { - "author_name": "Jason Hilton", - "author_inst": "University of Southampton, United Kingdom" - }, - { - "author_name": "Bastian Koller", - "author_inst": "High Performance Computing Center, Stuttgart, Germany" - }, - { - "author_name": "Mikko Myrskyla", - "author_inst": "Max Planck Institute for Demographic Research, Rostock, Germany" - }, - { - "author_name": "Francesco Scalone", - "author_inst": "University of Bologna, Italy" - }, - { - "author_name": "Martin Wolkewitz", - "author_inst": "University of Freiburg, Germany" - }, - { - "author_name": "Emilio Zagheni", - "author_inst": "Max Planck Institute for Demographic Research, Rostock, Germany" - }, - { - "author_name": "Michael M. Resch", - "author_inst": "High Performance Computing Center, Stuttgart, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.22.20248716", "rel_title": "On the main factors influencing COVID-19 spread and deaths in Mexico: A comparison between Phase I and II", @@ -989614,6 +995075,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.17.20248234", + "rel_title": "Airflow and air velocity measurements while playing wind instruments, with respect to risk assessment of a SARS-CoV-2 infection", + "rel_date": "2020-12-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.17.20248234", + "rel_abs": "Due to airborne transmission of infection with the coronavirus, the question arose as to how high the risk of spreading infectious particles can be while playing a wind instrument.\n\nTo contribute to this question and to help clarify the possible risks, we analyzed 14 wind instruments, first qualitative by making airflows visible while playing and second quantitative by measuring air velocities at three distances (1m, 1.5m and 2m) in direction of the instruments bell.\n\nMeasurements took place with wind instrumentalists of the Bamberg Symphony in their concert hall.\n\nOur findings highlight that while playing all wind instruments no airflow escaping from the instruments - from the bell with brass instruments, from the mouthpiece, keyholes and bell with woodwinds - was measured beyond a distance of 1.5m from the instruments bell, regardless of volume, pitch or what was played. With that, air velocity while playing corresponded to the usual value of hall-like rooms, of 0.1 m/s. For air-jet woodwinds, alto flute and piccolo, significant air movements were seen close to their mouthpieces, which escaped directly into the room without passing through the instrument and therefore generating directed air movements.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Claudia Spahn", + "author_inst": "Freiburg Institute for Musicians' Medicine" + }, + { + "author_name": "Anna Maria Hipp", + "author_inst": "Freiburg Institute for Musicians' Medicine" + }, + { + "author_name": "Bernd Schubert", + "author_inst": "Tintschl BioEnergie und Stroemungstechnik AG" + }, + { + "author_name": "Marcus Rudolf Axt", + "author_inst": "Bamberg Symphony" + }, + { + "author_name": "Markus Stratmann", + "author_inst": "Bamberg Symphony" + }, + { + "author_name": "Christian Schmoelder", + "author_inst": "Bamberg Symphony" + }, + { + "author_name": "Bernhard Richter", + "author_inst": "Freiburg Institute for Musicians' Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.12.21.20248608", "rel_title": "Adaptive immunity to SARS-CoV-2 in cancer patients: The CAPTURE study", @@ -990079,69 +995583,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.21.20248645", - "rel_title": "Renin-angiotensin system blockers and mortality in COVID-19: a territory-wide study from Hong Kong", - "rel_date": "2020-12-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248645", - "rel_abs": "AimsRenin-angiotensin system blockers such as angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) may increase the risk of adverse outcomes in COVID-19. In this study, the relationships between ACEI/ARB use and COVID-19 related mortality were examined.\n\nMethodsConsecutive patients diagnosed with COVID-19 by RT-PCR at the Hong Kong Hospital Authority between 1st January and 28th July 2020 were included.\n\nResultsThis study included 2774 patients. The mortality rate of the COVID-19 positive group was 1.5% (n=42). Those who died had a higher median age (82.3[76.5-89.5] vs. 42.9[28.2-59.5] years old; P<0.0001), more likely to have baseline comorbidities of cardiovascular disease, diabetes mellitus, hypertension, and chronic kidney disease (P<0.0001). They were more frequently prescribed ACEI/ARBs at baseline, and steroids, lopinavir/ritonavir, ribavirin and hydroxychloroquine during admission (P<0.0001). They also had a higher white cell count, higher neutrophil count, lower platelet count, prolonged prothrombin time and activated partial thromboplastin time, higher D-dimer, troponin, lactate dehydrogenase, creatinine, alanine transaminase, aspartate transaminase and alkaline phosphatase (P<0.0001). Multivariate Cox regression showed that age, cardiovascular disease, renal disease, diabetes mellitus, the use of ACEIs/ARBs and diuretics, and various laboratory tests remained significant predictors of mortality.\n\nConclusionsWe report that an association between ACEIs/ARBs with COVID-19 related mortality even after adjusting for cardiovascular and other comorbidities, as well as medication use. Patients with greater comorbidity burden and laboratory markers reflecting deranged clotting, renal and liver function, and increased tissue inflammation, and ACEI/ARB use have a higher mortality risk.\n\nKey PointsO_LIWe report that an association between ACEIs/ARBs with COVID-19 related mortality even after adjusting for cardiovascular and other comorbidities, as well as medication use.\nC_LIO_LIPatients with greater comorbidity burden and laboratory markers reflecting deranged clotting, renal and liver function, and increased tissue inflammation, and ACEI/ARB use have a higher mortality risk.\nC_LI", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Jiandong Zhou", - "author_inst": "City University of Hong Kong" - }, - { - "author_name": "Gary Tse", - "author_inst": "Tianjin Medical University" - }, - { - "author_name": "Sharen Lee", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Wing Tak Wong", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Xiansong Wang", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "William KK Wu", - "author_inst": "Chinese University of Hong Kong" - }, - { - "author_name": "Tong Liu", - "author_inst": "Tianjin Medical University" - }, - { - "author_name": "zhidong cao", - "author_inst": "Institute of Automation, Chinese Academy of Sciences" - }, - { - "author_name": "Daniel Dajin Zeng", - "author_inst": "Chinese Academy of Sciences" - }, - { - "author_name": "Ian CK Wong", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Bernard MY Cheung", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Qingpeng Zhang", - "author_inst": "City University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.21.20248684", "rel_title": "Macrolevel Association of COVID-19 with Non-Communicable Disease Risk Factors in India", @@ -991600,6 +997041,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.21.20248627", + "rel_title": "COVID-19 pandemic dynamics in Ukraine after September 1, 2020", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248627", + "rel_abs": "BackgroundThe threats of the COVID-19 pandemic require the mobilization of scientists, including mathematicians. To understand how the number of cases increases versus time, various models based on direct observations of a random number of new cases and differential equations can be used. Complex mathematical models contain many unknown parameters, the values of which must be determined using a limited number of observations of the disease over time. Even long-term monitoring of the epidemic may not provide reliable estimates of its parameters due to the constant change of testing conditions, isolation of infected and quarantine. Therefore, simpler approaches should also be used, for example, some smoothing of the dependence of the number of cases on time and the known SIR (susceptible-infected-removed) model. These approaches allowed to detect the waves of pandemic in different countries and regions and to make adequate predictions of the duration, hidden periods, reproduction numbers, and final sizes of its waves. In particular, seven waves of the COVID-19 pandemic in Ukraine were investigated.\n\nObjectiveWe will detect new epidemic waves in Ukraine that occurred after September 1, 2020 and estimate the epidemic characteristics with the use of generalized SIR model. Some predictions of the epidemic dynamics will be presented.\n\nMethodsIn this study we use the smoothing method for the dependence of the number of cases on time; the generalized SIR model for the dynamics of any epidemic wave, the exact solution of the linear differential equations and statistical approach developed before.\n\nResultsSeventh and eights epidemic waves in Ukraine were detected and the reasons of their appearance were discussed. The optimal values of the SIR model parameters were calculated. The prediction for the COVID-19 epidemic dynamics in Ukraine is not very optimistic: new cases will not stop appearing until June 2021. Only mass vaccination and social distancing can change this trend.\n\nConclusionsNew waves of COVID-19 pandemic can be detected, calculated and predicted with the use of rather simple mathematical simulations. The expected long duration of the pandemic forces us to be careful and in solidarity.The government and all Ukrainians must strictly adhere to quarantine measures in order to avoid fatal consequences.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Igor Nesteruk", + "author_inst": "Institute of Hydromechanics National Academy of sciences of Ukraine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.22.20248622", "rel_title": "Optimal strategies for combining vaccine prioritization and social distancing to reduce hospitalizations and mitigate COVID19 progression", @@ -991697,45 +997157,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.21.20248241", - "rel_title": "Mathematical Models for Assessing Vaccination Scenarios in Several Provinces in Indonesia", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248241", - "rel_abs": "To mitigate more casualties from the COVID-19 outbreak, this study assessed optimal vaccination scenarios, considering some existing healthcare conditions and some assumptions, by developing SIQRD (Susceptible-Infected-Quarantine-Recovery-Death) models for Jakarta, West Java, and Banten, in Indonesia. The models included an age-structured dynamic transmission model that naturally could give different treatments among age groups of population. The simulation results show that the timing and periods length of the vaccination should be well planned and prioritizing particular age groups will give significant impact on the total number of casualties.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Nuning Nuraini", - "author_inst": "Institut Teknologi Bandung" - }, - { - "author_name": "Kamal Khairudin", - "author_inst": "Institut Teknologi Bandung" - }, - { - "author_name": "Panji Hadisoemarto", - "author_inst": "Universitas Padjadjaran" - }, - { - "author_name": "Hadi Susanto", - "author_inst": "University of Essex" - }, - { - "author_name": "Agus Hasan", - "author_inst": "University of Southern Denmark" - }, - { - "author_name": "Novriana Sumarti", - "author_inst": "Institut Teknologi Bandung" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.19.20248573", "rel_title": "Modelling population-wide screening of SARS-CoV-2 infection for containing COVID-19 pandemic in Okinawa, Japan", @@ -992934,6 +998355,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.20.20248587", + "rel_title": "Predicting intention to receive COVID-19 vaccine among the general population using the Health Belief Model and the Theory of Planned Behavior Model", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.20.20248587", + "rel_abs": "BackgroundA novel coronavirus (COVID-19) was declared a global pandemic by the World Health Organization (WHO) in March, 2020. Until such time as a vaccine becomes available, it is important to identify the determining factors that influence the intention of the general public to accept a future COVID-19 vaccine. Consequently, we aim to explore behavioral-related factors predicting intention to receive COVID-19 vaccine among the general population using the Health Belief Model (HBM) and the Theory of Planned Behavior (TPB) model.\n\nMethodsAn online survey was conducted among adults aged 18 years and older from May 24 to June 24, 2020. The survey included socio-demographic and health-related questions, questions related to the HBM and TPB dimensions, and intention to receive COVID-19 vaccine. Associations between questionnaire variables and COVID-19 vaccination intention were assessed by univariate and multivariate analyses.\n\nResultsEighty percent of 398 eligible respondents stated their willingness to receive COVID-19 vaccine. A unified model including HBM and TPB covariates as well as demographic and health-related factors, proved to be a powerful predictor of intention to receive COVID-19 vaccine, explaining 78% of the variance (adjusted R2 = 0.78). Men (OR=4.35, 95% CI 1.58-11.93), educated respondents (OR=3.54, 95% CI 1.44-8.67) and respondents who had received the seasonal influenza vaccine in the previous year (OR=3.31, 95% CI 1.22-9.00) stated higher intention to receive COVID-19 vaccine. Participants were more likely to be willing to get vaccinated if they reported higher levels of perceived benefits of COVID-19 vaccine (OR=4.49, 95% CI 2.79-7.22), of perceived severity of COVID-19 infection (OR=2.36, 95% CI 1.58-3.51) and of cues to action (OR=1.99, 95% CI 1.38-2.87), according to HBM, and if they reported higher levels of subjective norms (OR=3.04, 95% CI 2.15-4.30) and self-efficacy (OR=2.05, 95% CI 1.54-2.72) according to TPB. Although half of the respondents reported they had not received influenza vaccine last year, 40% of them intended to receive influenza vaccine in the coming winter and 66% of them intended to receive COVID-19 vaccine.\n\nConclusionsProviding data on the public perspective and predicting intention for COVID-19 vaccination using HBM and TPB is important for health policy makers and healthcare providers and can help better guide compliance as the COVID-19 vaccine becomes available to the public.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Liora Shmueli", + "author_inst": "Bar-Ilan university" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.19.20248559", "rel_title": "Changes in UK hospital mortality in the first wave of COVID-19: the ISARIC WHO Clinical Characterisation Protocol prospective multicentre observational cohort study", @@ -993339,129 +998779,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.21.20248642", - "rel_title": "Identification of SARS-CoV-2-specific immune alterations in acutely ill patients", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248642", - "rel_abs": "Dysregulated immune profiles have been described in symptomatic SARS-CoV-2-infected patients. Whether the reported immune alterations are specific to SARS-CoV-2 infection or also triggered by other acute illnesses remains unclear. We performed flow cytometry analysis on fresh peripheral blood from a consecutive cohort of i) patients hospitalized with acute SARS-CoV-2 infection; ii) patients of comparable age/sex hospitalized for other acute disease (SARS-CoV-2 negative); and iii) healthy controls. Using both data-driven and hypothesis-driven analyses, we found several dysregulations in immune cell subsets (e.g. decreased proportion of T cells) that are similarly associated with acute SARS-CoV-2 infection and non-COVID-19 related acute illnesses. In contrast, we identified specific differences in myeloid and lymphocyte subsets that are associated with SARS-CoV-2 status (e.g. elevated proportion of ICAM-1+ mature/activated neutrophils, ALCAM+ monocytes, and CD38+CD8+ T cells). A subset of SARS-CoV-2-specific immune alterations correlated with disease severity, disease outcome at 30 days and mortality. Our data provides novel understanding of the immune dysregulation that are specifically associated with SARS-CoV-2 infection among acute care hospitalized patients. Our study lays the foundation for the development of specific biomarkers to stratify SARS-CoV-2+ patients at risk of unfavorable outcome and uncover novel candidate molecules to investigate from a therapeutic perspective.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Rose-Marie Rebillard", - "author_inst": "CRCHUM" - }, - { - "author_name": "Marc Charabati", - "author_inst": "CRCHUM" - }, - { - "author_name": "Camille Grasmuck", - "author_inst": "CRCHUM" - }, - { - "author_name": "Abdelali Filali-Mouhim", - "author_inst": "CRCHUM" - }, - { - "author_name": "Olivier Tastet", - "author_inst": "CRCHUM" - }, - { - "author_name": "Nathalie Brassard", - "author_inst": "CRCHUM" - }, - { - "author_name": "Audrey Daigneault", - "author_inst": "CRCHUM" - }, - { - "author_name": "Lyne Bourbonniere", - "author_inst": "CRCHUM" - }, - { - "author_name": "Renaud Balthazard", - "author_inst": "CRCHUM" - }, - { - "author_name": "Ana Carmena Moratalla", - "author_inst": "CRCHUM" - }, - { - "author_name": "Yves Carpentier Solorio", - "author_inst": "CRCHUM" - }, - { - "author_name": "Negar Farzam-kia", - "author_inst": "CRCHUM" - }, - { - "author_name": "Antoine Philippe Fournier", - "author_inst": "CRCHUM" - }, - { - "author_name": "Elizabeth Gowing", - "author_inst": "CRCHUM" - }, - { - "author_name": "Helene Jamann", - "author_inst": "CRCHUM" - }, - { - "author_name": "Florent Lemaitre", - "author_inst": "CRCHUM" - }, - { - "author_name": "Victoria Hannah Mamane", - "author_inst": "CRCHUM" - }, - { - "author_name": "Karine Thai", - "author_inst": "CRCHUM" - }, - { - "author_name": "Jean-Franois Cailhier", - "author_inst": "CRCHUM" - }, - { - "author_name": "Nicolas Chomont", - "author_inst": "CRCHUM" - }, - { - "author_name": "Andres Finzi", - "author_inst": "CRCHUM" - }, - { - "author_name": "Michael Chasse", - "author_inst": "CRCHUM" - }, - { - "author_name": "Madeleine Durand", - "author_inst": "CRCHUM" - }, - { - "author_name": "Nathalie Arbour", - "author_inst": "CRCHUM" - }, - { - "author_name": "Daniel E Kaufmann", - "author_inst": "CRCHUM" - }, - { - "author_name": "Alexandre Prat", - "author_inst": "CRCHUM" - }, - { - "author_name": "Catherine Larochelle", - "author_inst": "CRCHUM" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.19.20248567", "rel_title": "SARS-CoV-2 neutralizing antibodies; longevity, breadth, and evasion by emerging viral variants", @@ -995304,6 +1000621,85 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.12.22.423893", + "rel_title": "Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection", + "rel_date": "2020-12-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.22.423893", + "rel_abs": "SARS-CoV-2 uses subgenomic (sg)RNA to produce viral proteins for replication and immune evasion. We applied long-read RNA and cDNA sequencing to in vitro human and primate infection models to study transcriptional dynamics. Transcription-regulating sequence (TRS)-dependent sgRNA was upregulated earlier in infection than TRS-independent sgRNA. An abundant class of TRS-independent sgRNA consisting of a portion of ORF1ab containing nsp1 joined to ORF10 and 3UTR was upregulated at 48 hours post infection in human cell lines. We identified double-junction sgRNA containing both TRS-dependent and independent junctions. We found multiple sites at which the SARS-CoV-2 genome is consistently more modified than sgRNA, and that sgRNA modifications are stable across transcript clusters, host cells and time since infection. Our work highlights the dynamic nature of the SARS-CoV-2 transcriptome during its replication cycle. Our results are available via an interactive web-app at http://coinlab.mdhs.unimelb.edu.au/.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Jessie J.-Y. Chang", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Daniel Rawlinson", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Miranda E. Pitt", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "George Taiaroa", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Josie Gleeson", + "author_inst": "Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne" + }, + { + "author_name": "Chenxi Zhou", + "author_inst": "Department of Clinical Pathology, University of Melbourne," + }, + { + "author_name": "Francesca L. Mordant", + "author_inst": "Department of Clinical Pathology, University of Melbourne," + }, + { + "author_name": "Ricardo De Paoli-Iseppi", + "author_inst": "Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne" + }, + { + "author_name": "Leon Caly", + "author_inst": "Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Damian F. J. Purcell", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Tim P. Stinear", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Sarah L. Londrigan", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Michael B. Clark", + "author_inst": "Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne" + }, + { + "author_name": "Deborah A. Williamson", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Kanta Subbarao", + "author_inst": "WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Lachlan J M Coin", + "author_inst": "Department of Microbiology and Immunology, The University of Melbourne" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.22.423920", "rel_title": "Evolutionary tracking of SARS-CoV-2 genetic variants highlights intricate balance of stabilizing and destabilizing mutations", @@ -995517,65 +1000913,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.22.423917", - "rel_title": "T cell activation, highly armed cytotoxic cells and a sharp shift in monocytes CD300 receptors expression is characteristic of patients with severe COVID-19", - "rel_date": "2020-12-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.22.423917", - "rel_abs": "COVID-19 manifests with a wide diversity of clinical phenotypes characterized by dysfunctional and exaggerated host immune responses. Many results have been described on the status of the immune system of patients infected with SARS-CoV-2, but there are still aspects that have not been fully characterized. In this study, we have analyzed a cohort of patients with mild, moderate and severe disease. We performed flow cytometric studies and correlated the data with the clinical features and clinical laboratory values of patients. Both conventional and unsupervised data analyses concluded that patients with severe disease are characterized, among others, by a higher state of activation in all T cell subsets, higher expression of perforin and granzyme B in cytotoxic cells, expansion of adaptive NK cells and the accumulation of activated and immature dysfunctional monocytes which are identified by a low expression of HLA-DR and an intriguing abrupt change in the expression pattern of CD300 receptors. More importantly, correlation analysis showed a strong association between the alterations in the immune cells and the clinical signs of severity. These results indicate that patients with severe COVID-19 have a broad perturbation of their immune system, and they will help to understand the immunopathogenesis of severe COVID-19 as well as could be of special value for physicians to decide which specific therapeutic options are most effective for their patients.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Olatz Zenarruzabeitia", - "author_inst": "Biocruces Bizkaia Health Research Institute" - }, - { - "author_name": "Gabirel Astarloa-Pando", - "author_inst": "Biocruces Bizkaia Health Research Institute" - }, - { - "author_name": "I\u00f1igo Terr\u00e9n", - "author_inst": "Biocruces Bizkaia Health Research Institute" - }, - { - "author_name": "Ane Orrantia", - "author_inst": "Biocruces Bizkaia Health Research Institute" - }, - { - "author_name": "Raquel P\u00e9rez-Garay", - "author_inst": "Biocruces Bizkaia Health Research Institute" - }, - { - "author_name": "Iratxe Seijas-Betolaza", - "author_inst": "Biocruces Bizkaia Health Research Institute" - }, - { - "author_name": "Javier Nieto-Arana", - "author_inst": "Biocruces Bizkaia Health Research Institute" - }, - { - "author_name": "Natale Imaz-Ayo", - "author_inst": "Biocruces Bizkaia Health Research Institute" - }, - { - "author_name": "Silvia P\u00e9rez-Fern\u00e1ndez", - "author_inst": "Biocruces Bizkaia Health Research Institute" - }, - { - "author_name": "Eunate Arana-Arri", - "author_inst": "Biocruces Bizkaia Health Research Institute" - }, - { - "author_name": "Francisco Borrego", - "author_inst": "Biocruces Bizkaia Health Research Institute" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.12.21.423860", "rel_title": "Analyzing the vast coronavirus literature with CoronaCentral", @@ -997181,6 +1002518,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.19.423597", + "rel_title": "A comprehensive transcriptome analysis reveals broader but weaker host response of SARS-CoV-2 than SARS-CoV", + "rel_date": "2020-12-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.19.423597", + "rel_abs": "COVID-19, which has resulted a worldwide health crisis with more than 74.9 million confirmed cases worldwide by December 2020, is caused by a newly emerging coronavirus identified and named SARS-CoV-2 in February in Wuhan, China. Experiences in defeating SARS, which infested during 2002-2003, can be used in treating the new disease. However, comparative genomics and epidemiology studies have shown much difference between SARS-CoV and SARS-CoV-2, which underlies the different clinical features and therapies in between those two diseases. Further studies comparing transcriptomes infected by these two viruses to uncover the differences in host responses would be necessary. Here we conducted a comprehensive transcriptome analysis of SARS-CoV and SARS-CoV-2-infected human cell lines, including Caco-2, Calu-3, H1299. Clustering analysis and expression of ACE2 show that SARS-CoV-2 has broader but weaker infection, where the largest discrepancy occurs in the epithelial lung cancer cell, Calu-3. SARS-CoV-2 genes also show less tissue specificity than SARS-CoV genes. Furthermore, we detected more general but moderate immune responses in SARS-CoV-2 infected transcriptomes by comparing weighted gene co-expression networks and modules. Our results suggest a different immune therapy and treatment scheme for COVID-19 patients than the ones used on SARS patients. The wider but weaker permissiveness and host responses of virus infection may also imply a long-term existence of SARS-CoV-2 among human populations.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Chi Sum Leung", + "author_inst": "AmazingX Academy" + }, + { + "author_name": "Songhong Xie", + "author_inst": "AmazingX Academy" + }, + { + "author_name": "Jiali Feng", + "author_inst": "AmazingX Academy" + }, + { + "author_name": "Dongjing Chen", + "author_inst": "AmazingX Academy" + }, + { + "author_name": "Aimei Dai", + "author_inst": "School of Life Science, Sun Yat-sen University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.18.20248455", "rel_title": "The impact of the first UK Covid-19 lockdown on carers and people living with low prevalence dementia: results from the Rare Dementia Support survey", @@ -997478,69 +1002850,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.12.18.20248461", - "rel_title": "SARS-CoV-2-Specific Antibody Profiles Distinguish Patients with Moderate from Severe COVID-19", - "rel_date": "2020-12-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248461", - "rel_abs": "The production of SARS-CoV-2-specific neutralizing antibodies is widely considered as a key mechanism for COVID-19 resolution and protection. However, beyond their protective function, antibodies to SARS-CoV-2 may also participate in disease pathogenesis. To explore the potential relationship between virus-specific humoral responses and COVID-19 immunopathology, we measured serum antibody classes and subclasses to the receptor-binding domain of the SARS-CoV-2 spike protein and the nucleoprotein in a cohort of hospitalized COVID-19 patients with moderate to severe disease. We found that RBD-specific IgG1 and IgG3 dominated the humoral response to SARS-CoV-2, were more abundant in severe patients, and positively correlated with several clinical parameters of inflammation. In contrast, a virus-specific IgA2 response skewed toward RBD rather than NP associated with a more favorable clinical course. Interestingly, RBD-dominant IgA2 responses were mostly detected in patients with gastrointestinal symptoms, suggesting the possible involvement of intrinsically tolerogenic gut immune pathways in the attenuation of virus-induced inflammation and disease resolution.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Leire De Campos Mata", - "author_inst": "Translational clinical research program, Hospital del Mar Medical Research institute, Barcelona, Spain" - }, - { - "author_name": "Janet Pinero", - "author_inst": "Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu " - }, - { - "author_name": "Sonia Tejedor Vaquero", - "author_inst": "Translational clinical research program, Hospital del Mar Medical Research Institute (IMIM) Barcelona, Spain" - }, - { - "author_name": "Roser Tach\u00f3-Pi\u00f1ot", - "author_inst": "Translational clinical research program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain" - }, - { - "author_name": "Maria Kuksin", - "author_inst": "Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Itziar Arrieta Aldea", - "author_inst": "Department of Infectious Diseases, Hospital Del Mar, Barcelona, Spain" - }, - { - "author_name": "Natalia Rodrigo Melero", - "author_inst": "Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain" - }, - { - "author_name": "Carlo Carolis", - "author_inst": "Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader, Barcelona, Spain" - }, - { - "author_name": "Laura Furlong", - "author_inst": "Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Pompeu " - }, - { - "author_name": "Andrea Cerutti", - "author_inst": "Translational clinical research program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain/Department of Medicine, Immunology Institute, Icah" - }, - { - "author_name": "Judit Villar-Garcia", - "author_inst": "Department of Infectious Diseases, Hospital Del Mar, 08003, Barcelona, Spain" - }, - { - "author_name": "Giuliana Magri", - "author_inst": "Translational clinical research program, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.18.20248483", "rel_title": "Effects of obesity on serum levels of SARS-CoV-2-specific antibodies in COVID-19 patients", @@ -999171,6 +1004480,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.18.20248434", + "rel_title": "Excess deaths among Latino people in California during the COVID-19 pandemic", + "rel_date": "2020-12-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248434", + "rel_abs": "BackgroundLatino people in the US are experiencing higher excess deaths during the COVID-19 pandemic than any other racial/ethnic group, but it is unclear which subgroups within this diverse population are most affected. Such information is necessary to target policies that prevent further excess mortality and reduce inequities.\n\nMethodsUsing death certificate data for January 1, 2016 through February 29, 2020 and time-series models, we estimated the expected weekly deaths among Latino people in California from March 1 through October 3, 2020. We quantified excess mortality as observed minus expected deaths and risk ratios (RR) as the ratio of observed to expected deaths. We considered subgroups defined by age, sex, place of birth, education, occupation, and combinations of these factors.\n\nFindingsDuring the first seven months of the pandemic, Latino deaths in California exceeded expected deaths by 10,316, a 31% increase. Excess death rates were greatest for individuals born in Mexico (RR 1.44; 95% PI, 1.41, 1.48) or Central America (RR 1.49; 95% PI, 1.37, 1.64), with less than a high school degree (RR 1.41; 95% PI, 1.35, 1.46), or in food-and-agriculture (RR 1.60; 95% PI, 1.48, 1.74) or manufacturing occupations (RR 1.59; 95% PI, 1.50, 1.69). Immigrant disadvantages in excess death were magnified among working-age Latinos in essential occupations.\n\nInterpretationThe pandemic has disproportionately impacted mortality among Latino immigrants and Latinos in unprotected essential jobs; Interventions to reduce these disparities should include early vaccination, workplace safety enforcement, and expanded access to medical care.\n\nFundingNational Institute on Aging; UCSF\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSSeveral articles have suggested all-cause excess mortality estimates are superior to official COVID-19 counts for assessing the impact of the pandemic on marginalized populations that lack access to testing and healthcare. We searched PubMed, Google scholar, and the medRxiv preprint database through December 22, 2020 for studies of (\"excess mortality\" or \"excess death\") AND (\"COVID-19\" or \"coronavirus\") set in the United States and we identified two empirical studies with estimates of excess mortality among Latinos during the pandemic. The study set in California (from our research team) found per capita excess mortality was highest among Black and Latino people. The national study found percent excess mortality was significantly higher among Latino people than any other racial/ethnic group. Neither study further disaggregated the diverse Latino population or provided subgroup estimates to clarify why excess pandemic mortality is so high in this population. In the U.S., official COVID-19 statistics are rarely disaggregated by place of birth, education, or occupation which has resulted in a lack of evidence of how these factors have impacted mortality during the pandemic. No study to date of excess mortality in the U.S. has provided estimates for immigrant or occupational subgroups.\n\nAdded value of this studyOur population-based observational study of all-cause mortality during the COVID-19 pandemic provides the first estimates of within-group heterogeneity among the Latino population in California - one of the populations hardest hit by COVID-19 in the U.S. We provide the first subgroup estimates by place of birth and occupational sector, in addition to combined estimates by foreign-birth and participation in an essential job and education. In doing so, we reveal that Latino immigrants in essential occupations have the highest risk of excess death during the pandemic among working-age Latinos. We highlight the heightened risk of excess mortality associated with food/agriculture and manufacturing occupational sectors, essential sectors in which workers may lack COVID-19 protections.\n\nImplications of all the available evidenceOur study revealed stark disparities in excess mortality during the COVID-19 pandemic among Latinos, pointing to the particularly high vulnerability of Latino immigrants and Latinos in essential jobs. These findings may offer insight into the disproportionate COVID-19 mortality experienced by immigrants or similarly marginalized groups in other contexts. Interventions to reduce these disparities should include policies enforcing occupational safety, especially for immigrant workers, early vaccination, and expanded access to medical care.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Alicia R. Riley", + "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco" + }, + { + "author_name": "Yea-Hung Chen", + "author_inst": "Institute for Global Health Sciences, University of California, San Francisco" + }, + { + "author_name": "Ellicott C. Matthay", + "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco" + }, + { + "author_name": "M. Maria Glymour", + "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco" + }, + { + "author_name": "Jacqueline M. Torres", + "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco" + }, + { + "author_name": "Alicia Fernandez", + "author_inst": "Department of Medicine, University of California, San Francisco" + }, + { + "author_name": "Kirsten Bibbins-Domingo", + "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.18.20248449", "rel_title": "Coinfection with Respiratory Pathogens in COVID-19 in Korea", @@ -999328,53 +1004680,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.18.20248317", - "rel_title": "The COSEVAST Study: Unravelling the role of Arterial Stiffness in COVID-19 Disease severity.", - "rel_date": "2020-12-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248317", - "rel_abs": "BackgroundBased on the detailed review of available research and case studies reported in reputed international journals, it can be concluded that endothelial damage (En-dotheliitis) both in small and large arteries may be an important factor of morbidity and mortality in COVID-19 patients. Arterial stiffness due to Endothelial Dysfunction has been established as an independent and specific marker of various chronic cardiovascular diseases.\n\nObjectiveOur objective was to examine functional impairment of the arteries in COVID-19 disease and establish the non-invasive measurement of Arterial Stiffness as an independent marker of disease severity.\n\nMethodsWe recorded the Arterial Stiffness of 23 Mild, 21 Moderate and 20 Severe COVID-19 patients grouped on latest NIH severity criteria. We observed Arterial Stiffness of COVID-19 patients with standard parameters like non-invasive Carotid-Femoral Pulse Wave velocity (cfPWV), Age-Normalized increase in cfPWV (ANI_cfPWV).\n\nResultsModerate and Severe COVID-19 patients have extremely elevated arterial stiffness than Mild patients. In Mild patients, cfPWV (829.1 {+/-} 139.2 cm/s) was extremely significantly lower than both Moderate (1067 {+/-} 152.5 cm/s, P< 0.0001) and Severe (1416 {+/-} 253.9 cm/s, P < 0.0001) patients. ANI_cfPWV in Moderate and Severe patients was significantly higher than Mild patients. (Mild: 101.2 {+/-} 126.1 cm/s; Moderate: 279 {+/-} 114.4 cm/s; Severe: 580.1 {+/-} 216.4 cm/s; intergroup P <0.0001). Conclusion: Our findings strongly suggest that arterial stiffness can be an independent and accurate marker for objective risk stratification and therapeutic alleviation of the acute cardiovascular complications like MODS in COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sanjeev Kumar", - "author_inst": "All India Institute of Medical Sciences Patna" - }, - { - "author_name": "Neeraj Kumar", - "author_inst": "All India Institute of Medical Sciences Patna" - }, - { - "author_name": "Abhyuday Kumar", - "author_inst": "All India Institute of Medical Science Patna" - }, - { - "author_name": "Divendu Bhushan", - "author_inst": "All India Institute of Medical Science Patna" - }, - { - "author_name": "Amarjeet Kumar", - "author_inst": "All India Institute of Medical Science Patna" - }, - { - "author_name": "Ajeet Kumar", - "author_inst": "All India Institute of Medical Science Patna" - }, - { - "author_name": "Veena Singh", - "author_inst": "All India Institute of Medical Science Patna" - }, - { - "author_name": "Prabhat Kumar Singh", - "author_inst": "All India Institute of Medical Science Patna" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.12.18.20248454", "rel_title": "Lessons learned from Vietnam's COVID-19 response: the role of adaptive behavior change and testing in epidemic control", @@ -1001109,6 +1006414,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.12.17.20248382", + "rel_title": "Sub-national forecasts of COVID-19 vaccine acceptance across the UK: a large-scale cross-sectional spatial modelling study", + "rel_date": "2020-12-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.17.20248382", + "rel_abs": "The rollout of COVID-19 vaccines has begun to at-risk populations around the world. It is currently unclear whether rejection of the vaccine will pose challenges for achieving herd/community immunity either through large-scale rejection or localised pockets. Here we predict uptake of the vaccine at unprecedented spatial resolution across the UK using a large-scale survey of over 17,000 individuals. Although the majority of the UK population would likely take the vaccine, there is substantial heterogeneity in uptake intent across the UK. Large urban areas, including London and North West England, females, Black or Black British ethnicities, and Polish-speakers are among the least accepting. This study helps identify areas and socio-demographic groups where vaccination levels may not reach those levels required for herd immunity. Identifying clusters of non-vaccinators is extremely important in the context of achieving herd immunity as vaccination \"cold-spots\" can amplify epidemic spread and disproportionately increase vaccination levels required for herd protection.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Alex de Figueiredo", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.15.20247981", "rel_title": "SIREN protocol: Impact of detectable anti-SARS-CoV-2 on the subsequent incidence of COVID-19 in 100,000 healthcare workers: do antibody positive healthcare workers have less reinfection than antibody negative healthcare workers?", @@ -1001238,65 +1006562,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.17.20248377", - "rel_title": "Voxel-level forecast system for lesion development in patients with COVID-19", - "rel_date": "2020-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.17.20248377", - "rel_abs": "The global spread of COVID-19 seriously endangers human health and even lives. By predicting patients individualized disease development and further performing intervention in time, we may rationalize scarce medical resources and reduce mortality. Based on 1337 multi-stage ([≥]3) high-resolution chest computed tomography (CT) images of 417 infected patients from three centers in the epidemic area, we proposed a random forest + cellular automata (RF+CA) model to forecast voxel-level lesion development of patients with COVID-19. The model showed a promising prediction performance (Dice similarity coefficient [DSC] = 71.1%, Kappa coefficient = 0.612, Figure of Merit [FoM] = 0.257, positional accuracy [PA] = 3.63) on the multicenter dataset. Using this model, multiple driving factors for the development of lesions were determined, such as distance to various interstitials in the lung, distance to the pleura, etc. The driving processes of these driving factors were further dissected and explained in depth from the perspective of pathophysiology, to explore the mechanism of individualized development of COVID-19 disease. The complete codes of the forecast system are available at https://github.com/keyunj/VVForecast_covid19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Cheng Jin", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Yongjie Duan", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Yukun Cao", - "author_inst": "Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Hubei Province Key Laboratory of M" - }, - { - "author_name": "Jinyang Yu", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Zhanwei Xu", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Weixiang Chen", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Xiaoyu Han", - "author_inst": "Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Hubei Province Key Laboratory of M" - }, - { - "author_name": "Jia Liu", - "author_inst": "Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Hubei Province Key Laboratory of M" - }, - { - "author_name": "Jie Zhou", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Heshui Shi", - "author_inst": "Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Hubei Province Key Laboratory of M" - }, - { - "author_name": "Jianjiang Feng", - "author_inst": "Tsinghua University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.12.16.20248110", "rel_title": "Internal medicine clerkship amidst COVID-19 pandemic: clinical learning experience of undergraduate medical students at Makerere University, Uganda: a cross-sectional study", @@ -1002707,6 +1007972,45 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.12.17.423130", + "rel_title": "Suppression of miR-155 attenuates lung cytokine storm induced by SARS-CoV-2 infection in human ACE2-transgenic mice", + "rel_date": "2020-12-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.17.423130", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is a recent global pandemic. It is a deadly human viral disease, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with a high rate of infection, morbidity and mortality. Therefore, there is a great urgency to develop new therapies to control, treat and prevent this disease. Endogenous microRNAs (miRNAs, miRs) of the viral host are key molecules in preventing viral entry and replication, and building an antiviral cellular defense. Here, we have analyzed the role of miR-155, one of the most powerful drivers of host antiviral responses including immune and inflammatory responses, in the pathogenicity of SARS-CoV-2 infection. Subsequently, we have analyzed the potency of anti-miR-155 therapy in a COVID-19 mouse model (mice transgenic for human angiotensin I-converting enzyme 2 receptor (tg-mice hACE2)). We report for the first time that miR-155 expression is elevated in COVID-19 patients. Further, our data indicate that the viral load as well as miR-155 levels are higher in male relative to female patients. Moreover, we find that the delivery of anti-miR-155 to SARS-CoV-2-infected tg-mice hACE2 effectively suppresses miR-155 expression, and leads to improved survival and clinical scores. Importantly, anti-miR-155-treated tg-mice hACE2 infected with SARS-CoV-2 not only exhibit reduced levels of pro-inflammatory cytokines, but also have increased anti-viral and anti-inflammatory cytokine responses in the lungs. Thus, our study suggests anti-miR-155 as a novel therapy for mitigating the lung cytokine storm induced by SARS-CoV-2 infection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Dharmendra Kumar Soni", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Juan Cabrera-Luque", + "author_inst": "GeneDx" + }, + { + "author_name": "Swagata Kar", + "author_inst": "Bioqual Inc." + }, + { + "author_name": "Chaitali Sen", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Joseph Devaney", + "author_inst": "GeneDx" + }, + { + "author_name": "Roopa Biswas", + "author_inst": "Uniformed Services University of the Health Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.16.423166", "rel_title": "Molecular diversity analysis of the spike glycoprotein (S) gene from Hong Kong - China", @@ -1002796,37 +1008100,6 @@ "type": "new results", "category": "ecology" }, - { - "rel_doi": "10.1101/2020.12.14.20248201", - "rel_title": "Comparison of Healthcare costs and benefits of the UK's Covid-19 response with four European countries: Decision Modelling Study", - "rel_date": "2020-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20248201", - "rel_abs": "BackgroundIn responding to covid-19, governments have tried to balance protecting health while minimising Gross Domestic Product (GDP) losses. We compare health-related net benefit (HRNB) and GDP losses associated with government responses of the UK, Ireland, Germany, Spain, and Sweden from UK healthcare payer perspective.\n\nMethodsWe compared observed cases, hospitalisations, and deaths under \"mitigation\" to modelled events under \"no mitigation\" to 20th July 2020. We thus calculated healthcare costs, quality adjusted life years (QALYs), and HRNB at {pound}20,000/QALY saved by each country. On per population (i.e. per capita) basis, we compared HRNB with forecast reductions in 2020 GDP growth (overall or compared to Sweden as minimal mitigation country) and qualitatively and quantitatively described government responses.\n\nResultsThe UK saved 3.17 (0.32-3.65) million QALYs, {pound}33 (8-38) billion healthcare costs, and {pound}1416 (220-1637) HRNB per capita at {pound}20,000/QALY. Per capita, this is comparable to {pound}1,455 GDP loss using Sweden as comparator and offsets 46.1 (7.1-53.2)% of total {pound}3075 GDP loss.\n\nGermany, Spain, and Sweden had greater HRNB per capita. These also offset a greater percentage of total GDP losses per capita. Ireland fared worst on both measures. Countries with more mask wearing, testing, and population susceptibility had better outcomes. Highest stringency responses did not appear to have best outcomes.\n\nConclusionsOur exploratory analysis indicates the benefit of government covid-19 responses may outweigh their economic costs. The extent that HRNB offset economic losses appears to relate to population characteristics, testing levels, and mask wearing, rather than response stringency.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSOur research question was how the health-related net benefits and economic impacts of the UK response to the covid-19 epidemic first wave compared to other European countries. We searched PubMed, MedRxiv, and Arxiv for terms related to cost-effectivness, covid-19, and the UK.\n\nTwo studies compared predicted lives saved to predicted gross domestic product (GDP) losses. One found that lives saved by a lockdown would outweigh GDP losses, while another found a lockdown to cost {pound}10million per life saved. A later modelling study used quality adjusted life-years (QALYs), going beyond lives saved, and found cost per QALY was below {pound}50,000. A fourth, comparing observed to modelled deaths and hospitalisations, found the cost per QALY was at least {pound}220,000, and thus the UK response was not cost-effective. None of these were international comparisons. One international study found good health and economic outcomes to be correlated. Another found global trade reductions and voluntary behavioural changes to have greater impact on economic growth than government measures. Neither considered cost-effectiveness. However, they suggest comparison to GDP loss is naive as this is total loss and not that due to government restrictions.\n\nAdded value of this studyWe compare the UK to Ireland, Germany, Spain, and Sweden on health-related net benefits and economic impacts of government response from a UK National Health Service (NHS) perspective. We describe countries response measures. We compared model predictions of outcomes under \"no mitigation\" to observed outcomes under \"mitigation\" up to July 20th 2020. We estimated healthcare costs, QALYs, and health-related net benefit (HRNB) saved. We compared HRBN to GDP losses using Sweden as a \"minimal mitigation\" comparator and calculated the % of total GDP loss they offset.\n\nWe found the UK saved 3{middle dot}17 (0{middle dot}32-3{middle dot}65) million QALYs, {pound}33 ({pound}8-38) billion in healthcare costs, and {pound}1416 (220-1637) HRNB per capita at the NHS threshold of {pound}20,000/QALY. This is comparable to the {pound}1,455 GDP loss per capita using Sweden as comparator and offsets 46{middle dot}1% (7{middle dot}1-53{middle dot}2) of the total estimated {pound}3075 GDP loss per capita. We found that Germany, Spain, and probably Sweden had greater HRNB per capita and offset greater percentages of GDP loss per capita. Ireland fared worst on both measures. We found countries with more mask wearing, testing, and population susceptibility (e.g. older and more interpersonal contact) had better outcomes. Highest stringency responses did not appear to have best outcomes.\n\nImplications of all the available evidenceWe add to growing evidence that the total economic impact of covid-19 exceeds the HRNB of the UKs response. However, using Sweden as comparator and comparing across countries, we argue that GDP loss is not purely due to government restrictions and that due to restrictions may be outweighed by HRNB. We evaluated the extent to which countries have offset GDP losses, and these appear to be higher in countries with more at-risk populations, higher testing, and higher mask wearing, rather than those with most stringent restrictions.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Howard Thom", - "author_inst": "University of Bristol" - }, - { - "author_name": "Josephine Walker", - "author_inst": "University of Bristol" - }, - { - "author_name": "Peter Vickerman", - "author_inst": "University of Bristol" - }, - { - "author_name": "Will Hollingworth", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.12.14.20248155", "rel_title": "Investigating mental and physical disorders associated with COVID-19 in online health forums", @@ -1004429,6 +1009702,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.14.20248181", + "rel_title": "Predicting the need for escalation of care or death from repeated daily clinical observations and laboratory results in patients with SARS-CoV-2 during 2020: a retrospective population-based cohort study from the United Kingdom", + "rel_date": "2020-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20248181", + "rel_abs": "ObjectivesCurrently used prognostic tools for patients with SARS-CoV-2 infection are based on clinical and laboratory parameters measured at a single point in time, usually on admission. We aimed to determine how dynamic changes in clinical and laboratory parameters relate to SARS-CoV-2 prognosis.\n\nDesignretrospective, observational cohort study using routinely collected clinical data to model the dynamic change in prognosis of SARS-CoV-2.\n\nSettinga single, large hospital in England.\n\nParticipantsall patients with confirmed SARS-CoV-2 admitted to Nottingham University Hospitals (NUH) NHS Trust, UK from 1st February 2020 until 30th November 2020.\n\nMain outcome measuresIntensive Care Unit (ICU) admission, death and discharge from hospital.\n\nStatistical MethodsWe split patients into 1st (admissions until 30th June) and 2nd (admissions thereafter) waves. We incorporated all clinical observations, blood tests and other covariates from electronic patient records and follow up until death or 30 days from the point of hospital discharge. We modelled daily risk of admission to ICU or death with a time varying Cox proportional hazards model.\n\nResults2,964 patients with confirmed SARS-CoV-2 were included. Of 1,374 admitted during the 1st wave, 593 were eligible for ICU escalation, and 466 had near complete ascertainment of all covariates at admission. Our validation sample included 1,590 confirmed cases, of whom 958 were eligible for ICU admission. Our model had good discrimination of daily need for ICU admission or death (C statistic = 0.87 (IQR 0.85-0.90)) and predicted this daily prognosis better than previously published scores (NEWS2, ISCARIC 4C). In validation in the 2nd wave the score overestimated escalation (calibration slope 0.55), whilst retaining a linear relationship and good discrimination (C statistic = 0.88 (95% CI 0.81 -0.95)).\n\nConclusionsA bespoke SARS-CoV-2 escalation risk prediction score can predict need for clinical escalation better than a generic early warning score or a single estimation of risk at admission.\n\nWhat is already known on this topicSARS-CoV-2 is a recently emerged viral infection, which presents typically with flu like symptoms, can have severe sequelae and has caused a pandemic during 2020.\n\nA number of risk factors for poor outcomes including obesity, age and comorbidity have been recognized.\n\nRisk scores have been developed to stratify risk of poor outcome for patients with SARS-CoV-2 at admission, but these do not take account of dynamic changes in severity of disease on a daily basis.\n\nWhat this study addsWe have developed a dynamic risk score to predict escalation to ICU or death within the next 24 hours.\n\nOur score has good discrimination between those who will and not require ICU admission (or die) in both our derivation and validation cohorts.\n\nOur bespoke SARS-CoV-2 escalation risk prediction score can predict need for clinical escalation better than a generic early warning score or a single estimation of risk at admission.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Colin J Crooks", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Joe West", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Andrew Fogarty", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Joanne R Morling", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Matthew J Grainge", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Sherif Gonem", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Mark Simmonds", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Andrea Race", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Irene Juurlink", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Stephen Briggs", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Simon Cruikshank", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Susan Hammond-Pears", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Timothy R Card", + "author_inst": "University of Nottingham" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.15.20248279", "rel_title": "Shared genetic etiology between idiopathic pulmonary fibrosis and COVID-19 severity", @@ -1004574,45 +1009914,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.12.15.412809", - "rel_title": "Cyclic gallium-68 labeled peptides for specific detection of human angiotensin-converting enzyme 2", - "rel_date": "2020-12-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.15.412809", - "rel_abs": "In this study, we developed ACE2-specific, peptide-derived 68Ga-labeled radiotracers, motivated by the hypotheses that (1) ACE2 is an important determinant of SARS-CoV-2 susceptibility, and (2) that modulation of ACE2 in COVID-19 drives severe organ injury.\n\nMethodsA series of NOTA-conjugated peptides derived from the known ACE2 inhibitor DX600 were synthesized, with variable linker identity. Since DX600 bears two cystine residues, both linear and cyclic peptides were studied. An ACE2 inhibition assay was used to identify lead compounds, which were labeled with 68Ga to generate peptide radiotracers ([68Ga]NOTA-PEP). The aminocaproate-derived radiotracer [68Ga]NOTA-PEP4 was subsequently studied in a humanized ACE2 (hACE2) transgenic model.\n\nResultsCyclic DX-600 derived peptides had markedly lower IC50s than their linear counterparts. The three cyclic peptides with triglycine, aminocaproate, and polyethylene glycol linkers had calculated IC50s similar to, or lower than the parent DX600 molecule. Peptides were readily labeled with 68Ga, and the biodistribution of [68Ga]NOTA-PEP4 was determined in a hACE2 transgenic murine cohort. Pharmacologic concentrations of co-administered NOTA-PEP (\"blocking\") showed significant reduction of [68Ga]NOTA-PEP4 signals in the in the heart, liver, lungs, and small intestine. Ex vivo hACE2 activity in these organs was confirmed as a correlate to in vivo results.\n\nConclusionsNOTA-conjugated, cyclic peptides derived from the known ACE2 inhibitor DX600 retain their activity when N-conjugated for 68Ga chelation. In vivo studies in a transgenic hACE2 murine model using the lead tracer [68Ga]NOTA-PEP4 showed specific binding in the heart, liver, lungs and intestine - organs known to be affected in SARS-CoV-2 infection. These results suggest that [68Ga]NOTA-PEP4 could be used to detect organ-specific suppression of ACE2 in SARS-CoV-2 infected murine models and COVID-19 patients.\n\nTOC figure\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=44 SRC=\"FIGDIR/small/412809v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@f3047org.highwire.dtl.DTLVardef@12ab9a9org.highwire.dtl.DTLVardef@33f43org.highwire.dtl.DTLVardef@12e77ed_HPS_FORMAT_FIGEXP M_FIG For Table of Contents use only\n\nC_FIG", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Matthew Parker", - "author_inst": "UCSF" - }, - { - "author_name": "Joseph Blecha", - "author_inst": "UCSF" - }, - { - "author_name": "Oren Rosenberg", - "author_inst": "UCSF" - }, - { - "author_name": "Michael Ohliger", - "author_inst": "UCSF" - }, - { - "author_name": "Robert Flavell", - "author_inst": "UCSF" - }, - { - "author_name": "David Meybin Wilson", - "author_inst": "UCSF" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.12.15.422939", "rel_title": "Choice of assemblers has a critical impact on de novo assembly of SARS-CoV-2 genome and characterizing variants", @@ -1006095,6 +1011396,33 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.12.14.422793", + "rel_title": "Genomic diversity analysis of SARS-CoV-2 genomes in Rwanda", + "rel_date": "2020-12-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.14.422793", + "rel_abs": "COVID-19 (Coronavirus disease 2019) is an emerging pneumonia-like respiratory disease of humans and is recently spreading across the globe.\n\nObjectiveTo analyze the genome sequence of SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) isolated from Rwanda with other viral strains from African countries.\n\nMethodsWe downloaded 75 genomes sequences of clinical SARS-CoV-2 from the GISAID (global initiative on sharing all influenza data) database and we comprehensively analyzed these SARS-CoV-2 genomes sequences alongside with Wuhan SARS-CoV-2 sequences as the reference strains.\n\nResultsWe analyzed 75 genomes sequences of SARS-CoV-2 isolated in different African countries including 10 samples of SARS-CoV-2 isolated in Rwanda between July and August 2020. The phylogenetic analysis of the genome sequence of SARS-CoV-2 revealed a strong identity with reference strains between 90-95%. We identified a missense mutation in four proteins including orf1ab polyprotein, NSP2, 2-O-ribose methyltransferase and orf1a polyprotein. The most common changes in the base are C > T. We also found that all clinically SARS-CoV-2 isolated from Rwanda had genomes belonging to clade G and lineage B.1.\n\nConclusionsTracking the genetic evolution of SARS-CoV-2 over time is important to understand viral evolution pathogenesis. These findings may help to implement public health measures in curbing COVID-19 in Rwanda.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Nzungize Lambert", + "author_inst": "Synthetic Biology Rwanda" + }, + { + "author_name": "Ndishimye Pacifique", + "author_inst": "Rwanda Joint Task Force COVID-19, Rwanda Biomedical Center, Ministry of Health, Kigali, Rwanda." + }, + { + "author_name": "Fathiah Zakham", + "author_inst": "Laboratory of Virology, University of Helsinki, Helsinki 00014, Finland." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.12.10.20245944", "rel_title": "Azithromycin in Hospitalised Patients with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", @@ -1006308,81 +1011636,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.11.20247742", - "rel_title": "Changes in cardiovascular disease monitoring in English primary care during the COVID-19 pandemic: an observational cohort study", - "rel_date": "2020-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.11.20247742", - "rel_abs": "ObjectiveTo quantify the impact and recovery in cardiovascular disease monitoring in primary care associated with the first COVID-19 lockdown.\n\nDesignRetrospective nationwide primary care cohort study, utilising data from 1st January 2018 to 27th September 2020.\n\nSettingWe extracted primary care electronic health records data from 514 primary care practices in England contributing to the Oxford Royal College of General Practitioners Clinical Informatics Digital Hub (ORCHID). These practices were representative of English primary care across urban and non-urban practices.\n\nParticipantsThe ORCHID database included 6,157,327 active patients during the study period, and 13,938,390 patient years of observation (final date of follow-up 27th September 2020). The mean (SD) age was 38{+/-}24 years, 49.4% were male and the majority were of white ethnicity (65% [21.9% had unknown ethnicity])\n\nExposureThe primary exposure was the first national lockdown in the UK, starting on 23rd March 2020.\n\nMain outcome measuresRecords of cholesterol, blood pressure, HbA1c and International Normalised Ratio (INR) measurement derived from coded entries in the primary care electronic health record.\n\nResultsRates of cholesterol, blood pressure, HbA1c and INR recording dropped by 23-87% in the week following the first UK national lockdown, compared with the previous week. The largest decline was seen in cholesterol (IRR 0.13, 95% CI 0.11 to 0.15) and smallest for INR (IRR 0.77, 95% CI 0.72 to 0.81).\n\nFollowing the immediate drop, rates of recorded tests increased on average by 5-9% per week until 27th September 2020. However, the number of recorded measures remained below that expected for the time of year, reaching 51.8% (95% CI 51.8 to 51.9%) for blood pressure, 63.7%, (95% CI 63.7% to 63.8%) for cholesterol measurement and 70.3% (95% CI 70.2% to 70.4%) for HbA1c. Rates of INR recording declined throughout the previous two years, a trend that continued after lockdown. There were no differences in the times series trends based on sex, age, ethnicity or deprivation.\n\nConclusionsCardiovascular disease monitoring in English primary care declined substantially from the time of the first UK lockdown. Despite a consistent recovery in activity, there is still a substantial shortfall in the numbers of recorded measurements to those expected. Strategies are required to ensure cardiovascular disease monitoring is maintained during the COVID-19 pandemic.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Clare R Bankhead", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sarah Lay-Flurrie", - "author_inst": "University of Oxford" - }, - { - "author_name": "Brian D Nicholson", - "author_inst": "Nuffield Department of Primary Care Health Sciences" - }, - { - "author_name": "James P Sheppard", - "author_inst": "University of Oxford" - }, - { - "author_name": "Chris P Gale", - "author_inst": "University of Leeds" - }, - { - "author_name": "Harshana Liyanage", - "author_inst": "University of Oxford" - }, - { - "author_name": "Dylan McGagh", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mark Minchin", - "author_inst": "National Institute for Health and Care Excellence" - }, - { - "author_name": "Rafael Perera", - "author_inst": "University of Oxford" - }, - { - "author_name": "Julian Sherlock", - "author_inst": "University of Oxford" - }, - { - "author_name": "Margaret Smith", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nicholas PB Thomas", - "author_inst": "Royal College of General Practitioners" - }, - { - "author_name": "Cynthia Wright Drakesmith", - "author_inst": "University of Oxford" - }, - { - "author_name": "Simon D de Lusignan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Richard Hobbs", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2020.12.11.20242511", "rel_title": "Treatment provision for adults with ADHD during the COVID-19 pandemic: An exploratory study on patient and therapist experience with on-site sessions using face masks vs. telepsychiatric sessions", @@ -1007849,6 +1013102,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.14.20248160", + "rel_title": "Acceptability and feasibility of strategies to shield the vulnerable during the COVID-19 outbreak: a qualitative study in six Sudanese communities", + "rel_date": "2020-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20248160", + "rel_abs": "BackgroundShielding of high-risk groups from coronavirus disease (COVID-19), either within their households or safe communal structures, has been suggested as a realistic alternative to severe movement restrictions in response to the COVID-19 epidemic in low-income countries. To our knowledge, this concept has not been tested or evaluated in resource-poor settings. This study aimed to explore the acceptability and feasibility of strategies to shield persons at higher risk of severe COVID-19 outcomes, during the COVID-19 epidemic in six communities in Sudan.\n\nMethodsWe purposively sampled participants from six communities, illustrative of urban, rural and forcibly-displaced settings. In-depth telephone interviews were held with 59 members of households with one or more members at higher risk of severe COVID-19 outcomes. Follow-up interviews were held with 30 community members after movement restrictions were eased across the country. All interviews were audio-recorded, transcribed verbatim, and analysed using a two-stage deductive and inductive thematic analysis.\n\nResultsMost participants were aware that some people are at higher risk of severe COVID-19 outcomes but were unaware of the concept of shielding. Most participants found shielding acceptable and consistent with cultural inclinations to respect elders and protect the vulnerable. However, extra-household shielding arrangements were mostly seen as socially unacceptable. Participants reported feasibility concerns related to the social isolation of shielded persons and loss of income for shielding families. The acceptability and feasibility of shielding strategies were reduced after movement restrictions were eased, as participants reported lower perception of risk in their communities and increased pressure to comply with social commitments outside the house.\n\nConclusionShielding is generally acceptable in the study communities. Acceptability is influenced by feasibility, and by contextual changes in the epidemic and associated policy response. The promotion of shielding should capitalise on the cultural and moral sense of duty towards elders and vulnerable groups. Communities and households should be provided with practical guidance to implement feasible shielding options. Households must be socially, psychologically and financially supported to adopt and sustain shielding effectively.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nada Abdelmagid", + "author_inst": "London School of Hygiene and Tropical Medicine, (Department of Infectious Disease Epidemiology), London, (London), United Kingdom / Sudan COVID-19 Research Grou" + }, + { + "author_name": "Salma A.E. Ahmed", + "author_inst": "Independent public health researcher, Khartoum, (Khartoum), Sudan / Sudan COVID-19 Research Group" + }, + { + "author_name": "Nazik Nurelhuda", + "author_inst": "University of Khartoum, Faculty of Dentistry, Khartoum, (Khartoum), Sudan / Sudan COVID-19 Research Group" + }, + { + "author_name": "Israa Zainalabdeen", + "author_inst": "Y-PEER Sudan, Khartoum, (Khartoum), Sudan / Sudan COVID-19 Research Group" + }, + { + "author_name": "Aljaile Ahmed", + "author_inst": "Y-PEER Sudan, Khartoum, (Khartoum), Sudan / Sudan COVID-19 Research Group" + }, + { + "author_name": "Mahmoud Ali Fadlallah", + "author_inst": "Asian Institute of Technology, Bangkok, (Bangkok), Thailand / Public Health Institute (PHI), Khartoum, (Khartoum), Sudan / Sudan COVID-19 Research Group" + }, + { + "author_name": "Maysoon Dahab", + "author_inst": "London School of Hygiene and Tropical Medicine, (Department of Infectious Disease Epidemiology), London, (London), United Kingdom / Sudan COVID-19 Research Grou" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.11.20247262", "rel_title": "COVID-19 in persons affected by Hansen's disease in Brazil", @@ -1007982,129 +1013278,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.13.20248122", - "rel_title": "Screening for high amounts of SARS-CoV-2 identifies pre-symptomatic subjects among healthy healthcare workers", - "rel_date": "2020-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.13.20248122", - "rel_abs": "BackgroundPre-symptomatic subjects are spreaders of SARS-CoV-2 infection, and strategies that could identify these subjects, particularly in hospital settings, are needed.\n\nMethodsWe tested a cohort of 9449 employees at work at the Karolinska University Hospital, Stockholm, Sweden for SARS-CoV-2 RNA and antibodies, linked the screening results to sick leave records and examined the association between screening results and past or future sick leave using multinomial logistic regression.\n\nResultsWe found that healthcare workers with high amounts of SARS-CoV-2 virus, as indicated by the Cycle threshold (Ct) value in the PCR, had the highest risk for sick leave in the two weeks after testing (OR 11{middle dot}97 (CI 95% 6{middle dot}29-22{middle dot}80)) whereas subjects with low amounts of virus had the highest risk for sick leave in the past three weeks before testing (OR 6{middle dot}31 (4{middle dot}38-9{middle dot}08)). Only 2{middle dot}5% of employees were SARS-CoV-2 positive while 10{middle dot}5% were positive by serology and 1{middle dot}2% were positive in both tests. Serology-positive subjects were not at excess risk for future sick leave (OR 1{middle dot}06 (95% CI, 0{middle dot}71-1{middle dot}57)), but virus-positive subjects had a 7{middle dot}23 fold (95% CI, 4{middle dot}52-11{middle dot}57)) increased risk for sick leave within two weeks post testing.\n\nConclusionsScreening of asymptomatic healthcare workers for high amounts of SARS-CoV-2 virus using Ct values will identify pre-symptomatic subjects who will develop disease in the next few weeks. Identification of potentially contagious, pre-symptomatic subjects is likely critical for protecting patients and healthcare workers.\n\nMain pointHealthy healthcare workers with low amounts of SARS-CoV-2 nucleic acids will previously have had the disease. Presence of a high amount of SARS-CoV-2 nucleic acids predicts future symptomatic disease.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Joakim Dillner", - "author_inst": "Karolinska University Laboratory, Karolinska University Hospital" - }, - { - "author_name": "Miriam Elfstr\u00f6m", - "author_inst": "Karolinska University Laboratory, Karolinska University Hospital" - }, - { - "author_name": "Jonas Blomqvist", - "author_inst": "Karolinska University Hospital" - }, - { - "author_name": "Lars Engstrand", - "author_inst": "Karolinska University Hospital, Karolinska Institutet, Science for Life Laboratory" - }, - { - "author_name": "Mathias Uhl\u00e9n", - "author_inst": "Science for Life Laboratory" - }, - { - "author_name": "Carina Eklund", - "author_inst": "Karolinska University Laboratory, Karoliska University Hospital" - }, - { - "author_name": "Fredrik Boulund", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Camilla Lagheden", - "author_inst": "Karolinska University Laboratory, Karolinska University Hospital" - }, - { - "author_name": "Marica Hamsten", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Sara Nordqvist Kleppe", - "author_inst": "Karolinska University Laboratory, Karolinska University Hospital" - }, - { - "author_name": "Maike Seifert", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Cecilia Hellstr\u00f6m", - "author_inst": "KTH Royal Institute of Technology, Science for LifeLaboratory" - }, - { - "author_name": "Jennie Olofsson", - "author_inst": "KTH Royal Institute of Technology, Science for Life Laboratory" - }, - { - "author_name": "Eni Andersson", - "author_inst": "KTH Royal Institute of Technology, Science for Life Laboratory" - }, - { - "author_name": "August Jernbom Falk", - "author_inst": "KTH Royal Institute of Technology, Science for Life Laboratory" - }, - { - "author_name": "Sofia Bergstr\u00f6m", - "author_inst": "KTH Royal Institute of Technology, Science for Life Laboratory" - }, - { - "author_name": "Emilie Hultin", - "author_inst": "Karolinska University Laboratory, Karolinska University Hospital" - }, - { - "author_name": "Elisa Pin", - "author_inst": "KTH Royal Institute of Technology, Science for Life Laboratory" - }, - { - "author_name": "Ville N Pimenoff", - "author_inst": "Karolinska University Laboratory, Karolinska University Hospital" - }, - { - "author_name": "Sadaf Hassan", - "author_inst": "Karolinska University Laboratory, Karolinska University Hospital" - }, - { - "author_name": "Anna M\u00e5nberg", - "author_inst": "KTH Royal Institute of Technology, Science for Life Laboratory" - }, - { - "author_name": "Peter Nilsson", - "author_inst": "KTH Royal Institute of Technology, Science for Life Laboratory" - }, - { - "author_name": "My Hedhammar", - "author_inst": "KTH Royal Institute of Technology, Science for Life Laboratory" - }, - { - "author_name": "Sophia Hober", - "author_inst": "KTH Royal Institute of Technology" - }, - { - "author_name": "Johan Mattsson", - "author_inst": "Karolinska University Hospital" - }, - { - "author_name": "Sara Arroyo Muhr", - "author_inst": "Karolinska University Laboratory, Karolinska University Hospital" - }, - { - "author_name": "Kalle Conneryd Lundgren", - "author_inst": "Karolinska University Hospital" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.11.20247353", "rel_title": "Association of University Reopening Policies with New Confirmed COVID-19 Cases in the United States", @@ -1009590,6 +1014763,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, + { + "rel_doi": "10.1101/2020.11.22.20235184", + "rel_title": "Neurological Disorders associated with COVID-19 Hospital Admissions : Experience of a Single Tertiary Healthcare Centre", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.22.20235184", + "rel_abs": "BackgroundEarly reports have detailed a range of neurological symptoms in patients with the SARS-CoV-2 infection. However, there is a lack of detailed description and incidence of the neurological disorders amongst hospitalized COVID-19 patients. We describe a range of neurological disorders (other than non-specific neurological symptoms), including their clinical, radiological and laboratory findings, encountered in our cohort of COVID-19 patients admitted to a large tertiary institution.\n\nMethodsWe reviewed our prospectively collated database of all adult Neurology referrals, Neurology and Stroke admissions and Neurological multi-disciplinary team meetings for all hospitalized patients with suspected or proven COVID-19 from 17 March 2020 to 31 August 2020.\n\nResultsTwenty-nine of 1243 COVID-19 inpatients (2.3%) presented with COVID-19-related neurological disorders. The mean age was 68.9 +/- 13.5(SD) years, age range of 34-97 years, and there were 16 males. 22 patients had confirmed, 5 were probable and 2 had suspected COVID-19 infection according to the WHO case classification. Eight patients (27%) required critical care admission. Neurological symptoms at presentation included acute confusion and delirium, seizures, and new focal neurological deficits. Based on the pre-defined neurological phenotype, COVID-19 patients were grouped into four main categories. 16 patients had cerebrovascular events (13 with acute ischaemic stroke and 3 had haemorrhagic features), 7 patients were found to have inflammatory, non-inflammatory and autoimmune encephalopathy (including 2 with known Multiple Sclerosis), whilst disorders of movement and peripheral nervous system were diagnosed in 3 patients each.\n\nConclusionAlthough the exact prevalence and aetiology remain unclear, new onset of neurological disorders, in addition to anosmia, is non-sporadic during the acute COVID-19-infection. Longitudinal follow-up of these patients is required to determine the clinical and functional outcome, treatment response and long-term effects of the SARS-CoV-2 infection.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Permesh Singh Dhillon", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Robert Dineen", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Haley Morris", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Radu Tanasescu", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Esmaeil Nikfekr", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Jonathan Evans", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Cris S Constantinescu", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Akram A Hosseini", + "author_inst": "Nottingham University Hospitals NHS Trust" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.12.08.20246140", "rel_title": "How detection ranges and usage stops impact digital contact tracing effectiveness for COVID-19", @@ -1009747,45 +1014967,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.08.20245894", - "rel_title": "Why the SARS-CoV-2 antibody test results may be misleading: insights from a longitudinal analysis of COVID-19", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20245894", - "rel_abs": "To estimate the effectiveness of vaccines in development, a robust mechanism is required to understand immunity, risks of reinfection and measure the immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and how this may change over time. This study is a longitudinal analysis of COVID-19 infection rates using PCR, membrane immunoassay and chemiluminescent microparticle immunoassay (CMIA) diagnostic tests. Our data confirm that antibody levels wane in the three months after symptom onset. Comparison of the three methods used suggests that quantitative CMIA testing may exaggerate numbers of COVID-19 negative individuals.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jorg Taubel", - "author_inst": "Richmond Research Institute" - }, - { - "author_name": "Samuel Thomas Cole", - "author_inst": "Richmond Pharmacology Ltd" - }, - { - "author_name": "Christopher S Spencer", - "author_inst": "Richmond Research Institute" - }, - { - "author_name": "Anne Freier", - "author_inst": "Richmond Research Institute" - }, - { - "author_name": "Doroth\u00e9e Camilleri", - "author_inst": "Richmond Pharmacology Ltd" - }, - { - "author_name": "Ulrike Lorch", - "author_inst": "Richmond Pharmacology Ltd" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.08.20245134", "rel_title": "Low COVID-19 mortality in old age homes in western India: an empirical study", @@ -1011428,6 +1016609,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.10.20246884", + "rel_title": "SARS-CoV-2/COVID-19 hospitalised patients in Switzerland: a prospective cohort profile", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20246884", + "rel_abs": "BackgroundSARS-CoV-2/COVID-19, which emerged in China in late 2019, rapidly spread across the world causing several million victims in 213 countries. Switzerland was severely hit by the virus, with 43000 confirmed cases as of September 1st, 2020.\n\nAimIn cooperation with the Federal Office of Public Health, we set up a surveillance database in February 2020 to monitor hospitalised patients with COVID-19 in addition to their mandatory reporting system.\n\nMethodsPatients hospitalised for more than 24 hours with a positive PCR test, from 20 Swiss hospitals, are included. Data collection follows a custom Case Report Form based on WHO recommendations and adapted to local needs. Nosocomial infections were defined as infections for which the onset of symptoms started more than 5 days after the patients admission date.\n\nResultsAs of September 1st, 2020, 3645 patients were included. Most patients were male (2168 - 59.5%),and aged between 50 and 89 years (2778 - 76.2%), with a median age of 68 (IQR 54-79). Community infections dominated with 3249 (89.0%) reports. Comorbidities were frequently reported: hypertension (1481 - 61.7%), cardiovascular diseases (948 - 39.5%), and diabetes (660 - 27.5%) being the most frequent in adults; respiratory diseases and asthma (4 -21.1%), haematological and oncological diseases (3 - 15.8%) being the most frequent in children. Complications occurred in 2679 (73.4%) episodes, mostly for respiratory diseases (2470 - 93.2% in adults, 16 - 55.2% in children), renal (681 - 25.7%) and cardiac (631 - 23.8%) complication for adults. The second and third most frequent complications in children affected the digestive system and the liver (7 - 24.1%). A targeted treatment was given in 1299 (35.6%) episodes, mostly with hydroxychloroquine (989 - 76.1%). Intensive care units stays were reported in 578 (15.8%) episodes. 527 (14.5%) deaths were registered, all among adults.\n\nConclusionThe surveillance system has been successfully initiated and provides a very representative set of data for Switzerland. We therefore consider it to be a valuable addition to the existing mandatory reporting, providing more precise information on the epidemiology, risk factors, and clinical course of these cases.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Amaury Thiabaud", + "author_inst": "Institut de Sant\u00e9 Globale, Facult\u00e9 de M\u00e9decine de l'Universit\u00e9 de Gen\u00e8ve, Geneva, Switzerland" + }, + { + "author_name": "Anne Iten", + "author_inst": "Service de pr\u00e9vention et contr\u00f4le de l'infection, Direction m\u00e9dicale et qualit\u00e9, HUG, Geneva, Switzerland" + }, + { + "author_name": "Carlo Balmelli", + "author_inst": "Infection Control Programme, EOC Hospitals, Ticino, Switzerland" + }, + { + "author_name": "Laurence Senn", + "author_inst": "Service de m\u00e9decine pr\u00e9ventive hospitali\u00e8re, CHUV, Lausanne, Switzerland" + }, + { + "author_name": "Nicolas Troillet", + "author_inst": "Service of Infectious Diseases, Central Institute, Valais Hospitals, Sion, Switzerland" + }, + { + "author_name": "Andreas Widmer", + "author_inst": "Department of Infectious Diseases, University Hospital Basel, Basel, Switzerland" + }, + { + "author_name": "Domenica Flury", + "author_inst": "Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland" + }, + { + "author_name": "Peter W. Schreiber", + "author_inst": "Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Miriam V\u00e1zquez", + "author_inst": "Department of Infectious Diseases, Bern University Hospital (Inselspital), Bern, Switzerland" + }, + { + "author_name": "Lauro Damonti", + "author_inst": "Department of Infectious Diseases, Bern University Hospital (Inselspital), Bern, Switzerland" + }, + { + "author_name": "Michael Buettcher", + "author_inst": "Paediatric Infectious Diseases, Department of Paediatrics, Children's Hospital, Cantonal Hospital Lucerne, Switzerland" + }, + { + "author_name": "Danielle Vuichard-Gysin", + "author_inst": "Department of Infectious Diseases, Thurgau Cantonal Hospital, Thurgau, Switzerland" + }, + { + "author_name": "Christoph Kuhm", + "author_inst": "Department of Infectious Diseases, Thurgau Cantonal Hospital, Thurgau, Switzerland" + }, + { + "author_name": "Alexia Cusini", + "author_inst": "Department of Infectious Diseases, Cantonal Hospital Graubuenden, Chur, Switzerland" + }, + { + "author_name": "Thomas Riedel", + "author_inst": "Department of Pediatrics, Cantonal Hospital Graubuenden, Chur, Switzerland" + }, + { + "author_name": "Yvonne Nussbaumer", + "author_inst": "Klinik f\u00fcr Innere Medizin, Kantonsspital Spit\u00e4ler Schaffhausen, Schaffhausen, Switzerland" + }, + { + "author_name": "Roman Gaudenz", + "author_inst": "Innere Medizin und Infektiologie, Kantonsspital Nidwalden, Stans, Switzerland" + }, + { + "author_name": "Ulrich Heininger", + "author_inst": "Infectious Diseases and Vaccinology, University of Basel Children's Hospital, Basel, Switzerland" + }, + { + "author_name": "Christoph Berger", + "author_inst": "Division of Infectious Diseases, and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland" + }, + { + "author_name": "Franziska Zucol", + "author_inst": "Paediatric Infectious Diseases, Department of Paediatrics, Cantonal Hospital Winterthur, Winterthur, Switzerland" + }, + { + "author_name": "Sara Bernhard-Stirnemann", + "author_inst": "Children's Hospital Aarau, Aarau, Switzerland" + }, + { + "author_name": "Natascia Corti", + "author_inst": "Unit of General Internal Medicine, Hirslanden Clinic, Zurich, Switzerland" + }, + { + "author_name": "Petra Zimmermann", + "author_inst": "Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; and Department of Paediatrics, Fribourg Hospital HFR, Fribourg, Switzerland" + }, + { + "author_name": "Anita Uka", + "author_inst": "Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; and Department of Paediatrics, Fribourg Hospital HFR, Fribourg, Switzerland" + }, + { + "author_name": "Anita Niederer-Loher", + "author_inst": "Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland" + }, + { + "author_name": "C\u00e9line Gardiol", + "author_inst": "Swiss Federal Office of Public Health, Bern, Switzerland" + }, + { + "author_name": "Maroussia Roelens", + "author_inst": "Institut de Sant\u00e9 Globale, Facult\u00e9 de M\u00e9decine de l'Universit\u00e9 de Gen\u00e8ve, Geneva, Switzerland" + }, + { + "author_name": "Olivia Keiser", + "author_inst": "Institut de Sant\u00e9 Globale, Facult\u00e9 de M\u00e9decine de l'Universit\u00e9 de Gen\u00e8ve, Geneva, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.09.20246363", "rel_title": "Risk of adverse outcomes with COVID-19 in the Republic of Ireland", @@ -1011553,57 +1016861,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.09.20246520", - "rel_title": "Impact of Nasopharyngeal Specimen Quality on SARS-CoV-2 Test Performance", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.09.20246520", - "rel_abs": "BackgroundThe SARS-CoV-2 reverse-transcription polymerase chain reaction (RT-PCR) cycle of threshold (Ct) has been used to estimate quantitative viral load, with the goal of targeting isolation precautions for individuals with COVID-19 and guiding public health interventions. However, variability in specimen quality can alter the Ct values obtained from SARS-CoV-2 clinical assays. We sought to define how variable nasopharyngeal (NP) swab quality impacts clinical SARS-CoV-2 test sensitivity.\n\nMethodsWe performed amplification of a human gene target ({beta}-actin) in parallel with a clinical RT-PCR targeting the SARS-CoV-2 ORF1ab gene for 1311 NP specimens collected from patients with clinical concern for COVID-19. We evaluated the relationship between NP specimen quality, characterized by high Ct values for the human gene target {beta}-actin Ct, and the probability of SARS-CoV-2 detection via logistic regression, as well as the linear relationship between SARS-CoV-2 and {beta}-actin Ct.\n\nResultsLow quality NP swabs are less likely to detect SARS-CoV-2 (odds ratio 0.654, 95%CI 0.523 to 0.802). We observed a positive linear relationship between SARS-CoV-2 and {beta}-actin Ct values (slope 0.169, 95%CI 0.092 to 0.247). COVID-19 disease severity was not associated with {beta}-actin Ct values.\n\nConclusionsVariability in NP specimen quality accounts for significant differences in the sensitivity of clinical SARS-CoV-2 assays. If unrecognized, low quality NP specimens, which are characterized by a low level of amplifiable human DNA target, may limit the application of SARS-CoV-2 Ct values to direct infection control and public health interventions.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Melissa Richard-Greenblatt", - "author_inst": "Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Matthew J Ziegler", - "author_inst": "Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Valerie Bromberg", - "author_inst": "Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Elizabeth Huang", - "author_inst": "Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Hatem O Abdallah", - "author_inst": "Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Pam Tolomeo", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Ebbing Lautenbach", - "author_inst": "Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Laurel Glaser", - "author_inst": "Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania" - }, - { - "author_name": "Brendan J Kelly", - "author_inst": "Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.09.20246447", "rel_title": "COVID-19 vaccine confidence and hesitancy among healthcare workers: a cross-sectional survey from a MERS-CoV experienced nation", @@ -1013126,6 +1018383,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.10.20247361", + "rel_title": "COVID-19 prediction in South Africa: Understanding the unascertained cases -- the hidden part of the epidemiological iceberg", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20247361", + "rel_abs": "Understanding the impact of non-pharmaceutical interventions as well as acscounting for the unascertained cases remain critical challenges for epidemiological models for understanding the transmission dynamics of COVID-19 spread. In this paper, we propose a new epidemiological model (eSEIRD) that extends the widely used epidemiological models such as extended Susceptible-Infected-Removed model (eSIR) and SAPHIRE (initially developed and used for analyzing data from Wuhan). We fit these models to the daily ascertained infected (and removed) cases from March 15, 2020 to Dec 31, 2020 in South Africa that reported the largest number of confirmed COVID-19 cases and deaths from the WHO African region. Using the eSEIRD model, the COVID-19 transmission dynamics in South Africa was characterized by the estimated basic reproduction number (R0) starting at 3.22 (95%CrI: [3.19, 3.23]) then dropping below 2 following a mandatory lockdown implementation and subsequently increasing to 3.27 (95%CrI: [3.27, 3.27]) by the end of 2020. The initial decrease of effective reproduction number followed by an increase suggest the effectiveness of early interventions and the combined effect of relaxing strict interventions and emergence of a new coronavirus variant in South Africa. The low estimated ascertainment rate was found to vary from 1.65% to 9.17% across models and time periods. The overall infection fatality ratio (IFR) was estimated as 0.06% (95%CrI: [0.04%, 0.22%]) accounting for unascertained cases and deaths while the reported case fatality ratio was 2.88% (95% CrI: [2.45%, 6.01%]). The models predict that from December 31, 2020, to April 1, 2021, the predicted cumulative number of infected would reach roughly 70% of total population in South Africa. Besides providing insights on the COVID-19 dynamics in South Africa, we develop powerful forecasting tools that enable estimation of ascertainment rates and IFR while quantifying the effect of intervention measures on COVID-19 spread.\n\nAMS ClassificationPlace Classification here. Leave as is, if there is no classification", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Xuelin Gu", + "author_inst": "Department of Biostatistics, University of Michigan" + }, + { + "author_name": "Bhramar Mukherjee", + "author_inst": "Department of Biostatistics, University of Michigan; Department of Epidemiology, University of Michigan" + }, + { + "author_name": "Sonali Das", + "author_inst": "Department of Business Management, University of Pretoria" + }, + { + "author_name": "Jyotishka Datta", + "author_inst": "Department of Statistics, Virginia Polytechnic Institute and State University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.10.20247247", "rel_title": "Mathematical modelling projections versus the actual course of the COVID-19 epidemic following the nationwide lockdown in Kyrgyzstan", @@ -1013291,229 +1018579,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.11.20236919", - "rel_title": "Addressing Personal Protective Equipment (PPE) Decontamination: Methylene Blue and Light Inactivates SARS-CoV-2 on N95 Respirators and Masks with Maintenance of Integrity and Fit", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.11.20236919", - "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) pandemic has resulted in severe shortages of personal protective equipment (PPE) necessary to protect front-line healthcare personnel. These shortages underscore the urgent need for simple, efficient, and inexpensive methods to decontaminate SARS-CoV-2-exposed PPE enabling safe reuse of masks and respirators. Efficient decontamination must be available not only in low-resourced settings, but also in well-resourced settings affected by PPE shortages. Methylene blue (MB) photochemical treatment, hitherto with many clinical applications including those used to inactivate virus in plasma, presents a novel approach for widely applicable PPE decontamination. Dry heat (DH) treatment is another potential low-cost decontamination method.\n\nMethodsMB and light (MBL) and DH treatments were used to inactivate coronavirus on respirator and mask material. We tested three N95 filtering facepiece respirators (FFRs), two medical masks (MMs), and one cloth community mask (CM). FFR/MM/CM materials were inoculated with SARS-CoV-2 (a Betacoronavirus), murine hepatitis virus (MHV) (a Betacoronavirus), or porcine respiratory coronavirus (PRCV) (an Alphacoronavirus), and treated with 10 {micro}M MB followed by 50,000 lux of broad-spectrum light or 12,500 lux of red light for 30 minutes, or with 75{degrees}C DH for 60 minutes. In parallel, we tested respirator and mask integrity using several standard methods and compared to the FDA-authorized vaporized hydrogen peroxide plus ozone (VHP+O3) decontamination method. Intact FFRs/MMs/CM were subjected to five cycles of decontamination (5CD) to assess integrity using International Standardization Organization (ISO), American Society for Testing and Materials (ASTM) International, National Institute for Occupational Safety and Health (NIOSH), and Occupational Safety and Health Administration (OSHA) test methods.\n\nFindingsOverall, MBL robustly and consistently inactivated all three coronaviruses with at least a 4-log reduction. DH yielded similar results, with the exception of MHV, which was only reduced by 2-log after treatment. FFR/MM integrity was maintained for 5 cycles of MBL or DH treatment, whereas one FFR failed after 5 cycles of VHP+O3. Baseline performance for the CM was variable, but reduction of integrity was minimal.\n\nInterpretationMethylene blue with light and DH treatment decontaminated masks and respirators by inactivating three tested coronaviruses without compromising integrity through 5CD. MBL decontamination of masks is effective, low-cost and does not require specialized equipment, making it applicable in all-resource settings. These attractive features support the utilization and continued development of this novel PPE decontamination method.", - "rel_num_authors": 52, - "rel_authors": [ - { - "author_name": "Thomas S Lendvay", - "author_inst": "University of Washington School of Medicine, Department of Urology, Seattle Children's Hospital, Seattle, Washington, USA" - }, - { - "author_name": "James Chen", - "author_inst": "University of Washington School of Medicine, Department of Urology, Seattle, Washington, USA" - }, - { - "author_name": "Brian H Harcourt", - "author_inst": "Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for" - }, - { - "author_name": "Florine E.M. Scholte", - "author_inst": "Department of Infectious Diseases, Microbiology and Immunology, CRCHU de Qu\u00e9bec-Universit\u00e9, Laval, Qu\u00e9bec City, Qu\u00e9bec, Canada" - }, - { - "author_name": "F. Selcen Kilinc-Balci", - "author_inst": "National Personal Protective Technology Laboratory (NPPL), Nathional Institue for Occupational Safety and Health, Centers for Disease Control and Prevention, Pi" - }, - { - "author_name": "Ying Ling Lin", - "author_inst": "World Health Organization" - }, - { - "author_name": "Molly M Lamb", - "author_inst": "Center for Global Health, Colorado School of Public Health, Anschutz Medical Campus, Aurora, Colorado, USA" - }, - { - "author_name": "Larry F Chu", - "author_inst": "The AIM Lab, Stanford University School of Medicine, Stanford, California, USA" - }, - { - "author_name": "Amy Price", - "author_inst": "The AIM Lab, Stanford University School of Medicine, Palo Alto, California, USA" - }, - { - "author_name": "David Evans", - "author_inst": "Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada" - }, - { - "author_name": "Yi-Chan Lin", - "author_inst": "Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada" - }, - { - "author_name": "Christopher N Mores", - "author_inst": "Department of Global Health, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA" - }, - { - "author_name": "Jaya Sahni", - "author_inst": "Seattle Children's Research Institute, Seattle Children's Hospital, Seattle, Washington, USA" - }, - { - "author_name": "Kareem B Kabra", - "author_inst": "Department of Global Health, Milken Institute School of Public Health, The George Washington University,Washington, DC, USA" - }, - { - "author_name": "Eric Haubruge", - "author_inst": "Gembloux AgroBioTech, Terra Research Center, Universityof Li\u00e9ge, Gembloux, Belgium" - }, - { - "author_name": "Etienne Thiry", - "author_inst": "Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, University of Li\u00e9ge, Li\u00e9ge, Belgium" - }, - { - "author_name": "Belinda Heyne", - "author_inst": "Department of Chemistry, University of Calgary, Calgary, Alberta, Canada" - }, - { - "author_name": "Jan Laperre", - "author_inst": "Centexbel, Grace-Hollogne, Belgium" - }, - { - "author_name": "Sarah Simmons", - "author_inst": "W21C Research and Innovation Centre, University of Calgary, Calgary, Alberta, Canada" - }, - { - "author_name": "Jan Davies", - "author_inst": "W21C Research and Innovation Centre, University of Calgary, Calgary, Alberta, Canada. Alberta Health Services, Alberta, Canada. Department of Anesthesiology, Pe" - }, - { - "author_name": "Yi Cui", - "author_inst": "Department of Materials Science and Engineering, Stanford University, Stanford, California, USA" - }, - { - "author_name": "Thor Wagner", - "author_inst": "Seattle Children's Research Institute, Seattle Children's Hospital, Seattle, Washington, USA" - }, - { - "author_name": "Tanner Clark", - "author_inst": "University of Washington School of Medicine, Department of Radiology, Seattle, Washington, USA" - }, - { - "author_name": "Sarah J Smit", - "author_inst": "Nelson Laboratories, LLC, Salt Lake City, Utah, USA" - }, - { - "author_name": "Rod Parker", - "author_inst": "Stryker, Quebec, Canada" - }, - { - "author_name": "Thomas Gallagher", - "author_inst": "Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA" - }, - { - "author_name": "Emily Timm", - "author_inst": "Department of Microbiology and Immunology, Loyola University Chicago, Maywood, Illinois, USA" - }, - { - "author_name": "Louisa F Ludwig-Begall", - "author_inst": "Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, University of Li\u00e9ge, Li\u00e9ge, Belgium" - }, - { - "author_name": "Nicolas Macia", - "author_inst": "Department of Chemistry, University of Calgary, Calgary, Alberta, Canada" - }, - { - "author_name": "Cyrus Mackie", - "author_inst": "Department of Chemistry, University of Calgary, Calgary, Alberta, Canada" - }, - { - "author_name": "Karen Hope", - "author_inst": "Alberta Health Services, Alberta, Canada" - }, - { - "author_name": "Ken Page", - "author_inst": "Alberta Health Services, Alberta, Canada" - }, - { - "author_name": "Susan Reader", - "author_inst": "Alberta Health Services, Alberta, Canada" - }, - { - "author_name": "Peter Faris", - "author_inst": "Alberta Health Services, Alberta, Canada" - }, - { - "author_name": "Oliver Jolois", - "author_inst": "Centexbel, Grace-Hollogne, Belgium" - }, - { - "author_name": "Alpa Patel", - "author_inst": "Nelson Laboratories, LLC, Salt Lake City, Utah, USA" - }, - { - "author_name": "Jean-Luc Lemyre", - "author_inst": "Stryker, Quebec, Canada" - }, - { - "author_name": "Vanessa Molly-Simard", - "author_inst": "Stryker, Quebec, Canada" - }, - { - "author_name": "Kamonthip Homdayjanakul", - "author_inst": "Center for Global Health, Colorado School of Public Health, Anschutz Medical Campus, Aurora, Colorado, USA" - }, - { - "author_name": "Sarah R Tritsch", - "author_inst": "Department of Global Health, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA" - }, - { - "author_name": "Constance Wielick", - "author_inst": "Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, University of Li\u00e9ge, Li\u00e9ge, Belgium" - }, - { - "author_name": "Mark Mayo", - "author_inst": "British Standards Institution, London, UK" - }, - { - "author_name": "Rebecca Malott", - "author_inst": "W21C Research and Innovation Centre, University of Calgary, Calgary, Alberta, Canada" - }, - { - "author_name": "Jean-Francois Willaert", - "author_inst": "Stryker, Quebec, Canada" - }, - { - "author_name": "Hans Nauwynck", - "author_inst": "Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium" - }, - { - "author_name": "Lor\u00e9ne Dams", - "author_inst": "Department of Infectious and Parasitic Diseases, Faculty of Veterinary Medicine, University of Li\u00e9ge, Li\u00e9ge, Belgium" - }, - { - "author_name": "Simon De Jaeger", - "author_inst": "Gembloux AgroBioTech, Terra Research Center, University of Li\u00e9ge, Gembloux, Belgium" - }, - { - "author_name": "Lei Liao", - "author_inst": "4CAir, Inc., Sunnyvale, California, USA" - }, - { - "author_name": "Mervin Zhao", - "author_inst": "4CAir, Inc., Sunnyvale, California, USA" - }, - { - "author_name": "Steven Chu", - "author_inst": "Departments of Physics, Molecular and Cellular Physiology, Stanford University, Stanford, California, USA" - }, - { - "author_name": "John Conly", - "author_inst": "W21C Research and Innovation Centre, University of Calgary, Calgary, Alberta, Canada. Alberta Health Services, Alberta, Canada." - }, - { - "author_name": "May C Chu", - "author_inst": "Center for Global Health, Colorado School of Public Health, Anschutz Medical Campus, Aurora, Colorado, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.07.20234641", "rel_title": "Implementation of novel and conventional outbreak control measures in managing a COVID-19 outbreak in a large UK prison", @@ -1015285,6 +1020350,20 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.12.08.416677", + "rel_title": "Intranasal administration of SARS-CoV-2 neutralizing human antibody prevents infection in mice", + "rel_date": "2020-12-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.08.416677", + "rel_abs": "Prevention of SARS-CoV-2 infection at the point of nasal entry is a novel strategy that has the potential to help contain the ongoing pandemic. Using our proprietary technologies, we have engineered a human antibody that recognizes SARS-CoV-2 S1 spike protein with an enhanced affinity for mucin to improve the antibodys retention in respiratory mucosa. The modified antibody, when administered into mouse nostrils, was shown to block infection in mice that were exposed to high titer SARS-CoV-2 pseudovirus 10 hours after the initial antibody treatment. Our data show that the protection against SARS-CoV-2 infection is effective in both nasal and lung areas 7 days after viral exposure. The modified antibody is stable in a nasal spray formulation and maintains its SARS-CoV-2 neutralizing activity. Nasal spray of the modified antibody can be developed as an affordable and effective prophylactic product to protect people from infection by exposure to SARS-CoV-2 virus in the air.\n\nOne-sentence summaryA Fc-modified human antibody prevents SARS-CoV-2 viral infection via nasal administration", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2020.12.09.417741", "rel_title": "Characterization of protease activity of Nsp3 from SARS-CoV-2 and its in vitro inhibition by nanobodies", @@ -1015438,45 +1020517,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.07.20245514", - "rel_title": "Smoking, distress and COVID-19 in England: cross-sectional population surveys from 2016 to 2020", - "rel_date": "2020-12-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.07.20245514", - "rel_abs": "BackgroundChanges in the prevalence of mental health problems among smokers due to the COVID-19 pandemic in England have important implications for existing health inequalities. This study examined the prevalence of psychological distress among smokers following the onset of the pandemic compared with previous years.\n\nMethodsCross-sectional data were used from a representative survey of smokers (18+) in England (n = 2,927) during four months (April to July) in 2016, 2017 and 2020. Adjusted logistic regressions estimated the associations between past-month psychological distress across two time periods (2016/17 and 2020), and age. Weighted proportions, chi-squared statistics and stratified logistic regression models were used to compare the distributions of minimal, moderate and severe distress, respectively, within socio-demographic and smoking characteristic categories in 2016/17 and 2020.\n\nResultsThe prevalence of moderate and severe distress among past-year smokers was higher in 2020 (moderate: 28.79%, 95%CI 26.11-31.60; OR=2.08, 95%CI 1.34-3.25; severe: 11.04%, 9.30-13.12; OR=2.16, 1.13-4.07) than in 2016/17 (moderate: 20.66%, 19.02-22.43; severe: 8.23%, 7.16-9.47). While there was no overall evidence of an interaction between time period and age, young (16-24 years) and middle-age groups (45-54 years) may have experienced greater increases in moderate and older age groups (65+ years) in severe distress from 2016/17 to 2020. There were also increases in 2020 of moderate distress among those from more disadvantaged social grades and of both moderate and severe distress among women and those with low cigarette addiction.\n\nConclusionsBetween April-July 2016/17 and April-July 2020 in England there were increases in both moderate and severe distress among smokers. The distribution of distress differed between 2016/17 and 2020 and represents a widening of established inequalities, with increases in distress among socio-economically disadvantaged groups, women and diverging age groups.\n\nO_TEXTBOXWhat this paper adds\n\nO_LISurveys in the UK indicate that there has been a deterioration in mental health of the general population since the onset of the COVID-19 pandemic.\nC_LIO_LISmoking is strongly associated with poor mental health, and a deterioration in mental health among smokers has potentially damaging consequences for existing health inequalities in the UK.\nC_LIO_LIOur findings using data from a large population-based sample of adults in England show that between 2016/17 and 2020 there were increases in moderate and severe psychological distress among smokers.\nC_LI\n\nC_TEXTBOX", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Loren Kock", - "author_inst": "UCL" - }, - { - "author_name": "Lion Shahab", - "author_inst": "University College London" - }, - { - "author_name": "Jamie Brown", - "author_inst": "University College London" - }, - { - "author_name": "Graham Moore", - "author_inst": "Cardiff University" - }, - { - "author_name": "Marie Horton", - "author_inst": "Public Health England" - }, - { - "author_name": "Leonie Brose", - "author_inst": "Kings College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.08.20245787", "rel_title": "Stress-related emotional and behavioural impact following the first COVID-19 outbreak peak", @@ -1017058,6 +1022098,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.06.20243691", + "rel_title": "What is the probability that this patient, who presents to a UK hospital, will be diagnosed with Covid-19? Prospective validation of the open-source CovidCalculatorUK resource.", + "rel_date": "2020-12-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.06.20243691", + "rel_abs": "IntroductionThe novel coronavirus SARS-CoV2 and the associated disease, Covid-19, continue to pose a global health threat. The CovidCalculatorUK is an open-source online tool (covidcalculatoruk.org) that estimates the probability that an individual patient, who presents to a UK hospital, will later test positive for SARS-CoV2. The objective is to aid cohorting decisions and minimise nosocomial transmission of SARS-CoV2.\n\nMethodsThis n = 500 prospective, observational, multicentre, validation study compared the CovidCalculatorUKs estimated probability of Covid-19 with the first SARS-CoV2 oropharyngeal/nasopharyngeal swab result for individual patients admitted to hospital during the study period (01.04.20 - 18.05.20). A comparison with senior clinicians estimates of the probability of Covid-19 was also made.\n\nResultsPatients who were prospectively grouped, by the CovidCalculatorUK, into 0-30% estimated probability, 30-60% and 60-100% estimated probability went on to have first swab SARS-CoV2 positive results in: 15.7%, 30.5% and 61.9% of cases, respectively. CovidCalculatorUK performance demonstrated an area under the curve of 0.76 (95% CI 0.71 - 0.81) (p < 0.001). Senior clinician stratification of the estimated probability of Covid-19 performed similarly to the CovidCalculatorUK.\n\nConclusionThe CovidCalculatorUK provides a reasonably accurate estimate of the probability of an individual testing positive on their first SARS-CoV2 nasopharyngeal/oropharyngeal swab. The CovidCalculatorUK output performs similarly to a senior clinicians estimate. Further evolution of the calculator may improve performance.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "George A Chapman", + "author_inst": "Oxford University Hospitals NHS Trust" + }, + { + "author_name": "Lewis Mundell", + "author_inst": "Lanarkshire NHS Trust" + }, + { + "author_name": "Charlotte H Harrison", + "author_inst": "Oxford University Hospitals NHS Trust" + }, + { + "author_name": "Tamsin Cargill", + "author_inst": "Oxford University Hospitals NHS Trust" + }, + { + "author_name": "Odhran Keating", + "author_inst": "Buckinghamshire Healthcare NHS Trust" + }, + { + "author_name": "Mark Johnson", + "author_inst": "Buckinghamshire Healthcare NHS Trust" + }, + { + "author_name": "Andrew Smith", + "author_inst": "Lanarkshire NHS Trust" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.06.20244756", "rel_title": "Comparing Decision Tree-Based Ensemble Machine Learning Models for COVID-19 Death Probability Profiling", @@ -1017159,81 +1022242,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.07.20245308", - "rel_title": "Integrative analyses identify susceptibility genes underlying COVID-19 hospitalization", - "rel_date": "2020-12-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.07.20245308", - "rel_abs": "Despite rapid progress in characterizing the role of host genetics in SARS-Cov-2 infection, there is limited understanding of genes and pathways that contribute to COVID-19. Here, we integrated a genome-wide association study of COVID-19 hospitalization (7,885 cases and 961,804 controls from COVID-19 Host Genetics Initiative) with mRNA expression, splicing, and protein levels (n=18,502). We identified 27 genes related to inflammation and coagulation pathways whose genetically predicted expression was associated with COVID-19 hospitalization. We functionally characterized the 27 genes using phenome- and laboratory-wide association scans in Vanderbilt Biobank (BioVU; n=85,460) and identified coagulation-related clinical symptoms, immunologic, and blood-cell-related biomarkers. We replicated these findings across trans-ethnic studies and observed consistent effects in individuals of diverse ancestral backgrounds in BioVU, pan-UK Biobank, and Biobank Japan. Our study highlights putative causal genes impacting COVID-19 severity and symptomology through the host inflammatory response.\n\nSINGLE-SENTENCE SUMMARYLarge-scale genomic studies identify genes in the inflammation and coagulation pathways contributing to risk and symptomology of COVID-19 disease.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Gita A Pathak", - "author_inst": "Yale University" - }, - { - "author_name": "Kritika Singh", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Tyne W Miller-Fleming", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Frank Wendt", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Nava Ehsan", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Kangcheng Hou", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Ruth Johnson", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Zeyun Lu", - "author_inst": "University of Southern California" - }, - { - "author_name": "Shyamalika Gopalan", - "author_inst": "University of Southern California" - }, - { - "author_name": "Loic Yengo Dimbou", - "author_inst": "Institute for Molecular Bioscience, The University of Queensland" - }, - { - "author_name": "Pejman Mohammadi", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Bogdan Pasaniuc", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Renato Polimanti", - "author_inst": "Yale University" - }, - { - "author_name": "Lea K Davis", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Nicholas Mancuso", - "author_inst": "University of Southern California" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.12.07.20244103", "rel_title": "Seroprevalence of SARS-CoV-2 Antibodies in Seattle, Washington: October 2019-April 2020", @@ -1018575,6 +1023583,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.12.05.20244426", + "rel_title": "Exploring drugs and vaccines associated with altered risks and severity of COVID-19: a UK Biobank cohort study of all ATC level-4 drug categories", + "rel_date": "2020-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.05.20244426", + "rel_abs": "BackgroundCOVID-19 is a major public health concern, yet its risk factors are not well-understood and effective therapies are lacking. It remains unclear how different drugs may increase or decrease the risks of infection and severity of disease.\n\nMethodsWe studied associations of prior use of all level-4 ATC drug categories (including vaccines) with COVID-19 diagnosis and outcome, based on a prospective cohort of UK Biobank(UKBB). Drug history was based on general practitioner(GP) records. Effects of prescribed medications/vaccinations on the risk of infection, severity of disease and mortality were investigated separately. Hospitalized and fatal cases were categorized as severe infection. We also considered different study designs and conducted analyses within infected patients, tested subjects and the whole population respectively, and for 5 different time-windows of prescriptions. Missing data were accounted for by multiple imputation and inverse probability weighting was employed to reduce testing bias. Multivariable logistic regression was conducted which controls for main confounders.\n\nResultsWe placed a greater focus on protective associations here, as (residual) confounding by indication and comorbidities tends to bias towards harmful effects. Across all categories, statins showed the strongest and most consistent protective associations. Significant protective effects against severe infection were seen among infected subjects (OR for prescriptions within a 12-month window, same below: 0.50, 95% CI:0.42-0.60), tested subjects (OR=0.63, 0.54-0.73) or in the general population (OR=0.49, 0.42-0.57). A number of top-listed drugs with protective effects were also cardiovascular medications, such as angiotensin converting enzyme inhibitors, angiotensin receptor blockers, calcium channel blocker and beta-blockers. Some other drugs showing protective associations included biguanides (metformin), estrogens, thyroid hormones and proton pump inhibitors, among others.\n\nInterestingly, we also observed protective associations by numerous vaccines. The most consistent association was observed for influenza vaccines, which showed reduced odds of infection (OR= 0.73 for vaccination in past year, CI 0.65-0.83) when compared cases to general population controls or test-negative controls (OR=0.60, 0.53-0.68). Protective associations were also observed when severe or fatal infection was considered as the outcome. Pneumococcal, tetanus, typhoid and combined bacterial and viral vaccines (ATC code J07CA) were also associated with lower odds of infection/severity.\n\nFurther subgroup and interaction analyses revealed difference in protective effects in different clinical subgroups. For example, protective effects of flu and pneumococcal vaccines were weaker in obese individuals, while we observed stronger protective effects of statins in those with cardiometabolic disorders, such as diabetes, coronary artery disease, hypertension and obesity.\n\nConclusionsA number of drugs, including many for cardiometabolic disorders, may be associated with lower odds of infection/severity of infection. Several existing vaccines, especially flu vaccines, may be beneficial against COVID-19 as well. However, causal relationship cannot be established due to risk of confounding. While further studies are required to validate the findings, this work provides a useful reference for future meta-analyses, clinical trials or experimental studies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Yong XIANG", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Kenneth Chi-Yin WONG", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Hon-Cheong SO", + "author_inst": "Chinese University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pharmacology and therapeutics" + }, { "rel_doi": "10.1101/2020.12.04.20244327", "rel_title": "COVID-19 RELATED IMMUNIZATION DISRUPTIONS IN RAJASTHAN, INDIA: A RETROSPECTIVE OBSERVATIONAL STUDY", @@ -1018692,49 +1023727,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.12.04.20242073", - "rel_title": "Sulodexide in the treatment of patients with early stages of COVID-19: a randomised controlled trial", - "rel_date": "2020-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.04.20242073", - "rel_abs": "BackgroundTargeting endothelial cells has been suggested for the treatment of patients with COVID-19 and sulodexide has pleiotropic properties within the vascular endothelium that can prove beneficial to the same. We aimed to evaluate the effect of sulodexide when used in the early clinical stages of COVID-19.\n\nMethodsWe conducted a single-centre, outpatient setting, randomised controlled trial with a parallel-group design in Mexico. Including patients within three days of clinical symptom onset, who were at a high risk of severe clinical progression due to chronic comorbidities. Participants were randomly allocated to receive an oral dose of sulodexide (500 LRU twice a day) or the placebo for 21 days. Primary outcomes were need and length of hospitalisation, need and length of oxygen support.\n\nResultsBetween June 5 and August 30, 2020, 243 patients were included in the \"per-protocol\" analysis. One hundred twenty-four of them received sulodexide, while 119 received placeboes. At 21 days follow-up, 22 of 124 patients required hospitalisation in the sulodexide group compared to 35 of 119 in the placebo group [relative risk (RR), 0{middle dot}6; 95% confidence interval (CI), 0{middle dot}37-0{middle dot}96; p=0{middle dot}03]. Fewer patients required oxygen support in the sulodexide group [37 of 124 vs. 50 of 119; RR, 0{middle dot}71; 95% CI, 0{middle dot}5 to 1; p=0{middle dot}05], and for fewer days (9{+/-}7{middle dot}2 in the sulodexide group vs. 11{middle dot}5{+/-}9{middle dot}6 in the placebo group; p=0{middle dot}02). There was no between-group difference concerning the length of hospital stay.\n\nInterpretationEarly intervention in COVID-19 patients with sulodexide reduced hospital admissions and oxygen support requirements, although with no significant effect on mortality. This has beneficial implications in the patient well-being, making sulodexide a favourable medication until an effective vaccine or an antiviral becomes available.\n\nFundingResearcher independently initiated, partially funded by Alfasigma, Mexico.\n\nListed in the ISRCTN registry under ID ISRCTN59048638.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Alejandro J Gonzalez Ochoa", - "author_inst": "IMSS" - }, - { - "author_name": "Joseph D Raffetto", - "author_inst": "VA Boston Healthcare System" - }, - { - "author_name": "ana Gabriela Hernandez", - "author_inst": "CLINEDEM" - }, - { - "author_name": "Nestor A Zavala", - "author_inst": "IMSS 12" - }, - { - "author_name": "Obed Gutierrez", - "author_inst": "IMSS 12" - }, - { - "author_name": "Arturo Vargas", - "author_inst": "Hospital General San Luis RC" - }, - { - "author_name": "Jorge Loustaunau", - "author_inst": "IMSS 12" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.12.04.20240218", "rel_title": "Does HIV impact susceptibility to COVID-19 (SARS-CoV-2) infection and pathology? A review of the current literature", @@ -1020033,6 +1025025,73 @@ "type": "contradictory results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.06.413443", + "rel_title": "Efficient inhibition of SARS-CoV-2 strains by a novel ACE2-IgG4-Fc fusion protein with a stabilized hinge region", + "rel_date": "2020-12-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.06.413443", + "rel_abs": "The novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) enters its host cells after binding to the angiotensin-converting enzyme 2 (ACE2) via its spike glycoprotein. This interaction is critical for virus entry and virus-host membrane fusion. Soluble ACE2 ectodomains bind and neutralize the virus but the short in vivo half-lives of soluble ACE2 limits its therapeutic use. Fusion of the fragment crystallizable (Fc) part of human immunoglobulin G (IgG) to the ACE2 ectodomain can prolong the in vivo half-life but bears the risk of unwanted Fc-receptor activation and antibody-dependent disease enhancement. Here, we describe optimized ACE2-Fc fusion constructs that avoid Fc-receptor binding by using IgG4-Fc as a fusion partner. The engineered ACE2-IgG4-Fc fusion proteins described herein exhibit promising pharmaceutical properties and a broad antiviral activity at single-digit nanomolar concentration. In addition, they allow to maintain the beneficial enzymatic activity of ACE2 and thus are very promising candidate antivirals broadly acting against coronaviruses.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Hristo L Svilenov", + "author_inst": "Department of Chemistry, Technical University of Munich, Garching, Germany" + }, + { + "author_name": "Julia Sacherl", + "author_inst": "Institute of Virology, Technical University of Munich / Helmholtz Zentrum Munich, Munich, Germany" + }, + { + "author_name": "Alwin Reiter", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Lisa Wolff", + "author_inst": "Institute of Virology, Technical University of Munich / Helmholtz Zentrum Munich, Munich, Germany" + }, + { + "author_name": "Cho-Chin Chen", + "author_inst": "Institute of Virology, Technical University of Munich / Helmholtz Zentrum Munich, Munich, Germany / German Center for Infection Research, Munich partner site, M" + }, + { + "author_name": "Marcel Stern", + "author_inst": "Max von Pettenkofer Institute & Gene Center, Virology, LMU Muenchen, Munich, Germany / German Center for Infection Research, Munich partner site, Munich, German" + }, + { + "author_name": "Frank-Peter Wachs", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Nicole Simonavicius", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Susanne Pippig", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Florian Wolschin", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Johannes Buchner", + "author_inst": "Department of Chemistry, Technical University of Munich, Garching, Germany" + }, + { + "author_name": "Carsten Brockmeyer", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Ulrike Protzer", + "author_inst": "Institute of Virology, Technical University of Munich / Helmholtz Zentrum Munich, Munich, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.06.412759", "rel_title": "The new generation hDHODH inhibitor MEDS433 hinders the in vitro replication of SARS-CoV-2", @@ -1020202,133 +1025261,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.12.04.410589", - "rel_title": "Elevated SARS-CoV-2 Antibodies Distinguish Severe Disease in Early COVID-19 Infection", - "rel_date": "2020-12-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.04.410589", - "rel_abs": "BackgroundSARS-CoV-2 has caused over 36,000,000 cases and 1,000,000 deaths globally. Comprehensive assessment of the multifaceted anti-viral antibody response is critical for diagnosis, differentiation of severe disease, and characterization of long-term immunity. Initial observations suggest that severe disease is associated with higher antibody levels and greater B cell/plasmablast responses. A multi-antigen immunoassay to define the complex serological landscape and clinical associations is essential.\n\nMethodsWe developed a multiplex immunoassay and evaluated serum/plasma from adults with RT-PCR-confirmed SARS-CoV-2 infections during acute illness (N=52) and convalescence (N=69); and pre-pandemic (N=106) and post-pandemic (N=137) healthy adults. We measured IgA, IgG, and/or IgM against SARS-CoV-2 Nucleocapsid (N), Spike domain 1 (S1), receptor binding domain (S1-RBD) and S1-N-terminal domain (S1-NTD).\n\nResultsTo diagnose infection, the combined [IgA+IgG+IgM] or IgG for N, S1, and S1-RBD yielded AUC values -0.90 by ROC curves. From days 6-30 post-symptom onset, the levels of antigen-specific IgG, IgA or [IgA+IgG+IgM] were higher in patients with severe/critical compared to mild/moderate infections. Consistent with excessive concentrations of antibodies, a strong prozone effect was observed in sera from severe/critical patients. Notably, mild/moderate patients displayed a slower rise and lower peak in anti-N and anti-S1 IgG levels compared to severe/critical patients, but anti-RBD IgG and neutralization responses reached similar levels at 2-4 months.\n\nConclusionThis SARS-CoV-2 multiplex immunoassay measures the magnitude, complexity and kinetics of the antibody response against multiple viral antigens. The IgG and combined-isotype SARS-CoV-2 multiplex assay is highly diagnostic of acute and convalescent disease and may prognosticate severity early in illness.\n\nOne Sentence SummaryIn contrast to patients with moderate infections, those with severe COVID-19 develop prominent, early antibody responses to S1 and N proteins.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Natalie S. Haddad", - "author_inst": "Emory University" - }, - { - "author_name": "Doan C. Nguyen", - "author_inst": "Emory University" - }, - { - "author_name": "Merin E. Kuruvilla", - "author_inst": "Emory University" - }, - { - "author_name": "Andrea Morrison-Porter", - "author_inst": "Emory University" - }, - { - "author_name": "Fabliha Anam", - "author_inst": "Emory University" - }, - { - "author_name": "Kevin S. Cashman", - "author_inst": "Emory University" - }, - { - "author_name": "Richard P. Ramonell", - "author_inst": "Emory University" - }, - { - "author_name": "Shuya Kyu", - "author_inst": "Emory University" - }, - { - "author_name": "Ankur Singh Saini", - "author_inst": "Emory University" - }, - { - "author_name": "Monica Cabrera-Mora", - "author_inst": "Emory University" - }, - { - "author_name": "Andrew Derrico", - "author_inst": "Emory University" - }, - { - "author_name": "David Alter", - "author_inst": "Emory University" - }, - { - "author_name": "John D. Roback", - "author_inst": "Emory University" - }, - { - "author_name": "Michael Horwath", - "author_inst": "Emory University" - }, - { - "author_name": "Henry M. Wu", - "author_inst": "Emory University" - }, - { - "author_name": "An-Kwok Ian Wong", - "author_inst": "Emory University" - }, - { - "author_name": "Alexandra W. Dretler", - "author_inst": "Infectious Disease Specialists of Atlanta" - }, - { - "author_name": "Ria Gripaldo", - "author_inst": "Emory University" - }, - { - "author_name": "Andrea N. Lane", - "author_inst": "Emory University" - }, - { - "author_name": "Hao Wu", - "author_inst": "Emory University" - }, - { - "author_name": "Saeyun Lee", - "author_inst": "Emory University" - }, - { - "author_name": "Mindy Hernandez", - "author_inst": "Emory University" - }, - { - "author_name": "Vanessa Engineer", - "author_inst": "Emory University" - }, - { - "author_name": "John Varghese", - "author_inst": "Emory University" - }, - { - "author_name": "Sang Le", - "author_inst": "Emory University" - }, - { - "author_name": "I\u00f1aki Sanz", - "author_inst": "Emory University" - }, - { - "author_name": "John L. Daiss", - "author_inst": "MicroB-plex, Inc." - }, - { - "author_name": "Frances Eun-Hyung Lee", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.12.04.412494", "rel_title": "The aging whole blood transcriptome reveals a potential role of FASLG in COVID-19", @@ -1021903,6 +1026835,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.02.20242925", + "rel_title": "Mapping each pre-existing conditions association to short-term and long-term COVID-19 complications", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.02.20242925", + "rel_abs": "Understanding the relationships between pre-existing conditions and complications of COVID-19 infection is critical to identifying which patients will develop severe disease. Here, we leverage 1.1 million clinical notes from 1,903 hospitalized COVID-19 patients and deep neural network models to characterize associations between 21 pre-existing conditions and the development of 20 complications (e.g. respiratory, cardiovascular, renal, and hematologic) of COVID-19 infection throughout the course of infection (i.e. 0-30 days, 31-60 days, and 61-90 days). Pleural effusion was the most frequent complication of early COVID-19 infection (23% of 383 complications) followed by cardiac arrhythmia (12% of 383 complications). Notably, hypertension was the most significant risk factor associated with 10 different complications including acute respiratory distress syndrome, cardiac arrhythmia and anemia. Furthermore, novel associations between cancer (risk ratio: 3, p=0.02) or immunosuppression (risk ratio: 4.3, p=0.04) with early-onset heart failure have also been identified. Onset of new complications after 30 days is rare and most commonly involves pleural effusion (31-60 days: 24% of 45 patients, 61-90 days: 25% of 36 patients). Overall, the associations between pre-COVID conditions and COVID-associated complications presented here may form the basis for the development of risk assessment scores to guide clinical care pathways.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "AJ Venkatakrishnan", + "author_inst": "nference" + }, + { + "author_name": "Colin Pawlowski", + "author_inst": "nference" + }, + { + "author_name": "David Zemmour", + "author_inst": "nference" + }, + { + "author_name": "Travis Hughes", + "author_inst": "nference" + }, + { + "author_name": "Akash Anand", + "author_inst": "nference Labs" + }, + { + "author_name": "Gabriela Berner", + "author_inst": "nference" + }, + { + "author_name": "Nikhil Kayal", + "author_inst": "nference" + }, + { + "author_name": "Arjun Puranik", + "author_inst": "nference" + }, + { + "author_name": "Ian Conrad", + "author_inst": "nference" + }, + { + "author_name": "Sairam Bade", + "author_inst": "nference Labs" + }, + { + "author_name": "Rakesh Barve", + "author_inst": "nference Labs" + }, + { + "author_name": "Purushottam Sinha", + "author_inst": "nference Labs" + }, + { + "author_name": "Jack O'Horo", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew D Badley", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Venky Soundararajan", + "author_inst": "nference" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.02.20242958", "rel_title": "Longitudinal lab test analysis confirms pre-existing anemia as a severe risk factor for post-viral clearance hospitalization in COVID-19 patients", @@ -1022308,73 +1027315,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.12.04.407510", - "rel_title": "Comparative analysis of antigen-specific anti-SARS-CoV-2 antibody isotypes in COVID-19 patients", - "rel_date": "2020-12-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.04.407510", - "rel_abs": "Serological tests for detection of anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies in blood are expected to identify individuals who have acquired immunity against SARS-CoV-2 and indication of seroprevalence of SARS-CoV-2 infection. Many serological tests have been developed to detect antibodies against SARS-CoV-2. However, these tests have considerable variations in their specificity and sensitivity, and whether they can predict levels of neutralizing activity is yet to be determined. This study aimed to investigate the kinetics and neutralizing activity of various antigen-specific antibody isotypes against SARS-CoV-2 in serum of coronavirus disease 2019 (COVID-19) patients confirmed via polymerase chain reaction test. We developed IgG, IgM and IgA measurement assays for each antigen, including receptor-binding domain (RBD) of spike (S) protein, S1 domain, full length S protein, S trimer and nucleocapsid (N) domain, based on enzyme-linked immunosorbent assay. The assays of the S protein for all isotypes showed high specificity, while the assays for all isotypes against N protein showed lower specificity. The sensitivity of all antigen-specific antibody isotypes depended on the timing of the serum collection and all of them, except for IgM against N protein, reached more than 90% at 15-21 days post-symptom onset. The best correlation with virus neutralizing activity was found for IgG against RBD (RBD-IgG), and levels of RBD-IgG in sera from four severe COVID-19 patients increased concordantly with neutralizing activity. Our results provide valuable information regarding the selection of serological test for seroprevalence and vaccine evaluation studies.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Hidetsugu Fujigaki", - "author_inst": "Fujita Health University Graduate School of Health Sciences" - }, - { - "author_name": "Masato Inaba", - "author_inst": "Fujita Health University School of Medicine" - }, - { - "author_name": "Michiko Osawa", - "author_inst": "Fujita Health University Hospital" - }, - { - "author_name": "Saya Moriyama", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Yoshimasa Takahashi", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Tadaki Suzuki", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Kenya Yamase", - "author_inst": "FUJIFILM Wako Pure Chemical Corporation" - }, - { - "author_name": "Yukihiro Yoshida", - "author_inst": "FUJIFILM Wako Pure Chemical Corporation" - }, - { - "author_name": "Yo Yagura", - "author_inst": "FUJIFILM Wako Pure Chemical Corporation" - }, - { - "author_name": "Takayoshi Oyamada", - "author_inst": "FUJIFILM Corporation" - }, - { - "author_name": "Masao Takemura", - "author_inst": "Fujita Health University Graduate School of Health Sciences" - }, - { - "author_name": "Yohei Doi", - "author_inst": "Fujita Health University School of Medicine" - }, - { - "author_name": "Kuniaki Saito", - "author_inst": "Fujita Health University Graduate School of Health Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.12.03.410472", "rel_title": "Ca2+-dependent mechanism of membrane insertion and destabilization by the SARS-CoV-2 fusion peptide", @@ -1023557,6 +1028497,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, + { + "rel_doi": "10.1101/2020.12.03.20239681", + "rel_title": "Spatial risk factors for Pillar 1 COVID-19 case counts and mortality in rural eastern England, UK", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.03.20239681", + "rel_abs": "Understanding is still developing about risk factors for COVID-19 infection or mortality. This is especially true with respect to identifying spatial risk factors and therefore identifying which geographic areas have populations who are at greatest risk of acquiring severe disease. This is a secondary analysis of patient records in a confined area of eastern England, covering persons who tested positive for SARS-CoV-2 through end May 2020, including dates of death and residence area. For each residence area (local super output area), we obtained data on air quality, deprivation levels, care home bed capacity, age distribution, rurality, access to employment centres and population density. We considered these covariates as risk factors for excess cases and excess deaths in the 28 days after confirmation of positive covid status relative to the overall case load and death recorded for the study area as a whole. We used the conditional autoregressive Besag-York-Mollie model to investigate the spatial dependency of cases and deaths allowing for a Poisson error structure. Structural equation models were also applied to clarify relationships between predictors and outcomes. Excess case counts or excess deaths were both predicted by the percentage of population age 65 years, care home bed capacity and less rurality: older population and more urban areas saw excess cases. Greater deprivation did not correlate with excess case counts but was significantly linked to higher mortality rates after infection. Neither excess cases nor excess deaths were predicted by population density, travel time to local employment centres or air quality indicators. Only 66% of mortality could be explained by locally high case counts. The results show a clear link between greater deprivation and higher COVID-19 mortality that is separate from wider community prevalence and other spatial risk factors.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Julii S Brainard", + "author_inst": "university of east anglia" + }, + { + "author_name": "Steve Rushton", + "author_inst": "Newcastle University" + }, + { + "author_name": "Tim Winters", + "author_inst": "Norfolk County Council" + }, + { + "author_name": "Paul R Hunter", + "author_inst": "University of East Anglia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.03.20243535", "rel_title": "OpenSAFELY: impact of national guidance on switching from warfarin to direct oral anticoagulants (DOACs) in early phase of COVID-19 pandemic in England", @@ -1023782,89 +1028753,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.12.04.411389", - "rel_title": "Elevated temperature inhibits SARS-CoV-2 replication in respiratory epithelium independently of the induction of IFN-mediated innate immune defences", - "rel_date": "2020-12-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.04.411389", - "rel_abs": "The pandemic spread of SARS-CoV-2, the etiological agent of COVID-19, represents a significant and ongoing international health crisis. A key symptom of SARS-CoV-2 infection is the onset of fever, with a hyperthermic temperature range of 38 to 41{degrees}C. Fever is an evolutionarily conserved host response to microbial infection and inflammation that can influence the outcome of viral pathogenicity and regulation of host innate and adaptive immune responses. However, it remains to be determined what effect elevated temperature has on SARS-CoV-2 tropism and replication. Utilizing a 3D air-liquid interface (ALI) model that closely mimics the natural tissue physiology and cellular tropism of SARS-CoV-2 infection in the respiratory airway, we identify tissue temperature to play an important role in the regulation of SARS-CoV-2 infection. We show that temperature elevation induces wide-spread transcriptome changes that impact upon the regulation of multiple pathways, including epigenetic regulation and lncRNA expression, without disruption of general cellular transcription or the induction of interferon (IFN)-mediated antiviral immune defences. Respiratory tissue incubated at temperatures >37{degrees}C remained permissive to SARS-CoV-2 infection but severely restricted the initiation of viral transcription, leading to significantly reduced levels of intraepithelial viral RNA accumulation and apical shedding of infectious virus. To our knowledge, we present the first evidence that febrile temperatures associated with COVID-19 inhibit SARS-CoV-2 replication. Our data identify an important role for temperature elevation in the epithelial restriction of SARS-CoV-2 that occurs independently of the induction of canonical IFN-mediated antiviral immune defences and interferon-stimulated gene (ISG) expression.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Vanessa Herder", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Kieran Dee", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Joanna Wojtus", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Daniel Goldfarb", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Christoforos Rozario", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Quan Gu", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Ruth Jarrett", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Ilaria Epifano", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Andrew Stevenson", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Steven McFarlane", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Meredith Stewart", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Agnieszka Szemiel", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Rute Pinto", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Andreu Masdefiol Garriga", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Sheila Graham", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Pablo Murcia", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Chris Boutell", - "author_inst": "University of Glasgow" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.04.411330", "rel_title": "Quality of life and depressive symptoms among Peruvian university students during the COVID-19 pandemic", @@ -1025103,6 +1029991,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.01.20241885", + "rel_title": "Prediction of Covid-19 spreading and optimal coordination of counter-measures: From microscopic to macroscopic models to Pareto fronts", + "rel_date": "2020-12-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20241885", + "rel_abs": "The Covid-19 disease has caused a world-wide pandemic with more than 60 million positive cases and more than 1.4 million deaths by the end of November 2020. As long as effective medical treatment and vaccination are not available, non-pharmaceutical interventions such as social distancing, self-isolation and quarantine as well as far-reaching shutdowns of economic activity and public life are the only available strategies to prevent the virus from spreading. These interventions must meet conflicting requirements where some objectives, like the minimization of disease-related deaths or the impact on health systems, demand for stronger counter-measures, while others, such as social and economic costs, call for weaker counter-measures. Therefore, finding the optimal compromise of counter-measures requires the solution of a multi-objective optimization problem that is based on accurate prediction of future infection spreading for all combinations of counter-measures under consideration. We present a strategy for construction and solution of such a multi-objective optimization problem with real-world applicability. The strategy is based on a micro-model allowing for accurate prediction via a realistic combination of person-centric data-driven human mobility and behavior, stochastic infection models and disease progression models including micro-level inclusion of governmental intervention strategies. For this micro-model, a surrogate macro-model is constructed and validated that is much less computationally expensive and can therefore be used in the core of a numerical solver for the multi-objective optimization problem. The resulting set of optimal compromises between counter-measures (Pareto front) is discussed and its meaning for policy decisions is outlined.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Hanna Wulkow", + "author_inst": "Zuse Institute Berlin" + }, + { + "author_name": "Tim Conrad", + "author_inst": "Zuse Institute Berlin and Freie Universitaet Berlin" + }, + { + "author_name": "Natasa Djurdjevac Conrad", + "author_inst": "Zuse Institute Berlin" + }, + { + "author_name": "Sebastian Alexander Mueller", + "author_inst": "TU Berlin" + }, + { + "author_name": "Kai Nagel", + "author_inst": "TU Berlin" + }, + { + "author_name": "Christof Schuette", + "author_inst": "FU Berlin" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.01.20242289", "rel_title": "The COVID-19 herd immunity threshold is not low: A re-analysis of European data from spring of 2020", @@ -1025220,77 +1030147,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.01.20241877", - "rel_title": "Impact of social distancing regulations and epidemic risk perception on social contact and SARS-CoV-2 transmission potential in rural South Africa: analysis of repeated cross-sectional surveys", - "rel_date": "2020-12-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20241877", - "rel_abs": "BackgroundSouth Africa implemented rapid and strict physical distancing regulations to minimize SARS-CoV-2 epidemic spread. Evidence on the impact of such measures on interpersonal contact in rural and lower-income settings is limited.\n\nMethodsWe compared population-representative social contact surveys conducted in the same rural KwaZulu-Natal location once in 2019 and twice in mid-2020. Respondents reported characteristics of physical and conversational ( close interaction) contacts over 24 hours. We built age-mixing matrices and estimated the proportional change in the SARS-CoV-2 reproduction number (R0). Respondents also reported counts of others present at locations visited and transport used, from which we evaluated change in potential exposure to airborne infection due to shared indoor space ( shared air).\n\nResultsRespondents in March-December 2019 (n=1704) reported a mean of 7.4 close interaction contacts and 196 shared air person-hours beyond their homes. Respondents in June-July 2020 (n=216), as the epidemic peaked locally, reported 4.1 close interaction contacts and 21 shared air person-hours outside their home, with significant declines in others homes and public spaces. Adults aged over 50 had fewer close contacts with others over 50, but little change in contact with 15-29 year olds, reflecting ongoing contact within multigenerational households. We estimate potential R0 fell by 42% (95% plausible range 14-59%) between 2019 and June-July 2020.\n\nDiscussionExtra-household social contact fell substantially following imposition of Covid-19 distancing regulations in rural South Africa. Ongoing contact within intergenerational households highlighted the limitation of social distancing measures in protecting older adults.\n\nFundingWellcome Trust, UKRI, DFID, European Union", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Nicky McCreesh", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Vuyiswa Dlamini", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Anita Edwards", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Stephen Olivier", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Njabulo Dayi", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Keabetswe Dikgale", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Siyabonga Nxumalo", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Jaco Dreyer", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Kathy Baisley", - "author_inst": "London School of Hygiene & Tropical Medicine; Africa Health Research Institute" - }, - { - "author_name": "Mark Siedner", - "author_inst": "Africa Health Research Institute; Harvard Medical School; Massachusetts General Hospital" - }, - { - "author_name": "Richard G White", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Kobus Herbst", - "author_inst": "Africa Health Research Institute; DSI-MRC South African Population Research Infrastructure Network" - }, - { - "author_name": "Alison Grant", - "author_inst": "London School of Hygiene & Tropical Medicine; Africa Health Research Institute" - }, - { - "author_name": "Guy Harling", - "author_inst": "Africa Health Research Institute; University College London; Harvard T.H. Chan School of Public Health; University of the Witwatersrand" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.01.20241992", "rel_title": "How effective are face coverings in reducing transmission of COVID-19?", @@ -1026589,6 +1031445,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.12.01.20241570", + "rel_title": "The Acceleration Index as a Test-Controlled Reproduction Number: Application to COVID-19 in France", + "rel_date": "2020-12-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20241570", + "rel_abs": "We provide a novel way to correct the effective reproduction number for the time-varying amount of tests, using the acceleration index (Baunez et al., 2021) as a simple measure of viral spread dynamics. Not correcting results in the reproduction number being a biased estimate of viral acceleration and we provide a formal decomposition of the resulting bias, involving the useful notions of test and infectivity intensities. When applied to French data for the COVID-19 pandemic (May 13, 2020 - October 26, 2022), our decomposition shows that the reproduction number, when considered alone, characteristically underestimates the resurgence of the pandemic, compared to the acceleration index which accounts for the time-varying volume of tests. Because the acceleration index aggregates all relevant information and captures in real time the sizable time variation featured by viral circulation, it is a more parsimonious indicator to track the dynamics of an infectious disease outbreak in real time, compared to the equivalent alternative which would combine the reproduction number with the test and infectivity intensities.\n\nJEL Classification NumbersI18; H12", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Christelle Baunez", + "author_inst": "Institut Neurosciences Timone" + }, + { + "author_name": "Mickael Degoulet", + "author_inst": "Institut Neurosciences Timone" + }, + { + "author_name": "Stephane Luchini", + "author_inst": "Aix-Marseille School of Economics" + }, + { + "author_name": "Matteo Louis Pintus", + "author_inst": "AgroParisTech" + }, + { + "author_name": "Patrick Pintus", + "author_inst": "Aix-Marseille University and CNRS" + }, + { + "author_name": "Miriam Teschl", + "author_inst": "Aix-Marseille School of Economics" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.11.30.20240986", "rel_title": "A Net Benefit Approach for the Optimal Allocation of a COVID-19 Vaccine", @@ -1026698,73 +1031593,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.01.20241349", - "rel_title": "Performance of saliva specimens for the molecular detection of SARS-CoV-2 in the community setting: does sample collection method matter?", - "rel_date": "2020-12-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20241349", - "rel_abs": "BackgroundData on the performance of saliva specimens for diagnosing COVID-19 in ambulatory patients are scarce and inconsistent. We assessed saliva-based specimens for detecting SARS-CoV-2 by RT-PCR in the community setting and compared three different collection methods.\n\nMethodProspective study conducted in three primary care centres. RT-PCR was performed in paired nasopharyngeal swabs (NPS) and saliva samples collected from outpatients with a broad clinical spectrum of illness. To assess differences in collection methods, saliva specimens were obtained in a different way in each of the participating centres: supervised collection (SVC), oropharyngeal washing (OPW) and self-collection (SC).\n\nResultsNPS and saliva pairs of samples from 577 patients (median age 39 years, 44% men, 42% asymptomatic) were collected and tested, and 120 (20.8%) gave positive results. The overall agreement with NPS and kappa coefficients (K) for SVC, OPW and SC were 95% (=0.85), 93.4% (=0.76), and 93.3% (=0.76), respectively. The sensitivity (95% CI) of the saliva specimens varied from 86% (72.6-93.7) for SVC to 66.7% (50.4-80) for SC samples. The sensitivity was higher in samples with lower cycle threshold (Ct) values. The best performance of RT-PCR was observed for SVC, with sensitivity (95% CI) for Ct values [≤]32 of 97% (82.5-99.8) in symptomatic, and 88.9% (50.7-99.4) in asymptomatic individuals.\n\nConclusionsSaliva is an acceptable specimen for the detection of SARS-CoV-2 in the community setting. Specimens collected under supervision perform comparably to NPS and can effectively identify individuals with higher risk of transmission in real life conditions.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Marta Fern\u00e1ndez-Gonz\u00e1lez", - "author_inst": "Hospital General Universitario de Elche" - }, - { - "author_name": "Vanesa Agull\u00f3", - "author_inst": "Hospital General Universitario de Elche" - }, - { - "author_name": "Alba de la Rica", - "author_inst": "Hospital General Universitario de Elche" - }, - { - "author_name": "Ana Infante", - "author_inst": "Hospital Universitario de San Juan de Alicante" - }, - { - "author_name": "Mar Carvajal", - "author_inst": "Hospital General Universitario de Elche" - }, - { - "author_name": "Jos\u00e9 Alberto Garc\u00eda", - "author_inst": "Hospital General Universitario de Elche" - }, - { - "author_name": "Nieves Gonzalo-Jim\u00e9nez", - "author_inst": "Hospital General Universitario de Elche" - }, - { - "author_name": "Claudio Cuartero", - "author_inst": "Hospital Universitario de San Juan de Alicante" - }, - { - "author_name": "Montserrat Ruiz", - "author_inst": "Hospital General Universitario de Elche" - }, - { - "author_name": "Carlos de Gregorio", - "author_inst": "Department 20th Health" - }, - { - "author_name": "Manuel S\u00e1nchez", - "author_inst": "Department 20th Health" - }, - { - "author_name": "Mar Masi\u00e1", - "author_inst": "Hospital General Universitario de Elche" - }, - { - "author_name": "F\u00e9lix Guti\u00e9rrez", - "author_inst": "Hospital General Universitario de Elche" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.01.20241562", "rel_title": "Real-life evaluation of a rapid antigen test (Panbio COVID-19 Ag Rapid Test Device) for SARS-CoV-2 detection in asymptomatic close contacts of COVID-19 patients", @@ -1028215,6 +1033043,137 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2020.12.01.405738", + "rel_title": "Guidelines for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples", + "rel_date": "2020-12-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.01.405738", + "rel_abs": "BackgroundSARS-CoV-2 genotyping has been instrumental to monitor virus evolution and transmission during the pandemic. The reliability of the information extracted from the genotyping efforts depends on a number of aspects, including the quality of the input material, applied technology and potential laboratory-specific biases. These variables must be monitored to ensure genotype reliability. The current lack of guidelines for SARS-CoV-2 genotyping leads to inclusion of error-containing genome sequences in studies of viral spread and evolution.\n\nResultsWe used clinical samples and synthetic viral genomes to evaluate the impact of experimental factors, including viral load and sequencing depth, on correct sequence determination using an amplicon-based approach. We found that at least 1000 viral genomes are necessary to confidently detect variants in the genome at frequencies of 10% or higher. The broad applicability of our recommendations was validated in >200 clinical samples from six independent laboratories. The genotypes of clinical isolates with viral load above the recommended threshold cluster by sampling location and period. Our analysis also supports the rise in frequency of 20A.EU1 and 20A.EU2, two recently reported European strains whose dissemination was favoured by travelling during the summer 2020.\n\nConclusionsWe present much-needed recommendations for reliable determination of SARS-CoV-2 genome sequence and demonstrate their broad applicability in a large cohort of clinical samples.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Slawomir Kubik", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Ana Claudia Marques", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + }, + { + "author_name": "Xiaobin Xing", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + }, + { + "author_name": "Janine Silvery", + "author_inst": "LABCON-OWL GmbH, Siemensstrasse 40, D-32105 Bad Salzuflen, USt-IdNr. DE814960283, Germany" + }, + { + "author_name": "Claire Bertelli", + "author_inst": "Genomics and Metagenomics Laboratory, Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland" + }, + { + "author_name": "Flavio De Maio", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS, Universita Cattolica del Sacro Cuore, L.go Agostino Gemelli 8, 00168 Roma, Italy" + }, + { + "author_name": "Spyros Pournaras", + "author_inst": "Laboratory of Clinical Microbiology, Attikon University Hospital Medical School, National and Kapodistrian University of Athens, Athens, Rimini 1, Chaidari 124 " + }, + { + "author_name": "Tom Burr", + "author_inst": "Source BioScience, Units 24/25, William James House, Cowley Road, Cambridge, CB4 0WU, United Kingdom" + }, + { + "author_name": "Yannis Duffourd", + "author_inst": "Equipe GAD - Inserm U1231, CHU Francois Mitterrand; 21000 Dijon, France" + }, + { + "author_name": "Helena Siemens", + "author_inst": "LABCON-OWL GmbH, Siemensstrasse 40, D-32105 Bad Salzuflen, USt-IdNr. DE814960283, Germany" + }, + { + "author_name": "Chakib Alloui", + "author_inst": "Laboratoire de Virologie, CHU Avicenne, AP-HP, 93000 Bobigny, France" + }, + { + "author_name": "Lin Song", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + }, + { + "author_name": "Yvan Wenger", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Alexandra Saitta", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Morgane Macheret", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Ewan W Smith", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Philippe Menu", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + }, + { + "author_name": "Marion Brayer", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + }, + { + "author_name": "Lars M Steinmetz", + "author_inst": "Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA" + }, + { + "author_name": "Ali Si-Mohammed", + "author_inst": "Laboratoire de Virologie, CHU Francois Mitterrand; 2, rue Angelique Ducoudray, 2100 Dijon, France" + }, + { + "author_name": "Josiane Chuisseu", + "author_inst": "Source BioScience, Units 24/25, William James House, Cowley Road, Cambridge, CB4 0WU, United Kingdom" + }, + { + "author_name": "Richard Stevens", + "author_inst": "Source BioScience, Units 24/25, William James House, Cowley Road, Cambridge, CB4 0WU, United Kingdom" + }, + { + "author_name": "Pantelis Constantoulakis", + "author_inst": "BioAnalytica Genotypos SA, 3-5 Ilision str, 115 28 Athens, Greece" + }, + { + "author_name": "Michela Sali", + "author_inst": "Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Universita Cattolica del Sacro Cuore, Ro" + }, + { + "author_name": "Gilbert Greub", + "author_inst": "Genomics and Metagenomics Laboratory, Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland" + }, + { + "author_name": "Carsten Tiemann", + "author_inst": "LABCON-OWL GmbH, Siemensstrasse 40, D-32105 Bad Salzuflen, USt-IdNr. DE814960283, Germany" + }, + { + "author_name": "Vicent Pelechano", + "author_inst": "SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Solna, Sweden" + }, + { + "author_name": "Adrian Willig", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Zhenyu Xu", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.11.30.405340", "rel_title": "Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2", @@ -1028364,49 +1033323,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.12.01.405662", - "rel_title": "Differential effects of antiseptic mouth rinses on SARS-CoV-2 infectivity in vitro", - "rel_date": "2020-12-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.01.405662", - "rel_abs": "SARS-CoV-2 is detectable in saliva from asymptomatic individuals, suggesting a potential benefit from the use of mouth rinses to suppress viral load and reduce virus spread. Published studies on reduction of SARS-CoV-2-induced cytotoxic effects by antiseptics do not exclude antiseptic-associated cytotoxicity. Here, we determined the effect of commercially available mouth rinses and antiseptic povidone-iodine on the infectivity of SARS-CoV-2 virus and of a non-pathogenic, recombinant, SARS-CoV-2 infection vector (pseudotyped SARS-CoV-2 virus). We first determined the effect of mouth rinses on cell viability to ensure that antiviral activity was not a consequence of mouth rinse-induced cytotoxicity. Colgate Peroxyl (hydrogen peroxide) exhibited the most cytotoxicity, followed by povidone-iodine, chlorhexidine gluconate (CHG), and Listerine (essential oils and alcohol). Potent anti-viral activities of povidone iodine and Colgate peroxyl mouth rinses was the consequence of rinse-mediated cellular damage. The potency of CHG was greater when the product was not washed off after virus attachment, suggesting that the prolonged effect of mouth rinses on cells impacts anti-viral activity. To minimalize mouth rinse-associated cytotoxicity, mouth rinse was largely removed from treated-viruses by centrifugation prior to infection of cells. A 5% (v/v) dilution of Colgate Peroxyl or povidone-iodine completely blocked viral infectivity. A similar 5% (v/v) dilution of Listerine or CHG had a moderate suppressive effect on the virus, but a 50% (v/v) dilution of Listerine or CHG blocked viral infectivity completely. Prolonged incubation of virus with mouth rinses was not required for viral inactivation. Our results indicate that mouth rinses can significantly reduce virus infectivity, suggesting a potential benefit for reducing SARS-CoV-2 spread.\n\nImportanceSARS-CoV-2 is detectable in saliva from asymptomatic individuals, suggesting the potential necessity for the use of mouth rinses to suppress viral load to reduce virus spread. Published studies on anti-SARS-CoV-2 activities of antiseptics determined by virus-induced cytotoxic effects cannot exclude antiseptic-associated cytotoxicity. We found that all mouth rinses tested inactivated SARS-CoV-2 viruses. Listerine and CHG were less cytotoxic than Colgate Peroxyl or povidone-iodine and were active against the virus. When mouth rinses were present in the cell culture during the infection, the potent anti-viral effect of mouth rinses were in part due to the mouth rinse-associated cytotoxicity. Our results suggest that assessing anti-viral candidates including mouth rinses with minimal potential disruption of cells may help identify active agents that can reduce SARS-CoV-2 spread.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Chuan Xu", - "author_inst": "Rutgers University" - }, - { - "author_name": "Annie Wang", - "author_inst": "Rutgers University" - }, - { - "author_name": "Eileen R Hoskin", - "author_inst": "Rutgers University" - }, - { - "author_name": "Carla Cugini", - "author_inst": "Rutgers School of Dental Medicine" - }, - { - "author_name": "Kenneth Markowitz", - "author_inst": "Rutgers School of Dental Medicine" - }, - { - "author_name": "Theresa L Chang", - "author_inst": "Rutgers University-Newark" - }, - { - "author_name": "Daniel H Fine", - "author_inst": "Rutgers University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.01.406116", "rel_title": "A pomegranate peel extract as inhibitor of SARS-CoV-2 Spike binding to human ACE2 (in vitro): a promising source of novel antiviral drugs", @@ -1030257,6 +1035173,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.11.26.20239103", + "rel_title": "I'm alone but not lonely. U-shaped pattern of perceived loneliness during the COVID-19 pandemic in the UK and Greece", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.26.20239103", + "rel_abs": "Many countries have adopted lengthy lockdown measures to mitigate the spreading of the COVID-19 virus. In this study, we train a RandomForest model using 10 variables quantifying individuals living environment, physical and mental health statuses to predict how long each of the UK participants (N=382) had been in lockdown. Self-perceived loneliness was found to be the most important variable predicting time in lockdown and, therefore, the aspect most influenced by the time the participant spent in lockdown. Subsequent statistical analysis showed a significant U-shaped curve for the levels of perceived loneliness (p<0.012), specifically decreasing during the 4th and 5th lockdown weeks. The same pattern was found on data from Greek citizens (N=129, p<0.041). These results suggest that lockdown measures may have affected how people evaluated their social support while in lockdown, leading to a decreased sense of loneliness. Implications of this study should be reflected on policies and countermeasures to current and future pandemics.\n\nState of relevanceThis study aims to inform policies for the current and/or future pandemics, particularly those involving lockdown restrictions. It highlights that self-perceived loneliness was the trait most affected by the time spent in lockdown: data show that the very first period of lockdown was characterised by a decrease in levels of perceived loneliness. The machine learning approach adopted and the statistical validation on two different Western European countries ensure that the uncovered pattern is substantial. This result highlights the dissociation between objective social support and perceived loneliness: initially, restrictions may have triggered better social behaviours among communities or increased the level of gratitude for the social support people have always received. The short duration of these desirable effects suggests that measures and campaigns promoting better social support strategies could be potentially effective, even in social isolation, to keep the levels of perceived loneliness low.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Alessandro Carollo", + "author_inst": "University of Trento" + }, + { + "author_name": "Andrea Bizzego", + "author_inst": "University of Trento" + }, + { + "author_name": "Giulio Gabrieli", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Keri Ka-Yee Wong", + "author_inst": "Department of Psychology and Human Development, University College London, London, UK" + }, + { + "author_name": "Adrian Raine", + "author_inst": "Departments of Criminology, Psychiatry, and Psychology, University of Pennsylvania" + }, + { + "author_name": "Gianluca Esposito", + "author_inst": "Nanyang Technological University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.11.25.20238741", "rel_title": "I dont feel safe sitting in my own yard: Chicago resident experiences with urban rats during a COVID-19 stay-at-home order", @@ -1030418,81 +1035373,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.26.20152520", - "rel_title": "Design of COVID-19 Staged Alert Systems to Ensure Healthcare Capacity with Minimal Closures", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.26.20152520", - "rel_abs": "Community mitigation strategies to combat COVID-19, ranging from healthy hygiene to shelter-in-place orders, exact substantial socioeconomic costs. Judicious implementation and relaxation of restrictions amplify their public health benefits while reducing costs. We derive optimal strategies for toggling between mitigation stages using daily COVID-19 hospital admissions. With public compliance, the policy triggers ensure adequate intensive care unit capacity with high probability while minimizing the duration of strict mitigation measures. In comparison, we show that other sensible COVID-19 staging policies, including Frances ICU-based thresholds and a widely adopted indicator for reopening schools and businesses, require overly restrictive measures or trigger strict stages too late to avert catastrophic surges. As cities worldwide face future pandemic waves, our findings provide a robust strategy for tracking COVID-19 hospital admissions as an early indicator of hospital surges and enacting staged measures to ensure integrity of the health system, safety of the health workforce, and public confidence.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Haoxiang Yang", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "\u00d6zge S\u00fcrer", - "author_inst": "Northwestern University" - }, - { - "author_name": "Daniel Duque", - "author_inst": "Northwestern University" - }, - { - "author_name": "David Morton", - "author_inst": "Northwestern University" - }, - { - "author_name": "Bismark Singh", - "author_inst": "Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg" - }, - { - "author_name": "Spencer Fox", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Remy Pasco", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Kelly Pierce", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Paul Rathouz", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Zhanwei Du", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Michael Pignone", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Mark E. Escott", - "author_inst": "The City of Austin" - }, - { - "author_name": "Stephen I. Adler", - "author_inst": "The City of Austin" - }, - { - "author_name": "S.Clairborne Johnston", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Lauren Ancel Meyers", - "author_inst": "The University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.26.20239152", "rel_title": "Altered Smell and Taste: anosmia, parosmia and the long impact of Covid-19", @@ -1031923,6 +1036803,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.28.20240259", + "rel_title": "Threatening second wave of COVID-19 is imminent: A deep learning perspective", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.28.20240259", + "rel_abs": "When the entire world is waiting restlessly for a safe and effective COVID-19 vaccine that could soon become a reality, numerous countries around the globe are grappling with unprecedented surges of new COVID-19 cases. As the number of new cases is skyrocketing, pandemic fatigue and public apathy towards different intervention strategies are posing new challenges to the government officials to combat the pandemic. Henceforth, it is indispensable for the government officials to understand the future dynamics of COVID-19 flawlessly in order to develop strategic preparedness and resilient response planning. In light of the above circumstances, probable future outbreak scenarios in Brazil, Russia and the United kingdom have been sketched in this study with the help of four deep learning models: long short term memory (LSTM), gated recurrent unit (GRU), convolutional neural network (CNN) and multivariate convolutional neural network (MCNN). In our analysis, CNN algorithm has outperformed other deep learning models in terms of validation accuracy and forecasting consistency. It has been unearthed in our study that CNN can provide robust long term forecasting results in time series analysis due to its capability of essential features learning, distortion invariance and temporal dependence learning. However, the prediction accuracy of LSTM algorithm has been found to be poor as it tries to discover seasonality and periodic intervals from any time series dataset, which were absent in our studied countries. Our study has highlighted the promising validation of using convolutional neural networks instead of recurrent neural networks when it comes to forecasting with very few features and less amount of historical data.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Khondoker Nazmoon Nabi", + "author_inst": "Bangladesh University of Engineering and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.27.20240036", "rel_title": "Rapid disappearance of influenza following the implementation of COVID-19 mitigation measures in Hamilton, Ontario", @@ -1032020,93 +1036919,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.27.20239244", - "rel_title": "Prevalence of SARS-CoV-2 in household members and other close contacts of COVID-19 cases: a serologic study in canton of Vaud, Switzerland", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.27.20239244", - "rel_abs": "BackgroundUnderstanding community-based SARS-CoV-2 transmission is crucial to inform public health decisions. Research on SARS-CoV-2 transmission within households and other close settings using serological testing is scarce.\n\nMethodsWe invited COVID-19 cases diagnosed between February 27 and April 1, 2020 in canton of Vaud, Switzerland, to participate, along with household members and other close contacts. Anti-SARS-CoV-2 IgG antibodies were measured using a Luminex immunoassay. We estimated factors associated with serological status using generalized estimating equations.\n\nFindingsOverall, 219 COVID-19 index cases, 302 household members, and 69 other close contacts participated between May 4 and June 27, 2020. More than half of household members (57{middle dot}2%, 95%CI 49{middle dot}7-64{middle dot}3) had developed a serologic response to SARS-CoV-2, while 19{middle dot}0% (95%CI 10{middle dot}0-33{middle dot}2) of other close contacts were seropositive. After adjusting for individual and household characteristics, infection risk was higher in household members aged 65 or more than in younger adults (aOR 3{middle dot}63, 95%CI 1{middle dot}05-12{middle dot}60), and in those not strictly adhering to simple hygiene rules like hand washing (aOR 1{middle dot}80, 95%CI 1{middle dot}02-3{middle dot}17). The risk was lower when more than 5 people outside home were met during the semi-confinement, compared to none (aOR 0{middle dot}35, 95%CI 0{middle dot}16-0{middle dot}74). The individual risk of household members to be seropositive was lower in large households (22% less per each additional person).\n\nInterpretationWe find that, during semi-confinement, household members of a COVID-19 case were at very high risk of getting infected, 3 times more than close contacts outside home. This highlights the need to provide clear messages on specific protective measures applicable at home. For elderly couples, who were especially at risk, providing them external support for daily basic activities is essential.\n\nFundingCenter for Primary Care and Public Health (Unisante), Canton of Vaud, Leenaards Foundation, Fondation pour lUniversite de Lausanne. SerocoViD is part of Corona Immunitas coordinated by SSPH+.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Julien Dupraz", - "author_inst": "Center for Primary Care and Public Health (Unisante), University of Lausanne" - }, - { - "author_name": "Audrey Butty", - "author_inst": "Center for Primary Care and Public Health (Unisante), University of Lausanne" - }, - { - "author_name": "Olivier Duperrex", - "author_inst": "Center for Primary Care and Public Health (Unisante), University of Lausanne" - }, - { - "author_name": "Sandrine Estoppey", - "author_inst": "Center for Primary Care and Public Health (Unisante), University of Lausanne" - }, - { - "author_name": "Vincent Faivre", - "author_inst": "Center for Primary Care and Public Health (Unisante), University of Lausanne" - }, - { - "author_name": "Julien Thabard", - "author_inst": "Center for Primary Care and Public Health (Unisante), University of Lausanne" - }, - { - "author_name": "Claire Zuppinger", - "author_inst": "Center for Primary Care and Public Health (Unisante), University of Lausanne" - }, - { - "author_name": "Gilbert Greub", - "author_inst": "Lausanne University Hospital and University of Lausanne" - }, - { - "author_name": "Giuseppe Pantaleo", - "author_inst": "Lausanne University Hospital and University of Lausanne" - }, - { - "author_name": "Jerome Pasquier", - "author_inst": "Center for Primary Care and Public Health (Unisante), University of Lausanne" - }, - { - "author_name": "Valentin Rousson", - "author_inst": "Center for Primary Care and Public Health (Unisante), University of Lausanne" - }, - { - "author_name": "Malik Egger", - "author_inst": "Center for Primary Care and Public Health (Unisante), University of Lausanne" - }, - { - "author_name": "Amelie Steiner-Dubuis", - "author_inst": "Center for Primary Care and Public Health (Unisante), University of Lausanne" - }, - { - "author_name": "Sophie Vassaux", - "author_inst": "Center for Primary Care and Public Health (Unisante), University of Lausanne" - }, - { - "author_name": "Eric Masserey", - "author_inst": "Department of Health and Social Action, Canton of Vaud, Switzerland" - }, - { - "author_name": "Murielle Bochud", - "author_inst": "Center for Primary Care and Public Health (Unisante), University of Lausanne" - }, - { - "author_name": "Semira Gonseth Nussle", - "author_inst": "Center for Primary Care and Public Health (Unisante), University of Lausanne" - }, - { - "author_name": "Valerie D'Acremont", - "author_inst": "Center for Primary Care and Public Health (Unisante), University of Lausanne" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.28.20240366", "rel_title": "Second versus first wave of COVID-19 deaths: shifts in age distribution and in nursing home fatalities", @@ -1033409,6 +1038221,61 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2020.11.30.20240721", + "rel_title": "Remote working in mental health services: a rapid umbrella review of pre-COVID-19 literature", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20240721", + "rel_abs": "BackgroundTele-mental health care has been rapidly adopted to maintain services during the pandemic, and there is now substantial interest in its future role. Service planning and policy making for recovery from the pandemic and beyond should draw not only on COVID-19 experiences, but also on the substantial research evidence accumulated prior to this.\n\nAimsto conduct an umbrella review of systematic reviews of research literature and evidence-based guidance on remote working in mental health, including both qualitative and quantitative literature.\n\nMethodThree databases were searched between January 2010 and August 2020 for systematic reviews meeting pre-defined criteria. Reviews retrieved were independently screened and those meeting inclusion criteria were synthesised and assessed for risk of bias. Narrative synthesis was used to report findings\n\nResultsNineteen systematic reviews met inclusion criteria. Fifteen examined clinical effectiveness, eight reported on aspects of tele-mental health implementation, ten reported on acceptability to service users and clinicians, two on cost-effectiveness and one on guidance. Most reviews were assessed as low quality. Findings suggested that video-based communication could be as effective and acceptable as face-face formats, at least in the short-term. Evidence was lacking on extent of digital exclusion and how it can be overcome, or on significant context such as children and young people and inpatient settings.\n\nConclusionsThis umbrella review suggests that tele-mental health has potential to be an effective and acceptable form of service delivery. However, we found limited evidence on impacts of large-scale implementation across catchment areas. Combining previous evidence and COVID-19 experiences may allow realistic planning for future tele-mental health implementation.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Phoebe Barnett", + "author_inst": "University College London" + }, + { + "author_name": "Lucy Goulding", + "author_inst": "King's College London" + }, + { + "author_name": "Cecilia Casetta", + "author_inst": "King's College London" + }, + { + "author_name": "Harriet Jordan", + "author_inst": "King's College London" + }, + { + "author_name": "Luke Sheridan Rains", + "author_inst": "University College London" + }, + { + "author_name": "Thomas Steare", + "author_inst": "University College London" + }, + { + "author_name": "Julie Williams", + "author_inst": "King's College London" + }, + { + "author_name": "Lisa Wood", + "author_inst": "University College London" + }, + { + "author_name": "Fiona Gaughran", + "author_inst": "King's College London" + }, + { + "author_name": "Sonia Johnson", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.11.25.20234914", "rel_title": "The efficacy and safety of hydroxychloroquine in COVID19 patients : a multicenter national retrospective cohort", @@ -1033538,165 +1038405,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, - { - "rel_doi": "10.1101/2020.11.25.20237883", - "rel_title": "Clinical and immunological benefits of convalescent plasma therapy in severe COVID-19: insights from a single center open label randomised control trial", - "rel_date": "2020-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20237883", - "rel_abs": "IntroductionA single center open label phase II randomised control trial was done to assess the pathogen and host-intrinsic factors influencing clinical and immunological benefits of passive immunization using convalescent plasma therapy (CPT), in addition to standard of care (SOC) therapy in severe COVID-19 patients, as compared to patients only on SOC therapy.\n\nMethodsConvalescent plasma was collected from patients recovered from COVID-19 following a screening protocol which also included measuring plasma anti SARS-CoV2 spike IgG content. Retrospectively, neutralizing antibody content was measured and proteome was characterized by LC-MS/MS for all convalescent plasma units that were transfused to patients. Severe COVID-19 patients with evidence for acute respiratory distress syndrome (ARDS) with PaO2/FiO2 ratio 100-300 (moderate ARDS) were recruited and randomised into two parallel arms of SOC and CPT, N=40 in each arm. Peripheral blood samples were collected on the day of enrolment (T1) followed by day3/4 (T2) and day 7 (T3). RT-PCR and sequencing was done for SARS-CoV2 RNA isolated from nasopharyngeal swabs collected at T1. A panel of cytokines and neutralizing antibody content were measured in plasma at all three timepoints. Patients were followed up for 30 days post-admission to assess the primary outcomes of all cause mortality and immunological correlates for clinical benefits.\n\nResultsWhile across all age-groups no statistically significant clinical benefit was registered for patients in the CPT arm, significant immediate mitigation of hypoxia, reduction in hospital stay as well as survival benefit was recorded in severe COVID-19 patients with ARDS aged less than 67 years receiving convalescent plasma therapy. In addition to its neutralizing antibody content a prominent effect of convalescent plasma on attenuation of systemic cytokine levels possibly contributed to its benefits.\n\nConclusionPrecise targeting of severe COVID-19 patients is necessary for reaping the clinical benefits of convalescent plasma therapy.\n\nClinical trial registrationClinical Trial Registry of India No. CTRI/2020/05/025209", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Yogiraj Ray", - "author_inst": "Infectious Disease & Beleghata General Hospital, Kolkata, India" - }, - { - "author_name": "Shekhar Ranjan Paul", - "author_inst": "Infectious Disease & Beleghata General Hospital, Kolkata, India" - }, - { - "author_name": "Purbita Bandopadhyay", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Ranit D'Rozario", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Jafar Sarif", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Abhishake Lahiri", - "author_inst": "Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Debaleena Bhowmik", - "author_inst": "Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Janani Srinivasa Vasudevan", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology, Delhi, India" - }, - { - "author_name": "Ranjeet Maurya", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology, Delhi, India" - }, - { - "author_name": "Akshay Kanakan", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology, Delhi, India" - }, - { - "author_name": "Sachin Sharma", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology, Delhi, India" - }, - { - "author_name": "Manish Kumar", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology, Delhi, India" - }, - { - "author_name": "Praveen Singh", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology, Delhi, India" - }, - { - "author_name": "Rammohan Roy", - "author_inst": "Infectious Disease & Beleghata General Hospital, Kolkata, India" - }, - { - "author_name": "Kausik Chaudhury", - "author_inst": "Infectious Disease & Beleghata General Hospital, Kolkata, India" - }, - { - "author_name": "Rajsekhar Maiti", - "author_inst": "Infectious Disease & Beleghata General Hospital, Kolkata, India" - }, - { - "author_name": "Saugata Bagchi", - "author_inst": "Infectious Disease & Beleghata General Hospital, Kolkata, India" - }, - { - "author_name": "Ayan Maiti", - "author_inst": "Infectious Disease & Beleghata General Hospital, Kolkata, India" - }, - { - "author_name": "Md. Masoom Perwez", - "author_inst": "Infectious Disease & Beleghata General Hospital, Kolkata, India" - }, - { - "author_name": "Abhinandan Mondal", - "author_inst": "Infectious Disease & Beleghata General Hospital, Kolkata, India" - }, - { - "author_name": "Avinash Tewari", - "author_inst": "Infectious Disease & Beleghata General Hospital, Kolkata, India" - }, - { - "author_name": "Samik Mandal", - "author_inst": "Infectious Disease & Beleghata General Hospital, Kolkata, India" - }, - { - "author_name": "Arpan Roy", - "author_inst": "Infectious Disease & Beleghata General Hospital, Kolkata, India" - }, - { - "author_name": "Moumita Saha", - "author_inst": "Infectious Disease & Beleghata General Hospital, Kolkata, India" - }, - { - "author_name": "Durba Biswas", - "author_inst": "Department of Immunohematology & Blood Transfusion, Medical College Hospital, Kolkata, India" - }, - { - "author_name": "Chikam Maiti", - "author_inst": "Department of Immunohematology & Blood Transfusion, Medical College Hospital, Kolkata, India" - }, - { - "author_name": "Sayantan Chakraborty", - "author_inst": "Department of Critical Care Medicine, Tata Medical Center, Kolkata, India." - }, - { - "author_name": "Biswanath Sharma Sarkar", - "author_inst": "Infectious Disease & Beleghata General Hospital, Kolkata, India" - }, - { - "author_name": "Anima Haldar", - "author_inst": "Infectious Disease & Beleghata General Hospital, Kolkata, India" - }, - { - "author_name": "Bibhuti Saha", - "author_inst": "Department of Tropical Medicine, School of Tropical Medicine, Kolkata, India" - }, - { - "author_name": "Shantanu Sengupta", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology, Delhi, India" - }, - { - "author_name": "Rajesh Pandey", - "author_inst": "CSIR-Institute of Genomics and Integrative Biology, Delhi, India" - }, - { - "author_name": "Shilpak Chatterjee", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Prasun Bhattacharya", - "author_inst": "Department of Immunohematology & Blood Transfusion, Medical College Hospital, Kolkata, India" - }, - { - "author_name": "Sandip Paul", - "author_inst": "Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - }, - { - "author_name": "Dipyaman Ganguly", - "author_inst": "IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.24.20238287", "rel_title": "A Test-Based Strategy for Safely Shortening Quarantine for COVID-19", @@ -1034699,6 +1039407,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.24.20238139", + "rel_title": "Prediction of evolution of the second wave of Covid-19 pandemic in Italy", + "rel_date": "2020-11-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20238139", + "rel_abs": "A relevant problem in the study of the Covid-19 pandemic is the study of its temporal evolution. Such evolution depends on a number of factors, among which the average rate of contacts between susceptible and infected individuals, the duration of infectiousness and the transmissibility, that is the probability of infection after a contact between susceptible and infected individuals. In a previous study, we analyzed the potentiality of a number of distributions to describe the evolution of the pandemic and the potentiality of each distribution to mathematically predict the evolution of the pandemic in Italy. Since the number of daily tests was changing and increasing with time, we used the ratio of the new daily cases per swab. We considered distributions of the type of Gauss (normal), Gamma, Beta, Weibull, Lognormal and in addition of the type of the Planck blackbody radiation law. The Planck law, describing the amount of energy of the electromagnetic radiation emitted by a black body at each wavelength or at each frequency, marked in 1900 the beginning of Quantum Mechanics. The result of our analysis was that, among the considered distributions, the Planck law has the best potentiality to mathematically predict the evolution of the pandemic and the best fitting capability. In this paper, we analyze the time evolution of the second wave of the Covid-19 pandemic in Italy and in particular we predict the ratio of the new daily cases per swab at Christmas 2020 using the data in the interval from 17 Oct to 21 Nov. According to Figure 4 and Figure 8, the prediction for such a ratio around Christmas is approximately within 6% and 7%. In this study there is also an attempt to account for the effects of the governmental containment measures.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ignazio Ciufolini", + "author_inst": "University of Salento" + }, + { + "author_name": "Antonio Paolozzi", + "author_inst": "School of Aerospace Engineering, Sapienza University of Rome" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.25.20237776", "rel_title": "Body mass index and risk of COVID-19 diagnosis, hospitalisation, and death: a population-based multi-state cohort analysis including 2,524,926 people in Catalonia, Spain", @@ -1034808,45 +1039539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.11.24.20235721", - "rel_title": "Cytokine ranking via mutual information algorithm correlates cytokine profiles with disease severity in patients with COVID-19", - "rel_date": "2020-11-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20235721", - "rel_abs": "Although the range of immune responses to COVID-19 infection is variable, cytokine storm is observed in many affected individuals. To further understand the disease pathogenesis and, consequently, to develop an additional tool for clinicians to evaluate patients for presumptive intervention we sought to compare plasma cytokine levels between a range of donor and patient samples grouped by a COVID-19 Severity Score (CSS) based on need for hospitalization and oxygen requirement. Here we utilize a mutual information algorithm that classifies the information gain for CSS prediction provided by cytokine expression levels and clinical variables. Using this methodology, we found that a small number of clinical and cytokine expression variables are predictive of presenting COVID-19 disease severity, raising questions about the mechanism by which COVID-19 creates severe illness. The variables that were the most predictive of CSS included clinical variables such as age and abnormal chest x-ray as well as cytokines such as macrophage colony-stimulating factor (M-CSF), interferon-inducible protein 10 (IP-10) and Interleukin-1 Receptor Antagonist (IL-1RA). Our results suggest that SARS-CoV-2 infection causes a plethora of changes in cytokine profiles and that particularly in severely ill patients, these changes are consistent with the presence of Macrophage Activation Syndrome and could furthermore be used as a biomarker to predict disease severity.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kelsey Huntington", - "author_inst": "Brown University" - }, - { - "author_name": "Anna Louie", - "author_inst": "Brown University" - }, - { - "author_name": "Chun Geun Lee", - "author_inst": "Brown University" - }, - { - "author_name": "Jack A. Elias", - "author_inst": "Brown University" - }, - { - "author_name": "Eric A. Ross", - "author_inst": "Fox Chase Cancer Center" - }, - { - "author_name": "Wafik S. El-Deiry", - "author_inst": "Brown University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.11.24.20231324", "rel_title": "Evaluation of SARS-CoV2 antibody Rapid Diagnostic Test kits (RDTs) and Real Time-Polymerase Chain Reaction (Rt-PCR) for COVID-19 Diagnosis in Kaduna, Nigeria", @@ -1036653,6 +1041345,49 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.11.25.399055", + "rel_title": "Triple Combination Nitazoxanide, Ribavirin, and Hydroxychloroquine results in the multiplicative reduction of in vitro SARS-CoV-2 viral replication", + "rel_date": "2020-11-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.25.399055", + "rel_abs": "BackgroundAn immediate unmet medical need exists to test and develop existing approved drugs against SARS-COV-2. Despite many efforts, very little progress has been made regarding finding low-cost oral medicines that can be made widely available worldwide to address the global pandemic.\n\nMethodsWe sought to examine if a triple combination of nitazoxanide (using its active metabolite tizoxanide), ribavirin, and hydroxychloroquine would lead to a multiplicative effects on viral replication of SARS-COV-2 resulting in a significant reduction of virus yield using VERO E6 cells as a model of viral replication.\n\nResultsVirus yield measured in PFU/ml was ~ 2 logs lower with triple combination versus either drug alone, resulting in the prolongation of time to peak cytopathic effects (CPE). The time to produce 50% CPE increased from 2.8 days for viral controls versus 5.3 days for triple combination therapy. Finally, for each 1-log reduction in virus yield 24 hours post-infection, there was an additional 0.7-day delay in onset of CPE.\n\nConclusionsA triple combination of tizoxanide, ribavirin, and hydroxychloroquine produced a reduction in SARS-COV-2 viral replication in Vero E6 cells, warranting exploration in additional cell lines as well as human clinical trials.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Elena Lian", + "author_inst": "Colorado State University" + }, + { + "author_name": "Carley McAlister", + "author_inst": "Colorado State University" + }, + { + "author_name": "Gabriela Ramirez", + "author_inst": "Colorado State University" + }, + { + "author_name": "David N Chernoff", + "author_inst": "Synavir Corporation" + }, + { + "author_name": "Gregory Went", + "author_inst": "Synavir Corporation" + }, + { + "author_name": "Justin Hoopes", + "author_inst": "Synavir Corporation" + }, + { + "author_name": "Rushika Perera", + "author_inst": "Colorado State University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.26.399436", "rel_title": "Host-directed FDA-approved drugs with antiviral activity against SARS-CoV-2 identified by hierarchical in silico/in vitro screening methods", @@ -1036810,53 +1041545,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, - { - "rel_doi": "10.1101/2020.11.23.394114", - "rel_title": "A Nasal Spray Solution of Grapefruit Seed Extract plus Xylitol Displays Virucidal Activity Against SARS-Cov-2 In Vitro", - "rel_date": "2020-11-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.23.394114", - "rel_abs": "ABSTARCTThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the ongoing pandemic coronavirus disease 2019 (COVID-19) has triggered worldwide concerted efforts in an attempt to identify effective therapies. In the present study, we have identified two candidate agents with potential activity against SARS-CoV-2 which can be administered intranasally, namely, xylitol and grape seed fruit extract (GSE). A commercially available nasal spray (Xlear) combining xylitol and GSE has been available for years, but the antiviral effects of this solution have not been documented. This in vitro study examined the virucidal effect of Xlear against SARS-CoV-2. To this end, two independent sets of experiments were carried out to test the hypothesis that Xlear is an effective (Experiment I) and replicable (Experiment II) means to deactivate SARS-CoV-2. When tested against SARS-CoV-2, the test compound GSE 0.2% was the only compound effective at reducing >3 log10 CCID50 infectious virus from, 3.67 log10 CCID50/0.1 mL to an undetectable amount of infectious virus. The present results validated by two independent sets of experiments, performed by different labs, on different viral strains, provide early evidence to encourage further pilot and clinical studies aimed at investigating the use of Xlear as a potential treatment for COVID-19", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Gustavo A Ferrer", - "author_inst": "Nova Southeastern University" - }, - { - "author_name": "Arian Betancour", - "author_inst": "Aventura Pulmonary Institute" - }, - { - "author_name": "Camille C Go", - "author_inst": "Aventura Pulmonary Institute" - }, - { - "author_name": "Hector Vazquez", - "author_inst": "Aventura Pulmonary Institute" - }, - { - "author_name": "Jonna B Westover", - "author_inst": "Utah State University" - }, - { - "author_name": "Valeria Cagno", - "author_inst": "University of Geneva" - }, - { - "author_name": "Caroline Tapparel", - "author_inst": "University of Geneva" - }, - { - "author_name": "Marcos A Sanchez-Gonzalez", - "author_inst": "Lake Erie College of Osteopathic Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.11.24.393629", "rel_title": "Double Lock of a Potent Human Monoclonal Antibody against SARS-CoV-2", @@ -1038367,6 +1043055,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.11.23.20237198", + "rel_title": "The sensitivity of SARS-CoV-2 antigen tests in the view of large-scale testing", + "rel_date": "2020-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.23.20237198", + "rel_abs": "ObjectivesAntigen tests have recently emerged as an interesting alternative to SARS-CoV-2 diagnostic PCR, thought to be valuable especially for the screening of bigger communities. To check appropriateness of the antigen based testing, we determined sensitivity of two point-of-care antigen tests when applied to a cohort of COVID-19 symptomatic, COVID-19 asymptomatic and healthy persons.\n\nMethodsWe examined nasopharyngeal swabs with antigen test 1 (Panbio Covid-19 Ag Rapid Test, Abbott) and antigen test 2 (Standard F Covid-19 Ag FIA, SD Biosensor). An additional nasopharyngeal and oropharyngeal swab of the same individual was checked with PCR (Allplex SARS-nCoV-2, Seegene). Within a 4-day period in October 2020, we collected specimens from 591 subjects. Of them, 290 had COVID-19 associated symptoms.\n\nResultsWhile PCR positivity was detected in 223 cases, antigen test 1 and antigen test 2 were found positive in 148 (sensitivity 0.664, 95% CI 0.599 - 0.722) and 141 (sensitivity 0.623, 95% CI 0.558 - 0.684) patients, respectively. When only symptomatic patients were analysed, sensitivity increased to 0.738 (95% CI 0.667 - 0.799) for the antigen test 1 and to 0.685 (95% CI 0.611 - 0.750) for the antigen test 2. The substantial drop in sensitivity to 12.9% (95% CI 0.067 - 0.234) was observed for samples with the PCR threshold cycle above > 30.\n\nConclusionsLow sensitivity of antigen tests leads to the considerable risk of false negativity. It is advisable to implement repeated testing with high enough frequency if the antigen test is used as a frontline screening tool.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Pavel Drevinek", + "author_inst": "2nd Faculty of Medicine, Charles University and Motol University Hospital" + }, + { + "author_name": "Jakub Hurych", + "author_inst": "2nd Faculty of Medicine, Charles University and Motol University Hospital" + }, + { + "author_name": "Zdenek Kepka", + "author_inst": "Motol University Hospital" + }, + { + "author_name": "Ales Briksi", + "author_inst": "Motol University Hospital" + }, + { + "author_name": "Michal Kulich", + "author_inst": "Faculty of Mathematics and Physics, Charles University" + }, + { + "author_name": "Miroslav Zajac", + "author_inst": "Motol University Hospital" + }, + { + "author_name": "Petr Hubacek", + "author_inst": "2nd Faculty of Medicine, Charles University and Motol University Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.24.20237560", "rel_title": "Demography, social contact patterns and the COVID-19 burden in different settings of Ethiopia: a modeling study", @@ -1038600,85 +1043331,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.23.20236901", - "rel_title": "SalivaSTAT: Direct-PCR and pooling of saliva samples collected in healthcare and community setting for SARS-CoV-2 mass surveillance.", - "rel_date": "2020-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.23.20236901", - "rel_abs": "BackgroundThe limitations of widespread current COVID-19 diagnostic testing lie at both pre-analytical and analytical stages. Collection of nasopharyngeal swabs is invasive and is associated with exposure risk, high cost, and supply-chain constraints. Additionally, the RNA extraction in the analytical stage is the most significant rate-limiting step in the entire testing process. To alleviate these limitations, we developed a universal saliva processing protocol (SalivaSTAT) that would enable an extraction free RT-PCR test using any of the commercially available RT-PCR kits.\n\nMethodsWe optimized saliva collection devices, heat-shock treatment and homogenization. The effect of homogenization on saliva samples for extraction-free RT-PCR assay was determined by evaluating samples with and without homogenization and preforming viscosity measurements. Saliva samples (872) previously tested using the FDA-EUA method were reevaluated with the optimized SalivaSTAT protocol using two widely available commercial RT-PCR kits. Further, a five-sample pooling strategy was evaluated as per FDA guidelines using the SalivaSTAT protocol.\n\nResultsThe saliva collection (done without any media) performed comparable to the FDA-EUA method. The SalivaSTAT protocol was optimized by incubating saliva samples at 95{degrees}C for 30-minutes and homogenization, followed by RT-PCR assay. The clinical sample evaluation of 630 saliva samples using the SalivaSTAT protocol with PerkinElmer (600-samples) and CDC (30-samples) RT-PCR assay achieved positive (PPA) and negative percent agreement (NPA) of 95.8% and 100%, respectively. The LoD was established as [~]20-60 copies/ml by absolute quantification. Further, a five-sample pooling evaluation using 250 saliva samples achieved a PPA and NPA of 92% and 100%, respectively.\n\nConclusionWe have optimized an extraction-free direct RT-PCR assay for saliva samples that demonstrated comparable performance to FDA-EUA assay (Extraction and RT-PCR). The SalivaSTAT protocol is a rapid, sensitive, and cost-effective method that can be adopted globally, and has the potential to meet testing needs and may play a significant role in management of the current pandemic.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Nikhil Shri Shri Sahajpal", - "author_inst": "Augusta University" - }, - { - "author_name": "Ashis K Mondal", - "author_inst": "Augusta University" - }, - { - "author_name": "Sudha Ananth", - "author_inst": "Augusta University" - }, - { - "author_name": "Allan Njau", - "author_inst": "Aga Khan University Hospital" - }, - { - "author_name": "Pankaj Ahluwalia", - "author_inst": "Augusta University" - }, - { - "author_name": "Gary Newnam", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Adriana Lozoya-Colinas", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Nicholas V Hud", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Vamsi Kota", - "author_inst": "Augusta University" - }, - { - "author_name": "Ted M Ross", - "author_inst": "University System of Georgia" - }, - { - "author_name": "Michelle D Reid", - "author_inst": "Emory University" - }, - { - "author_name": "Sadanand Fulzele", - "author_inst": "Augusta University" - }, - { - "author_name": "Alka Chaubey", - "author_inst": "Augusta University" - }, - { - "author_name": "Madhuri Hegde", - "author_inst": "PerkinElmer" - }, - { - "author_name": "Amyn M Rojiani", - "author_inst": "Augusta University" - }, - { - "author_name": "Ravindra Kolhe", - "author_inst": "Augusta University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.23.20236968", "rel_title": "Novel early-warning system for evaluating control and elimination of SARS-CoV-2 reveals alignment of policy with local transmission in New Zealand", @@ -1040141,6 +1044793,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.20.20233890", + "rel_title": "A Data Driven Change-point Epidemic Model for Assessing the Impact of Large Gathering and Subsequent Movement Control Order on COVID-19 Spread in Malaysia", + "rel_date": "2020-11-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20233890", + "rel_abs": "The second wave of COVID-19 in Malaysia is largely attributed to a mass gathering held in Sri Petaling between February 27, 2020 and March 1, 2020, which contributed to an exponential rise of COVID-19 cases in the country. Starting March 18, 2020, the Malaysian government introduced four consecutive phases of a Movement Control Order (MCO) to stem the spread of COVID-19. The MCO was implemented through various non-pharmaceutical interventions (NPIs). The reported number of cases reached its peak by the first week of April and then started to reduce, hence proving the effectiveness of the MCO. To gain a quantitative understanding of the effect of MCO on the dynamics of COVID-19, this paper develops a class of mathematical models to capture the disease spread before and after MCO implementation in Malaysia. A heterogeneous variant of the Susceptible-Exposed-Infected-Recovered (SEIR) model is developed with additional compartments for asymptomatic transmission. Further, a change-point is incorporated to model the before and after disease dynamics, and is inferred based on data. Related statistical analyses for inference are developed in a Bayesian framework and are able to provide quantitative assessments of (1) the impact of the Sri Petaling gathering, and (2) the extent of decreasing transmission during the MCO period. The analysis here also quantitatively demonstrates how quickly transmission rates fall under effective NPI implemention within a short time period.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sarat Chandra Dass", + "author_inst": "Heriot-Watt University Malaysia Campus" + }, + { + "author_name": "Wai Meng Kwok", + "author_inst": "Heriot-Watt University Malaysia Campus" + }, + { + "author_name": "Gavin J Gibson", + "author_inst": "Heriot-Watt University Edinburgh Campus" + }, + { + "author_name": "Balvinder S Gill", + "author_inst": "Institute for Medical Research Malaysia" + }, + { + "author_name": "Bala M Sundram", + "author_inst": "Institute for Medical Research Malaysia" + }, + { + "author_name": "Sarbhan Singh", + "author_inst": "Institute for Medical Research Malaysia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.20.20220749", "rel_title": "Community Transmission of SARS-CoV-2 by Fomites: Risks and Risk Reduction Strategies", @@ -1040258,93 +1044949,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.11.20.20235697", - "rel_title": "Long-Term Persistence of Spike Antibody and Predictive Modeling of Antibody Dynamics Following Infection with SARS-CoV-2", - "rel_date": "2020-11-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20235697", - "rel_abs": "BackgroundAntibodies to Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) have been shown to neutralize the virus in-vitro. Similarly, animal challenge models suggest that neutralizing antibodies isolated from SARS-CoV-2 infected individuals prevent against disease upon re-exposure to the virus. Understanding the nature and duration of the antibody response following SARS-CoV-2 infection is therefore critically important.\n\nMethodsBetween April and October 2020 we undertook a prospective cohort study of 3555 healthcare workers in order to elucidate the duration and dynamics of antibody responses following infection with SARS-CoV-2. After a formal performance evaluation against 169 PCR confirmed cases and negative controls, the Meso-Scale Discovery assay was used to quantify in parallel, antibody titers to the SARS-CoV-2 nucleoprotein (N), spike (S) protein and the receptor-binding-domain (RBD) of the S-protein. All seropositive participants were followed up monthly for a maximum of 7 months; those participants that were symptomatic, with known dates of symptom-onset, seropositive by the MSD assay and who provided 2 or more monthly samples were included in the analysis. Survival analysis was used to determine the proportion of sero-reversion (switching from positive to negative) from the raw data. In order to predict long-term antibody dynamics, two hierarchical longitudinal Gamma models were implemented to provide predictions for the lower bound (continuous antibody decay to zero, \"Gamma-decay\") and upper bound (decay-to-plateau due to long lived plasma cells, \"Gamma-plateau\") long-term antibody titers.\n\nResultsA total of 1163 samples were provided from 349 of 3555 recruited participants who were symptomatic, seropositive by the MSD assay, and were followed up with 2 or more monthly samples. At 200 days post symptom onset, 99% of participants had detectable S-antibody whereas only 75% of participants had detectable N-antibody. Even under our most pessimistic assumption of persistent negative exponential decay, the S-antibody was predicted to remain detectable in 95% of participants until 465 days [95% CI 370-575] after symptom onset. Under the Gamma-plateau model, the entire posterior distribution of S-antibody titers at plateau remained above the threshold for detection indefinitely. Surrogate neutralization assays demonstrated a strong positive correlation between antibody titers to the S-protein and blocking of the ACE-2 receptor in-vitro [R2=0.72, p<0.001]. By contrast, the N-antibody waned rapidly with a half-life of 60 days [95% CI 52-68].\n\nDiscussionThis study has demonstrated persistence of the spike antibody in 99% of participants at 200 days following SARS-CoV-2 symptoms and rapid decay of the nucleoprotein antibody. Diagnostic tests or studies that rely on the N-antibody as a measure of seroprevalence must be interpreted with caution. Our lowest bound prediction for duration of the spike antibody was 465 days and our upper bound predicted spike antibody to remain indefinitely in line with the long-term seropositivity reported for SARS-CoV infection. The long-term persistence of the S-antibody, together with the strong positive correlation between the S-antibody and viral surrogate neutralization in-vitro, has important implications for the duration of functional immunity following SARS-CoV-2 infection.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Louis Grandjean", - "author_inst": "University College London, Institute of Child Health" - }, - { - "author_name": "Anja Saso", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Arturo Torres Ortiz", - "author_inst": "Imperial College London" - }, - { - "author_name": "Tanya Lam", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "James Hatcher", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Rosie Thistlethwaite", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Mark Harris", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Timothy Best", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Marina Johnson", - "author_inst": "University College London" - }, - { - "author_name": "Helen Wagstaffe", - "author_inst": "University College London" - }, - { - "author_name": "Elizabeth Ralph", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Annabelle Mai", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Caroline Colijn", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Judith Breuer", - "author_inst": "University College London" - }, - { - "author_name": "Matthew Buckland", - "author_inst": "Great Ormond Street Hospital" - }, - { - "author_name": "Kimberly Gilmour", - "author_inst": "kimberly.gilmour@gosh.nhs.uk" - }, - { - "author_name": "David Goldblatt", - "author_inst": "University College London" - }, - { - "author_name": "- The Co-Stars Study Team", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.21.20235283", "rel_title": "Aerial transmission of SARS-CoV-2 virus (and pathogens in general) through environmental e-cigarette aerosol", @@ -1041547,6 +1046151,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.21.392555", + "rel_title": "Interactions of anti-COVID-19 drug candidates with multispecific ABC and OATP drug transporters", + "rel_date": "2020-11-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.21.392555", + "rel_abs": "In the COVID-19 epidemic, several repurposed drugs have been proposed to alleviate the major health effects of the disease. These drugs are often applied together with analgesics or non-steroid anti-inflammatory compounds, and co-morbid patients may also be treated with anticancer, cholesterol-lowering or antidiabetic agents. Since drug ADME-tox properties may be significantly affected by multispecific transporters, here we examined the interactions of the repurposed drugs with the key human multidrug transporters, present in the major tissue barriers and strongly affecting pharmacokinetics. Our in vitro studies, using a variety of model systems, explored the interactions of the antimalarial agents chloroquine and hydroxychloroquine, the antihelmintic ivermectin, and the proposed antiviral compounds, ritonavir, lopinavir, favipiravir and remdesivir with the ABCB1/Pgp, ABCG2/BCRP and ABCC1/MRP1 exporters, as well as the OATP2B1 and OATP1A2 uptake transporters. The results presented here show numerous pharmacologically relevant transporter interactions and may provide a warning for the potential toxicities of these repurposed drugs, especially in drug combinations at the clinic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Agnes Telbisz", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Csilla Ambrus", + "author_inst": "Solvo Biotechnology Ltd" + }, + { + "author_name": "Orsolya Mozner", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Edit Szabo", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Gyorgy Varady", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Eva Bakos", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Balazs Sarkadi", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Csilla Ozvegy-Laczka", + "author_inst": "Research Centre for Natural Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.11.21.392670", "rel_title": "A repurposed, blood gene signature is associated with poor outcomes in SARS-CoV-2", @@ -1041680,41 +1046331,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2020.11.22.393587", - "rel_title": "A Synthetic Defective Interfering SARS-CoV-2", - "rel_date": "2020-11-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.22.393587", - "rel_abs": "Viruses thrive by exploiting the cells they infect but must also produce viral proteins to replicate and infect other cells. As a consequence, they are also susceptible to exploitation by defective versions of themselves that do not produce such proteins. A defective viral genome with deletions in protein-coding genes could still replicate in cells coinfected with full-length viruses, and even replicate faster due to its shorter size, interfering with the replication of the virus. We have created a synthetic defective interfering version of SARS-CoV-2, the virus causing the recent Covid-19 pandemic, assembling parts of the viral genome that do not code for any functional protein but enable it to be replicated and packaged. This synthetic defective genome replicates three times faster than SARS-CoV-2 in coinfected cells, and interferes with it, reducing the viral load of a cell by half in 24 hours. The synthetic genome is transmitted as efficiently as the full-length genome, confirming the location of the putative packaging signal of SARS-CoV-2. A version of such a synthetic construct could be used as a self-promoting antiviral therapy: by enabling replication of the synthetic genome, the virus promotes its own demise.\n\nO_FIG O_LINKSMALLFIG WIDTH=153 HEIGHT=200 SRC=\"FIGDIR/small/393587v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (42K):\norg.highwire.dtl.DTLVardef@60aa77org.highwire.dtl.DTLVardef@57a965org.highwire.dtl.DTLVardef@132574dorg.highwire.dtl.DTLVardef@18e2e_HPS_FORMAT_FIGEXP M_FIG Graphic summary C_FIG", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Shun Yao", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Anoop Narayanan", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Sydney Majowicz", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Joyce Jose", - "author_inst": "Pennsylvania State University" - }, - { - "author_name": "Marco Archetti", - "author_inst": "Pennsylvania State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "synthetic biology" - }, { "rel_doi": "10.1101/2020.11.22.389056", "rel_title": "Stable neutralizing antibody levels six months after mild and severe COVID-19 episode", @@ -1043305,6 +1047921,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.19.20234849", + "rel_title": "Community factors and excess mortality in first wave of the COVID-19 pandemic.", + "rel_date": "2020-11-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234849", + "rel_abs": "Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Bethan Davies", + "author_inst": "Imperial College London" + }, + { + "author_name": "Brandon L Parkes", + "author_inst": "Imperial College London" + }, + { + "author_name": "James Bennett", + "author_inst": "Imperial College London" + }, + { + "author_name": "Daniela Fecht", + "author_inst": "Imperial College London" + }, + { + "author_name": "Marta Blangiardo", + "author_inst": "Imperial College London" + }, + { + "author_name": "Majid Ezzati", + "author_inst": "Imperial College London" + }, + { + "author_name": "Paul Elliott", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.21.392639", "rel_title": "Anti-COVID-19 efficacy of ivermectin in the golden hamster", @@ -1043494,469 +1048153,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.20.20234013", - "rel_title": "Prevention of severe COVID-19 in the elderly by early high-titer plasma", - "rel_date": "2020-11-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20234013", - "rel_abs": "BackgroundTherapies to interrupt progression of early COVID-19 remain elusive. Among them, convalescent plasma in hospitalized patients was unsuccessful, perhaps because antibody should be administered earlier. We advanced plasma infusions to the first 72 hours of symptoms to arrest COVID-19 progression.\n\nMethodsA randomized, double-blind, placebo-controlled trial of convalescent plasma with high IgG titers against SARS-CoV2 in elderly subjects within 72 hours of mild COVID-19 symptoms. The primary endpoint was severe respiratory disease defined as a respiratory rate [≥]30 and/or an O2 sat<93% in room air. The study was interrupted at 76% of its projected sample size, because cases in the region decreased considerably and steady enrollment of study subjects became virtually impossible.\n\nResults160 patients underwent randomization. In the intention-to-treat analysis (ITT), 13/80(16.2%) patients receiving plasma vs. 25/80(31.2%) receiving placebo experienced severe respiratory disease [RR(95%CI)= 0.52(0.29,0.94); p=0.026)] with an RRR=48%.\n\nA modified ITT analysis, excluding six subjects who experienced the primary endpoint before infusion, showed a larger effect size [RR(95%CI) = 0.40(0.20, 0.81), p=0.007]. High- and low-titer donor analyses, based on a median IgG titer=1:3,200, evidenced a dose-dependent response with an RRR=73.3% for recipients of high-titer plasma (p=0.016) and a number needed to treat (NNT)=4.4. All secondary endpoints exhibited trends towards protection. No solicited adverse events were observed.\n\nConclusionsEarly administration of high-titer convalescent plasma against SARS-CoV2 to mildly ill infected seniors reduced COVID-19 progression. This safe, inexpensive, outpatient intervention facilitates access to treatment from industrialized to LMIC, can decompress demands on hospitals, and may contribute to save lives.\n\nFunded by The Bill & Melinda Gates Foundation and The Fundacion INFANT Pandemic Fund. Registered in the Direccion de Sangre y Medicina Transfusional del Ministerio de Salud (PAEPCC19), Plataforma PRIISA (1421), and clinicaltrials.gov (NCT04479163).\n\nAll authors have completed the ICMJE uniform disclosure form at www.icmje.org/coi_disclosure.pdf and declare: no support from any organization for the submitted work; RL, GPM, DW and FPP are investigators in a phase 3 SARS CoV2 trial from Pfizer; no other relationships or activities that could appear to have influenced the submitted work.", - "rel_num_authors": 112, - "rel_authors": [ - { - "author_name": "Romina Libster", - "author_inst": "Fundacion INFANT, iTrials" - }, - { - "author_name": "Gonzalo Perez Marc", - "author_inst": "iTrials, Hospital Militar Central Cirujano Mayor Dr Cosme Argerich, Maternal and Child Department" - }, - { - "author_name": "Diego Wappner", - "author_inst": "iTrials, Swiss Medical Group" - }, - { - "author_name": "Silvina Coviello", - "author_inst": "Fundacion INFANT, iTrials" - }, - { - "author_name": "Alejandra Bianchi", - "author_inst": "Fundacion INFANT, iTrials" - }, - { - "author_name": "Virginia Braem", - "author_inst": "iTrials, Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Ignacio Esteban", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Mauricio Tomas Caballero", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Cristian J Wood", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Mabel Berrueta", - "author_inst": "Instituto de Efectividad Clinica y Sanitaria" - }, - { - "author_name": "Anibal Rondan", - "author_inst": "Hospital Zonal General de Agudos Dr Carlos Bocalandro" - }, - { - "author_name": "Gabriela Lescano", - "author_inst": "Hospital General Zonal de Agudos Dr Carlos Bocalandro" - }, - { - "author_name": "Pablo Cruz", - "author_inst": "Centro Gallego de Buenos Aires" - }, - { - "author_name": "Ivonne Ritou", - "author_inst": "Hospital Interzonal Especializado de Agudos y Cronicos San Juan de Dios" - }, - { - "author_name": "Valeria Fernandez Vina", - "author_inst": "Hospital Zonal General de Agudos Simplemente Evita" - }, - { - "author_name": "Damian Alvarez Paggi", - "author_inst": "Fundacion INFANT, CONICET" - }, - { - "author_name": "Sebastian Esperante", - "author_inst": "Fundacion INFANT, CONICET" - }, - { - "author_name": "Adrian Ferretti", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Gaston Ofman", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Alvaro Ciganda", - "author_inst": "Instituto de Efectividad Clinica y Sanitaria" - }, - { - "author_name": "Rocio Rodriguez", - "author_inst": "Instituto de Efectividad Clinica y Sanitaria" - }, - { - "author_name": "Jorge Lantos", - "author_inst": "Swiss Medical Group" - }, - { - "author_name": "Ricardo Valentini", - "author_inst": "CEMIC" - }, - { - "author_name": "Nicolas Itcovici", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Alejandra Hintze", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Laura Oyarvide", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Candela Etchegaray", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Alejandra Neira", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Ivonne Name", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Julieta Alfonso", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Rocio Lopez Castelo", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Gisela Caruso", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Sofia Rapelius", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Fernando Alvez", - "author_inst": "Fundacion Hematologica Sarmiento" - }, - { - "author_name": "Federico Cesar Etchenique", - "author_inst": "Swiss Medical Group" - }, - { - "author_name": "Federico Dimase", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Dario Raul Alvarez", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Sofia Sol Aranda", - "author_inst": "Fundacion INFANT, iTrials" - }, - { - "author_name": "Clara Sanchez Yanotti", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Julian DeLuca", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Sofia Jarez Baglivo", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Sofia Lujan Laudanno", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Florencia Nowogrodzki", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Florencia Izetta", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Maria Teresa Paniguetti", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Paula Fernandez Estrella", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Maria Emilia Gutierrez Meyer", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Viviana Dominguez", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Marcela Balduzzi", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Romina Militerno", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Jimena Ochoa", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Sebastian Perez Marc", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Lucila DiNunzio", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Mariano Aizpurua", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Romina Zadoff", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Carla Marchionatti", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Natalia Garcia Escude", - "author_inst": "Fundacion INFANT" - }, - { - "author_name": "Romina Romero", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Noelia Iraizos", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Emmanuel Ezequiel Valls", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Patricia Rearte Carvalho", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Jimena Franco", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Natali Estrada", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Juan Rusconi", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Guido Ochoa", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Maria Veronica Paz", - "author_inst": "Swiss Medical Group" - }, - { - "author_name": "Patricia Lesch", - "author_inst": "Swiss Medical Group" - }, - { - "author_name": "Maria Fernanda Caracciolo", - "author_inst": "Hospital Zonal General de Agudos Dr Carlos Bocalandro" - }, - { - "author_name": "Maria Eugenia Macaneo", - "author_inst": "Hospital Zonal General de Agudos Dr Carlos Bocalandro" - }, - { - "author_name": "Lia Pocket", - "author_inst": "Centro Gallego de Buenos Aires" - }, - { - "author_name": "Silvana Marquez", - "author_inst": "Hospital Interzonal Especializado en Agudos y Cronicos San Juan de Dios" - }, - { - "author_name": "Gaston Pellegrino", - "author_inst": "Hospital Interzonal Especializado en Agudos y Cronicos San Juan de Dios" - }, - { - "author_name": "Jorge Geffner", - "author_inst": "Universidad de Buenos Aires Facultad de Medicina" - }, - { - "author_name": "Rocio Zarlenga", - "author_inst": "Universidad de Buenos Aires Facultad de Medicina" - }, - { - "author_name": "Camila Witteveen", - "author_inst": "Universidad de Buenos Aires Facultad de Medicina" - }, - { - "author_name": "Agustina Venditti", - "author_inst": "Universidad de Buenos Aires Facultad de Medicina" - }, - { - "author_name": "Indira Pichetto Olanda", - "author_inst": "Universidad de Buenos Aires Facultad de Medicina" - }, - { - "author_name": "Juan Mauricio Vargas", - "author_inst": "Universidad de Buenos Aires Facultad de Medicina" - }, - { - "author_name": "Micaela Piani", - "author_inst": "Universidad de Buenos Aires Facultad de Medicina" - }, - { - "author_name": "Daniela Carolina Galnarez", - "author_inst": "Universidad de Buenos Aires Facultad de Medicina" - }, - { - "author_name": "Florencia De la Fuente", - "author_inst": "Universidad de Buenos Aires Facultad de Medicina" - }, - { - "author_name": "Andrea Gamarnik", - "author_inst": "FUNDACION INSTITUTO LELOIR" - }, - { - "author_name": "Maria del Carmen Nigro", - "author_inst": "Hospital Zonal General de Agudos Simplemente Evita" - }, - { - "author_name": "Susana Villaroel", - "author_inst": "Hospital Zonal General de Agudos Simplemente Evita" - }, - { - "author_name": "Cristina Soler Riera", - "author_inst": "CEMIC" - }, - { - "author_name": "Leonel Langellotti", - "author_inst": "Hospital Municipal San Isidro" - }, - { - "author_name": "Clarisa Taffarel", - "author_inst": "Hospital Municipal San Isidro" - }, - { - "author_name": "Jose L Scapellato", - "author_inst": "Sanatorio Anchorena" - }, - { - "author_name": "Mariano Girasolli", - "author_inst": "Sanatorio Sagrado Corazon OSECAC" - }, - { - "author_name": "Maximiliano de Zan", - "author_inst": "Sanatorio Sagrado Corazon OSECAC" - }, - { - "author_name": "Juan Sebastian Riera", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Enio Garcia", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Mario Rovere", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires." - }, - { - "author_name": "Juan Canela", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Agostina Pagella", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Cecilia Pampuro", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Yanina Miragaya", - "author_inst": "Programa de Atencion Medica Integral PAMI" - }, - { - "author_name": "Silvina Kuperman", - "author_inst": "Hospital Garrahan" - }, - { - "author_name": "Alfonso Raggio", - "author_inst": "Ministerio de Salud Provincia de Buenos Aires" - }, - { - "author_name": "Ramiro Manuel Larrea", - "author_inst": "Hospital Central de San Isidro" - }, - { - "author_name": "Maria Dolores Silveyra", - "author_inst": "Sanatorio Anchorena" - }, - { - "author_name": "Gabriela Leberzstein", - "author_inst": "Sanatorio Sagrado Corazon OSECAC" - }, - { - "author_name": "Alejandra Debonis", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Juan Molinos", - "author_inst": "Clinica Olivos" - }, - { - "author_name": "Miguel Gonzalez", - "author_inst": "Sanatorio Finochietto" - }, - { - "author_name": "Eduardo Perez", - "author_inst": "PAMI" - }, - { - "author_name": "Nicolas Kreplak", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires" - }, - { - "author_name": "Susana Pastor Arguello", - "author_inst": "Hospital Militar Central Cirujano Mayor Dr Cosme Argerich" - }, - { - "author_name": "Luz Gibbons", - "author_inst": "Instituto de Efectividad Clinica y Sanitaria" - }, - { - "author_name": "Fernando Althabe", - "author_inst": "Instituto de Efectividad Clinica y Sanitaria, World Health Organization" - }, - { - "author_name": "Eduardo Bergel", - "author_inst": "Instituto de Efectividad Clinica y Sanitaria" - }, - { - "author_name": "Fernando P Polack", - "author_inst": "Fundacion INFANT, iTRIALS" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.20.391011", "rel_title": "Modeling the frequency and number of persons to test to detect and control COVID-19 outbreaks in congregate settings", @@ -1045803,6 +1049999,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.18.20225029", + "rel_title": "The Invasive Respiratory Infection Surveillance (IRIS) Initiative reveals significant reductions in invasive bacterial infections during the COVID-19 pandemic", + "rel_date": "2020-11-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20225029", + "rel_abs": "BackgroundStreptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis are leading causes of invasive diseases including bacteraemic pneumonia and meningitis, and of secondary infections post-viral respiratory disease. They are typically transmitted via respiratory droplets. We investigated rates of invasive disease due to these pathogens during the early phase of the COVID-19 pandemic.\n\nMethodsLaboratories in 26 countries across six continents submitted data on cases of invasive disease due to S pneumoniae, H influenzae and N meningitidis from 1 January 2018 to 31 May 2020. Weekly cases in 2020 vs 2018-2019 were compared. Streptococcus agalactiae data were collected from nine laboratories for comparison to a non-respiratory pathogen. The stringency of COVID-19 containment measures was quantified by the Oxford COVID-19 Government Response Tracker. Changes in population movements were assessed by Google COVID-19 Community Mobility Reports. Interrupted time series modelling quantified changes in rates of invasive disease in 2020 relative to when containment measures were imposed.\n\nFindingsAll countries experienced a significant, sustained reduction in invasive diseases due to S pneumoniae, H influenzae and N meningitidis, but not S agalactiae, in early 2020, which coincided with the introduction of COVID-19 containment measures in each country. Similar impacts were observed across most countries despite differing stringency in COVID-19 control policies. There was no evidence of a specific effect due to enforced school closures.\n\nInterpretationThe introduction of COVID-19 containment policies and public information campaigns likely reduced transmission of these bacterial respiratory pathogens, leading to a significant reduction in life-threatening invasive diseases in many countries worldwide.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Angela B Brueggemann", + "author_inst": "University of Oxford" + }, + { + "author_name": "Melissa J Jansen van Rensburg", + "author_inst": "University of Oxford" + }, + { + "author_name": "David Shaw", + "author_inst": "University of Oxford" + }, + { + "author_name": "Noel D McCarthy", + "author_inst": "University of Warwick" + }, + { + "author_name": "Keith A Jolley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Martin CJ Maiden", + "author_inst": "University of Oxford" + }, + { + "author_name": "Mark PG van der Linden", + "author_inst": "University Hospital RWTH Aachen" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.18.388140", "rel_title": "Detecting SARS-CoV-2 variants with SNP genotyping", @@ -1045992,145 +1050231,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.18.20234369", - "rel_title": "Antibodies to SARS-CoV-2 are associated with protection against reinfection", - "rel_date": "2020-11-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20234369", - "rel_abs": "BackgroundIt is critical to understand whether infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) protects from subsequent reinfection.\n\nMethodsWe investigated the incidence of SARS-CoV-2 PCR-positive results in seropositive and seronegative healthcare workers (HCWs) attending asymptomatic and symptomatic staff testing at Oxford University Hospitals, UK. Baseline antibody status was determined using anti-spike and/or anti-nucleocapsid IgG assays and staff followed for up to 30 weeks. We used Poisson regression to estimate the relative incidence of PCR-positive results and new symptomatic infection by antibody status, accounting for age, gender and changes in incidence over time.\n\nResultsA total of 12219 HCWs participated and had anti-spike IgG measured, 11052 were followed up after negative and 1246 after positive antibody results including 79 who seroconverted during follow up. 89 PCR-confirmed symptomatic infections occurred in seronegative individuals (0.46 cases per 10,000 days at risk) and no symptomatic infections in those with anti-spike antibodies. Additionally, 76 (0.40/10,000 days at risk) anti-spike IgG seronegative individuals had PCR-positive tests in asymptomatic screening, compared to 3 (0.21/10,000 days at risk) seropositive individuals. Overall, positive baseline anti-spike antibodies were associated with lower rates of PCR-positivity (with or without symptoms) (adjusted rate ratio 0.24 [95%CI 0.08-0.76, p=0.015]). Rate ratios were similar using anti-nucleocapsid IgG alone or combined with anti-spike IgG to determine baseline status.\n\nConclusionsPrior SARS-CoV-2 infection that generated antibody responses offered protection from reinfection for most people in the six months following infection. Further work is required to determine the long-term duration and correlates of post-infection immunity.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Sheila F Lumley", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nicole E Stoesser", - "author_inst": "University of Oxford" - }, - { - "author_name": "Philippa C Matthews", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alison Howarth", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stephanie B Hatch", - "author_inst": "University of Oxford" - }, - { - "author_name": "Brian D Marsden", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stuart Cox", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "Tim James", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "Fiona Warren", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "Liam J Peck", - "author_inst": "University of Oxford" - }, - { - "author_name": "Thomas G Ritter", - "author_inst": "University of Oxford" - }, - { - "author_name": "Zoe de Toledo", - "author_inst": "University of Oxford" - }, - { - "author_name": "Laura Warren", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "David Axten", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "Richard J Cornall", - "author_inst": "University of Oxford" - }, - { - "author_name": "E Yvonne Jones", - "author_inst": "University of Oxford" - }, - { - "author_name": "David I Stuart", - "author_inst": "University of Oxford" - }, - { - "author_name": "Gavin Screaton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Daniel Ebner", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sarah Hoosdally", - "author_inst": "University of Oxford" - }, - { - "author_name": "Meera Chand", - "author_inst": "Public Health England" - }, - { - "author_name": "- Oxford University Hospitals Staff Testing Group", - "author_inst": "" - }, - { - "author_name": "Derrick W Crook", - "author_inst": "University of Oxford" - }, - { - "author_name": "Christopher P Conlon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Koen B Pouwels", - "author_inst": "University of Oxford" - }, - { - "author_name": "A Sarah Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tim EA Peto", - "author_inst": "University of Oxford" - }, - { - "author_name": "Susan Hopkins", - "author_inst": "Public Health England" - }, - { - "author_name": "Tim M Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Katie Jeffery", - "author_inst": "University of Oxford" - }, - { - "author_name": "David W Eyre", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.19.20234682", "rel_title": "Social patterning and stability of COVID-19 vaccination acceptance in Scotland: Will those most at risk accept a vaccine?", @@ -1047437,6 +1051537,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.16.20232850", + "rel_title": "The impact of COVID-19 employment shocks on suicide and poverty alleviation programs: An early-stage investigation", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232850", + "rel_abs": "This paper examines whether the COVID-19-induced employment shocks are associated with increases in suicides and safety net use in the second and third quarters of 2020. We exploit plausibly exogenous regional variation in the magnitude of the employment shocks in Japan and adopt a difference-in-differences research design to examine and control for possible confounders. Our preferred point estimates suggest that a one-percentage-point increase in the unemployment rate in the second quarter of 2020 is associated with, approximately, an additional 0.52 suicides, 28 unemployment benefit recipients, 88 recipients of a temporary loan program, and 10 recipients of public assistance per 100,000 population per month. A simple calculation based on these estimates suggests that if a region experienced a one-percentage-point increase in the unemployment rate caused by the COVID-19 crisis in the second quarter of 2020, which is roughly equivalent to the third-highest regional employment shock, this would be associated with 37.4%, 60.5%, and 26.5% increases in the total, female, and male suicide rates respectively in July 2020 compared with July 2019. Our baseline findings are robust to several different model specifications, although we do not assert that our research design perfectly solves the problem of estimation bias.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Michihito Ando", + "author_inst": "Rikkyo University" + }, + { + "author_name": "Masato Furuichi", + "author_inst": "Teikyo University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.11.16.20227389", "rel_title": "Designing Efficient Contact Tracing Through Risk-Based Quarantining", @@ -1047570,113 +1051693,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.17.20232827", - "rel_title": "Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 transmission identifies community social distancing as the dominant intervention reducing outbreaks", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20232827", - "rel_abs": "Many healthcare facilities report SARS-CoV-2 outbreaks but transmission analysis is complicated by the high prevalence of infection and limited viral genetic diversity. The contribution of different vectors to nosocomial infection or the effectiveness of interventions is therefore currently unclear. Detailed epidemiological and viral nanopore sequence data were analysed from 574 consecutive patients with a PCR positive SARS-CoV-2 test between March 13th and March 31st, when the pandemic first impacted on a large, multisite healthcare institution in London. During this time the first major preventative interventions were introduced, including progressive community social distancing (CSD) policies leading to mandatory national lockdown, exclusion of hospital visitors, and introduction of universal surgical facemask-use by healthcare-workers (HCW). Incidence of nosocomial cases, community SARS-CoV-2 cases and infection in a cohort of 228 HCWs followed the same dynamic course, decreasing shortly after introduction of CSD measures and prior to the main hospital-based interventions. We investigated clusters involving nosocomial cases based on overlapping ward-stays during the 14-day incubation period and SARS-CoV-2 genome sequence similarity. Our method placed 63 (79%) of 80 sequenced probable and definite nosocomial cases into 14 clusters containing a median of 4 patients (min 2, max 19) No genetic support was found for the majority of epidemiological clusters (31/44, 70%) and genomics revealed multiple contemporaneous outbreaks within single epidemiological clusters. We included a measure of hospital enrichment compared to community cases to increase confidence in our clusters, which were 1-14 fold enriched. Applying genomics, we could provide a robust estimate of the incubation period for nosocomial transmission, with a median lower bound and upper bound of 6 and 9 days respectively. Six (43%) clusters spanned multiple wards, with evidence of cryptic transmission, and community-onset cases could not be identified in more than half the clusters, particularly on the elective hospital site, implicating HCW as vectors of transmission. Taken together these findings suggest that CSD had the dominant impact on reducing nosocomial transmission by reducing HCW infection.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Luke B Snell", - "author_inst": "Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London" - }, - { - "author_name": "Chloe L Fisher", - "author_inst": "Genomics Innovation Unit, Guy's and St. Thomas' NHS Foundation Trust" - }, - { - "author_name": "Usman Taj", - "author_inst": "Directorate of Infection, Guy's and St Thomas' NHS Foundation Trust" - }, - { - "author_name": "Blair Merrick", - "author_inst": "Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London" - }, - { - "author_name": "Adela Alcolea-Medina", - "author_inst": "Infection Sciences, Viapath, St Thomas' Hospital, London" - }, - { - "author_name": "Themoula Charalampous", - "author_inst": "Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London" - }, - { - "author_name": "Adrian W Signell", - "author_inst": "Department of Infectious Diseases, King's College London" - }, - { - "author_name": "Harry D Wilson", - "author_inst": "Department of Infectious Diseases, King's College London" - }, - { - "author_name": "Gilberto Betancor", - "author_inst": "Department of Infectious Diseases, King's College London" - }, - { - "author_name": "Mark Tan Kia Ik", - "author_inst": "Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London" - }, - { - "author_name": "Emma Cunningham", - "author_inst": "Infection Sciences, Viapath, St Thomas' Hospital, London" - }, - { - "author_name": "Penelope R Cliff", - "author_inst": "Infection Sciences, Viapath, St Thomas' Hospital, London" - }, - { - "author_name": "Suzanne Pickering", - "author_inst": "Department of Infectious Diseases, King's College London" - }, - { - "author_name": "Rui Pedro Galao", - "author_inst": "Department of Infectious Diseases, King's College London" - }, - { - "author_name": "Rahul Batra", - "author_inst": "Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London" - }, - { - "author_name": "Stuart J D Neil", - "author_inst": "Department of Infectious Diseases, King's College London" - }, - { - "author_name": "Michael H Malim", - "author_inst": "Department of Infectious Diseases, King's College London" - }, - { - "author_name": "Katie J Doores", - "author_inst": "Department of Infectious Diseases, King's College London" - }, - { - "author_name": "Sam T Douthwaite", - "author_inst": "Directorate of Infection, Guy's and St Thomas' NHS Foundation Trust" - }, - { - "author_name": "Gaia Nebbia", - "author_inst": "Directorate of Infection, Guy's and St Thomas' NHS Foundation Trust" - }, - { - "author_name": "Jonathan D Edgeworth", - "author_inst": "Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London" - }, - { - "author_name": "Ali R Awan", - "author_inst": "Genomics Innovation Unit, Guy's and St. Thomas' NHS Foundation Trust" - }, - { - "author_name": "- The COVID-19 Genomics UK (COG-UK) consortium", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.17.20228155", "rel_title": "Community prevalence of antibodies to SARS-CoV-2 and correlates of protective immunity in five localities in an Indian metropolitan city", @@ -1048855,6 +1052871,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.16.20232884", + "rel_title": "Comparative Efficacy and Safety of Current Drugs against COVID-19: a Systematic Review and Net-work Meta Analysis", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232884", + "rel_abs": "The rapid spread of coronavirus disease (COVID-19) has greatly disrupted the livelihood of many people around the world. To date, more than 35.16 million COVID-19 cases with 1.037million total deaths have been reported worldwide. Compared with China, where the disease was first reported, cases of COVID-19, the number of confirmed cases for the disease in the rest of the world have been incredibly high. Even though several dugs have been suggested to be used against the disease, the said interventions should be backed by empirical clinical evidence. Therefore, this paper provides a systematic review and a meta-analysis of efficacy and safety of different COVID-19 drugs.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSCurrently, Covid-19 is one of the most urgent and significant health challenge, globally. However, so far there is no specific and effective treatment strategy against the disease. Nonetheless, there are numerous debates over the effectiveness and potential adverse effects of different COVID-19 antivirals. In general, there is invaluable need to continually report on new advances and successes against COVID-19, apparently to aid in managing the pandemic.\n\nAdded value of this studyThis study provides a comprehensive, evidence-based guide on the management of multiple COVID-19 symptoms. In particular, we provide a review of 14 drugs, placebos and standard treatments against COVID 19. Meanwhile, we also performed a meta-analysis based on four clinical outcome indicators, to measure and compare the efficacy and safety of current interventions.\n\nImplications of all the available evidenceFindings of this research will guide clinical decision in COVID-19 patients. It will also provide a basis for predicting clinical outcomes such as efficacy, mortality and safety of interventions against the disease.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Yi Li", + "author_inst": "China Pharmaceutical University" + }, + { + "author_name": "Wei He", + "author_inst": "China Pharmaceutical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.17.20233080", "rel_title": "COVID-19: more than a little flu? Insights from the Swiss hospital-based surveillance of Influenza and COVID-19", @@ -1049056,73 +1053095,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.17.20233262", - "rel_title": "COVID-19 critical care simulations: An international cross-sectional survey", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20233262", - "rel_abs": "IntroductionMany healthcare systems initiated rapid training with COVID-19 simulations for their healthcare workers (HCWs) to build surge capacity and optimize infection control measures. This study aimed to describe COVID-19 simulation drills in international healthcare centers.\n\nMethodsThis is cross-sectional, international survey among simulation team leaders and HCWs, based on each centers debriefing reports from simulation centers from 30 countries in all WHO regions where COVID-19 simulation drills were conducted. The main outcome measures were the COVID-19 simulations characteristics, outcomes, facilitators, obstacles and challenges encountered during the simulation sessions.\n\nResultsInvitation was sent to 500 simulation team leaders and HCWs, 343 responded, and 121 completed the survey. Those who completed the study were from East Mediterranean (EMRO) countries (41.3%); Southeast Asian countries (SERO) (25.6%); and Europe (12.4%) and the remainder from other regions. The frequency of simulation sessions was monthly (27.1%), weekly (24.8%), twice weekly (19.8%), or daily (21.5%). Among participants, 55.6% reported teams full engagement in the simulation sessions. The average session length was 30-60 minutes. The most commonly reported debriefing leaders were ICU staff, simulation lab staff, and ER facilitators, and the least common were infection control staff. A total of 80% reported \"a lot\" to \"a great improvement\" in terms of clinical preparedness after simulation sessions, and 70% were satisfied with the COVID-19 simulation sessions and thought they were better than expected. Most of the perceived issues reported were related to infection control measures, followed by team dynamics, logistics, and patient transport issues.\n\nConclusionSimulation centers team leaders and HCWs reported positive feedback on COVID- 19 simulation sessions. The presence of multiprofessional personnel during drills is warranted. These drills are a valuable tool for rehearsing safe dynamics of HCWs on the frontline of COVID-19.\n\nSummary boxexplaining the significance of their study by providing each of the following key questions:\n\nWhat is already known?O_LISimulation enhances healthcare systems safety.\nC_LIO_LIPreparedness to potential disasters includes training for personal protection techniques, environmental contamination, medical management, and training of HCWs.\nC_LI\n\nWhat are the new findings?O_LIMany hospitals conducted COVID-19 simulations in all WHO regions.\nC_LIO_LIMost of the team leaders and HCWs reported full engagement and significant clinical preparedness improvement after the COVID-19 simulation sessions.\nC_LI\n\nWhat do the new findings imply?O_LIThe presence of multiprofessional personnel, including infection control experts, during COVID-19 drills is warranted.\nC_LIO_LISimulation are a valuable tool for rehearsing safe dynamics of HCWs on the frontline of COVID-19.\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Mohamad Hani Temsah", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Abdulkarim Alrabiaah", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Ayman Al-Eyadhy", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Fahad Al-Sohime", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Abdullah Al Huzaimi", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Nurah Alamro", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Khalid Alhasan", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Vaibhavi Upadhye", - "author_inst": "Deenanath Mangeshkar Hospital and Research Centre, Pune, India" - }, - { - "author_name": "Amr Jamal", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Fadi Aljamaan", - "author_inst": "King Saud University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Yaseen M Arabi", - "author_inst": "King Abdullah International Medical Research Center, Riyadh, Saudi Arabia" - }, - { - "author_name": "Marc Lazarovici", - "author_inst": "Society for Simulation in Europe (SESAM), LMU University Hospital Simulation Centre, Munich, Germany" - }, - { - "author_name": "Abdulaziz M Boker", - "author_inst": "King Abdulaziz University, Jeddah, Saudi Arabia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.11.17.20233643", "rel_title": "Estimating COVID-19 Virus Prevalence from Records of Testing Rate and Test Positivity", @@ -1050493,6 +1054465,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.11.16.20231100", + "rel_title": "Deconditioning in people living with dementia during the COVID-19 pandemic: findings from the Promoting Activity, Independence and Stability in Early Dementia (PrAISED) process evaluation", + "rel_date": "2020-11-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20231100", + "rel_abs": "BackgroundRestrictions introduced in response to the COVID-19 pandemic led to increased risk of deconditioning in the general population. No empirical evidence of this effect however has been empirically gathered in people living with dementia.\n\nObjectiveThis study aims to identify the causes and effects of COVID-19-related deconditioning in people living with dementia.\n\nDesignLongitudinal phenomenological qualitative study.\n\nSubjectsParticipants living with dementia, their carers and therapists involved in the Promoting Activity, Independence and Stability in Early Dementia (PrAISED) process evaluation during the COVID-19 pandemic.\n\nMethodsQualitative interviews with participants were conducted remotely at two time points. The data were analysed through deductive thematic analysis.\n\nResultsTwenty-four participants living with dementia, 19 carers and 15 therapists took part in the study. A self-reinforcing pattern was common, whereby lockdown made the person apathetic, demotivated, socially-disengaged, and frailer. This reduced activity levels, which in turn reinforced the effects of deconditioning over time. Without external supporters, most participants lacked the motivation / cognitive abilities to keep active. Provided the proper infrastructure and support, some participants could use tele-rehabilitation to combat deconditioning.\n\nConclusionThe added risks and effects of deconditioning on people with dementia require considerable efforts from policy makers and clinicians to ensure that they initiate and maintain physical activity in prolonged periods of social distancing. Delivering rehabilitation in the same way as before the pandemic might not be feasible or sustainable and innovative approaches must be found. Digital support for this population has shown promising results, but still remains a challenge.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Claudio Di Lorito", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Tahir Masud", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "John Gladman", + "author_inst": "University of Notitngham" + }, + { + "author_name": "Maureen Godfrey", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Marianne Dunlop", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Rowan H Harwood", + "author_inst": "University of Nottingham" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "geriatric medicine" + }, { "rel_doi": "10.1101/2020.11.16.20232009", "rel_title": "The total number and mass of SARS-CoV-2 virions in an infected person", @@ -1050642,89 +1054653,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.16.20232397", - "rel_title": "Effect of Vitamin D3 Supplementation vs Placebo on Hospital Length of Stay in Patients with Severe COVID-19: A Multicenter, Double-blind, Randomized Controlled Trial.", - "rel_date": "2020-11-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232397", - "rel_abs": "ImportancePatients with COVID-19 may exhibit 25-hydroxyvitamin D deficiency, but the beneficial effects of vitamin D3 supplementation in this disease remain to be proven by randomized controlled trials.\n\nObjectiveTo investigate the efficacy and safety of vitamin D3 supplementation in patients with severe COVID-19.\n\nDesign, Setting, and ParticipantsThis is a multicenter, double-blind, randomized, placebo-controlled trial conducted in two centers (a quaternary hospital and a field hospital) in Sao Paulo, Brazil. The trial included 240 hospitalized patients with severe COVID-19. The study was conducted from June 2, 2020 to October 7, 2020.\n\nInterventionsPatients were randomly allocated (1:1 ratio) to receive either a single oral dose of 200,000 IU of vitamin D3 or placebo.\n\nMain Outcomes and MeasuresThe primary outcome was hospital length of stay, defined as hospital discharge from the date of randomization or death. Secondary outcomes were mortality, admission to ICU, mechanical ventilation requirement, and serum levels of 25-hydroxyvitamin D, creatinine, calcium, C-reactive protein, and D-dimer.\n\nResultsOf 240 randomized patients (mean age, 56 years; 56% men), 232 (96.7%) were included in the primary analysis. Log-rank test showed that hospital length of stay was comparable between the vitamin D3 supplementation and placebo groups (7.0 days [95% CI, 6.1 to 7.9] and 7.0 days [95% CI, 6.2 to 7.8 days]; hazard ratio, 1.12 [95% CI, 0.9 to 1.5]; P = .379; respectively). The rate of mortality (7.0% vs 5.1%; P = .590), admission to ICU (15.8% vs 21.2%; P = .314), and mechanical ventilation requirement (7.0% vs 14.4%; P = .090) did not significantly differ between groups. Vitamin D3 supplementation significantly increased serum 25-hydroxyvitamin D levels compared to placebo (difference, 24.0 ng/mL [95% CI, 21.0% to 26.9%]; P = .001). No adverse events were observed.\n\nConclusions and RelevanceAmong hospitalized patients with severe COVID-19, vitamin D3 supplementation was safe and increased 25-hydroxyvitamin D levels, but did not reduce hospital length of stay or any other relevant outcomes vs placebo. This trial does not support the use of vitamin D3 supplementation as an adjuvant treatment of patients with COVID-19.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSCan vitamin D3 supplementation reduce hospital length of stay in hospitalized patients with severe COVID-19?\n\nFindingsIn this double-blind, randomized, placebo-controlled trial involving 240 hospitalized patients with severe COVID-19, a single dose of 200,000 IU of vitamin D3 supplementation was safe and effective in increasing 25-hydroxyvitamin D levels, but did not significantly reduce hospital length of stay (hazard ratio, 1.12) or any other clinically-relevant outcomes compared with placebo.\n\nMeaningVitamin D3 supplementation does not confer therapeutic benefits among hospitalized patients with severe COVID-19.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Igor H. Murai", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Alan L. Fernandes", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Lucas P. Sales", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Ana J. Pinto", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Karla F. Goessler", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Camila S. C. Duran", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Carla B. R. Silva", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Andre S. Franco", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Marina B. Macedo", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Henrique H. H. Dalmolin", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Janaina Baggio", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Guilherme G. M. Balbi", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Bruna Z. Reis", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Leila Antonangelo", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Valeria F. Caparbo", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Bruno Gualano", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Rosa M. R. Pereira", - "author_inst": "Universidade de Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "rheumatology" - }, { "rel_doi": "10.1101/2020.11.15.20231001", "rel_title": "Central and peripheral nervous system complications of COVID-19: A prospective tertiary center cohort with 3-month follow-up", @@ -1052595,6 +1056523,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.12.20230912", + "rel_title": "Prevalence of IgG antibodies against the severe acute respiratory syndrome coronavirus-2 among healthcare workers in Tennessee during May and June, 2020", + "rel_date": "2020-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.12.20230912", + "rel_abs": "SARS-CoV-2 seroprevalence was low (<1%) in this large population of healthcare workers (HCWs) across the state of Tennessee (n=11,787) in May-June 2020. Among those with PCR results, 81.5% of PCR and antibody test results were concordant. SARS-CoV-2 seroprevalence was higher among HCWs working in high-community-transmission regions and among younger workers.\n\nImportanceThese results may be seen as a baseline assessment of SARS-CoV-2 seroprevalence among HCWs in the American South during a period of growth, but not yet saturation, of infections among susceptible populations. In fact, this period of May-June 2020 was marked by the extension of renewed and sustained community-wide transmission after mandatory quarantine periods expired in several more populous regions of Tennessee. Where community transmission remains low, HCWs may still be able to effectively mitigate SARS-CoV-2 transmission, preserving resources for populations at high risk of severe disease, and these sorts of data help highlight such strategies.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Peter F Rebeiro", + "author_inst": "Vanderbilt University School of Medicine, Department of Medicine, Divisions of Infectious Diseases & Epidemiology; Department of Biostatistics" + }, + { + "author_name": "Kara J Levinson", + "author_inst": "Tennessee Department of Health, Division of Laboratory Services" + }, + { + "author_name": "Lindsay Jolly", + "author_inst": "Tennessee Department of Health, Division of Laboratory Services" + }, + { + "author_name": "Elizabeth Kassens", + "author_inst": "Tennessee Department of Health, Division of Laboratory Services" + }, + { + "author_name": "George J Dizikes", + "author_inst": "Tennessee Department of Health, Division of Laboratory Services" + }, + { + "author_name": "Richard S Steece", + "author_inst": "Tennessee Department of Health, Division of Laboratory Services" + }, + { + "author_name": "David C Metzger", + "author_inst": "Ballad Health" + }, + { + "author_name": "Matthew Loos", + "author_inst": "Ballad Health" + }, + { + "author_name": "Ron Buchheit", + "author_inst": "Department Of Emergency Medicine, University Of Tennessee College of Medicine Chattanooga, Erlanger Health System" + }, + { + "author_name": "Lisa D Duncan", + "author_inst": "University of Tennessee Medical Center, Department of Pathology" + }, + { + "author_name": "Lori A Rolando", + "author_inst": "Vanderbilt University School of Medicine, Department of Medicine, Division of General Internal Medicine & Public Health and Vanderbilt Health and Wellness" + }, + { + "author_name": "Jonathan Schmitz", + "author_inst": "Vanderbilt University School of Medicine , Department of Pathology, Microbiology and Immunology" + }, + { + "author_name": "Heather A Hart", + "author_inst": "Vanderbilt University School of Medicine, Department of Surgery, Division of Trauma" + }, + { + "author_name": "David M Aronoff", + "author_inst": "Vanderbilt University School of Medicine, Department of Medicine, Division of Infectious Diseases; Department of Pathology, Microbiology and Immunology" + }, + { + "author_name": "- Tennessee COVID-19 Serology Study Team", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.12.20230656", "rel_title": "Development and validation of a highly sensitive and specific electrochemical assay to quantify anti-SARS-CoV-2 IgG antibodies to facilitate pandemic surveillance and monitoring of vaccine response", @@ -1052852,57 +1056855,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.11.13.20231266", - "rel_title": "Estimating the cumulative incidence of SARS-CoV-2 infection and the infection fatality ratio in light of waning antibodies", - "rel_date": "2020-11-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.13.20231266", - "rel_abs": "BackgroundSerology tests can identify previous infections and facilitate estimation of the number of total infections. However, immunoglobulins targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been reported to wane below the detectable level of serological assays. We estimate the cumulative incidence of SARS-CoV-2 infection from serology studies, accounting for expected levels of antibody acquisition (seroconversion) and waning (seroreversion), and apply this framework using data from New York City (NYC) and Connecticut.\n\nMethodsWe estimated time from seroconversion to seroreversion and infection fatality ratio (IFR) using mortality data from March-October 2020 and population-level cross-sectional seroprevalence data from April-August 2020 in NYC and Connecticut. We then estimated the daily seroprevalence and cumulative incidence of SARS-CoV-2 infection.\n\nFindingsThe estimated average time from seroconversion to seroreversion was 3-4 months. The estimated IFR was 1.1% (95% credible interval: 1.0-1.2%) in NYC and 1.4% (1.1-1.7%) in Connecticut. The estimated daily seroprevalence declined after a peak in the spring. The estimated cumulative incidence reached 26.8% (24.2-29.7%) and 8.8% (7.1-11.3%) at the end of September in NYC and Connecticut, higher than maximum seroprevalence measures (22.1% and 6.1%), respectively.\n\nInterpretationThe cumulative incidence of SARS-CoV-2 infection is underestimated using cross-sectional serology data without adjustment for waning antibodies. Our approach can help quantify the magnitude of underestimation and adjust estimates for waning antibodies.\n\nFundingThis study was supported by the US National Science Foundation and the National Institute of Allergy and Infectious Diseases.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Kayoko Shioda", - "author_inst": "Emory University" - }, - { - "author_name": "Max SY Lau", - "author_inst": "Emory University" - }, - { - "author_name": "Alicia NM Kraay", - "author_inst": "Emory University" - }, - { - "author_name": "Kristin N Nelson", - "author_inst": "Emory University" - }, - { - "author_name": "Aaron J Siegler", - "author_inst": "Emory University" - }, - { - "author_name": "Patrick S Sullivan", - "author_inst": "Emory University" - }, - { - "author_name": "Matthew H Collins", - "author_inst": "Emory University" - }, - { - "author_name": "Joshua S Weitz", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Benjamin A Lopman", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.13.20231472", "rel_title": "Role of air temperature and humidity in the transmission of SARS-CoV-2 in the United States", @@ -1054241,6 +1058193,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.11.13.20231571", + "rel_title": "No evidence of increase in suicide in Greece during the first wave of Covid-19", + "rel_date": "2020-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.13.20231571", + "rel_abs": "Background and ObjectiveMental health outcomes have reportedly worsened in several countries during the Covid-19 pandemic and associated lockdowns. In the present study we examined whether suicides increased in Greece during the first wave of the pandemic.\n\nMethodsWe used daily suicide estimates from a Suicide Observatory in Greece from 2015-2020 and followed three methodologies: A descriptive approach, an interrupted time series analysis, and a differences-in-differences econometric model.\n\nResultsWe did not find any empirical evidence of any increase in suicides during the first wave of Covid-19 and the lockdown in any of the three approaches used.\n\nConclusionsSuicides did not seem to increase during the first wave of covid-19 and lockdown in Greece. However, this does not mean that mental health did not deteriorate, or that we will not observe an increase in suicides during the second wave. Protective factors for Greece during the first wave may include working from home (for those able to tele-work), strong family ties, advertising of a suicide hotline and income support for the unemployed.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Sotiris Vandoros", + "author_inst": "King's College London and Harvard T.H. Chan School of Public Health, Harvard University" + }, + { + "author_name": "Olga Theodorikakou", + "author_inst": "Suicide Prevention Center, KLIMAKA NGO" + }, + { + "author_name": "Kyriakos Katsadoros", + "author_inst": "Suicide Prevention Center, KLIMAKA NGO" + }, + { + "author_name": "Dimitra Zafeiropoulou", + "author_inst": "Suicide Prevention Center, KLIMAKA NGO" + }, + { + "author_name": "Ichiro Kawachi", + "author_inst": "Harvard T.H. Chan School of Public Health, Harvard University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.14.20229096", "rel_title": "Chest CT features of COVID-19 in the region of Abu Dhabi, UAE- A single institute study", @@ -1054346,65 +1058333,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.11.14.382770", - "rel_title": "Discovery of rhodomyrtone as a broad-spectrum antiviral inhibitor with anti-SARS-CoV-2 activity", - "rel_date": "2020-11-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.14.382770", - "rel_abs": "The outbreak of new viruses, such as serve acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as well as the emerging of drug-resistance viruses highlight the urgent need for the development of broad-spectrum antiviral drugs. Herein, we report the discovery of a plant-derived small molecule, 6,8-dihydroxy-9-isobutyl-2,2,4,4-tetramethyl-7-(3-methylbutanoyl)-4,9-dihydro-1H-xanthene-1,3(2H)-dione (rhodomyrtone, RDT), which exhibited potent broad-spectrum antiviral activities against several RNA and DNA viruses, including SARS-CoV-2, respiratory syncytial virus (RSV), herpes simplex virus type 1 (HSV-1), herpes simplex virus type 2 (HSV-2), varicella-zoster virus (VZV), human cytomegalovirus (HCMV), and Kaposis sarcoma-associated herpesvirus (KSHV). RDT can significantly suppress viral gene expression and show the low possibility to elicit drug-resistant variants. Mechanistic study implied that RDT inhibited viral infection by disturbing the cellular factors that essential for viral gene expression. Our results suggested that RDT might be a promising lead compound for the development of broad-spectrum antiviral drugs.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Wei Tang", - "author_inst": "Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drugs Research, College of Pharmacy, Jinan University, G" - }, - { - "author_name": "Jing Lu", - "author_inst": "Guangdong Provincial Institution of Public Health, Guangdong Provincial Center for Disease Control & Prevention, Guangzhou, China" - }, - { - "author_name": "Qiao-Yun Song", - "author_inst": "Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drugs Research, College of Pharmacy, Jinan University, G" - }, - { - "author_name": "Man-Mei Li", - "author_inst": "Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drugs Research, College of Pharmacy, Jinan University, G" - }, - { - "author_name": "Li-Feng Chen", - "author_inst": "Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drugs Research, College of Pharmacy, Jinan University, G" - }, - { - "author_name": "Li-Jun Hu", - "author_inst": "Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drugs Research, College of Pharmacy, Jinan University, G" - }, - { - "author_name": "Shao-Min Yang", - "author_inst": "Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drugs Research, College of Pharmacy, Jinan University, G" - }, - { - "author_name": "Dong-Mei Zhang", - "author_inst": "Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drugs Research, College of Pharmacy, Jinan University, G" - }, - { - "author_name": "Ying Wang", - "author_inst": "Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drugs Research, College of Pharmacy, Jinan University, G" - }, - { - "author_name": "Yao-Lan Li", - "author_inst": "Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drugs Research, College of Pharmacy, Jinan University, G" - }, - { - "author_name": "Wen-Cai Ye", - "author_inst": "Guangdong Province Key Laboratory of Pharmacodynamic Constituents of Traditional Chinese Medicine & New Drugs Research, College of Pharmacy, Jinan University, G" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.11.14.382416", "rel_title": "Novel gene-specific translation mechanism of dysregulated, chronic inflammation reveals promising, multifaceted COVID-19 therapeutics", @@ -1056183,6 +1060111,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.11.20229815", + "rel_title": "Excess mortality for care home residents during the first 23 weeks of the COVID-19 pandemic in England: a national cohort study", + "rel_date": "2020-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20229815", + "rel_abs": "BackgroundTo estimate excess mortality for care home residents during the COVID-19 pandemic in England, exploring associations with care home characteristics.\n\nMethodsDaily number of deaths in all residential and nursing homes in England notified to the Care Quality Commission (CQC) from 1st January 2017 to 7th August 2020. Care home level data linked with CQC care home register to identify homes characteristics: client type (over 65s/children and adults), ownership status (for-profit/not-for-profit; branded/independent), and size (small/medium/large).\n\nExcess deaths computed as the difference between observed and predicted deaths using local authority fixed-effect Poisson regressions on pre-pandemic data. Fixed-effect logistic regressions were used to model odds of experiencing COVID-19 suspected/confirmed deaths.\n\nFindingsUp to 7th August 2020 there were 29,542 (95%CI: 25,176 to 33,908) excess deaths in all care homes. Excess deaths represented 6.5% (95%CI: 5.5% to 7.4%) of all care home beds, higher in nursing (8.4%) than residential (4.6%) homes. 64.7% (95%CI: 56.4% to 76.0%) of the excess deaths were confirmed/suspected COVID-19. Almost all excess deaths were recorded in the quarter (27.4%) of homes with any COVID-19 fatalities.\n\nThe odds of experiencing COVID-19 attributable deaths were higher in homes providing nursing services (OR: 1.8, 95%CI: 1.6 to 2.0); to older people and/or with dementia (OR: 5.5, 95%CI: 4.4 to 6.8); among larger (vs. small) homes (OR: 13.3, 95%CI: 11.5 to 15.4); belonging to a large provider/brand (OR: 1.2, 95%CI: 1.1 to 1.3). There was no significant association with for-profit status of providers.\n\nInterpretationTo limit excess mortality, policy should be targeted at care homes to minimise the risk of ingress of disease and limit subsequent transmission. Our findings provide specific characteristic targets for further research on mechanisms and policy priority.\n\nFundingNIHR.\n\nSummary boxO_ST_ABSEvidence before this studyC_ST_ABSGlobally, residents in care homes have experienced disproportionately high morbidity and mortality from COVID-19. Excess mortality incorporates all direct and indirect mortality effects of the pandemic.\n\nWe searched MEDLINE for published literature, pre-publication databases (medRxiv and Lancet pre-print) and grey literature (ONS and Google) for care homes AND COVID-19 AND mortality, to 31st October 2020. We screened for evidence on excess deaths in care homes in England, and international evidence of the association of COVID-19 deaths and outbreaks with care home characteristics.\n\nOfficial estimates from England and Wales have reported aggregated excess deaths by place of occurrence, but we identified no peer-reviewed excess deaths study in this setting. These aggregates, however, do not account for care home residents dying in other settings (e.g. hospital), nor provide sufficient information to reflect on the impacts of enacted policies over the period, or to inform new policies for future virus waves.\n\nPrevious peer-reviewed and pre-publication studies have also shown the heterogeneous effects of COVID-19 by care home characteristics in other countries. Particularly important from the current literature appears to be care home size, with larger care homes tending to be associated with more negative outcomes in studies with smaller sample sizes. A study from the Lothian region of Scotland additionally found excess deaths concentrated in a minority of homes that experienced an outbreak. However, a national breakdown of excess deaths by care home characteristics is largely lacking from the current literature in England, with a specific market structure and policy context.\n\nAdded value of this studyWe use nationally representative administrative data from all care homes in England to estimate overall excess deaths and by care home characteristics: setting type (nursing or residential home), client types (offering services for people aged 65+ and/or people with dementia or offering services to children and adults), ownership status (whether not-for-profit - charity/NHS/LA-run homes - or for-profit), whether known to be affiliated to a large provider/brand or independent, and classification according to their registered maximum bed capacity (small, medium and large).\n\nWe then used multivariable logistic regression to estimate the adjusted odds of a care home experiencing a suspected or confirmed COVID-19 death across these characteristics.\n\nWe found that only 65% of excess deaths were flagged as officially confirmed/suspected COVID-19 attributed. However, almost all excess deaths occurred in the roughly quarter of care homes that reported at least one suspected/confirmed COVID-19 death. After adjusting for other care home characteristics, larger care homes (vs. small) had the highest odds of experiencing at least one suspected/confirmed COVID-19 death. These findings confirm those from the previous literature, in a unique policy context and with national data.\n\nImplications of all the available evidenceThe fact that nearly all excess deaths occurred in care homes with at least one COVID-19 attributed death suggests that directly-attributed deaths are very likely to be under-recorded. It also suggests that any indirect mortality effect, of COVID-19 and any enacted policies, were predominantly constrained to those homes experiencing an outbreak.\n\nLarger homes are likely to experience higher footfall in general, and so higher probability of contact with an infected individual, which is likely a contributing factor to the association. Furthermore, it might be easier to ensure person-centred protocols in small care homes due to the scale.\n\nThere is an urgent need for further research to explore the mechanisms in relation to care home characteristics. Also, to empirically test effective interventions, in consideration of additional impacts on quality of life and psychological wellbeing. However, until this is possible, prioritising existing resources, such as testing and PPE equipment, for care homes to prevent ingress of disease is key to preventing large excess mortality.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Marcello Morciano", + "author_inst": "University of Manchester" + }, + { + "author_name": "Jonathan M Stokes", + "author_inst": "University of Manchester" + }, + { + "author_name": "Evangelos Kontopantelis", + "author_inst": "University of Manchester" + }, + { + "author_name": "Ian Hall", + "author_inst": "University of Manchester" + }, + { + "author_name": "Alexander J Turner", + "author_inst": "University of Manchester" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.11.20229393", "rel_title": "Using Convergent Sequential Design for Rapid Complex Case Study Descriptions: Example of Public Health Briefings During the Onset of the COVID-19 Pandemic", @@ -1056380,101 +1060343,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.11.20229500", - "rel_title": "Association of social distancing and masking with risk of COVID-19", - "rel_date": "2020-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20229500", - "rel_abs": "Given the continued burden of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) disease (COVID-19) across the U.S., there is a high unmet need for data to inform decision-making regarding social distancing and universal masking. We examined the association of community-level social distancing measures and individual masking with risk of predicted COVID-19 in a large prospective U.S. cohort study of 198,077 participants. Individuals living in communities with the greatest social distancing had a 31% lower risk of predicted COVID-19 compared with those living in communities with poor social distancing. Self-reported masking was associated with a 63% reduced risk of predicted COVID-19 even among individuals living in a community with poor social distancing. These findings provide support for the efficacy of mask-wearing even in settings of poor social distancing in reducing COVID-19 transmission. In the current environment of relaxed social distancing mandates and practices, universal masking may be particularly important in mitigating risk of infection.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Sohee Kwon", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Amit D. Joshi", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Chun-Han Lo", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "David Alden Drew", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Long Nguyen", - "author_inst": "Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Chuan-Guo Guo", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Wenjie Ma", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Raaj S. Mehta", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Erica T. Warner", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Christina M. Astley", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Jordi Merino", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Benjamin Murray", - "author_inst": "King's College London" - }, - { - "author_name": "Jonathan Wolf", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Sebastien Ourselin", - "author_inst": "King's College London" - }, - { - "author_name": "Claire Steves", - "author_inst": "King's College London" - }, - { - "author_name": "Timothy Spector", - "author_inst": "King's College London" - }, - { - "author_name": "Jaime E. Hart", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Mingyang Song", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Trang VoPham", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Andrew T. Chan", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.11.20229708", "rel_title": "Mortality in Norway and Sweden before and after the Covid-19 outbreak: a cohort study", @@ -1057885,6 +1061753,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.10.20229005", + "rel_title": "Non-occupational and occupational factors associated with specific SARS-CoV-2 antibodies among Hospital Workers - a multicentre cross-sectional study", + "rel_date": "2020-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.10.20229005", + "rel_abs": "ObjectivesProtecting healthcare workers (HCW) from Coronavirus Disease-19 (COVID-19) is critical to preserve the functioning of healthcare systems. We therefore assessed seroprevalence and identified risk factors for Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) seropositivity in this population.\n\nMethodsBetween June 22nd and August 15th 2020, HCW from institutions in Northern/Eastern Switzerland were screened for SARS-CoV-2 antibodies. We recorded baseline characteristics, non-occupational and occupational risk factors. We used pairwise tests of associations and multivariable logistic regression to identify factors associated with seropositivity.\n\nResultsAmong 4664 HCW from 23 healthcare facilities, 139 (3%) were seropositive. Non-occupational exposures independently associated with seropositivity were contact with a COVID-19-positive household (adjusted OR=54, 95%-CI: 31-97) and stay in a COVID-19 hotspot (aOR=2.2, 95%-CI: 1.1-3.9). Blood group 0 vs. non-0 (aOR=0.4, 95%-CI: 0.3-0.7), active smoking (aOR=0.5, 95%-CI: 0.3-0.9) and living with children <12 years (aOR=0.3, 95%-CI: 0.2-0.6) were associated with decreased risk. Occupational risk factors were close contact to COVID-19 patients (aOR=2.8, 95%-CI: 1.5-5.5), exposure to COVID-19-positive co-workers (aOR=2.0, 95%-CI: 1.2-3.1), poor knowledge of standard hygiene precautions (aOR=2.0, 95%-CI: 1.3-3.2), and frequent visits to the hospital canteen (aOR=1.9, 95%-CI: 1.2-3.1).\n\nConclusionsLiving with COVID-19-positive households showed by far the strongest association with SARS-CoV-2 seropositivity. We identified several potentially modifiable risk factors, which might allow mitigation of the COVID-19 risk among HCW. The lower risk among those living with children, even after correction for multiple confounders, is remarkable and merits further study.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Christian R. Kahlert", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland; Children's Hospital of Eastern Switzerland, Depa" + }, + { + "author_name": "Raphael Persi", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Sabine Guesewell", + "author_inst": "Clinical Trials Unit, Cantonal Hospital of St. Gallen, St. Gallen, Switzerland" + }, + { + "author_name": "Thomas Egger", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Onicio B. Leal-Neto", + "author_inst": "Epitrack, Recife, Brazil; Department of Economics, University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Johannes Sumer", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Domenica Flury", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Angela Brucher", + "author_inst": "Psychiatry Services of the Canton of St. Gallen (South), Switzerland" + }, + { + "author_name": "Eva Lemmenmeier", + "author_inst": "Clienia Littenheid AG, Private Clinic for Psychiatry and Psychotherapy, Littenheid, Switzerland" + }, + { + "author_name": "Carsten Moeller", + "author_inst": "Rehabilitation Clinic, Zihlschlacht, Switzerland" + }, + { + "author_name": "Philip Rieder", + "author_inst": "Hirslanden Clinic, Zurich, Switzerland" + }, + { + "author_name": "Reto Stocker", + "author_inst": "Hirslanden Clinic, Zurich, Switzerland" + }, + { + "author_name": "Danielle Vuichard-Gysin", + "author_inst": "Thurgau Hospital Group, Division of Infectious Diseases and Hospital Epidemiology, Muensterlingen, Switzerland; Swiss National Center for Infection Prevention (" + }, + { + "author_name": "Benedikt Wiggli", + "author_inst": "Kantonsspital Baden, Division of Infectious Diseases and Hospital Epidemiology, Baden, Switzerland" + }, + { + "author_name": "Werner C. Albrich", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Baharak Babouee Flury", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Ulrike Besold", + "author_inst": "Geriatric Clinic St. Gallen, St. Gallen, Switzerland" + }, + { + "author_name": "Jan Fehr", + "author_inst": "Department of Public and Global Health, University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Stefan P. Kuster", + "author_inst": "Federal Office of Public Health, Bern, Switzerland; University Hospital and University of Zurich, Division of Infectious Diseases and Hospital Epidemiology, Zur" + }, + { + "author_name": "Allison McGeer", + "author_inst": "Sinai Health System, Toronto, Canada" + }, + { + "author_name": "Lorenz Risch", + "author_inst": "Labormedizinisches Zentrum Dr Risch Ostschweiz AG, Buchs, Switzerland; Private Universitaet im Fuerstentum Liechtenstein, Triesen, Liechtenstein; Center of Labo" + }, + { + "author_name": "Matthias Schlegel", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Pietro Vernazza", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Andree Friedl", + "author_inst": "Kantonsspital Baden, Division of Infectious Diseases and Hospital Epidemiology, Baden, Switzerland" + }, + { + "author_name": "Philipp Kohler", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.10.20228973", "rel_title": "Comparison of SARS-COV-2 nasal antigen test to nasopharyngeal RT-PCR in mildly symptomatic patients", @@ -1058058,29 +1062041,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.10.20215145", - "rel_title": "The Change in Seroprevalence in the US plus Puerto Rico between May and September of SARS-CoV-2 Antibody in the Asymptomatic Population", - "rel_date": "2020-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.10.20215145", - "rel_abs": "As the COVID-19 pandemic continues to ravage the world there is a great need to understand the dynamics of spread. Currently the seroprevalence of asymptomatic COVID-19 doubles every 3 months, this silent epidemic of new infections may be the main driving force behind the rapid increase in SARS-CoV-2 cases.\n\nPublic health official quickly recognized that clinical cases were just the tip of the iceberg. In fact a great deal of the spread was being driven by the asymptomatically infected who continued to go out, socialize and go to work. While seropositivity is an insensitive marker for acute infection it does tell us about the prevalence COVID-19 in the population.\n\nObjectiveDescribe the seroprevalence of SARS-CoV-2 infection in the United States over time.\n\nMethodologyRepeated convenience samples from a commercial laboratory dedicated to the assessment of life insurance applicants were tested for the presence of antibodies to SARS-CoV-2, in several time periods between May and December of 2020. US census data were used to estimate the population prevalence of seropositivity.\n\nResultsThe raw seroprevalence in the May-June, September, and December timeframes were 3.0%, 6.6% and 10.4%, respectively. Higher rates were noted in younger vs. older age groups. Total estimated seroprevalence in the US is estimated at 25.7 million cases.\n\nConclusionsThe seroprevalence of SARS-CoV-2 demonstrates a significantly larger pool of individuals who have contract COVID-19 and recovered, implying a lower case rate of hospitalizations and deaths than have been reported so far.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Robert Stout", - "author_inst": "Clinical Reference Laboratory" - }, - { - "author_name": "Steven Rigatti", - "author_inst": "Clinical Reference Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.10.20228403", "rel_title": "Do predictors of adherence to pandemic guidelines change over time? A panel study of 21,000 UK adults during the COVID-19 pandemic", @@ -1059723,6 +1063683,49 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.11.08.20227819", + "rel_title": "Detection of COVID-19 Disease from Chest X-Ray Images: A Deep Transfer Learning Framework", + "rel_date": "2020-11-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.08.20227819", + "rel_abs": "World economy as well as public health have been facing a devastating effect caused by the disease termed as Coronavirus (COVID-19). A significant step of COVID-19 affected patients treatment is the faster and accurate detection of the disease which is the motivation of this study. In this paper, implementation of a deep transfer learning-based framework using a pre-trained network (ResNet-50) for detecting COVID-19 from the chest X-rays was done. Our dataset consists of 2905 chest X-ray images of three categories: COVID-19 affected (219 cases), Viral Pneumonia affected (1345 cases), and Normal Chest X-rays (1341 cases). The implemented neural network demonstrates significant performance in classifying the cases with an overall accuracy of 96%. Most importantly, the model has shown a significantly good performance over the current research-based methods in detecting the COVID-19 cases in the test dataset (Precision = 1.00, Recall = 1.00, F1-score = 1.00 and Specificity = 1.00). Therefore, our proposed approach can be adapted as a reliable method for faster and accurate COVID-19 affected case detection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Shadman Sakib", + "author_inst": "Leading University" + }, + { + "author_name": "Md. Abu Bakr Siddique", + "author_inst": "International University of Business Agriculture and Technology" + }, + { + "author_name": "Mohammad Mahmudur Rahman Khan", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Nowrin Yasmin", + "author_inst": "Ahsanullah University of Science and Technology" + }, + { + "author_name": "Anas Aziz", + "author_inst": "Military Institute of Science and Technology" + }, + { + "author_name": "Madiha Chowdhury", + "author_inst": "Bangladesh University of Engineering and Technology" + }, + { + "author_name": "Ihtyaz Kader Tasawar", + "author_inst": "BRAC University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.08.20227884", "rel_title": "Host genetic liability for severe COVID-19 overlaps with alcohol drinking behavior and diabetic outcomes and in over 1 million participants", @@ -1059824,45 +1063827,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.11.06.20223040", - "rel_title": "Innovation of Audio-Visual Triage system in Combating the Spread of COVID-19 Infection and its efficacy: A Novel Strategy", - "rel_date": "2020-11-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20223040", - "rel_abs": "During the novel coronavirus pandemic, also known as SARS-CoV-2 or COVID-19 pandemic, frontline healthcare professionals suffered psychological as well as pathological trauma due to the lack of preparation to cope with this unforeseen situation. The protocols to prevent the spread of this disease proved to be less effective than anticipated. In these circumstances, improvement of the existing triage system was felt and an AUDIO-VISUAL TRIAGE (AVT) system was introduced to enhance confidence as well as increase the safety of frontline healthcare professionals. The current analysis was performed from March 21, 2020, to April 28, 2020, until the completion of sixty response forms, at Bahria Town International Hospital, Lahore. Thirty participants (Group A) deployed on visual triage and other thirty (Group B) on AVT for screening suspected cases of COVID-19 infection. Anxiety levels were measured by using the GAD-7 scoring system and the participants of both groups were periodically tested for COVID-19 infection by PCR. Independent t-test was used to evaluate the significance of different variables at a confidence level of 95%. The result of the current study revealed the effectiveness of AVT for the screening of COVID-19 patients. There was a statistically significant increase in anxiety levels and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection rate in group A as compared to group B. Almost all participants in group A wanted to shift their place of work or ready to quit the job if they were forced to perform their duties at the same visual triage. AVT system for COVID-19 screening found to be more safe and less stressful than visual triage. It is not only a simple and effective way to prevent the spread of diseases but also boosted the confidence of frontline healthcare professionals to fight against coronavirus spread.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Muhammad Mansoor Hafeez", - "author_inst": "Institute of Molecular Biology and Biotechnology, The University of Lahore" - }, - { - "author_name": "Mohammad Azhar", - "author_inst": "Bahria International Hospital Lahore" - }, - { - "author_name": "Hafiz Razwan Zafar", - "author_inst": "Bahria International Hospital Lahore" - }, - { - "author_name": "Muhammad Asim Rana", - "author_inst": "Bahria International Hospital, Lahore" - }, - { - "author_name": "Sulayman Waquar", - "author_inst": "Institute of Molecular Biology and Biotechnology, The University of Lahore" - }, - { - "author_name": "Arif Malik", - "author_inst": "Institute of Molecular Biology and Biotechnology, The University of Lahore" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2020.11.08.20222638", "rel_title": "Mathematical analysis of Cordoba calcifediol trial suggests strong role for Vitamin D in reducing ICU admissions of hospitalized COVID-19 patients", @@ -1061701,6 +1065665,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.11.09.20228684", + "rel_title": "Retrospective Analyses of Interventions to Epidemics using a Continuously Updated Model, with Application to the COVID-19 Crisis in New York City", + "rel_date": "2020-11-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.09.20228684", + "rel_abs": "Retrospective analyses of interventions to epidemics, in which the effectiveness of strategies implemented are compared to hypothetical alternatives, are valuable for performing the cost-benefit calculations necessary to optimize infection countermeasures. SIR (susceptible-infected-removed) models are useful in this regard but are limited by the challenge of deciding how and when to update the numerous parameters as the epidemic changes in response to population behaviors. Behaviors of particular interest include facemasks adoption (at various levels) and social distancing. We present a method that uses a \"dynamic spread function\" to systematically capture the continuous variation in the population behavior, and the gradual change in infection evolution, resulting from interventions. No parameter updates are made by the user. We use the tool to quantify the reduction in infection rate realizable from the population of New York City adopting different facemask strategies during COVID-19. Assuming a baseline facemask of 67% filtration efficiency, calculations show that increasing the efficiency to 80% could have reduced the roughly 5000 new infections per day occurring at the peak of the epidemic to around 4000. Population behavior that may not be varied as part of the retrospective analysis, such as social distancing in a facemask analysis, are automatically captured as part of the calibration of the dynamic spread function.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jenna Osborn", + "author_inst": "U. S. FDA" + }, + { + "author_name": "Shayna Berman", + "author_inst": "U. S. FDA" + }, + { + "author_name": "Sara Bender_Bier", + "author_inst": "U. S. FDA" + }, + { + "author_name": "Gavin D'Souza", + "author_inst": "U. S. FDA" + }, + { + "author_name": "Matthew Myers", + "author_inst": "U. S. FDA" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.09.20228098", "rel_title": "Peginterferon-lambda for the treatment of COVID-19 in outpatients", @@ -1061962,73 +1065961,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.09.20223792", - "rel_title": "The Individual and Social Determinants of COVID-19 in Ontario, Canada: A Population-Wide Study", - "rel_date": "2020-11-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.09.20223792", - "rel_abs": "BackgroundOptimizing the public health response to reduce coronavirus disease 2019 (COVID-19) burden necessitates characterizing population-level heterogeneity of COVID-19 risks. However, heterogeneity in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing may introduce biased estimates depending on analytic design.\n\nMethodsWe explored the potential for collider bias and characterized individual, environmental, and social determinants of testing and diagnosis using cross-sectional analyses among 14.7 million community-dwelling people in Ontario, Canada. Among those diagnosed, we used separate analytic designs to compare predictors of: 1) individuals testing positive versus negative; 2) symptomatic individuals only testing positive versus testing negative; and 3) individuals testing positive versus individuals not testing positive (i.e., testing negative or not being tested). Analyses included tests conducted between March 1 and June 20, 2020.\n\nResultsOf a total of 14,695,579 individuals, 758,691 were tested for SARS-CoV-2, of whom 25,030 (3.3%) tested positive. The further the odds of testing from the null, the more variability observed in the odds of diagnosis across analytic design, particularly among individual factors. There was less variability in testing by social determinants across analytic designs. Residing in areas with highest household density (adjusted odds ratio [aOR]: 1.86; 95%CI: 1.75-1.98), highest proportion of essential workers (aOR: 1.58; 95%CI: 1.48-1.69), lowest educational attainment (aOR: 1.33; 95%CI: 1.26-1.41), and highest proportion of recent immigrants (aOR: 1.10; 95%CI: 1.05-1.15) were consistently related to increased odds of SARS-CoV-2 diagnosis regardless of analytic design.\n\nInterpretationWhere testing is limited, risk factors may be better estimated using population comparators rather than test-negative comparators. Optimizing COVID-19 responses necessitates investment and sufficient coverage of structural interventions tailored to heterogeneity in social determinants of risk, including household crowding, occupation, and structural racism.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Maria Sundaram", - "author_inst": "ICES" - }, - { - "author_name": "Andrew Calzavara", - "author_inst": "ICES" - }, - { - "author_name": "Sharmistha Mishra", - "author_inst": "University of Toronto" - }, - { - "author_name": "Rafal Kustra", - "author_inst": "University of Toronto" - }, - { - "author_name": "Adrienne Chan", - "author_inst": "University of Toronto, Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Mackenzie A. Hamilton", - "author_inst": "ICES" - }, - { - "author_name": "Mohamed Djebli", - "author_inst": "ICES" - }, - { - "author_name": "Laura A. Rosella", - "author_inst": "University of Toronto" - }, - { - "author_name": "Tristan Watson", - "author_inst": "ICES" - }, - { - "author_name": "Hong Chen", - "author_inst": "ICES, University of Toronto" - }, - { - "author_name": "Branson Chen", - "author_inst": "ICES" - }, - { - "author_name": "Stefan Baral", - "author_inst": "JHSPH" - }, - { - "author_name": "Jeff Kwong", - "author_inst": "ICES" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.09.20228494", "rel_title": "Changes in sexual behavior, PrEP adherence, and access to sexual health services due to the COVID-19 pandemic among a cohort of PrEP-using MSM in the South", @@ -1063939,6 +1067871,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.07.20227462", + "rel_title": "Synthetic Reproduction and Augmentation of COVID-19 Case Reporting Data by Agent-Based Simulation", + "rel_date": "2020-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.07.20227462", + "rel_abs": "We generate synthetic data documenting COVID-19 cases in Austria by the means of an agent-based simulation model. The model simulates the transmission of the SARS-CoV-2 virus in a statistical replica of the population and reproduces typical patient pathways on an individual basis while simultaneously integrating historical data on the implementation and expiration of population-wide countermeasures. The resulting data semantically and statistically aligns with an official epidemiological case reporting data set and provides an easily accessible, consistent and augmented alternative. Our synthetic data set provides additional insight into the spread of the epidemic by synthesizing information that cannot be recorded in reality.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Nikolas Popper", + "author_inst": "Information and Software Engineering, Vienna University of Technology" + }, + { + "author_name": "Melanie Zechmeister", + "author_inst": "DEXHELPP - Decision Support for Health Policy and Planning" + }, + { + "author_name": "Dominik Brunmeir", + "author_inst": "dwh simulation services" + }, + { + "author_name": "Claire Rippinger", + "author_inst": "dwh simulation services" + }, + { + "author_name": "Nadine Weibrecht", + "author_inst": "DEXHELPP - Decision Support for Health Policy and Planning" + }, + { + "author_name": "Christoph Urach", + "author_inst": "dwh simulation services" + }, + { + "author_name": "Martin Bicher", + "author_inst": "Information and Software Engineering, Vienna University of Technology" + }, + { + "author_name": "G\u00fcnter Schneckenreither", + "author_inst": "Information and Software Engineering, Vienna University of Technology" + }, + { + "author_name": "Andreas Rauber", + "author_inst": "Information and Software Engineering, Vienna University of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.06.20227330", "rel_title": "The COVID-19 epidemic in the Czech Republic: retrospective analysis of measures (not) implemented during the spring first wave", @@ -1064080,49 +1068063,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.11.06.20227314", - "rel_title": "Asymptomatic Employee Screening for SARS-CoV-2: Implementation of and Reactions to an Employer-Based Testing Program.", - "rel_date": "2020-11-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20227314", - "rel_abs": "IntroductionAsymptomatic testing for SARS-CoV-2 among healthcare workers or other essential personnel could remove infected carriers from the workforce, decreasing chances for transmission and workplace outbreaks. Results from one-time testing programs have been reported but data regarding longitudinal testing, including information about employees reactions to such programs, is not readily available.\n\nMethodsTo identify asymptomatic carriers of SARS-CoV-2, we implemented a longitudinal screening program for critical on-site employees within our research institute in early April 2020. We conducted a survey of both on-site employees and those working from home in order to measure their reactions to the testing program. Statistical analysis of the survey was conducted with general linear regression and Pearsons Chi-Square tests.\n\nResultsDespite an ongoing high community prevalence rate of COVID-19, to date only two asymptomatic employees tested positive out of 1050 tests run during 7 months of the program. However, 12 symptomatic employees not participating in the program have tested positive. The employee survey was completed by 132/306 (43%) employees, with 93% agreeing that asymptomatic employee screening led to a better and safer working environment and 75% agreeing with on-site public health measures to help contain the virus, but only 58% feeling COVID-19 was a serious threat to their health.\n\nConclusionOur results suggest that a longitudinal asymptomatic employee screening program for SARS-CoV-2 can be accepted by employees and can be used to maintain the health of the workforce, potentially keeping positivity rates below community levels in the face of the ongoing COVID-19 pandemic.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Laura Goetz", - "author_inst": "TGen" - }, - { - "author_name": "Tyler L DeLaughder", - "author_inst": "TGen" - }, - { - "author_name": "Kathleen L Kennedy", - "author_inst": "TGen" - }, - { - "author_name": "Nicholas Schork", - "author_inst": "The Translational Genomics Research Institute (TGen)" - }, - { - "author_name": "Timothy McDaniel", - "author_inst": "TGen" - }, - { - "author_name": "Jeffrey Trent", - "author_inst": "TGen" - }, - { - "author_name": "David Engelthaler", - "author_inst": "TGen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.11.06.20223206", "rel_title": "The smartphone: an evolution or revolution in virtual patient healthcare during and beyond the COVID-19 pandemic ? An evaluation and comparison of the smartphone against other currently available wearable technologies in a secondary care setting during the COVID-19 pandemic.", @@ -1065501,6 +1069441,93 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.11.10.376673", + "rel_title": "SARS-CoV-2 infection causes transient olfactory dysfunction in mice", + "rel_date": "2020-11-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.10.376673", + "rel_abs": "Olfactory dysfunction caused by SARS-CoV-2 infection represents as one of the most predictive and common symptoms in COVID-19 patients. However, the causal link between SARS-CoV-2 infection and olfactory disorders remains lacking. Herein we demonstrate intranasal inoculation of SARS-CoV-2 induces robust viral replication in the olfactory epithelium (OE), resulting in transient olfactory dysfunction in humanized ACE2 mice. The sustentacular cells and Bowmans gland cells in OE were identified as the major targets of SARS-CoV-2 before the invasion into olfactory sensory neurons. Remarkably, SARS-CoV-2 infection triggers cell death and immune cell infiltration, and impairs the uniformity of OE structure. Combined transcriptomic and proteomic analyses reveal the induction of antiviral and inflammatory responses, as well as the downregulation of olfactory receptors in OE from the infected animals. Overall, our mouse model recapitulates the olfactory dysfunction in COVID-19 patients, and provides critical clues to understand the physiological basis for extrapulmonary manifestations of COVID-19.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Cheng-Feng Qin", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Qing Ye", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Jia Zhou", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Guan Yang", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Rui-Ting Li", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Qi He", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Yao Zhang", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Shu-Jia Wu", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Qi Chen", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Jia-Hui Shi", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Rong-Rong Zhang", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Hui-Min Zhu", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Hong-Ying Qiu", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Tao Zhang", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Yong-Qiang Deng", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Xiao-Feng Li", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Ping Xu", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Xiao Yang", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.05.20224436", "rel_title": "Anxiety and depression among people living in quarantine centers during COVID-19 pandemic: A mixed method study from western Nepal", @@ -1065650,57 +1069677,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.11.05.20225052", - "rel_title": "Symptomatic SARS-CoV-2 re-infection of a health care worker in a Belgian nosocomial outbreak despite primary neutralizing antibody response.", - "rel_date": "2020-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20225052", - "rel_abs": "BackgroundIt is currently unclear whether SARS-CoV-2 re-infection will remain a rare event, only occurring in individuals who fail to mount an effective immune response, or whether it will occur more frequently when humoral immunity wanes following primary infection.\n\nMethodsA case of re-infection was observed in a Belgian nosocomial outbreak involving 3 patients and 2 health care workers. To distinguish re-infection from persistent infection and detect potential transmission clusters, whole genome sequencing was performed on nasopharyngeal swabs of all individuals including the re-infection cases first episode. IgA, IgM, and IgG and neutralizing antibody responses were quantified in serum of all individuals, and viral infectiousness was measured in the swabs of the reinfection case.\n\nResultsRe-infection was confirmed in a young, immunocompetent health care worker as viral genomes derived from the first and second episode belonged to different SARS-CoV-2 clades. The symptomatic re-infection occurred after an interval of 185 days, despite the development of an effective humoral immune response following symptomatic primary infection. The second episode, however, was milder and characterized by a fast rise in serum IgG and neutralizing antibodies. Although contact tracing and virus culture remained inconclusive, the health care worker formed a transmission cluster with 3 patients and showed evidence of virus replication but not of neutralizing antibodies in her nasopharyngeal swabs.\n\nConclusionIf this case is representative of most Covid-19 patients, long-lived protective immunity against SARS-CoV-2 might not be likely.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Philippe Selhorst", - "author_inst": "Institute of Tropical Medicine Belgium" - }, - { - "author_name": "Sabrina van Ierssel", - "author_inst": "Antwerp University Hospital" - }, - { - "author_name": "Jo Michiels", - "author_inst": "Institute of Tropical Medicine, Antwerp, Belgium" - }, - { - "author_name": "Joachim Mari\u00ebn", - "author_inst": "Institute of Tropical Medicine, Antwerp, Belgium" - }, - { - "author_name": "Koen Bartholomeeusen", - "author_inst": "Institute of Tropical Medicine, Antwerp, Belgium" - }, - { - "author_name": "Eveline Dirinck", - "author_inst": "Antwerp University Hospital" - }, - { - "author_name": "Sarah Vandamme", - "author_inst": "Antwerp University Hospital, Edegem, Belgium" - }, - { - "author_name": "Hilde Jansens", - "author_inst": "Antwerp University Hospital, Edegem, Belgium" - }, - { - "author_name": "Kevin K. Ari\u00ebn", - "author_inst": "Institute of Tropical Medicine Antwerp" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.06.20205799", "rel_title": "Non applicability of validated predictive models for intensive care admission and death of COVID-19 patients in a secondary care hospital in Belgium", @@ -1067182,6 +1071158,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.11.06.20226977", + "rel_title": "Team contact sports in times of the COVID-19 pandemic- a scientific concept for the Austrian football league", + "rel_date": "2020-11-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20226977", + "rel_abs": "BackgroundSince the beginning of the COVID -19 pandemic, many contact sport teams are facing major challenges to safely continue training and competition.\n\nObjectiveWe present the design and implementation of a structured monitoring concept for the Austrian national football league\n\nMethods146 professional players from five clubs of the professional Austrian football league were monitored for a period of 12 weeks. Subjective health parameters, PCR- test results and data obtained from a geo-tracking app were collected. Simulations modelling the consequences of a COVID-19 case with increasing reproduction number were computed.\n\nResultsNo COVID-19 infection occurred during the observation period in the players. Infections in the nearer surroundings lead to increased perceived risk of infection. Geo tracking was particularly hindered due to technical problems and reluctance of users. Simulation models suggested a hypothetical shut-down of all training and competition activities.\n\nConclusionsA structured monitoring concept can help to continue contact sports safely in times of a pandemic. Cooperation of all involved is essential.\n\nTrial registrationID: DRKS00022166 15/6/2020 https://www.who.int/ictrp/search/en/\n\nKey Points- The results of this study can inform the development of future prevention and monitoring strategies in professional football and beyond, potentially serving as a blueprint for the safe continuation of sports and physical activity, across a broad range of settings, during and following a pandemic such as COVID-19.\n- Health parameters should be digitally recorded and closely monitored to enable quick response in case of a COVID-19 infection.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Antje van der Zee-Neuen", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Dagmar Schaffler-Schaden", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Juergen Herfert", + "author_inst": "Red Bull Athlete Performance Centre" + }, + { + "author_name": "James O Brien", + "author_inst": "Red Bull Athlete Performance Centre" + }, + { + "author_name": "Tim Johansson", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Patrick Kutschar", + "author_inst": "patrick.kutschar@pmu.ac.at" + }, + { + "author_name": "Alexander Seymer", + "author_inst": "University of Salzburg" + }, + { + "author_name": "Stephan Ludwig", + "author_inst": "University of Muenster" + }, + { + "author_name": "Thomas Stoeggl", + "author_inst": "University of Salzburg" + }, + { + "author_name": "David Keeley", + "author_inst": "Electronic Caregiver" + }, + { + "author_name": "Herbert Resch", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Juergen Osterbrink", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Maria Flamm", + "author_inst": "Paracelsus Medical University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.05.20226654", "rel_title": "Multiplexed, quantitative serological profiling of COVID-19 from a drop of blood by a point-of-care test", @@ -1067447,97 +1071490,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.06.20149690", - "rel_title": "Healthcare strain and intensive care during the COVID-19 outbreak in the Lombardy region: a retrospective observational study on 43,538 hospitalized patients", - "rel_date": "2020-11-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20149690", - "rel_abs": "BackgroundDuring the spring of 2020, the SARS-CoV-2 epidemic has caused significant resource strain in hospitals of Lombardy, Italy, with the demand for intensive care beds for COVID-19 patients exceeding the overall pre-crisis capacity. In this study, we evaluate the effect of healthcare strain on ICU admission and survival.\n\nMethodsWe used data on 43,538 patients admitted to a hospital in the region between February 20 and July 12, 2020, of which 3,993 (9.2%) were admitted to an ICU. We applied logistic regression to model the probability of being admitted to an ICU and the probability of survival among ICU patients. Negative binomial regressions were used to model the time between hospital and ICU admission and the length of stay in ICU.\n\nResultsDuring the period of highest hospital strain (March 16 - April 22), individuals older than 70 years had a significantly lower probability of being admitted to an ICU and significantly longer times between hospital and ICU admission, indicating elective admission due to constrained resources. Healthcare strain did not have a clear effect on mortality, with the overall proportion of deaths declining from 52.1% (95%CI 49.8-54.5) for ICU patients admitted to the hospital before March 16, to 43.4% (95%CI 41.5-45.6) between March 16 and April 22, to 27.6% (95%CI 20.0-35.2) after April 22.\n\nConclusionsThese data demonstrate and quantify the adoption of elective admission to ICUs during the peak phase of the SARS-CoV-2 epidemic in Lombardy. However, we show that for patients admitted to ICUs, clinical outcomes progressively improved despite the saturation of healthcare resources.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Filippo Trentini", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Valentina Marziano", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Giorgio Guzzetta", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Marcello Tirani", - "author_inst": "Directorate General for Health, Lombardy Region, Milano, Italy; Health Protection Agency of Pavia, Pavia, Italy" - }, - { - "author_name": "Danilo Cereda", - "author_inst": "Directorate General for Health, Lombardy Region, Milano, Italy" - }, - { - "author_name": "Piero Poletti", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Antonio Barone", - "author_inst": "Regional Agency for Innovation and Procurement, Milano, Italy" - }, - { - "author_name": "Giuseppe Preziosi", - "author_inst": "Regional Agency for Innovation and Procurement, Milano, Italy" - }, - { - "author_name": "Fabio Arduini", - "author_inst": "Regional Agency for Innovation and Procurement, Milano, Italy" - }, - { - "author_name": "Petra Della Valle", - "author_inst": "Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy" - }, - { - "author_name": "Alberto Zanella", - "author_inst": "Department of Pathophysiology and Transplantation, University of Milan, Milano, Italy" - }, - { - "author_name": "Alessandra Piatti", - "author_inst": "Directorate General for Health, Lombardy Region, Milano, Italy" - }, - { - "author_name": "Raffaella Piccarreta", - "author_inst": "Bocconi University, Dondena Centre for Research on Social Dynamics and Public Policy, Milan, Italy" - }, - { - "author_name": "Giacomo Grasselli", - "author_inst": "Department of Pathophysiology and Transplantation, University of Milan, Milano, Italy; Department of Anesthesia, Intensive Care and Emergency, Fondazione IRCCS " - }, - { - "author_name": "Aida Andreassi", - "author_inst": "Directorate General for Health, Lombardy Region, Milano, Italy" - }, - { - "author_name": "Alessia Melegaro", - "author_inst": "Bocconi University, Dondena Centre for Research on Social Dynamics and Public Policy, Milan, Italy" - }, - { - "author_name": "Maria Gramegna", - "author_inst": "Directorate General for Health, Lombardy Region, Milano, Italy" - }, - { - "author_name": "Marco Ajelli", - "author_inst": "Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington, IN, USA" - }, - { - "author_name": "Stefano Merler", - "author_inst": "Fondazione Bruno Kessler" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.05.20226662", "rel_title": "Risk mitigating behaviours in people with inflammatory joint and skin disease during the COVID-19 pandemic differ by treatment type: a cross-sectional patient survey", @@ -1068984,6 +1072936,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.11.05.20226472", + "rel_title": "How has Covid-19 affected mental health nurses and the delivery of mental health nursing care in the UK? Results of a mixed methods study", + "rel_date": "2020-11-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20226472", + "rel_abs": "IntroductionWhile evidence has emerged concerning the impact of Covid-19 on the general population and the challenges facing health services, much less is known regarding how the pandemic has directly affected the delivery of mental health nursing care.\n\nAimThis paper aims to explore how Covid-19 has affected the ability of mental health nurses to deliver care in community and inpatient mental health services in the UK.\n\nMethodWe investigated staff reports regarding the impact of the Covid-19 pandemic on mental healthcare and mental health service users in the UK, using a mixed methods online survey. A total of 897 nurses across a range of inpatient and community settings participated.\n\nDiscussionKey themes within the data explore: new ways of working; remote working; risks of infection/infection control challenges; and the impact on service users. Targeted guidelines are required to support mental health nurses providing care and support during a pandemic to people in severe mental distress, often in unsuitable environments.\n\nImplications for PracticeService developments need to occur alongside tailored guidance and support for staff welfare supported by clear leadership. These findings identify areas requiring attention and investment to prepare for future crises and the consequences of the pandemic.\n\nAccessible SummaryO_ST_ABSWhat is known on the subject?C_ST_ABSDuring the Covid-19 pandemic there has been research considering the impact on medical healthcare professionals and the mental health needs of the general population. However, limited focus has been placed on mental health services or mental health staff providing care in the community and in hospitals. Whilst nurses make up the largest section of the mental health workforce in the UK, the impact that this pandemic has had on their work has been largely ignored.\n\nWhat the paper adds to existing knowledge?This paper provides a unique insight into the experiences and impact that the Covid-19 pandemic has had on mental health nurses across a range of community and inpatient settings to understand what has changed in their work and the care they can and do provide during this crisis. This includes exploring how services have changed, the move to remote working, the impact of the protective equipment crisis on nurses, and the difficult working conditions facing those in inpatient settings where there is minimal guidance provided.\n\nWhat are the implications for practice?By understanding the impact the pandemic has had on mental health nursing care, we can understand the gaps in guidance that exist, the challenges being faced, and the impact the crisis has had on care for mental health service users. By doing so we can plan for the ongoing nature of this pandemic as well as the aftermath that the crisis may leave for our service users and workforce alike.\n\nRelevance StatementThis paper provides insight into the impact that the Covid-19 pandemic has had on the service and care that mental health nurses are expected to and can provide. As a workforce that often requires ongoing face to face contact with service users, many in serious distress, in inpatient and community settings, it is important that we understand their experiences and the challenges and risks that face this workforce. This will enable us to ensure that future planning, guidance, support and safeguarding can take place during the ongoing and future crises.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Una Foye", + "author_inst": "King's College London" + }, + { + "author_name": "Christian Dalton-Locke", + "author_inst": "University College London" + }, + { + "author_name": "Jasmine Harju-Seppanen", + "author_inst": "University College London" + }, + { + "author_name": "Rebecca Lane", + "author_inst": "Kings College London" + }, + { + "author_name": "Lewys Beams", + "author_inst": "South London and Maudsley Foundation Trust" + }, + { + "author_name": "Norha Vera San Juan", + "author_inst": "King's College London" + }, + { + "author_name": "Sonia Johnson", + "author_inst": "University College London" + }, + { + "author_name": "Alan Simpson", + "author_inst": "Kings College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nursing" + }, { "rel_doi": "10.1101/2020.11.04.20226118", "rel_title": "Elevated COVID-19 outcomes among persons living with diagnosed HIV infection in New York State: Results from a population-level match of HIV, COVID-19, and hospitalization databases", @@ -1069261,121 +1073260,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.05.20223289", - "rel_title": "Longitudinal proteomic profiling of high-risk patients with COVID-19 reveals markers of severity and predictors of fatal disease", - "rel_date": "2020-11-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20223289", - "rel_abs": "End-stage kidney disease (ESKD) patients are at high risk of severe COVID-19. We measured 436 circulating proteins in serial blood samples from hospitalised and non-hospitalised ESKD patients with COVID-19 (n=256 samples from 55 patients). Comparison to 51 non-infected patients revealed 221 differentially expressed proteins, with consistent results in a separate subcohort of 46 COVID-19 patients. 203 proteins were associated with clinical severity, including IL6, markers of monocyte recruitment (e.g. CCL2, CCL7), neutrophil activation (e.g. proteinase-3) and epithelial injury (e.g. KRT19). Machine learning identified predictors of severity including IL18BP, CTSD, GDF15, and KRT19. Survival analysis with joint models revealed 69 predictors of death. Longitudinal modelling with linear mixed models uncovered 32 proteins displaying different temporal profiles in severe versus non-severe disease, including integrins and adhesion molecules. These data implicate epithelial damage, innate immune activation, and leucocyte-endothelial interactions in the pathology of severe COVID-19 and provide a resource for identifying drug targets.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Jack Gisby", - "author_inst": "Imperial College London" - }, - { - "author_name": "Candice L Clarke", - "author_inst": "Imperial College London" - }, - { - "author_name": "Nicholas Medjeral-Thomas", - "author_inst": "Imperial College London" - }, - { - "author_name": "Talat H Malik", - "author_inst": "Imperial College London" - }, - { - "author_name": "Artemis Papadaki", - "author_inst": "Imperial College London" - }, - { - "author_name": "Paige M Mortimer", - "author_inst": "Imperial College London" - }, - { - "author_name": "Norzawani B Buang", - "author_inst": "Imperial College London" - }, - { - "author_name": "Shanice Lewis", - "author_inst": "Imperial College London" - }, - { - "author_name": "Marie Pereira", - "author_inst": "Imperial College London" - }, - { - "author_name": "Frederic Toulza", - "author_inst": "Imperial College London" - }, - { - "author_name": "Ester Fagnano", - "author_inst": "Imperial College London" - }, - { - "author_name": "Marie-Anne Mawhin", - "author_inst": "Imperial College London" - }, - { - "author_name": "Emma E Dutton", - "author_inst": "Imperial College London" - }, - { - "author_name": "Lunnathaya Tapeng", - "author_inst": "Imperial College London" - }, - { - "author_name": "Arianne C Richard", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Paul Kirk", - "author_inst": "MRC Biostatistics Unit University of Cambridge" - }, - { - "author_name": "Jacques Behmoaras", - "author_inst": "Imperial College London" - }, - { - "author_name": "Eleanor Sandhu", - "author_inst": "Imperial College London" - }, - { - "author_name": "Stephen P McAdoo", - "author_inst": "Imperial College London" - }, - { - "author_name": "Maria F Prendecki", - "author_inst": "Imperial College London" - }, - { - "author_name": "Matthew C Pickering", - "author_inst": "Imperial College London" - }, - { - "author_name": "Marina Botto", - "author_inst": "Imperial College London" - }, - { - "author_name": "Michelle Willicombe", - "author_inst": "Imperial College London" - }, - { - "author_name": "David C Thomas", - "author_inst": "Imperial College London" - }, - { - "author_name": "James E. Peters", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.04.20226282", "rel_title": "Phase 1 trial of a Candidate Recombinant Virus-Like Particle Vaccine for Covid-19 Disease Produced in Plants", @@ -1070966,6 +1074850,125 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.11.06.370676", + "rel_title": "Potent SARS-CoV-2 neutralizing antibodies selected from a human antibody library constructed decades ago", + "rel_date": "2020-11-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.06.370676", + "rel_abs": "Combinatorial antibody libraries not only effectively reduce antibody discovery to a numbers game, but enable documentation of the history of antibody responses in an individual. The SARS-CoV-2 pandemic has prompted a wider application of this technology to meet the public health challenge of pandemic threats in the modern era. Herein, we used a combinatorial human antibody library constructed 20 years before the COVID-19 pandemic to discover three highly potent antibodies that selectively bind SARS-CoV-2 spike protein and neutralize authentic SARS-CoV-2 virus. Compared to neutralizing antibodies from COVID-19 patients with generally low somatic hypermutation (SHM), these antibodies contain over 13-22 SHMs, many of which are involved in specific interactions in crystal structures with SARS-CoV-2 spike RBD. The identification of these somatically mutated antibodies in a pre-pandemic library raises intriguing questions about the origin and evolution of human immune responses to SARS-CoV-2.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Min Qiang", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Peixiang Ma", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Yu Li", + "author_inst": "ShanghaiTech University; Chinese Academy of Sciences; University of Chinese Academy of Sciences" + }, + { + "author_name": "Hejun Liu", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Adam Harding", + "author_inst": "University of Oxford" + }, + { + "author_name": "Chenyu Min", + "author_inst": "Velox Pharmaceuticals" + }, + { + "author_name": "Lili Liu", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Meng Yuan", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Qun Ji", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Pingdong Tao", + "author_inst": "ShanghaiTech University; Chinese Academy of Sciences; University of Chinese Academy of Sciences" + }, + { + "author_name": "Xiaojie Shi", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Zhean Li", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Fulian Wang", + "author_inst": "ShanghaiTech University; Chinese Academy of Sciences; University of Chinese Academy of Sciences" + }, + { + "author_name": "Yu Zhang", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Nicholas C. Wu", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Chang-Chun D. Lee", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Xueyong Zhu", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Javier Gilbert-Jaramillo", + "author_inst": "University of Oxford" + }, + { + "author_name": "Abhishek Saxena", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Xingxu Huang", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Hou Wang", + "author_inst": "ShOx Science Limited" + }, + { + "author_name": "William James", + "author_inst": "University of Oxford" + }, + { + "author_name": "Raymond A. Dwek", + "author_inst": "Oxford Glycobiology Institute" + }, + { + "author_name": "Ian A. Wilson", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Guang Yang", + "author_inst": "ShanghaiTech University;Velox Pharmaceuticals" + }, + { + "author_name": "Richard A. Lerner", + "author_inst": "The Scripps Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.03.367391", "rel_title": "Evolution of Antibody Immunity to SARS-CoV-2", @@ -1071239,137 +1075242,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.11.04.364315", - "rel_title": "SARS-CoV-2 Infects Human Engineered Heart Tissues and Models COVID-19 Myocarditis", - "rel_date": "2020-11-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.04.364315", - "rel_abs": "Epidemiological studies of the COVID-19 pandemic have revealed evidence of cardiac involvement and documented that myocardial injury and myocarditis are predictors of poor outcomes. Nonetheless, little is understood regarding SARS-CoV-2 tropism within the heart and whether cardiac complications result directly from myocardial infection. Here, we develop a human engineered heart tissue model and demonstrate that SARS-CoV-2 selectively infects cardiomyocytes. Viral infection is dependent on expression of angiotensin-I converting enzyme 2 (ACE2) and endosomal cysteine proteases, suggesting an endosomal mechanism of cell entry. After infection with SARS-CoV-2, engineered tissues display typical features of myocarditis, including cardiomyocyte cell death, impaired cardiac contractility, and innate immune cell activation. Consistent with these findings, autopsy tissue obtained from individuals with COVID-19 myocarditis demonstrated cardiomyocyte infection, cell death, and macrophage-predominate immune cell infiltrate. These findings establish human cardiomyocyte tropism for SARS-CoV-2 and provide an experimental platform for interrogating and mitigating cardiac complications of COVID-19.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Adam L Bailey", - "author_inst": "Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "Oleksandr Dmytrenko", - "author_inst": "Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "Lina Greenberg", - "author_inst": "Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "Andrea L Bredemeyer", - "author_inst": "Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "Pan Ma", - "author_inst": "Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "Jing Liu", - "author_inst": "Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "Vinay Penna", - "author_inst": "Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "Lulu Lai", - "author_inst": "Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "Emma S Winkler", - "author_inst": "Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "Sanja Sviben", - "author_inst": "Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "Erin Brooks", - "author_inst": "Department of Pathology & Laboratory Medicine, University of Wisconsin Hospital and Clinics, Madison, Wisconsin, USA" - }, - { - "author_name": "Ajith P Nair", - "author_inst": "Department of Medicine, Baylor College of Medicine, Houston, Texas, USA" - }, - { - "author_name": "Kent A Heck", - "author_inst": "Department of Pathology, Baylor College of Medicine, Houston, Texas, USA" - }, - { - "author_name": "Aniket S Rali", - "author_inst": "Department of Medicine, Vanderbilt University, Nashville, Tennessee, USA" - }, - { - "author_name": "Leo Simpson", - "author_inst": "Department of Medicine, Baylor College of Medicine, Houston, Texas, USA" - }, - { - "author_name": "Mehrdad Saririan", - "author_inst": "Valleywise Health/Creighton University, Phoenix, AZ, USA" - }, - { - "author_name": "Dan Hobohm", - "author_inst": "Valleywise Health/Creighton University, Phoenix, AZ, USA" - }, - { - "author_name": "W. Tom Stump", - "author_inst": "Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "James A Fitzpatrick", - "author_inst": "Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "Xuping Xie", - "author_inst": "Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA" - }, - { - "author_name": "J Travis Hinson", - "author_inst": "epartments of Cardiology and Genetics and Genome Sciences, UConn Health, Farmington, CT." - }, - { - "author_name": "Weng-Tein Gi", - "author_inst": "Department of Internal Medicine III, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Constanze Schmidt", - "author_inst": "Department of Internal Medicine III, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Florian Leuschner", - "author_inst": "Department of Internal Medicine III, University Hospital Heidelberg, University of Heidelberg, Heidelberg, Germany" - }, - { - "author_name": "Chieh-Yu Lin", - "author_inst": "Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "Michael S Diamond", - "author_inst": "Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "Michael J Greenberg", - "author_inst": "Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "Kory J Lavine", - "author_inst": "Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.11.03.367516", "rel_title": "The translational landscape of SARS-CoV-2 and infected cells", @@ -1073487,6 +1077359,101 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.11.05.370239", + "rel_title": "SARS-CoV-2 Assembly and Egress Pathway Revealed by Correlative Multi-modal Multi-scale Cryo-imaging", + "rel_date": "2020-11-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.05.370239", + "rel_abs": "Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified recombinant viral components and inactivated viruses. However, investigation of the SARS-CoV-2 infection in the native cellular context is scarce, and there is a lack of comprehensive knowledge on SARS-CoV-2 replicative cycle. Understanding the genome replication, assembly and egress of SARS-CoV-2, a multistage process that involves different cellular compartments and the activity of many viral and cellular proteins, is critically important as it bears the means of medical intervention to stop infection. Here, we investigated SARS-CoV-2 replication in Vero cells under the near-native frozen-hydrated condition using a unique correlative multi-modal, multi-scale cryo-imaging approach combining soft X-ray cryo-tomography and serial cryoFIB/SEM volume imaging of the entire SARS-CoV-2 infected cell with cryo-electron tomography (cryoET) of cellular lamellae and cell periphery, as well as structure determination of viral components by subtomogram averaging. Our results reveal at the whole cell level profound cytopathic effects of SARS-CoV-2 infection, exemplified by a large amount of heterogeneous vesicles in the cytoplasm for RNA synthesis and virus assembly, formation of membrane tunnels through which viruses exit, and drastic cytoplasm invasion into nucleus. Furthermore, cryoET of cell lamellae reveals how viral RNAs are transported from double-membrane vesicles where they are synthesized to viral assembly sites; how viral spikes and RNPs assist in virus assembly and budding; and how fully assembled virus particles exit the cell, thus stablishing a model of SARS-CoV-2 genome replication, virus assembly and egress pathways.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Luiza Mendonca", + "author_inst": "University of Oxford" + }, + { + "author_name": "Andrew Howe", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "James B Gilchrist", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Dapeng Sun", + "author_inst": "University of Oxford" + }, + { + "author_name": "Michael Knight", + "author_inst": "University of Oxford" + }, + { + "author_name": "Laura C Zanetti-Domingues", + "author_inst": "Science and Technology Facility Council" + }, + { + "author_name": "Benji Bateman", + "author_inst": "Science and Technology Facility Council" + }, + { + "author_name": "Anna-Sophia Krebs", + "author_inst": "University of Oxford" + }, + { + "author_name": "Long Chen", + "author_inst": "University of Oxford" + }, + { + "author_name": "Julika Radecke", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Yuewen Sheng", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Vivian D Li", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Tao Ni", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ilias Kounatidis", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Mohamed A Koronfel", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Marta Szynkiewicz", + "author_inst": "Science and Technology Facility Council" + }, + { + "author_name": "Maria Harkiolaki", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Marisa L Martin-Fernandez", + "author_inst": "Science and Technology Facility Council" + }, + { + "author_name": "William James", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peijun Zhang", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.05.368647", "rel_title": "SLAMF7 engagement super-activates macrophages in acute and chronic inflammation", @@ -1073588,69 +1077555,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2020.10.30.20223461", - "rel_title": "SARS-CoV-2 Infection Hospitalization Rate and Infection Fatality Rate among the Non-Congregant Population in Connecticut", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20223461", - "rel_abs": "ImportanceCOVID-19 case fatality and hospitalization rates, calculated using the number of confirmed cases of COVID-19, have been described widely in the literature. However, the number of infections confirmed by testing underestimates the total infections as it is biased based on the availability of testing and because asymptomatic individuals may remain untested. The infection fatality rate (IFR) and infection hospitalization rate (IHR), calculated using the estimated total infections based on a representative sample of a population, is a better metric to assess the actual toll of the disease.\n\nObjectiveTo determine the IHR and IFR for COVID-19 using the statewide SARS-CoV-2 seroprevalence estimates for the non-congregate population in Connecticut.\n\nDesignCross-sectional.\n\nSettingAdults residing in a non-congregate setting in Connecticut between March 1 and June 1, 2020.\n\nParticipantsIndividuals aged 18 years or above.\n\nExposureEstimated number of adults with SARS-CoV-2 antibodies.\n\nMain Outcome and MeasuresCOVID-19-related hospitalizations and deaths among adults residing in a non-congregate setting in Connecticut between March 1 and June 1, 2020.\n\nResultsOf the 2.8 million individuals residing in the non-congregate settings in Connecticut through June 2020, 113,515 (90% CI 56,758-170,273) individuals had SARS-CoV-2 antibodies. There were a total of 9425 COVID-19-related hospitalizations and 4071 COVID-19-related deaths in Connecticut between March 1 and June 1, 2020, of which 7792 hospitalizations and 1079 deaths occurred among the non-congregate population. The overall COVID-19 IHR and IFR was 6.86% (90% CI, 4.58%-13.72%) and 0.95% (90% CI, 0.63%-1.90%) among the non-congregate population. Older individuals, men, non-Hispanic Black individuals and those belonging to New Haven and Litchfield counties had a higher burden of hospitalization and deaths, compared with younger individuals, women, non-Hispanic White or Hispanic individuals, and those belonging to New London county, respectively.\n\nConclusion and RelevanceUsing representative seroprevalence estimates, the overall COVID-19 IHR and IFR were estimated to be 6.86% and 0.95% among the non-congregate population in Connecticut. Accurate estimation of IHR and IFR among community residents is important to guide public health strategies during an infectious disease outbreak.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Shiwani Mahajan", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Cesar Caraballo", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Shu-Xia Li", - "author_inst": "Center for Outcomes Research and Evaluation, Yale-New Haven Hospital" - }, - { - "author_name": "Claire Dong", - "author_inst": "Center for Outcomes Research and Evaluation, Yale-New Haven Hospital" - }, - { - "author_name": "Lian Chen", - "author_inst": "Center for Outcomes Research and Evaluation, Yale-New Haven Hospital" - }, - { - "author_name": "Sara K Huston", - "author_inst": "The Gallup Organization" - }, - { - "author_name": "Rajesh Srinivasan", - "author_inst": "The Gallup Organization" - }, - { - "author_name": "Carrie A Redlich", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Albert I Ko", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Jeremy S Faust", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Howard P Forman", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Harlan M Krumholz", - "author_inst": "Yale School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.30.20223222", "rel_title": "Forecasting new daily confirmed cases infected by COVID-19 in Italy from April 9th to May 18th 2020", @@ -1074945,6 +1078849,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.11.02.20224519", + "rel_title": "Are Mobile Phones part of the chain of transmission of SARS-CoV-2 in the hospital?", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20224519", + "rel_abs": "SARS-CoV-2 cross-transmission has become an concern in hospitals. We investigate healthcare workers(HCWs) knowledge about SARS-CoV-2 cross-transmission and conceptions whether the virus can remain on HCWs mobile phones(MPs) and be part of the chain of transmission.\n\nA cross-sectional study was conducted at a COVID-19 Intensive Care Unit of a teaching-hospital. Fifty-one MPs were swabbed and a questionnaire about hand hygiene and MP use and disinfection was applied after an educational campaign. Although most of HCWs believed on the importance of cross-transmission and increased hand hygiene adhesion and MP disinfection during the pandemic, SARS-CoV-2 RNA was detected in two MPs(culture of the samples was negative).\n\nImplementation of official hospital policies to guide HCWs regarding disinfection and care of personal MP are needed.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Evelyn Patricia Sanchez Espinoza", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Marina Farrel Cortes", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Saidy Vasconez Nogueira", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Anderson Vincente de Paula", + "author_inst": "LIM52 Virology Laboratory, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Thais Guimaraes", + "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Lucy Santos Vilas Boas", + "author_inst": "LIM52 Virology Laboratory, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Marcelo Park", + "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Cristina Carvalho da Silva", + "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Ingra Morales", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Lauro Vieira Perdigao Neto", + "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Tania Regina Tozetto-Mendoza", + "author_inst": "Instituto de Medicina Tropical de Sao Paulo. Universidade de Sao Paulo." + }, + { + "author_name": "Icaro Boszczowski", + "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Ester Sabino", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Maria Cassia Mendes-Correa", + "author_inst": "LIM52 Virology Laboratory, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Anna Sara Shafferman Levin", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil." + }, + { + "author_name": "Silvia Figueiredo Costa", + "author_inst": "Department of Infectious diseases, Instituto de Medicina Tropical, Universidade de Sao Paulo, Sao Paulo, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.11.01.20214122", "rel_title": "Simulation model for productivity, risk and GDP impact forecasting of the COVID-19 portfolio vaccines", @@ -1075034,29 +1079017,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.11.01.20194233", - "rel_title": "Cohorting of Non-Critically Ill COVID-19 Patients: A Multicenter Survey Study (COVID-COHORT)", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.01.20194233", - "rel_abs": "The COVID-19 pandemic has posed novel infection-control challenges for hospitals around the globe. One infection-control strategy that has been widely used in the context of other outbreaks is patient cohorting. This strategy refers to the placement of all patients exposed to the same laboratory-confirmed infectious agent in one location within the hospital. Little is known about the current utilization of this strategy with non-critically ill COVID-19 patients. An international multicenter, survey study was conducted to identify what strategies are planned or in place for patients with COVID-19 who are not critically ill. The survey was distributed from March 23-29th, 2020 to GIM physicians in Canada, USA, Denmark, Singapore, Hong Kong, and England. Of the 31 hospitals, 29 (94%) indicated that they plan on cohorting all GIM patients with COVID-19 to one location in the hospital. Among these 29 hospitals, 23 (79%) had implemented the plan at the time of the survey. The primary reasons for this decision were to limit the spread of COVID-19 and conserve PPE use. In conclusion, in the face of a novel virus there is near unanimity in the practice of patient cohorting as a potential mitigation strategy.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ushma Purohit", - "author_inst": "University of Toronto, Faculty of Medicine, Toronto, Canada" - }, - { - "author_name": "Michael Fralick", - "author_inst": "Sinai Health System and the Department of Medicine, University of Toronto, Toronto, ON, Canada" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.02.20224485", "rel_title": "High attack rates of SARS-CoV-2 infection through household-transmission: a prospective study", @@ -1076543,6 +1080503,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.11.02.20224642", + "rel_title": "Vascular Thrombosis in COVID-19: A Potential Association with Antiphospholipid Antibodies. A Rapid Systematic Review", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20224642", + "rel_abs": "BackgroundVascular thrombosis is common in patients with coronavirus disease 2019 (COVID-19). Etiologies underlying this complication are unclear.\n\nPurposeTo determine the prevalence of antiphospholipid (aPL), including lupus anticoagulant, anti-cardiolipin and anti-{beta}2-glycoprotein-1 antibodies, and its possible association with thrombotic manifestations of COVID-19.\n\nData SourcesWe searched MEDLINE indexed journals on September 24, 2020 using the tool LitCovid and the pre-print server medRxIV.\n\nStudy SelectionOriginal investigations (cross-sectional studies, cohort studies, case series, and research letters) on COVID-19 and thrombosis were included.\n\nData ExtractionData were independently extracted, and compiled into spreadsheets based on the PRISMA principles.\n\nData SynthesisHospitalized patients with COVID-19 showed a higher prevalence of lupus anticoagulant compared to non-COVID-19 patients. Temporally, lupus anticoagulant was generally positive early in the course of illness, whereas anti-cardiolipin and anti-{beta}2-glycoprotein-1 antibodies appeared to emerge later in the disease. Some patients who were aPL-negative at an early time-point after disease onset became aPL-positive at a later time-point. Lupus anticoagulant was independently associated with thrombosis in 60 COVID-19 patients in New York had who had 32 thrombotic events (8 arterial and 24 venous). In 88 patients in Wuhan, who had more than 20 each of arterial and venous thrombotic events, medium/high positivity for multiple aPL was significantly associated with arterial thrombosis. However, the association of aPL with thrombosis was not evident in reports that had an overall lower number of or predominantly venous thrombotic events. Analysis of pooled patients revealed that aPL were significantly more frequent in COVID-19 patients with stroke than stroke patients in the general population. Furthermore, injection of IgG aPL fractions from COVID-19 patients into mice accelerated venous thrombosis.\n\nLimitationLimited data and paucity of prospective studies.\n\nConclusionThe aPL are prevalent in patients with COVID-19 and their presence is associated with thrombosis. Importantly, these antibodies may be a key mechanism of thrombosis in COVID-19. Follow-up studies are required to understand the relationship between aPL and the spectrum of vascular thrombosis during and after infection with SARS-CoV-2.\n\nPrimary Funding SourceNone.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Aneesh S Kallapur", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Eric Y Yen", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Ram Raj Singh", + "author_inst": "UCLA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.11.02.20224709", "rel_title": "Gender-affirming care, mental health, and economic stability in the time of COVID-19: a global cross-sectional study of transgender and non-binary people", @@ -1076668,93 +1080655,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.11.02.20221622", - "rel_title": "Reproducibility and sensitivity of 36 methods to quantify the SARS-CoV-2 genetic signal in raw wastewater: findings from an interlaboratory methods evaluation in the U.S.", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20221622", - "rel_abs": "1In response to COVID-19, the international water community rapidly developed methods to quantify the SARS-CoV-2 genetic signal in untreated wastewater. Wastewater surveillance using such methods has the potential to complement clinical testing in assessing community health. This interlaboratory assessment evaluated the reproducibility and sensitivity of 36 standard operating procedures (SOPs), divided into eight method groups based on sample concentration approach and whether solids were removed. Two raw wastewater samples were collected in August 2020, amended with a matrix spike (betacoronavirus OC43), and distributed to 32 laboratories across the U.S. Replicate samples analyzed in accordance with the projects quality assurance plan showed high reproducibility across the 36 SOPs: 80% of the recovery-corrected results fell within a band of +/- 1.15-log10 genome copies/L with higher reproducibility observed within a single SOP (standard deviation of 0.13-log10). The inclusion of a solids removal step and the selection of a concentration method did not show a clear, systematic impact on the recovery-corrected results. Other methodological variations (e.g., pasteurization, primer set selection, and use of RT-qPCR or RT-dPCR platforms) generally resulted in small differences compared to other sources of variability. These findings suggest that a variety of methods are capable of producing reproducible results, though the same SOP or laboratory should be selected to track SARS-CoV-2 trends at a given facility. The methods showed a 7-log10 range of recovery efficiency and limit of detection highlighting the importance of recovery correction and the need to consider method sensitivity when selecting methods for wastewater surveillance.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Brian M Pecson", - "author_inst": "Trussell Technologies Inc." - }, - { - "author_name": "Emily Darby", - "author_inst": "Trussell Technologies Inc." - }, - { - "author_name": "Charles N Haas", - "author_inst": "Drexel University" - }, - { - "author_name": "Yamrot Amha", - "author_inst": "Trussell Technologies Inc." - }, - { - "author_name": "Mitchel Bartolo", - "author_inst": "Trussell Technologies Inc." - }, - { - "author_name": "Richard Danielson", - "author_inst": "Cel Analytical Inc." - }, - { - "author_name": "Yeggie Dearborn", - "author_inst": "Cel Analytical Inc." - }, - { - "author_name": "George Di Giovanni", - "author_inst": "Metropolitan Water District of Southern California" - }, - { - "author_name": "Christobel Ferguson", - "author_inst": "The Water Research Foundation" - }, - { - "author_name": "Stephanie Fevig", - "author_inst": "The Water Research Foundation" - }, - { - "author_name": "Erica Gaddis", - "author_inst": "Utah Department of Environmental Quality" - }, - { - "author_name": "Don Gray", - "author_inst": "East Bay Municipal Utilities District" - }, - { - "author_name": "George Lukasik", - "author_inst": "BCS Laboratories Inc." - }, - { - "author_name": "Bonnie Mull", - "author_inst": "BCS Laboratories Inc." - }, - { - "author_name": "Liana Olivas", - "author_inst": "Trussell Technologies Inc." - }, - { - "author_name": "Adam Olivieri", - "author_inst": "EOA Inc." - }, - { - "author_name": "Yan Qu", - "author_inst": "Trussell Technologies Inc." - }, - { - "author_name": "- SARS-CoV-2 Interlaboratory Consortium", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.03.20208322", "rel_title": "The mental health of critical care and anaesthetic staff during COVID-19", @@ -1078145,6 +1082045,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.28.20221077", + "rel_title": "Simple discrete-time self-exciting models can describe complex dynamic processes: a case study of COVID-19", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221077", + "rel_abs": "Hawkes processes are a form of self-exciting process that has been used in numerous applications, including neuroscience, seismology, and terrorism. While these self-exciting processes have a simple formulation, they are able to model incredibly complex phenomena. Traditionally Hawkes processes are a continuous-time process, however we enable these models to be applied to a wider range of problems by considering a discrete-time variant of Hawkes processes. We illustrate this through the novel coronavirus disease (COVID-19) as a substantive case study. While alternative models, such as compartmental and growth curve models, have been widely applied to the COVID-19 epidemic, the use of discrete-time Hawkes processes allows us to gain alternative insights. This paper evaluates the capability of discrete-time Hawkes processes by retrospectively modelling daily counts of deaths as two distinct phases in the progression of the COVID-19 outbreak: the initial stage of exponential growth and the subsequent decline as preventative measures become effective. We consider various countries that have been adversely affected by the epidemic, namely, Brazil, China, France, Germany, India, Italy, Spain, Sweden, the United Kingdom and the United States. These countries are all unique concerning the spread of the virus and their corresponding response measures, in particular, the types and timings of preventative actions. However, we find that this simple model is useful in accurately capturing the dynamics of the process, despite hidden interactions that are not directly modelled due to their complexity, and differences both within and between countries. The utility of this model is not confined to the current COVID-19 epidemic, rather this model could be used to explain many other complex phenomena. It is of interest to have simple models that adequately describe these complex processes with unknown dynamics. As models become more complex, a simpler representation of the process can be desirable for the sake of parsimony.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Raiha Browning", + "author_inst": "Queensland University of Technology" + }, + { + "author_name": "Deborah Sulem", + "author_inst": "University of Oxford" + }, + { + "author_name": "Kerrie Mengersen", + "author_inst": "Queensland University of Technology" + }, + { + "author_name": "Vincent Rivoirard", + "author_inst": "Universit\u00e9 Paris-Dauphine" + }, + { + "author_name": "Judith Rousseau", + "author_inst": "University of Oxford; Universit\u00e9 Paris-Dauphine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.28.20221408", "rel_title": "ROLE OF CYTOKINES AND OTHER PROPHETIC VARIABLES IN THE DEVELOPMENT AND PROGRESSION OF DISEASE IN PATIENTS SUFFERING FROM COVID-19", @@ -1078298,81 +1082233,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.28.20221879", - "rel_title": "Surveillance study of acute neurological manifestations among 439 Egyptian patients with COVID-19 in Assiut and Aswan university hospitals", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221879", - "rel_abs": "BackgroundCOVID-19 can be accompanied by acute neurological complications of both central and peripheral nervous systems (CNS and PNS). In this study we estimate the frequency of such complications among hospital in-patients with COVID-19 in Assiut and Aswan University Hospitals.\n\nMaterial and MethodsWe screened all patients with suspected COVID-19 admitted from 1 June to 10 August 2020 to the university hospitals of Assiut and Aswan in Upper Egypt. Clinical and laboratory data, CT/MRI of chest and brain, and neurophysiology were performed for each patient if indicated.\n\nResults439 patients had confirmed/probable COVID-19; neurological manifestations occurred in 222. Of these 117 had acute neurological disease; the remainder had non-specific neuropsychiatric symptoms such as headache, vertigo, and depression. The CNS was affected in 75 patients: 55 had stroke; the others had convulsions (5), encephalitis (6), hypoxic encephalopathy (4), cord myelopathy (2), relapse of RR-MS (2), and meningoencephalitis (1). The PNS was affected in 42 patients: the majority had anosmia and ageusia (31); the others had GBS (4), peripheral neuropathy (3), myasthenia gravis (2), or myositis (2). Fever, respiratory symptoms and headache, were the most common general symptoms. Hypertensions, Diabetes Mellitus, ischemic heart disease were the most common comorbidities in patients with CNS affection.\n\nConclusionIn COVID19, both the CNS and PNS are affected. Stroke was the most common complication for CNS and anosmia and/or ageusia were common for PNS diseases. However there were 6 cases encephalitis, 2 cases of spinal cord myelopathy, 2 cases of MG and 2 cases of myositis.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Eman Mohamed khedr", - "author_inst": "Assiut University hospital, Department of Neuropsychiatry" - }, - { - "author_name": "Noha Abo-Elfetoh", - "author_inst": "Professor of Neurology, Faculty of Medicine, Assiut University Hospital, Assiut/EGYPT" - }, - { - "author_name": "Enas Deaf", - "author_inst": "Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Egypt" - }, - { - "author_name": "Hebatallah M Hassan", - "author_inst": "Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Egypt" - }, - { - "author_name": "Mariam T Amin", - "author_inst": "Department of Public Health and Community Medicine, Faculty of Medicine, Assiut University Hospital" - }, - { - "author_name": "Radwa K Soliman", - "author_inst": "Department of Radiology, Faculty of Medicine, Assiut University Hospital" - }, - { - "author_name": "Alaa A Attia", - "author_inst": "Department of Anesthesia and Intensive Care, Assiut University, Faculty of Medicine, Assiut, EgyptI" - }, - { - "author_name": "Amro A Zarzour", - "author_inst": "Department of Anesthesia and Intensive Care, Assiut University, Faculty of Medicine, Assiut, EgyptI" - }, - { - "author_name": "Mohamed Zain", - "author_inst": "Department of Internal Medicine, Faculty of Medicine, Assiut University Hospital" - }, - { - "author_name": "Aliae Mohamed-Hussein", - "author_inst": "Chest department, Faculty of medicine, Assiut University" - }, - { - "author_name": "Maiada K Hashem", - "author_inst": "Department of Chest, Faculty of Medicine, Assiut University Hospital" - }, - { - "author_name": "Sahar M Hassany", - "author_inst": "Department of Tropical Medicine and GIT, Faculty of Medicine, Assiut University Hospital" - }, - { - "author_name": "Ahmed Aly", - "author_inst": "Department of Neurosurgery, Faculty of Medicine, Aswan University Hospital" - }, - { - "author_name": "Ahmed Shoap", - "author_inst": "Department of Neuropsychiatry, Faculty of Medicine, Aswan University Hospital" - }, - { - "author_name": "Mostafa Saber", - "author_inst": "Department of Neuropsychiatry, Faculty of Medicine, Aswan University Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.28.20221721", "rel_title": "A Time-dependent mathematical model for COVID-19 transmission dynamics and analysis of critical and hospitalized cases with bed requirements", @@ -1080083,6 +1083943,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.29.20222505", + "rel_title": "The use of compassionate Ivermectin in the management of symptomatic outpatients and hospitalized patients with clinical diagnosis of COVID-19 at the Medical Center Bournigal and the Medical Center Punta Cana, Rescue Group, Dominican Republic, from may 1 to august 10, 2020.", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.29.20222505", + "rel_abs": "No antiviral has been shown to reduce mortality in SARS-COV-2 patients to date. In the present observational and retrospective report, 3,099 patients with a definitive or highly probable diagnosis of infection due to COVID-19 were evaluated between May 1st to August 10th, 2020, at Centro Medico Bournigal (CMBO) and Centro Medico Punta Cana (CMPC), and all received compassionate treatment with Ivermectin. A total of 2,706 (87.3%) were discharged for outpatient treatment, all with mild severity of the infection. In 2,688 (99.33%) with outpatient treatment, the disease did not progress to warrant further hospitalization and there were no deaths. In 16 (0.59%) with outpatient treatment, it was necessary their subsequent hospitalization to a room without any death. In 2 (0.08%) with outpatient treatment, it was necessary their admission to the Intensive Care Unit (ICU) and 1 (0.04%) patient died. There were 411 (13.3%) patients hospitalized, being admitted at a COVID-19 room with a moderate disease 300 (9.7%) patients of which 3 (1%) died; and with a severe to critical disease were hospitalized in the ICU 111 (3.6%), 34 (30.6%) of whom died. The mortality percentage of patients admitted to the ICU of 30.6%, is similar with the percentage found in the literature of 30.9%. Total mortality was 37 (1.2%) patients, which is much lower than that reported in world statistics, which are around 3%.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Jose Morgenstern", + "author_inst": "Rescue Group" + }, + { + "author_name": "Jose N Redondo", + "author_inst": "Rescue Group" + }, + { + "author_name": "Albida De Leon", + "author_inst": "Rescue Group" + }, + { + "author_name": "Juan M Canela", + "author_inst": "Rescue Group" + }, + { + "author_name": "Nelson Torres", + "author_inst": "Rescue Group" + }, + { + "author_name": "Johnny Tavares", + "author_inst": "Rescue Group" + }, + { + "author_name": "Migulina Minaya", + "author_inst": "Rescue Group" + }, + { + "author_name": "Oscar Lopez", + "author_inst": "Rescue Group" + }, + { + "author_name": "Ana M Placido", + "author_inst": "Rescue Group" + }, + { + "author_name": "Ana Castillo", + "author_inst": "Rescue Group" + }, + { + "author_name": "Rafael Pena Cruz", + "author_inst": "Rescue Group" + }, + { + "author_name": "Yudelka Merrete", + "author_inst": "Rescue Group" + }, + { + "author_name": "Marlenin Toribio", + "author_inst": "Rescue Group" + }, + { + "author_name": "Juan A Francisco", + "author_inst": "Rescue Group" + }, + { + "author_name": "Santiago Roca", + "author_inst": "Rescue Group" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.29.20219931", "rel_title": "A longitudinal comparison of spike and nucleocapsid SARS-CoV-2 antibody responses in a tertiary hospitals laboratory workers with validation of DBS specimen analysis.", @@ -1080195,73 +1084130,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.30.20221465", - "rel_title": "The challenges of caring for people dying from COVID-19: a multinational,observational study of palliative and hospice services (CovPall)", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20221465", - "rel_abs": "BackgroundSystematic data on the care of people dying with COVID-19 are scarce. We studied the response of and challenges for palliative care services during the COVID-19 pandemic.\n\nMethodsWe surveyed palliative care and hospice services, contacted via relevant organisations. Multivariable logistic regression identified associations with key challenges. Content analysis explored free text.\n\nFindings458 services responded; 277 UK, 85 rest of Europe, 95 rest of the world (1 country unreported); 81% cared for patients with suspected or confirmed COVID-19, 77% had staff with suspected or confirmed COVID-19; 48% reported shortages of Personal Protective Equipment (PPE), 40% staff shortages, 24% medicines shortages, 14% shortages of other equipment. Services provided direct care and education in symptom management and communication; 91% changed how they worked. Care often shifted to increased community and hospital care, with fewer admissions to inpatient palliative care units. Factors associated with increased odds of PPE shortages were: charity rather than public management (OR 3{middle dot}07, 95% CI 1{middle dot}81-5{middle dot}20), inpatient palliative care unit rather than other setting (OR 2{middle dot}34, 95% CI 1{middle dot}46-3{middle dot}75). Being outside the UK was associated with lower odds of staff shortages (OR 0{middle dot}44, 95% CI 0{middle dot}26-0{middle dot}76). Staff described increased workload, concerns for their colleagues who were ill, whilst expending time struggling to get essential equipment and medicines, perceiving they were not a front-line service.\n\nInterpretationAcross all settings palliative care services were often overwhelmed, yet felt ignored in the COVID-19 response. Palliative care needs better integration with health care systems when planning and responding to future epidemics/pandemics.\n\nFundingMRC grant number MR/V012908/1, Cicely Saunders International and NIHR ARC South London.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSSystematic data on the response of palliative care services during COVID-19 are lacking. A search of PubMed on 27 August 2020 (start date: 01 December 2019) using keywords (palliative care OR end of life care OR hospice) and (COVID-19 OR coronavirus) and (multinational OR international) identified no studies that reported multinational or international data; there were 79 articles, mostly opinion pieces, single centre case studies or reports. A search for systematic reviews about palliative care and hospice services during pandemics of PubMed, with the same time periods and the keywords (palliative care OR end of life care OR hospice) and (COVID-19 OR coronavirus OR SARS-CoV-2) and (systematic review OR meta-analysis), identified one systematic review by Etkind et al, which underpinned this research and shares two senior authors (Higginson, Sleeman). Of 3094 articles identified, 10 studies, all observational, considered the palliative care response in pandemics. Studies were from single units or countries: West Africa, Taiwan, Hong Kong, Singapore, the U.S. (a simulation), and Italy (the only one considering COVID-19). The review concluded hospice and palliative care services are essential in the response to COVID-19 but systematic data are urgently needed to inform how to improve care for those who are likely to die, and/or have severe symptoms.\n\nAdded value of this studyWe found a high response by palliative care services during the COVID-19 pandemic. Services cared for a surge in patients dying from and with severe symptoms due to COVID-19 in three main categories: patients with underlying conditions and/or multimorbid disease not previously known to palliative care (70% of services), patients already known to palliative care services (47% of services), and patients, previously healthy, now dying from COVID-19 (37% of services). More than three quarters of services reported having staff with suspected or confirmed COVID-19. We found high levels of shortages of Personal Protective Equipment (PPE), staff, medicines and other equipment, with different effects according to service management, care settings and world regions. Mitigating these challenges was extremely time consuming, limiting the palliative care response.\n\nImplications of all the available evidenceDespite actively supporting dying patients, those with severe symptoms, their families/carers, and supporting other clinicians, palliative care professionals felt ignored by national health systems during the COVID-19 pandemic. Palliative care services need equipment, medicines and adequate staff to contribute fully to the pandemic response. Their crucial role must be better recognised and integrated, including into infection disease management, with improved workforce planning and management, so that patients and families can be better supported.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Adejoke O Oluyase", - "author_inst": "Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, King's College London, London, UK" - }, - { - "author_name": "Mevhibe B Hocaoglu", - "author_inst": "Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, King's College London, London, UK" - }, - { - "author_name": "Rachel L Cripps", - "author_inst": "Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, King's College London, London, UK" - }, - { - "author_name": "Matthew Maddocks", - "author_inst": "Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, King's College London, London, UK" - }, - { - "author_name": "Catherine Walshe", - "author_inst": "International Observatory on End of Life Care, Division of Health Research, Lancaster University, Lancaster, UK" - }, - { - "author_name": "Lorna K Fraser", - "author_inst": "Health Sciences, University of York, York, North Yorkshire, UK" - }, - { - "author_name": "Nancy Preston", - "author_inst": "International Observatory on End of Life Care, Division of Health Research, Lancaster University, Lancaster, UK" - }, - { - "author_name": "Lesley Dunleavy", - "author_inst": "International Observatory on End of Life Care, Division of Health Research, Lancaster University, Lancaster, UK" - }, - { - "author_name": "Andy Bradshaw", - "author_inst": "Wolfson Palliative Care Research Centre, Hull York Medical School, University of Hull, Hull, UK" - }, - { - "author_name": "Fliss EM Murtagh", - "author_inst": "Wolfson Palliative Care Research Centre, Hull York Medical School, University of Hull, Hull, UK & Cicely Saunders Institute of Palliative Care, Policy and Rehab" - }, - { - "author_name": "Sabrina Bajwah", - "author_inst": "Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, King's College London, London, UK" - }, - { - "author_name": "Katherine E Sleeman", - "author_inst": "Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, King's College London, London, UK" - }, - { - "author_name": "Irene J Higginson", - "author_inst": "Cicely Saunders Institute of Palliative Care, Policy and Rehabilitation, King's College London, London, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "palliative medicine" - }, { "rel_doi": "10.1101/2020.10.30.20222901", "rel_title": "COVID-19, a social disease in Paris: a socio-economic wide association study on hospitalized patients highlights low-income neighbourhood as a key determinant of severe COVID-19 incidence during the first wave of the epidemic", @@ -1081764,6 +1085632,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.27.20220707", + "rel_title": "Association of Mass Gatherings and COVID-19 Hospitalization", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20220707", + "rel_abs": "We examined COVID-19 hospitalizations following mass gatherings in Wisconsin and Minnesota, United States (September 17-18, 2020). We found that the hospitalization rate increased 15-fold in the Minnesota gathering county, and 12.7-fold in the Wisconsin gathering county. On the state level, it increased 2-fold in Minnesota, and 2.3-fold in Wisconsin, while not increasing significantly in states without gatherings. Our findings suggest that mass gatherings are followed by increased COVID-19 hospitalizations, and that precautions should be taken.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Oren Miron", + "author_inst": "Ben Gurion University" + }, + { + "author_name": "Kun-Hsing Yu", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Rachel Wilf-Miron", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Nadav Davidovitch", + "author_inst": "Ben Gurion University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.03.366609", "rel_title": "Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design", @@ -1082025,49 +1085924,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2020.11.02.365833", - "rel_title": "Zinc-embedded fabrics inactivate SARS-CoV-2 and influenza A virus", - "rel_date": "2020-11-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.02.365833", - "rel_abs": "Infections with respiratory viruses can spread via liquid droplets and aerosols, and cause diseases such as influenza and COVID-19. Face masks and other personal protective equipment (PPE) can act as barriers that prevent the spread of respiratory droplets containing these viruses. However, influenza A viruses and coronaviruses are stable for hours on various materials, which makes frequent and correct disposal of these PPE important. Metal ions embedded into PPE may inactivate respiratory viruses, but confounding factors such as absorption of viruses make measuring and optimizing the inactivation characteristics difficult. Here we used polyamide 6.6 (PA66) fibers that had zinc ions embedded during the polymerisation process and systematically investigated if these fibers can absorb and inactivate pandemic SARS-CoV-2 and influenza A virus H1N1. We find that these viruses are readily absorbed by PA66 fabrics and inactivated by zinc ions embedded into this fabric. The inactivation rate (pfu{middle dot}gram-1{middle dot}min-1) exceeds the number of active virus particles expelled by a cough and supports a wide range of viral loads. Moreover, we found that the zinc content and the virus inactivating property of the fabric remain stable over 50 standardized washes. Overall, these results provide new insight into the development of \"pathogen-free\" PPE and better protection against RNA virus spread.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Vikram Gopal", - "author_inst": "Ascend Performance Materials" - }, - { - "author_name": "Benjamin E Nilsson-Payant", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Hollie French", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Jurre Y Siegers", - "author_inst": "Erasmus University Medical Centre" - }, - { - "author_name": "Wai-shing Yung", - "author_inst": "Ascend Performance Materials" - }, - { - "author_name": "Matthew Hardwick", - "author_inst": "ResInnova Laboratories" - }, - { - "author_name": "Aartjan J.W. te Velthuis", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.11.03.366666", "rel_title": "Looking for pathways related to COVID-19 phenotypes: Confirmation of pathogenic mechanisms by SARS-CoV-2 - Host interactome.", @@ -1083610,6 +1087466,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.28.20221093", + "rel_title": "Features of creatine-kinase in COVID-19 patients with different ages, clinical types and outcomes: A cohort study", + "rel_date": "2020-11-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221093", + "rel_abs": "ObjectivesTo study the features of creatine-kinase (CK) in COVID-19 patients with different ages, clinical types and outcomes and quantify the relationship between CK value and clinical type.\n\nMethodsAll laboratory confirmed COVID-19 patients hospitalized in Xiangyang No.1 Peoples Hospital were included. Patients general information, clinical type, all CK values and outcome were collected.\n\nResultsThe peak median value of CK in cases aged [≥] 71 years old (appeared at T2) was higher than that in cases aged [≤] 70 years old. There was statistical difference between the two groups (P=0.001). Similarly, the peak in critical cases (appeared at T2) was higher than moderate and severe types, and significant difference were existed among moderate, severe, and critical types (P=0.000). Moreover, the peak value in death group (appeared at T2) was higher than those in survival group. Significant difference was also found between them (P=0.000). According to the optimal scale regression model, the CK value (P=0.000) and age (P=0.000) were associated with the clinical type.\n\nConclusionsDifference of the CK in different ages, clinical types, and outcomes were significant. The results of the optimal scale regression model are helpful to judge the clinical type of COVID-19 patients.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Shanshan Wan", + "author_inst": "Postgraduate Training Basement of Jinzhou Medical University, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Gaojing Qu", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Hui Yu", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Haoming Zhu", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Guoxin Huang", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Lei Chen", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Meiling Zhang", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Jiangtao Liu", + "author_inst": "Department of Orthopedics, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Bin Pei", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.28.20221069", "rel_title": "Psychological and social impact of COVID-19 in Pakistan: Need for Gender Responsive Policies", @@ -1083695,41 +1087602,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.10.31.363309", - "rel_title": "Molecular dynamics and in silico mutagenesis on the reversible inhibitor-bound SARS-CoV-2 Main Protease complexes reveal the role of lateral pocket in enhancing the ligand affinity", - "rel_date": "2020-11-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.31.363309", - "rel_abs": "The 2019 novel coronavirus pandemic caused by SARS-CoV-2 remains a serious health threat to humans and a number of countries are already in the middle of the second wave of infection. There is an urgent need to develop therapeutics against this deadly virus. Recent scientific evidences have suggested that the main protease (Mpro) enzyme in SARS-CoV-2 can be an ideal drug target due to its crucial role in the viral replication and transcription processes. Therefore, there are ongoing research efforts to identify drug candidates against SARS-CoV-2 Mpro that resulted in hundreds of X-ray crystal structures of ligand bound Mpro complexes in the protein data bank (PDB) that describe structural details of different chemotypes of fragments binding within different sites in Mpro. In this work, we perform rigorous molecular dynamics (MD) simulation of 62 reversible ligand-Mpro complexes in the PDB to gain mechanistic insights about their interactions at atomic level. Using a total of ~2.25 s long MD trajectories, we identified and characterized different pockets and their conformational dynamics in the apo Mpro structure. Later, using the published PDB structures, we analyzed the dynamic interactions and binding affinity of small ligands within those pockets. Our results identified the key residues that stabilize the ligands in the catalytic sites and other pockets in Mpro. Our analyses unraveled the role of a lateral pocket in the catalytic site in Mpro that is critical for enhancing the ligand binding to the enzyme. We also highlighted the important contribution from HIS163 in this lateral pocket towards ligand binding and affinity against Mpro through computational mutation analyses. Further, we revealed the effects of explicit water molecules and Mpro dimerization in the ligand association with the target. Thus, comprehensive molecular level insights gained from this work can be useful to identify or design potent small molecule inhibitors against SARS-CoV-2 Mpro.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Ying Li Weng", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Shiv Rakesh Naik", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Nadia Dingelstad", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Subha Kalyaanamoorthy", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Aravindhan Ganesan", - "author_inst": "University of Waterloo" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.10.30.362749", "rel_title": "Mechanism of ligand recognition by human ACE2 receptor", @@ -1085192,6 +1089064,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.27.20220731", + "rel_title": "Mental Health Impact of the First Wave of COVID-19 Pandemic on Spanish Healthcare Workers: a Large Cross-sectional Survey", + "rel_date": "2020-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20220731", + "rel_abs": "IntroductionHealthcare workers are vulnerable to adverse mental health impacts of COVID-19. We assessed prevalence of mental disorders and associated factors during the first wave of the pandemic among healthcare professionals in Spain.\n\nMethodsAll workers in 18 healthcare institutions (6 AACC) in Spain were invited to a series of online surveys assessing a wide range of individual characteristics, COVID-19 infection status and exposure, and mental health status. Here we report: current mental disorders (Major Depressive Disorder-MDD- [PHQ-8[≥]10], Generalized Anxiety Disorder-GAD- [GAD-7[≥]10], Panic attacks, Posttraumatic Stress Disorder -PTSD- [PCL-5[≥]7]; and Substance Use Disorder -SUD-[CAGE-AID[≥]2]. Severe disability assessed by the Sheehan Disability Scale was used to identify \"disabling\" current mental disorders.\n\nResults9,138 healthcare workers participated. Prevalence of screen-positive disorder: 28.1% MDD; 22.5% GAD, 24.0% Panic; 22.2% PTSD; and 6.2% SUD. Overall 45.7% presented any current and 14.5% any disabling current mental disorder. Healthcare workers with prior lifetime mental disorders had almost twice the prevalence of current disorders than those without. Adjusting for all other variables, odds of any disabling mental disorder were: prior lifetime disorders (TUS: OR=5.74; 95%CI 2.53-13.03; Mood: OR=3.23; 95%CI:2.27-4.60; Anxiety: OR=3.03; 95%CI:2.53-3.62); age category 18-29 years (OR=1.36; 95%CI:1.02-1.82), caring \"all of the time\" for COVID-19 patients (OR=5.19; 95%CI: 3.61-7.46), female gender (OR=1.58; 95%CI: 1.27-1.96) and having being in quarantine or isolated (OR= 1.60; 95CI:1.31-1.95).\n\nConclusionsCurrent mental disorders were very frequent among Spanish healthcare workers during the first wave of COVID-19. As the pandemic enters its second wave, careful monitoring and support is needed for healthcare workers, especially those with previous mental disorders and those caring COVID-19 very often.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Jordi Alonso", + "author_inst": "Health Services Research Unit, IMIM-Institut Hospital del Mar d'Investigacions M\u00e8diques" + }, + { + "author_name": "Gemma Vilagut", + "author_inst": "Health Services Research Unit, IMIM-Institut Hospital del Mar d'Investigacions M\u00e8diques" + }, + { + "author_name": "Philippe Mortier", + "author_inst": "Health Services Research Unit, IMIM-Institut Hospital del Mar d'Investigacions M\u00e8diques" + }, + { + "author_name": "Montse Ferrer", + "author_inst": "Health Services Research Unit, IMIM-Institut Hospital del Mar d'Investigacions M\u00e8diques" + }, + { + "author_name": "Itxaso Alayo", + "author_inst": "Health Services Research Unit, IMIM-Institut Hospital del Mar d'Investigacions M\u00e8diques" + }, + { + "author_name": "Andr\u00e9s Arag\u00f3n-Pe\u00f1a", + "author_inst": "Epidemiology Unit, Regional Ministry of Health, Community of Madrid" + }, + { + "author_name": "Enric Aragon\u00e8s", + "author_inst": "Institut d'Investigaci\u00f3 en Atenci\u00f3 Prim\u00e0ria IDIAP Jordi Gol" + }, + { + "author_name": "Mireia Campos", + "author_inst": "Service of Prevention of Labor Risks, Medical Emergencies System, Generalitat de Catalunya" + }, + { + "author_name": "Isabel del Cura-Gonz\u00e1lez", + "author_inst": "Research Unit. Primary Care Management. Madrid Health Service" + }, + { + "author_name": "Jos\u00e9 I. Emparanza", + "author_inst": "Hospital Universitario Donostia" + }, + { + "author_name": "Meritxell Espuga", + "author_inst": "Occupational Health Service. Hospital Universitari Vall d'Hebron" + }, + { + "author_name": "Joao Forjaz", + "author_inst": "National Center of Epidemiology, Instituto de Salud Carlos III (ISCIII)" + }, + { + "author_name": "Ana Gonz\u00e1lez Pinto", + "author_inst": "Hospital Universitario Araba-Santiago" + }, + { + "author_name": "Josep M. Haro", + "author_inst": "Parc Sanitari Sant Joan de D\u00e9u" + }, + { + "author_name": "Nieves L\u00f3pez Fresne\u00f1a", + "author_inst": "Hospital General Universitario Gregorio Mara\u00f1\u00f3n" + }, + { + "author_name": "Alma Mart\u00ednez de Sal\u00e1zar", + "author_inst": "UGC Salud Mental, Hospital Universitario Torrec\u00e1rdenas" + }, + { + "author_name": "Juan D. Molina", + "author_inst": "Villaverde Mental Health Center. Clinical Management Area of Psychiatry and Mental Health, Psychiatric Service, Hospital Universitario 12 de Octubre" + }, + { + "author_name": "Rafael M. Ort\u00ed Lucas", + "author_inst": "Hospital Cl\u00ednic Universitari de Valencia" + }, + { + "author_name": "Mara Parellada", + "author_inst": "Hospital General Universitario Gregorio Mara\u00f1\u00f3n" + }, + { + "author_name": "Jos\u00e9 Maria Pelayo-Ter\u00e1n", + "author_inst": "Hospital El Bierzo" + }, + { + "author_name": "Aurora P\u00e9rez Zapata", + "author_inst": "Pr\u00edncipe de Asturias University Hospital" + }, + { + "author_name": "Jos\u00e9 I. Pijoan", + "author_inst": "Hospital Universitario Cruces/ OSI EEC" + }, + { + "author_name": "Nieves Plana", + "author_inst": "Pr\u00edncipe de Asturias University Hospital" + }, + { + "author_name": "Teresa Puig", + "author_inst": "Department of Epidemiology and Public Health, Hospital de la Santa Creu i Sant Pau" + }, + { + "author_name": "Cristina Rius", + "author_inst": "Ag\u00e8ncia de Salut P\u00fablica de Barcelona" + }, + { + "author_name": "Carmen Rodriguez-Blazquez", + "author_inst": "National Center of Epidemiology, Instituto de Salud Carlos III (ISCIII)" + }, + { + "author_name": "Ferran Sanz", + "author_inst": "Research Progamme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)" + }, + { + "author_name": "Consol Serra", + "author_inst": "Parc de Salut Mar PSMAR" + }, + { + "author_name": "Ronald C. Kessler", + "author_inst": "Department of Health Care Policy, Harvard Medical School" + }, + { + "author_name": "Ronny Bruffaerts", + "author_inst": "Center for Public Health Psychiatry, Universitair Psychiatrisch Centrum, KU Leuven" + }, + { + "author_name": "Eduard Vieta", + "author_inst": "Fundaci\u00f3 Cl\u00ednic per a la Recerca Biom\u00e8dica de Barcelona" + }, + { + "author_name": "V\u00edctor P\u00e9rez-Sol\u00e1", + "author_inst": "Parc de Salut Mar PSMAR" + }, + { + "author_name": "- MINDCOVID Working group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.29.20222372", "rel_title": "The COVID-19 Healthcare Personnel Study (CHPS): Overview, Methods and Preliminary Report", @@ -1085333,41 +1089352,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.27.20220723", - "rel_title": "The psychological impact of coronavirus on university students and its socio-economic determinants in Malaysia", - "rel_date": "2020-10-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20220723", - "rel_abs": "This article examines the impact of coronavirus disease 2019 (COVID-19) upon university students anxiety level and finds the factors associated with the anxiety disorder in Malaysia. We collected data from 958 students from 16 different universities using an originally designed questionnaire. The Generalized Anxiety Disorder Scale 7-item (GAD-7) was used to estimate the anxiety. We find that 12.3% students were normal, whereas 30.5% were experiencing mild, 31.1% moderate, and 26.1% severe anxiety. Surprisingly, only 37.2% of students were aware of mental health support which was provided by their universities. Moreover, it was found that gender as male (Odds Ratio (OR= 0.798, 95% Confidence Interval (CI)= 0.61 - 1.04)) and having internet access (OR = 0.44, 95% CI= 0.24 - 0.80) were alleviating factors for the anxiety. Whereas, age above than 20 years (OR= 1.30, 95% CI= 0.96 - 1.75), ethnicity Chinese (OR=1.72, 95% CI= 0.95 - 3.1), any other disease (OR=2.0, 95% CI=1.44 - 2.79), decreased family income (OR=1.71, 95% CI=1.34 - 2.17), more time spent on watching COVID-19 related news (OR=1.52, 95% CI=1.17 - 1.97), and infected relative or friends (OR=1.62, 95% CI=1.06 - 2.50) were risk factors for anxiety among students. We suggest that the government of Malaysia should monitor the mental health of the universities students more closely and universities should open online mental health support clinics to avoid the adverse impacts of the anxiety disorder.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Muhammad Irfan", - "author_inst": "Xiamen University Malaysia" - }, - { - "author_name": "Faizah Shahudin", - "author_inst": "Xiamen University Malaysia" - }, - { - "author_name": "VINCENT HOOPER", - "author_inst": "Xiamen University Malaysia" - }, - { - "author_name": "Waqar Akram", - "author_inst": "Sukkur Institute of Business" - }, - { - "author_name": "Rosmaiza Ghani", - "author_inst": "MARA University of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.10.29.352450", "rel_title": "Brilacidin, a COVID-19 Drug Candidate, Exhibits Potent In Vitro Antiviral Activity Against SARS-CoV-2", @@ -1088002,6 +1091986,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.10.28.355305", + "rel_title": "5-amino levulinic acid inhibits SARS-CoV-2 infection in vitro", + "rel_date": "2020-10-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.28.355305", + "rel_abs": "The current COVID-19 pandemic requires urgent development of effective therapeutics. 5-amino levulinic acid (5-ALA) is a naturally synthesized amino acid and has been used for multiple purposes including as an anticancer therapy and as a dietary supplement due to its high bioavailability. In this study, we demonstrated that 5-ALA treatment potently inhibited infection of SARS-CoV-2, a causative agent of COVID-19. The antiviral effects could be detected in both human and non-human cells, without significant cytotoxicity. Therefore, 5-ALA is a candidate as an oral antiviral drug for COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yasuteru Sakurai", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Mya Myat Ngwe Tun", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Yohei Kurosaki", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Takaya Sakura", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Daniel Ken Inaoka", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Kiyotaka Fujine", + "author_inst": "neopharma Japan Co., Ltd." + }, + { + "author_name": "Kiyoshi Kita", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Kouichi Morita", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Jiro Yasuda", + "author_inst": "Nagasaki University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.28.359257", "rel_title": "In vitro assessment of the virucidal activity of four mouthwashes containing Cetylpyridinium Chloride, ethanol, zinc and a mix of enzyme and proteins against a human coronavirus", @@ -1088159,45 +1092194,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.10.27.20220665", - "rel_title": "ACE2 Netlas: In-silico functional characterization and drug-gene interactions of ACE2 gene network to understand its potential involvement in COVID-19 susceptibility", - "rel_date": "2020-10-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20220665", - "rel_abs": "Angiotensin-converting enzyme-2 (ACE2) receptor has been identified as the key adhesion molecule for the transmission of the SARS-CoV-2. However, there is no evidence that human genetic variation in ACE2 is singularly responsible for COVID-19 susceptibility. Therefore, we performed a multi-level characterization of genes that interact with ACE2 (ACE2-gene network) for their over-represented biological properties in the context of COVID-19.\n\nThe phenome-wide association of 51 genes including ACE2 with 4,756 traits categorized into 26 phenotype categories, showed enrichment of immunological, respiratory, environmental, skeletal, dermatological, and metabolic domains (p<4e-4). Transcriptomic regulation of ACE2-gene network was enriched for tissue-specificity in kidney, small intestine, and colon (p<4.7e-4). Leveraging the drug-gene interaction database we identified 47 drugs, including dexamethasone and spironolactone, among others.\n\nConsidering genetic variants within {+/-} 10 kb of ACE2-network genes we characterized functional consequences (among others) using miRNA binding-site targets. MiRNAs affected by ACE2-network variants revealed statistical over-representation of inflammation, aging, diabetes, and heart conditions. With respect to variants mapped to the ACE2-network, we observed COVID-19 related associations in RORA, SLC12A6 and SLC6A19 genes.\n\nOverall, functional characterization of ACE2-gene network highlights several potential mechanisms in COVID-19 susceptibility. The data can also be accessed at https://gpwhiz.github.io/ACE2Netlas/", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Gita A Pathak", - "author_inst": "Yale University" - }, - { - "author_name": "Frank Wendt", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Aranyak Goswami", - "author_inst": "Yale University" - }, - { - "author_name": "Flavio De Angelis", - "author_inst": "Yale Univeristy" - }, - { - "author_name": "- COVID-19 Host Genetics Initiative", - "author_inst": "" - }, - { - "author_name": "Renato Polimanti", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.10.22.20217539", "rel_title": "Evaluation of a Modified Early Warning Score (MEWS) adjusted for COVID-19 patients (CEWS) to identify risk of ICU admission or death.", @@ -1089568,6 +1093564,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.23.20218255", + "rel_title": "Characteristics and outcomes of hospitalized adult COVID-19 patients in Georgia", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.23.20218255", + "rel_abs": "ObjectiveDescribe presenting characteristics of hospitalized patients and explore factors associated with in-hospital mortality during the first wave of pandemic in Georgia.\n\nMethodsThis retrospective study included 582 adult patients admitted to 9 dedicated COVID-19 hospitals as of July 30, 2020 (72% of all hospitalizations). Data were abstracted from medical charts. Factors associated with mortality were evaluated in multivariable Poisson regression analysis.\n\nResultsAmong 582 adults included in this analysis 14.9% were 65+ years old, 49.1% were women, 59.3% had uni- or bi-lateral lung involvement on chest computed tomography, 27.1% had any co-morbidity, 13.2% patients had lymphopenia, 4.1% had neutophilosis, 4.8% had low platelet count, 37.6% had d-dimer levels of >0.5 mcg/l. Overall mortality was 2.1% (12/582). After excluding mild infections, mortality among patients with moderate-to-critical disease was 3.0% (12/399), while among patients with severe-to-critical disease mortality was 12.7% (8/63). Baseline characteristics associated with increased risk of mortality in multivariate regression analysis included: age [≥]65 years (RR: 10.38, 95% CI: 1.30-82.75), presence of any chronic co-morbidity (RR: 20.71, 95% CI: 1.58-270.99), lymphopenia (RR: 4.76, 95% CI: 1.52-14.93), neutrophilosis (RR: 7.22, 95% CI: 1.27-41.12), low platelet count (RR: 6.92, 95% CI: 1.18-40.54), elevated d-dimer (RR: 4.45, 95% CI: 1.48-13.35), elevated AST (RR: 6.33, 95% CI: 1.18-33.98).\n\nConclusionIn-hospital mortality during the first wave of pandemic in Georgia was low. We identified several risk factors (older age, co-morbidities and laboratory abnormalities) associated with poor outcome that should provide guidance for planning health sector response as pandemic continues to evolve.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Tengiz Tsertsvadze", + "author_inst": "1) Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia; 2) Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia" + }, + { + "author_name": "Marina Ezugbaia", + "author_inst": "Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia" + }, + { + "author_name": "Marina Endeladze", + "author_inst": "Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia" + }, + { + "author_name": "Levani Ratiani", + "author_inst": "First University Clinic, Tbilisi, Georgia" + }, + { + "author_name": "Neli Javakhishvili", + "author_inst": "Giorgi Abramishvili Military Hospital, Gori, Georgia" + }, + { + "author_name": "Lika Mumladze", + "author_inst": "St. King Mirian and Queen Nana Mtskheta Regional Medical Center, Georgia" + }, + { + "author_name": "Manana Khotcholava", + "author_inst": "Childrens Infectious Diseases Hospital, Tbilisi, Georgia" + }, + { + "author_name": "Maiko Janashia", + "author_inst": "University Clinic Rukhi, Georgia" + }, + { + "author_name": "Diana Zviadadze", + "author_inst": "LJ Clinic, Kutaisi, Georgia" + }, + { + "author_name": "Levan Gopodze", + "author_inst": "Central Republican Hospital, Tbilisi, Georgia" + }, + { + "author_name": "Alex Gokhelashvili", + "author_inst": "Medalpha Clinic, Batumi, Georgia" + }, + { + "author_name": "Revaz Metchurchtlishvili", + "author_inst": "Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia" + }, + { + "author_name": "Akaki Abutidze", + "author_inst": "1) Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia; 2) Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia" + }, + { + "author_name": "Nikoloz Chkhartishvili", + "author_inst": "1) Infectious Diseases, AIDS and Clinical Immunology Research Center; 2) Caucasus International University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.23.20218164", "rel_title": "SARS-CoV-2 seroprevalence in healthcare workers of dedicated COVID hospitals and non COVID hospitals of District Srinagar, Kashmir", @@ -1089705,45 +1093772,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.23.20218230", - "rel_title": "Abnormal liver tests in admitted patients with SARS-Cov-2 or other respiratory viruses- prognostic similarities and temporal disparities", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.23.20218230", - "rel_abs": "Background and AimsAbnormal liver tests are common in patients with severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) infection, but their association with short-term outcomes is controversial. We aimed to compare the pattern of abnormal liver tests in SARS-CoV-2 patients with those of patients infected with influenza or respiratory syncytial virus (RSV), two non-hepatotropic respiratory viruses, and their association with in-hospital mechanical ventilation or death.\n\nMethodsA retrospective cohort study of 1271 hospitalized patients (872 influenza, 218 RSV, and 181 SARS-Cov-2) in a tertiary medical center. We defined abnormal liver tests as GPT, GOT or GGT[≥]40IU/ML at any time-point during hospitalization.\n\nResultsAbnormal liver tests were mild-moderate in the majority of patients regardless of infection type but the majority of patients with influenza or RSV had a transaminases peak earlier during hospitalization compared to patients with SARS-Cov-2. Abnormal liver tests correlated with markers of severe disease across all types of infections, and were associated with mechanical ventilation or death, occurring mainly in patients with severe liver tests abnormalities (>200IU/L) (27.2%, 39.4% and 55.6% of patients with influenza, RSV or SARS-Cov-2). In multivariate analysis, controlling for age, gender, lymphopenia and CRP, liver tests abnormalities remained significantly associated with mechanical ventilation or death for influenza (OR= 3.047, 95% CI 1.518-6.117) and RSV (OR= 3.402, 95% CI 1.032-11.220) but not for SARS-Cov-2 (OR= 0.995, 95% CI 0.198-4.989). These results were confirmed upon propensity score matching.\n\nConclusionsAbnormal liver tests during hospitalization with different viral respiratory infections are common, may differ in their time-course and reflect disease severity. They are associated with worse outcomes, mainly in patients with severe liver test abnormalities, regardless of infection type.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Noa Shafran", - "author_inst": "Rabin Medical Center" - }, - { - "author_name": "Assaf Issachar", - "author_inst": "Rabin Medical Center" - }, - { - "author_name": "Tzippy Shochat", - "author_inst": "Rabin Medical Center" - }, - { - "author_name": "Inbal Haya Shafran", - "author_inst": "Medical University of Vienna" - }, - { - "author_name": "Michael Bursztyn", - "author_inst": "The Hebrew University" - }, - { - "author_name": "Amir Shlomai", - "author_inst": "Rabin Medical Center, Beilinson hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2020.10.23.20218297", "rel_title": "Perceived Risk and Distress related to COVID-19: Comparing Healthcare versus non-Healthcare Workers of Pakistan", @@ -1091134,6 +1095162,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.24.20218685", + "rel_title": "Increasing SARS-CoV-2 RT-qPCR testing capacity by sample pooling", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.24.20218685", + "rel_abs": "ObjectivesLimited testing capacity has characterized the ongoing COVID-19 pandemic in Spain, hampering a timely control of outbreaks and the possibilities to reduce the escalation of community transmissions. Here we investigated the potential of using pooling of samples followed by one-step retrotranscription and quantitative PCR (RT-qPCR) to increase SARS-CoV-2 testing capacity.\n\nMethodsWe first evaluated different sample pooling (1:5, 1:10 and 1:15) prior to RNA extractions followed by standard RT-qPCR for SARS-CoV-2/COVID-19 diagnosis. The pool size achieving reproducible results in independent tests was then used for assessing nasopharyngeal samples in a tertiary hospital during August 2020.\n\nResultsWe found that pool size of five samples achieved the highest sensitivity compared to pool sizes of 10 and 15, showing a mean ({+/-} SD) Ct shift of 3.5 {+/-} 2.2 between the pooled test and positive samples in the pool. We then used a pool size of five to test a total of 895 pools (4,475 prospective samples) using two different RT-qPCR kits available at that time. The Real Accurate Quadruplex corona-plus PCR Kit (PathoFinder) reported the lowest mean Ct ({+/-} SD) shift (2.2 {+/-} 2.4) among the pool and the individual samples. The strategy allows detecting individual samples in the positive pools with Cts in the range of 16.7-39.4.\n\nConclusionsWe found that pools of five samples combined with RT-qPCR solutions helped to increase SARS-CoV-2 testing capacity with minimal loss of sensitivity compared to that resulting from testing the samples independently.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Julia Alcoba-Florez", + "author_inst": "Servicio de Microbiologia, Hospital Universitario Nuestra Senora de Candelaria" + }, + { + "author_name": "Helena Gil-Campesino", + "author_inst": "Servicio de Microbiologia, Hospital Universitario Nuestra Senora de Candelaria" + }, + { + "author_name": "Diego Garcia-Martinez de Artola", + "author_inst": "Servicio de Microbiologia, Hospital Universitario Nuestra Senora de Candelaria" + }, + { + "author_name": "Oscar Diez-Gil", + "author_inst": "Servicio de Microbiologia, Hospital Universitario Nuestra Senora de Candelaria" + }, + { + "author_name": "Agustin Valenzuela-Fernandez", + "author_inst": "Laboratorio de Inmunologia Celular y Viral, Unidad de Farmacologia, Universidad de La Laguna" + }, + { + "author_name": "Rafaela Gonzalez-Montelongo", + "author_inst": "Genomics Division, Instituto Tecnologico y de Energias Renovables" + }, + { + "author_name": "Laura Ciuffreda", + "author_inst": "Unidad de Investigacion, Hospital Universitario Nuestra Senora de Candelaria" + }, + { + "author_name": "Carlos Flores", + "author_inst": "Hospital Universitario Nuestra Senora de Candelaria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.24.20218974", "rel_title": "Low serum vitamin D level and COVID-19 infection and outcomes, a multivariate meta-analysis", @@ -1091235,41 +1095310,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.24.20218321", - "rel_title": "COVID-19 Infections Following Physical School Reopening", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.24.20218321", - "rel_abs": "BackgroundSchool reopened in August-September 2020 and their effect on COVID-19 infections is unclear.\n\nMethodsWe examined Coronavirus Disease-19 incidence following school reopening in Florida.\n\nResultsWe found that counties teaching physically had 1.2-fold incidence increase in elementary schools and 1.3-fold increase in high schools, while counties teaching remotely had no increase.\n\nConclusionsOur results suggest that counties teaching physically could consider teaching remotely, especially in high school, until it is safe to teach physically.\n\nWhat was knownSchools reopened in August-September 2020, with some teaching remotely, since the effect of physical reopening on COVID-19 infections is unclear.\n\nWhat we addedcounties teaching physically had 1.2-fold incidence increase in elementary schools and 1.3-fold increase in high schools. This suggests that counties teaching physically could consider teaching remotely instead, especially at the high school level.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Oren Miron", - "author_inst": "Ben Gurion University" - }, - { - "author_name": "Kun-Hsing Yu", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Rachel Wilf-Miron", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Isaac Kohane", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Nadav Davidovitch", - "author_inst": "Ben Gurion University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2020.10.25.20219071", "rel_title": "Causes of death in mental health service users during the first wave of the COVID-19 pandemic: South London and Maudsley data from March to June 2020, compared with 2015-2019.", @@ -1092608,6 +1096648,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.26.20219626", + "rel_title": "Hyper-Exponential Growth of COVID-19 during Resurgence of the Disease in Russia", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219626", + "rel_abs": "In Russia, COVID-19 has currently been growing hyper-exponentially. This type of a spread pattern was not seen during the first wave of the pandemic the world over. Indeed when the disease had first appeared, in the accelerating stage the spread pattern was observed to have followed a highly nonlinear pattern that could be said to be approximately exponential or sub-exponential. As to why in the resurgence the growth has become hyper-exponential is another matter. But this has been happening in Europe and how long this would continue cannot be predicted. It may so happen that in the countries in which retardation has already been taking place, there may be resurgence of the disease. It was observed that in the World as a whole, retardation was on the threshold during the second half of September. But if the resurgence happens to follow the hyper-exponential growth pattern in different countries, there may be resurgence in the World as a whole.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Hemanta Kumar Baruah", + "author_inst": "The Assam Royal Global University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.22.20184630", "rel_title": "COVID-19 infections following outdoor mass gatherings in low incidence areas: retrospective cohort study", @@ -1092829,41 +1096888,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.26.20219543", - "rel_title": "Disruptions to schistosomiasis programmes due to COVID-19: an analysis of potential impact and mitigation strategies", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219543", - "rel_abs": "BackgroundThe 2030 goal for schistosomiasis is elimination as a public health problem (EPHP), with mass drug administration (MDA) of praziquantel to school-aged children (SAC) a central pillar of the strategy. However, due to COVID-19, many mass treatment campaigns for schistosomiasis have been halted with uncertain implications for the programmes.\n\nMethodWe use mathematical modelling to explore how postponement of MDA and various mitigation strategies affect achievement of the EPHP goal for Schistosoma mansoni and S. haematobium.\n\nResultsIn moderate and some high prevalence settings, the disruption may delay the goal by up to two years. In some high prevalence settings EPHP is not achievable with current strategies, and so the disruption will not impact this. Here, increasing SAC coverage and treating adults can achieve the goal.\n\nThe impact of MDA disruption and the appropriate mitigation strategy varies according to the baseline prevalence prior to treatment, the burden of infection in adults and stage of the programme.\n\nConclusionsSchistosomiasis MDA programmes in medium and high prevalence areas should restart as soon as is feasible, and mitigation strategies may be required in some settings.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "KLODETA KURA", - "author_inst": "Imperial College London" - }, - { - "author_name": "Diepreye Ayabina", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jaspreet Toor", - "author_inst": "University of Oxford" - }, - { - "author_name": "T. Deirdre Hollingsworth", - "author_inst": "University of Oxford" - }, - { - "author_name": "Roy M Anderson", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.26.20219691", "rel_title": "Implications of the COVID-19 pandemic on eliminating trachoma as a public health problem", @@ -1094786,6 +1098810,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.27.357954", + "rel_title": "Tuning Intrinsic Disorder Predictors for Virus Proteins", + "rel_date": "2020-10-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.27.357954", + "rel_abs": "Many virus-encoded proteins have intrinsically disordered regions that lack a stable folded threedimensional structure. These disordered proteins often play important functional roles in virus replication, such as down-regulating host defense mechanisms. With the widespread availability of next-generation sequencing, the number of new virus genomes with predicted open reading frames is rapidly outpacing our capacity for directly characterizing protein structures through crystallography. Hence, computational methods for structural prediction play an important role. A large number of predictors focus on the problem of classifying residues into ordered and disordered regions, and these methods tend to be validated on a diverse training set of proteins from eukaryotes, prokaryotes and viruses. In this study, we investigate whether some predictors outperform others in the context of virus proteins. We evaluate the prediction accuracy of 21 methods, many of which are only available as web applications, on a curated set of 126 proteins encoded by viruses. Furthermore, we apply a random forest classifier to these predictor outputs. Based on cross-validation experiments, this ensemble approach confers a substantial improvement in accuracy, e.g., a mean 36% gain in Matthews correlation coefficient. Lastly, we apply the random forest predictor to SARS-CoV-2 ORF6, an accessory gene that encodes a short (61 AA) and moderately disordered protein that inhibits the host innate immune response.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Gal Almog", + "author_inst": "Department of Pathology & Laboratory Medicine, Western University, London, Canada" + }, + { + "author_name": "Abayomi Samuel Olabode", + "author_inst": "Department of Pathology & Laboratory Medicine, Western University, London, Canada" + }, + { + "author_name": "Art FY Poon", + "author_inst": "Department of Pathology & Laboratory Medicine, Western University, London, Canada" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.27.357731", "rel_title": "SARS-CoV-2 viroporin triggers the NLRP3 inflammatory pathway", @@ -1095071,37 +1099122,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.10.27.357350", - "rel_title": "Binding Mode of SARS-CoV2 Fusion Peptide to Human Cellular Membrane", - "rel_date": "2020-10-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.27.357350", - "rel_abs": "Infection of human cells by the SARS-CoV2 relies on its binding to a specific receptor and subsequent fusion of the viral and host cell membranes. The fusion peptide (FP), a short peptide segment in the spike protein, plays a central role in the initial penetration of the virus into the host cell membrane, followed by the fusion of the two membranes. Here, we use an array of molecular dynamics (MD) simulations taking advantage of the Highly Mobile Membrane Mimetic (HMMM) model, to investigate the interaction of the SARS-CoV2 FP with a lipid bilayer representing mammalian cellular membranes at an atomic level, and to characterize the membrane-bound form of the peptide. Six independent systems were generated by changing the initial positioning and orientation of the FP with respect to the membrane, and each system was simulated in five independent replicas, each for 300 ns. In 73% of the simulations, the FP reaches a stable, membrane-bound configuration where the peptide deeply penetrated into the membrane. Clustering of the results reveals three major membrane binding modes (binding modes 1-3) where binding mode 1 populates over half of the data points. Taking into account the sequence conservation among the viral FPs and the results of mutagenesis studies establishing the role of specific residues in the helical portion of the FP in membrane association, the significant depth of penetration of the whole peptide, and the dense population of the respective cluster, we propose that the most deeply inserted membrane-bound form (binding mode 1) represents more closely the biologically relevant form. Analysis of FP-lipid interactions shows the involvement of specific residues, previously described as the \"fusion active core residues\", in membrane binding. Taken together, the results shed light on a key step involved in SARS-CoV2 infection with potential implications in designing novel inhibitors.\n\nSignificanceA key step in cellular infection by the SARS-CoV2 virus is its attachment to and penetration into the plasma membrane of human cells. These processes hinge upon the membrane interaction of the viral fusion peptide, a segment exposed by the spike protein upon its conformational changes after encountering the host cell. In this study, using molecular dynamics simulations, we describe how the fusion peptide from the SARS-CoV2 virus binds human cellular membranes and characterize, at an atomic level, lipid-protein interactions important for the stability of its membrane-bound state.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Defne Gorgun", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Muyun Lihan", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Karan Kapoor", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Emad Tajkhorshid", - "author_inst": "University of Illinois at Urbana-Champaign" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.10.27.357426", "rel_title": "A booster dose enhances immunogenicity of the COVID-19 vaccine candidate ChAdOx1 nCoV-19 in aged mice", @@ -1096380,6 +1100400,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.25.354571", + "rel_title": "Comparison of the in vitro-efficacy of different mouthwash solutions targeting SARS-CoV-2 based on the European Standard EN 14476", + "rel_date": "2020-10-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.25.354571", + "rel_abs": "The SARS-Cov-2 pandemic is triggering a global health emergency alert, and recent research is indicating the relevance of aerosols in the spread of SARS-CoV-2. Thus, in this study antiseptic mouthwashes based on the actives chlorhexidine (CHX) and octenidine (OCT) were investigated regarding their efficacy against SARS-CoV-2 using EN 14476. Based on the requirement of EN 14476 (i.e. reduction of viral titer by [≥] 4 log 10), the OCT-based formulation was effective within only 15 sec against SARS-CoV-2, and thus constitutes an interesting candidate for future clinical studies to prove its effectiveness in a potential prevention of SARS-CoV-2 transmission by aerosols.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Katrin Steinhauer", + "author_inst": "Department Research & Scientific Services, Schuelke & Mayr GmbH, Norderstedt, Germany; Faculty of Mechanical Engineering, Kiel University of Applied Sciences, K" + }, + { + "author_name": "Toni Luise Meister", + "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany" + }, + { + "author_name": "Daniel Todt", + "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany; European Virus Bioinformatics Center (EVBC), 07743 Jena, Germany" + }, + { + "author_name": "Adalbert Krawczyk", + "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany; European Virus Bioinformatics Center (EVBC), 07743 Jena, Germany" + }, + { + "author_name": "Lars Passvogel", + "author_inst": "Department Research & Scientific Services, Schuelke & Mayr GmbH, Norderstedt, Germany" + }, + { + "author_name": "Britta Becker", + "author_inst": "Dr. Brill + Partner GmbH Institut for Hygiene and Microbiology, Hamburg, Germany" + }, + { + "author_name": "Dajana Paulmann", + "author_inst": "Dr. Brill + Partner GmbH Institut for Hygiene and Microbiology, Hamburg, Germany" + }, + { + "author_name": "Birte Bischoff", + "author_inst": "Dr. Brill + Partner GmbH Institut for Hygiene and Microbiology, Hamburg, Germany" + }, + { + "author_name": "Stephanie Pfaender", + "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany" + }, + { + "author_name": "Florian Brill", + "author_inst": "Dr. Brill + Partner GmbH Institut for Hygiene and Microbiology, Hamburg, Germany" + }, + { + "author_name": "Eike Steinmann", + "author_inst": "Ruhr University Bochum" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.23.353219", "rel_title": "The papain-like protease of coronaviruses cleaves ULK1 to disrupt host autophagy", @@ -1096513,41 +1100592,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.21.20215418", - "rel_title": "COVID-19 in regions with low prevalence and low density of population. An uncertainty dynamic modeling approach.", - "rel_date": "2020-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20215418", - "rel_abs": "The coronavirus disease 2019 (COVID-19) that emerged in China at the end of 2019 has spread worldwide. In this article, we present a mathematical SEIR model focused on analysing the transmission dynamics of COVID-19, the patients circulating in the hospitals and evaluating the effects of health policies and vaccination on the control of the pandemic. We tested the model using registered cases and population data from the province of Granada (Spain), that represents a population size near 1 million citizens with low density of population and low prevalence. After calibrating the model with the data obtained from 15 March to 22 September 2020, we simulate different vaccination scenarios - including effectiveness and availability date - in order to study the possible evolution of the disease. The results show that: 1) infected will increase until 5.6% - 7.4% of the total population over next 3-4 months (2nd wave); 2) vaccination seems not to be enough to face the pandemic and other strategies should be used; 3) we also support the claim of the WHO about the effectiveness of the vaccine, that should be, at least, of 50% to represent a substantial progress against the COVID-19; 4) after the 2nd wave, the return to normal life should be controlled and gradual to avoid a 3rd wave. The proposed study may be a useful tool for giving insight into the transmission dynamics of SARS-CoV-2 and to design vaccination and health policies.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jos\u00e9 M. Garrido", - "author_inst": "Department of Surgery and Surgical Specialties, University of Granada, Granada, Spain" - }, - { - "author_name": "David Mart\u00ednez-Rodr\u00edguez", - "author_inst": "Instituto Universitario de Matem\u00e1tica Multidisciplinar, Universitat Polit\u00e8cnica de Val\u00e8ncia" - }, - { - "author_name": "Fernando Rodr\u00edguez-Serrano", - "author_inst": "Institute of Biopathology and Regenerative Medicine (IBIMER), University of Granada, Granada, Spain" - }, - { - "author_name": "Javier D\u00edez-Domingo", - "author_inst": "Fundaci\u00f3n para el Fomento de la Investigaci\u00f3n Sanitaria y Biom\u00e9dica de la Comunitat Valenciana (FISABIO), Valencia, Spain" - }, - { - "author_name": "Rafael J. Villanueva", - "author_inst": "Instituto Universitario de Matem\u00e1tica Multidisciplinar, Universitat Polit\u00e8cnica de Val\u00e8ncia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.21.20215434", "rel_title": "SARS-CoV-2 surveillance in untreated wastewater: first detection in a low-resource community in Buenos Aires, Argentina.", @@ -1097722,6 +1101766,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.10.20.20215608", + "rel_title": "Evidence for secondary thrombotic microangiopathy in COVID-19", + "rel_date": "2020-10-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20215608", + "rel_abs": "The causes of coagulopathy associated with COVID-19 disease are poorly understood. We aimed to investigate the relationship between markers of endothelial activation, intravascular hemolysis, coagulation, and organ damage in COVID-19 patients and study their association with disease severity and mortality. We conducted a retrospective study of 181 hospitalized COVID-19 patients randomly selected with equal distribution of survivors and non-survivors. Patients who died had significantly lower ADAMTS13 activity, significantly higher LDH, schistocytes and von Willebrand Factor levels compared to patients discharged alive. Only 30% of patients with an initial ADAMTS13 activity <43% survived vs. 60% with ADAMTS13 [≥]43% who survived. In conclusion, COVID-19 may manifest as a TMA-like illness in a subset of hospitalized patients. Presence of schistocytes on admission may warrant a work-up for TMA. These findings indicate the need for future investigation to study the relationship between endothelial and coagulation activation and the efficacy of TMA treatments in COVID-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Joseph Sweeney", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Mohammad Barouqa", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Gregory J J Krause", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Jesus Gonzalez Lugo", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Shafia Rahman", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Morayma Reyes Gil", + "author_inst": "Montefiore Medical Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2020.10.21.20216192", "rel_title": "Broadly-targeted autoreactivity is common in severe SARS-CoV-2 Infection", @@ -1097939,137 +1102022,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.21.20217208", - "rel_title": "Early use of nitazoxanide in mild Covid-19 disease: randomized, placebo-controlled trial", - "rel_date": "2020-10-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20217208", - "rel_abs": "The antiparasitic drug nitazoxanide is widely available and exerts broad-spectrum antiviral activity in vitro. However, there is no evidence of its impact on SARS-CoV-2 infection.\n\nIn a multicenter, randomized, double-blind, placebo-controlled trial, adult patients who presented up to 3 days after onset of Covid-19 symptoms (dry cough, fever, and/or fatigue) were enrolled. After confirmation of SARS-CoV2 infection by RT-PCR on nasopharyngeal swab, patients were randomized 1:1 to receive either nitazoxanide (500 mg) or placebo, TID, for 5 days. The primary outcome was complete resolution of symptoms. Secondary outcomes were viral load, general laboratory tests, serum biomarkers of inflammation, and hospitalization rate. Adverse events were also assessed.\n\nFrom June 8 to August 20, 2020, 1,575 patients were screened. Of these, 392 (198 placebo, 194 nitazoxanide) were analyzed. Median time from symptom onset to first dose of study drug was 5 (4-5) days. At the 5-day study visit, symptom resolution did not differ between the nitazoxanide and placebo arms. However, at the 1-week follow-up, 78% in the nitazoxanide arm and 57% in the placebo arm reported complete resolution of symptoms (p=0.048). Swabs collected were negative for SARS-CoV-2 in 29.9% of patients in the nitazoxanide arm versus 18.2% in the placebo arm (p=0.009). Viral load was also reduced after nitazoxanide compared to placebo (p=0.006). No serious adverse events were observed.\n\nIn patients with mild Covid-19, symptom resolution did not differ between the nitazoxanide and placebo groups after 5 days of therapy. However, early nitazoxanide therapy was safe and reduced viral load significantly.\n\nTake home messageThis was the first study to evaluate the effect of early nitazoxanide therapy in mild Covid-19. Nitazoxanide did not accelerate symptom resolution after 5 days of therapy; however, reduced viral load significantly with no serious adverse events.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Patricia Rieken Macedo Rocco", - "author_inst": "Federal University of Rio de Janeiro, Rio de Janeiro, Brazil" - }, - { - "author_name": "Pedro Leme Silva", - "author_inst": "Federal University of Rio de Janeiro, Rio de Janeiro, Brazil" - }, - { - "author_name": "Fernanda Ferreira Cruz", - "author_inst": "Federal University of Rio de Janeiro, Rio de Janeiro, Brazil" - }, - { - "author_name": "Marco Antonio C.M. Junior", - "author_inst": "Hospital Municipal de Emergencias Albert Sabin, Sao Caetano, Sao Paulo, Brazil" - }, - { - "author_name": "Paulo Fernando Guimaraes Morando Marzocchi Tierno", - "author_inst": "Hospital Municipal de Barueri Dr Francisco Moran, Barueri, Sao Paulo, Brazil" - }, - { - "author_name": "Marcos de Assis Moura", - "author_inst": "Hospital e Maternidade Therezinha de Jesus, Juiz de Fora, Minas Gerais, Brazil" - }, - { - "author_name": "Luis Frederico Gerbase De Oliveira", - "author_inst": "Hospital Santa Casa de Misericordia de Sorocaba, Sorocaba, Sao Paulo, Brazil" - }, - { - "author_name": "Cristiano Cleidson Lima", - "author_inst": "Secretaria de Estado de Saude do Distrito Federal, Brasilia, Distrito Federal, Brazil" - }, - { - "author_name": "Ezequiel Aparecido Dos Santos", - "author_inst": "Secretaria Municipal de Saude de Bauru, Bauru, Sao Paulo, Brazil" - }, - { - "author_name": "Walter Freitas Junior", - "author_inst": "Secretaria Municipal de Saude de Guarulhos, Guarulhos, Sao Paulo, Brazil" - }, - { - "author_name": "Ana Paula Salles Moura Fernandes", - "author_inst": "Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Kleber Gomes Franchini", - "author_inst": "Brazilian National Biosciences Laboratory (LNBio) and Brazilian Center for Energy and Materials Research (CNPEM), Campinas, Brazil" - }, - { - "author_name": "Erick Magri", - "author_inst": "Hospital Municipal de Emergencias Albert Sabin, Sao Caetano, Sao Paulo, Brazil" - }, - { - "author_name": "Nara Franzin de Moraes", - "author_inst": "Hospital Municipal de Barueri Dr Francisco Moran, Barueri, Sao Paulo, Brazil" - }, - { - "author_name": "Jose Mario de Jesus Goncalves", - "author_inst": "Hospital e Maternidade Therezinha de Jesus, Juiz de Fora, Minas Gerais, Brazil." - }, - { - "author_name": "Melanie Nogueira Carbonieri", - "author_inst": "Hospital Santa Casa de Misericordia de Sorocaba, Sorocaba, Sao Paulo, Brazil" - }, - { - "author_name": "Ivonise Sampaio Dos Santos", - "author_inst": "Secretaria de Estado de Saude do Distrito Federal, Brasilia, Distrito Federal, Brazil" - }, - { - "author_name": "Natalia de Fatima Paes", - "author_inst": "Secretaria Municipal de Saude de Bauru, Bauru, Sao Paulo, Brazil" - }, - { - "author_name": "Paula Veronica Martini Maciel", - "author_inst": "Secretaria Municipal de Saude de Guarulhos, Guarulhos, Sao Paulo, Brazil" - }, - { - "author_name": "Raissa Prado Rocha", - "author_inst": "Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Alex Fiorini de Carvalho", - "author_inst": "Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Pedro Augusto Alves", - "author_inst": "Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Jose Luiz Proenca Modena", - "author_inst": "Brazilian National Biosciences Laboratory (LNBio) and Brazilian Center for Energy and Materials Research (CNPEM), Campinas, Brazil" - }, - { - "author_name": "Artur Torres Cordeiro", - "author_inst": "Brazilian National Biosciences Laboratory (LNBio) and Brazilian Center for Energy and Materials Research (CNPEM), Campinas, Brazil" - }, - { - "author_name": "Daniela Barreto Barbose Trivella", - "author_inst": "Brazilian National Biosciences Laboratory (LNBio) and Brazilian Center for Energy and Materials Research (CNPEM), Campinas, Brazil" - }, - { - "author_name": "Rafael Elias Marques", - "author_inst": "Brazilian National Biosciences Laboratory (LNBio) and Brazilian Center for Energy and Materials Research (CNPEM), Campinas, Brazil" - }, - { - "author_name": "Ronir R Luiz", - "author_inst": "Federal University of Rio de Janeiro, Rio de Janeiro, Brazil" - }, - { - "author_name": "Paolo Pelosi", - "author_inst": "Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Genoa, Italy" - }, - { - "author_name": "Jose Roberto Lapa e Silva", - "author_inst": "Federal University of Rio de Janeiro, Rio de Janeiro, Brazil" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.21.20208728", "rel_title": "Decrease in Hospitalizations for COVID-19 after Mask Mandates in 1083 U.S. Counties", @@ -1099448,6 +1103400,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.10.21.20216960", + "rel_title": "Emergency Response for Evaluating SARS-CoV-2 Immune Status, Seroprevalence and Convalescent Plasma in Argentina", + "rel_date": "2020-10-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216960", + "rel_abs": "We report the emergency development and application of a robust serologic test to evaluate acute and convalescent antibody responses to SARS-CoV-2 in Argentina. The assays, COVIDAR IgG and IgM, which were produced and provided for free to health authorities, private and public health institutions and nursing homes, use a combination of a trimer stabilized spike protein and the receptor binding domain (RBD) in a single enzyme-linked immunosorbent assay (ELISA) plate. Over half million tests have already been distributed to detect and quantify antibodies for multiple purposes, including assessment of immune responses in hospitalized patients and large seroprevalence studies in neighborhoods, slums and health care workers, which resulted in a powerful tool for asymptomatic detection and policy making in the country. Analysis of antibody levels and longitudinal studies of symptomatic and asymptomatic SARS-CoV-2 infections in over one thousand patient samples provided insightful information about IgM and IgG seroconversion time and kinetics, and IgM waning profiles. At least 35% of patients showed seroconversion within 7 days, and 95% within 45 days of symptoms onset, with simultaneous or close sequential IgM and IgG detection. Longitudinal studies of asymptomatic cases showed a wide range of antibody responses with median levels below those observed in symptomatic patients. Regarding convalescent plasma applications, a protocol was standardized for the assessment of end point IgG antibody titers with COVIDAR with more than 500 plasma donors. The protocol showed a positive correlation with neutralizing antibody titers, and was used to assess antibody titers for clinical trials and therapies across the country. Here, we demonstrate the importance of providing a robust and specific serologic assay for generating new information about antibody kinetics in infected individuals and mitigation policies to cope with pandemic needs.\n\nAUTHOR SUMMARYThe development of robust and specific serologic assays to detect antibodies to SARS-CoV-2 is essential to understand the pandemic evolution and to stablish mitigation strategies. Here, we report the emergency development, production and application of a versatile ELISA test for detecting antibodies against the whole spike protein and its receptor binding domain. Over half million tests have been freely distributed in public and private health institutions of Argentina for evaluating immune responses, convalescent plasma programs and for large seroprevalence studies in neighborhoods and health care workers. We are still learning how and when to use serologic testing in different epidemiological settings. This program allowed us to produce large amount of high quality data on antibody levels in symptomatic and asymptomatic SARS-CoV-2 infections and generate relevant information about IgM and IgG seroconversion time and kinetics. We also present standardized protocols for antibody quantification as guidance for convalescent donor plasma selection in hospitals throughout the country for compassionate use and clinical trials. Here, we provide a framework for generating widely available tools, protocols and information of antibody responses for pandemic management.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Diego Ojeda", + "author_inst": "Fundacion Instituto Leloir-CONICET" + }, + { + "author_name": "Maria Mora Gonzalez Lopez Ledesma", + "author_inst": "Fundacion Instituto Leloir CONICET" + }, + { + "author_name": "Horacio Palleres", + "author_inst": "Fundacion Instituto Leloir-CONICET" + }, + { + "author_name": "Guadalupe Costa Navarro", + "author_inst": "Fundacion Instituto Leloir-CONICET" + }, + { + "author_name": "Lautaro Sanchez", + "author_inst": "Fundacion Instituto Leloir CONICET" + }, + { + "author_name": "Beatriz Perazzi", + "author_inst": "Facultad de Farmacia y Bioquimica UBA" + }, + { + "author_name": "Sergio Villordo", + "author_inst": "Fundacion Instituto Leloir" + }, + { + "author_name": "Diego Alvarez", + "author_inst": "Instituto de Investigaciones Biotecnologicas, Universidad Nacional de San Martin" + }, + { + "author_name": "- BioBanco Working Group", + "author_inst": "" + }, + { + "author_name": "Marcela Echavarria", + "author_inst": "Centro de Educacion Medica e Investigaciones Clinicas" + }, + { + "author_name": "Kasopefoluwa Y. Oguntuyo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Christian Stevens", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Benhur Lee", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jorge Carradori", + "author_inst": "Laboratorio Lemos" + }, + { + "author_name": "Julio Caramelo", + "author_inst": "Fundacion Instituto Leloir CONICET" + }, + { + "author_name": "Marcelo Yanovsky", + "author_inst": "Fundacion Instituto Leloir" + }, + { + "author_name": "Andrea Gamarnik", + "author_inst": "FUNDACION INSTITUTO LELOIR" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.21.20216945", "rel_title": "The effect of COVID-19 on critical care research: A prospective longitudinal multinational survey", @@ -1099593,29 +1103628,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.10.20.20216143", - "rel_title": "The incubation period of COVID-19: A scoping review and meta-analysis to aid modelling and planning", - "rel_date": "2020-10-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20216143", - "rel_abs": "BackgroundAn accurate estimate of the distribution of the incubation period for COVID-19 is the foundational building block for modelling the spread of the SARS COV2 and the effectiveness of mitigation strategies on affected communities. Initial estimates were based on early infections, the aim of this study was to provide an updated estimate and meta-analysis of the incubation period distribution for COVID-19.\n\nMethodsThe review was conducted according to the PRISMA Scoping Review guidelines. Five databases were searched; CINAHL, MEDLINE, PUBMED, EMBASE, ASSIA, and Global Index Medicus for studies published between 1 January 2020 - 27 July 2020.\n\nResultsA total of 1,084 articles were identified through the database searches and 1 article was identified through the reference screening of retrieved articles. After screening 64 articles were included. The studies combined had a sample of 45,151 people. The mean of the incubation periods was 6.71 days with 95% CIs ranging from 1 to 12.4 days. The median was 6 days and IQR ranging from 1.8 to 16.3. The resulting parameters for a Gamma Distribution modelling the incubation period were {Gamma}(, {lambda}) = {Gamma}(2.810,0.419) with mean, = /{lambda}.\n\nConclusionGovernments are planning their strategies on a maximum incubation period of 14 days. While our results are limited to primarily Chinese research studies, the findings highlight the variability in the mean period and the potential for further incubation beyond 14 days. There is an ongoing need for detailed surveillance on the timing of self-isolation periods and related measures protecting communities as incubation periods may be longer.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Prakashini Banka", - "author_inst": "Trinity College Dublin" - }, - { - "author_name": "Catherine M Comiskey", - "author_inst": "Trinity College Dublin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.20.20216309", "rel_title": "Diagnostic utility of a Ferritin-to-Procalcitonin Ratio to differentiate patients with COVID-19 from those with Bacterial Pneumonia: A multicenter study", @@ -1101062,6 +1105074,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.19.20213421", + "rel_title": "PREVALENCE OF ANTIBODIES AGAINST SARS-CoV-2 IN PROFESSIONALS OF A PUBLIC HEALTH LABORATORY AT SAO PAULO, SP, BRAZIL", + "rel_date": "2020-10-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.19.20213421", + "rel_abs": "BackgroundCovid-19 Serology may document exposure and perhaps protection to the virus and serological test may help understand epidemic dynamics. We tested health workers form a public laboratory to evaluate previous exposure to the virus and estimate the prevalence of antibodies against-SARS-CoV-2 in Adolfo Lutz Institute, State of Sao Paulo, Brazil.\n\nMethodsThis study was an open, prospective evaluation among professionals of Adolfo Lutz Institute some administrative personnel from the Secretary of Health that shares common areas with the institute. We used a lateral flow immunoassay (rapid test) to detect IgG and IgM for SARS-CoV-2; positive samples were further evaluated using Roche Electrochemiluminescence assay. SARS-CoV-2 RNA by real time reverse transcriptase polymerase chain reaction (RT-PCR) was also offered to participants.\n\nResultsA total of 406 HPs participated. Thirty five (8.6%) tested positive on rapid test and 32 these rapid test seropositive cases were confirmed by ECLIA. 43 HPs had SARS-CoV-2 RNA detected at a median of 33 days, and the three cases not reactive at Roche ECLIA had a previous positive RNA. Outsourced professionals (34% seropositive), males (15%) workers referring COVID-19 patients at home (22%) and those living farther form the institute tended to have higher prevalence of seropositivity, but in multivariable logistic analysis only outsourced workers and those with COVID patients at home remained independently associated to seropositivity. We observed no relation of seropositivity to COVID samples handling. Presence of at least one symptom was common but some clinical manifestations as anosmia/dysgeusia. Fatigue, cough and fever were associated to seropositivity.\n\nConclusionsWe documented a relatively high (8.6%) of anti-SARS-CoV-2 serological reactivity in this population, higher among outsourced workers and those residing with COVID-19 patients. COVID related work did not increased seropositivity. Some symptoms show strong association to COVID-19 serology and may be used in scoring tools for screening or diagnosis in resort limited settings.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Valeria Oliveira Silva", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Elaine Lopes de Oliveira", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Marcia Jorge Castejon", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Rosemeire Yamashiro", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Cintia Mayumi Ahagon", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Giselle Ibette Lopez-Lopes", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Edilene Peres Real da Silveira", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Marisa Ailin Hong", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Maria do Carmo Timenetsky", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Carmem aparecida de Freitas Oliveira", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Luis Fernando de Macedo Brigido", + "author_inst": "Instituto Adolfo Lutz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.20.20212522", "rel_title": "Analytical solution of equivalent SEIR and agent-based model of COVID-19; showing the bounds of contact tracing", @@ -1101158,33 +1105229,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, - { - "rel_doi": "10.1101/2020.10.19.20215517", - "rel_title": "An agent-based model of spread of a pandemic with validation using COVID-19 data from New York State", - "rel_date": "2020-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.19.20215517", - "rel_abs": "We introduce a simple agent based model where each agent carries an effective viral load that captures the instantaneous state of infection of the agent and simulate the spread of a pandemic and subsequently validate it by using publicly available COVID-19 data. Our simulation tracks the temporal evolution of a virtual city or community of agents in terms of contracting infection, recovering asymptomatically, or getting hospitalized. The virtual community is divided into family groups with 2-6 individuals in each group. Agents interact with other agents in virtual public places like at grocery stores, on public transportation and in offices. We initially seed the virtual community with a very small number of infected individuals and then monitor the disease spread and hospitalization over a period of fifty days, which is a typical time-frame for the initial spread of a pandemic. An uninfected or asymptomatic agent is randomly selected from a random family group in each simulation step for visiting a random public space. An uninfected agent contracts infection if the public place is occupied by other infected agents. We have calibrated our simulation rounds according to the size of the population of the virtual community for simulating realistic exposure of agents to a contagion. Our simulation results are consistent with the publicly available hospitalization and ICU patient data from different communities of varying sizes in New York state. Our model can predict the trend in epidemic spread and hospitalization from a set of simple parameters and could be potentially useful in exploring strategies to keep a community safe.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Amitava Datta", - "author_inst": "University of Western Australia" - }, - { - "author_name": "Peter Winkelstein", - "author_inst": "State University of New York, Buffalo" - }, - { - "author_name": "Surajit Sen", - "author_inst": "State University of New York, Buffalo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.10.20.20213272", "rel_title": "Clinical symptoms among ambulatory patients tested for SARS-CoV-2", @@ -1102647,6 +1106691,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.14.20212662", + "rel_title": "Antibody Immunological Imprinting on COVID-19 Patients", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212662", + "rel_abs": "While the current pandemic remains a thread to human health, the polyclonal nature of the antibody response against SARS-CoV-2 is not fully understood. Other than SARS-CoV-2, humans are susceptible to six different coronaviruses, and previous exposure to antigenically related and divergent seasonal coronaviruses is frequent. We longitudinally profiled the early humoral immune response against SARS-CoV-2 on hospitalized COVID-19 patients, and quantify levels of pre-existing immunity to OC43, HKU1 and 223E seasonal coronaviruses. A strong back-boosting effect to conserved, but not variable regions of OC43 and HKU1 betacoronaviruses spike protein was observed. All patients developed antibodies against SARS-CoV-2 spike and nucleoprotein, with peak induction at day 7 post hospitalization. However a negative correlation was found between antibody memory boost to human coronaviruses and induction of IgG and IgM against SARS-CoV-2 spike. Our findings provide evidence of immunological imprinting that determine the antibody profile to COVID-19 patients in an original antigenic sin fashion.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Teresa Aydillo", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York;" + }, + { + "author_name": "Alexander Rombauts", + "author_inst": "Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, LHospitalet de Llo" + }, + { + "author_name": "Daniel Stadlbauer", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Sadaf Aslam", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Gabriela Abelenda-Alonso", + "author_inst": "Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, LHospitalet de Llo" + }, + { + "author_name": "Alba Escalera", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Fatima Amanat", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Kaijun Jiang", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Jordi Carratala", + "author_inst": "Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, LHospitalet de Llo" + }, + { + "author_name": "Adolfo Garcia-Sastre", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.15.20213223", "rel_title": "Prediction of Covid-19 Infections Through December 2020 for 10 US States Incorporating Outdoor Temperature and School Re-Opening Effects-September Update", @@ -1102724,113 +1106827,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.15.20212712", - "rel_title": "A Multiplexed, Next Generation Sequencing Platform for High-Throughput Detection of SARS-CoV-2", - "rel_date": "2020-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.15.20212712", - "rel_abs": "Population scale sweeps of viral pathogens, such as SARS-CoV-2, that incorporate large numbers of asymptomatic or mild symptom patients present unique challenges for public health agencies trying to manage both travel and local spread. Physical distancing is the current major strategy to suppress spread of the disease, but with enormous socio-economic costs. However, modelling and studies in isolated jurisdictions suggest that active population surveillance through systematic molecular diagnostics, combined with contact tracing and focused quarantining can significantly suppress disease spread1-3 and has significantly impacted disease transmission rates, the number of infected people, and prevented saturation of the healthcare system4-7. However, reliable systems allowing for parallel testing of 10-100,000s of patients in larger urban environments have not yet been employed. Here we describe \"COVID-19 screening using Systematic Parallel Analysis of RNA coupled to Sequencing\" (C19-SPAR-Seq), a scalable, multiplexed, readily automated next generation sequencing (NGS) platform8 that is capable of analyzing tens of thousands of COVID-19 patient samples in a single instrument run. To address the strict requirements in clinical diagnostics for control of assay parameters and output, we employed a control-based Precision-Recall and predictive Receiver Operator Characteristics (coPR) analysis to assign run-specific quality control metrics. C19-SPAR-Seq coupled to coPR on a trial cohort of over 600 patients performed with a specificity of 100% and sensitivity of 91% on samples with low viral loads and a sensitivity of > 95% on high viral loads associated with disease onset and peak transmissibility. Our study thus establishes the feasibility of employing C19-SPAR-Seq for the large-scale monitoring of SARS-CoV-2 and other pathogens.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Marie-Ming Aynaud", - "author_inst": "Lunenfeld Tanenbaum Research Institute - Mount Sinai Hospital" - }, - { - "author_name": "J. Javier Hernandez", - "author_inst": "Lunenfeld Tanenbaum Research Institute - Mount Sinai Hospital" - }, - { - "author_name": "Seda Barutcu", - "author_inst": "Lunenfeld Tanenbaum Research Institute - Mount Sinai Hospital" - }, - { - "author_name": "Ulrich Braunschweig", - "author_inst": "Donnelly Centre for Cellular and Biomolecular Research, University of Toronto" - }, - { - "author_name": "Kin Chan", - "author_inst": "Lunenfeld Tanenbaum Research Institute - Mount Sinai Hospital" - }, - { - "author_name": "Joel D Pearson", - "author_inst": "Lunenfeld Tanenbaum Research Institute - Mount Sinai Hospital" - }, - { - "author_name": "Daniel Trcka", - "author_inst": "Lunenfeld Tanenbaum Research Institute - Mount Sinai Hospital" - }, - { - "author_name": "Suzanna L Prosser", - "author_inst": "Lunenfeld Tanenbaum Research Institute - Mount Sinai Hospital" - }, - { - "author_name": "Jaeyoun Kim", - "author_inst": "Lunenfeld Tanenbaum Research Institute - Mount Sinai Hospital" - }, - { - "author_name": "Miriam Barrios-Rodiles", - "author_inst": "Lunenfeld Tanenbaum Research Institute - Mount Sinai Hospital" - }, - { - "author_name": "Mark Jen", - "author_inst": "Lunenfeld Tanenbaum Research Institute - Mount Sinai Hospital" - }, - { - "author_name": "Siyuan Song", - "author_inst": "Donnelly Centre for Cellular and Biomolecular Research, University of Toronto" - }, - { - "author_name": "Jess Shen", - "author_inst": "Lunenfeld Tanenbaum Research Institute - Mount Sinai Hospital" - }, - { - "author_name": "Christine Bruce", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Bryn Hazlett", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Susan Poutanen", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Lilliana Attisano", - "author_inst": "Donnelly Centre for Cellular and Biomolecular Research, University of Toronto" - }, - { - "author_name": "Rod Bremner", - "author_inst": "Lunefeld Tanenbaum Research Institute - Mount Sinai Hospital" - }, - { - "author_name": "Benjamin Blencowe", - "author_inst": "Donnelly Centre for Cellular and Biomolecular Research, University of Toronto" - }, - { - "author_name": "Tony Mazzulli", - "author_inst": "Mount Sinai Hospital" - }, - { - "author_name": "Hong Han", - "author_inst": "Donnelly Centre for Cellular and Biomolecular Research, University of Toronto" - }, - { - "author_name": "Laurence Pelletier", - "author_inst": "Lunenfeld Tanenbaum Research Institute - Mount Sinai Hospital" - }, - { - "author_name": "Jeffrey L Wrana", - "author_inst": "Lunenfeld Tanenbaum Research Institute - Mount Sinai Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.14.20212761", "rel_title": "Characteristics of COVID-19 Clinical Trials in India Based on the Registration Data on CTRI (Clinical Trials Registry- India): a cross-sectional analysis", @@ -1104397,6 +1108393,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.17.20214312", + "rel_title": "Echo chambers as early warning signals of widespread vaccine refusal in social-epidemiological networks", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.17.20214312", + "rel_abs": "Sudden shifts in population health and vaccination rates occur as the dynamics of some epidemiological models go through a critical point; literature shows that this is sometimes foreshadowed by early warning signals (EWS). We investigate different structural measures of a network as candidate EWS of infectious disease outbreaks and changes in popular vaccine sentiment. We construct a multiplex disease model coupling infectious disease spread and social contact dynamics. We find that the number and mean size of echo chambers predict transitions in the infection dynamics, as do opinion-based communities. Graph modularity also gives early warnings, though the clustering coefficient shows no significant pre-outbreak changes. Change point tests applied to the EWS show decreasing efficacy as social norms strengthen. Therefore, many measures of social network connectivity can predict approaching critical changes in vaccine uptake and aggregate health, thereby providing valuable tools for improving public health.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Brendon C Phillips", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Chris Bauch", + "author_inst": "University of Waterloo" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.16.20214049", "rel_title": "Quantifying Asymptomatic Infection and Transmission of COVID-19 in New York City using Observed Cases, Serology and Testing Capacity", @@ -1104534,25 +1108553,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.16.20213892", - "rel_title": "Why do per capita COVID-19 Case Rates Differ Between U.S. States?", - "rel_date": "2020-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.16.20213892", - "rel_abs": "BackgroundThe popular press has explored the differences among U.S. states in rates of COVID-19 cases, mostly focusing on political party differences, and often mentioning that political party differences in health outcomes are confounded by demographic and socio-economic differences between Democratic areas and Republican areas. The purpose of this paper is to present a thorough analysis of these issues.\n\nDesign and MethodsState-specific COVID-19 cases per 100,000 people was the main outcome studied, with explanatory variables from Bureau of Census surveys, including percentages of the state population that were Hispanic, black, below poverty level, had at least a bachelors degree, or were uninsured, along with median age, median income, population density, and degree of urbanization. We also included political party in power as an explanatory variable in multiple linear regression. The units of analysis in this study are the 50 U.S. states.\n\nResultsAll explanatory variables were at least marginally statistically significantly associated with case rate in univariate regression analysis, except for population density and urbanization. All the census characteristics were at least marginally associated with party in power in one factor analysis of variance, except for percentage black. In a forward stepwise procedure in a multivariable model for case rate, percentages of the state population that were Hispanic or black, median age, median income, population density, and (residual) percentage poverty were retained as statistically significant and explained 62% of the variation between states in case rates. In a model with political party in power included, along with any additional variables that notably affected the adjusted association between party in power and case rate, 69% of the variance between states in case rates was explained, and adjusted case rates per 100,000 people were 2155 for states with Democratic governments, 2269 for states with mixed governments, and 2738 for Republican-led states. These estimates are based on data through October 8, 2020.\n\nConclusionsU.S. state-specific demographic and socio-economic variables are strongly associated with the states COVID-19 case rates, so must be considered in analysis of variation in case rates between the states. Adjusting for these factors, states with Democrats as the party in power have lower case rates than Republican-led states.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Lloyd Chambless", - "author_inst": "Retired" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.16.20212753", "rel_title": "Statistical deconvolution for inference of infection time series", @@ -1105947,6 +1109947,113 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.15.20208041", + "rel_title": "Analysis of respiratory and systemic immune responses in COVID-19 reveals mechanisms of disease pathogenesis", + "rel_date": "2020-10-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.15.20208041", + "rel_abs": "Immune responses to respiratory viruses like SARS-CoV-2 originate and function in the lung, yet assessments of human immunity are often limited to blood. Here, we conducted longitudinal, high-dimensional profiling of paired airway and blood samples from patients with severe COVID-19, revealing immune processes in the respiratory tract linked to disease pathogenesis. Survival from severe disease was associated with increased CD4+T cells and decreased monocyte/macrophage frequencies in the airway, but not in blood. Airway T cells and macrophages exhibited tissue-resident phenotypes and activation signatures, including high level expression and secretion of monocyte chemoattractants CCL2 and CCL3 by airway macrophages. By contrast, monocytes in blood expressed the CCL2-receptor CCR2 and aberrant CD163+ and immature phenotypes. Extensive accumulation of CD163+monocyte/macrophages within alveolar spaces in COVID-19 lung autopsies suggested recruitment from circulation. Our findings provide evidence that COVID-19 pathogenesis is driven by respiratory immunity, and rationale for site-specific treatment and prevention strategies.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Peter A. Szabo", + "author_inst": "Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Pranay Dogra", + "author_inst": "Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Joshua I. Gray", + "author_inst": "Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Steven B. Wells", + "author_inst": "Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Thomas J. Connors", + "author_inst": "Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Stuart P. Weisberg", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Izabela Krupska", + "author_inst": "Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Rei Matsumoto", + "author_inst": "Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Maya M.L. Poon", + "author_inst": "Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032 and Medical Scientist Training Program, Columbia Univer" + }, + { + "author_name": "Emma Idzikowski", + "author_inst": "Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Sinead E. Morris", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Pasin Chloe", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Andrew J. Yates", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Amy Ku", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Michael Chait", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Julia M. Davis-Porada", + "author_inst": "Medical Scientist Training Program, Columbia University" + }, + { + "author_name": "Jing Zhou", + "author_inst": "IsoPlexis Corporation, Branford, CT 06405" + }, + { + "author_name": "Matthew Steinle", + "author_inst": "IsoPlexis Corporation, Branford, CT 06405" + }, + { + "author_name": "Sean Mackay", + "author_inst": "IsoPlexis Corporation, Branford, CT 06405" + }, + { + "author_name": "Anjali Saqi", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Matthew R. Baldwin", + "author_inst": "Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Peter A. Sims", + "author_inst": "Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032 and Department of Biochemistry and Molecular Biophysics, Columbia U" + }, + { + "author_name": "Donna L Farber", + "author_inst": "Columbia University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.17.343863", "rel_title": "Development and pre-clinical characterization of two therapeutic equine formulations towards SARS-CoV-2 proteins for the potential treatment of COVID-19", @@ -1106204,49 +1110311,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.10.19.345363", - "rel_title": "SARS-CoV and SARS-CoV-2 are transmitted through the air between ferrets over more than one meter distance", - "rel_date": "2020-10-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.19.345363", - "rel_abs": "SARS-CoV-2 emerged in late 2019 and caused a pandemic, whereas the closely related SARS-CoV was contained rapidly in 2003. Here, a newly developed experimental set-up was used to study transmission of SARS-CoV and SARS-CoV-2 through the air between ferrets over more than a meter distance. Both viruses caused a robust productive respiratory tract infection resulting in transmission of SARS-CoV-2 to two of four indirect recipient ferrets and SARS-CoV to all four. A control pandemic A/H1N1 influenza virus also transmitted efficiently. Serological assays confirmed all virus transmission events. Although the experiments did not discriminate between transmission via small aerosols, large droplets and fomites, these results demonstrate that SARS-CoV and SARS-CoV-2 can remain infectious while travelling through the air. Efficient virus transmission between ferrets is in agreement with frequent SARS-CoV-2 outbreaks in mink farms. Although the evidence for airborne virus transmission between humans under natural conditions is absent or weak for SARS-CoV and SARS-CoV-2, ferrets may represent a sensitive model to study interventions aimed at preventing virus transmission.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jasmin S Kutter", - "author_inst": "Erasmus Medical Center, Rotterdam" - }, - { - "author_name": "Dennis de Meulder", - "author_inst": "Erasmus Medical Center, Rotterdam" - }, - { - "author_name": "Theo M Bestebroer", - "author_inst": "Erasmus Medical Center, Rotterdam" - }, - { - "author_name": "Pascal Lexmond", - "author_inst": "Erasmus Medical Center, Rotterdam" - }, - { - "author_name": "Ard Mulders", - "author_inst": "Erasmus Medical Center, Rotterdam" - }, - { - "author_name": "Ron AM Fouchier", - "author_inst": "Erasmus Medical Center, Rotterdam" - }, - { - "author_name": "Sander Herfst", - "author_inst": "Erasmus Medical Center, Rotterdam" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.10.17.343749", "rel_title": "On Classification and Taxonomy of Coronaviruses (Riboviria, Nidovirales, Coronaviridae) with the special focus on severe acute respiratory syndrome-related coronavirus 2 (SARS-Cov-2)", @@ -1107508,6 +1111572,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.10.14.20212449", + "rel_title": "TREATMENT PROFILES AND CLINICAL OUTCOMES OF COVID-19 PATIENTS AT PRIVATE HOSPITAL IN JAKARTA", + "rel_date": "2020-10-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212449", + "rel_abs": "BackgroundSevere Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a virus that causes COVID-19, which has become a worldwide pandemic. However, until now, there is no vaccine or specific drug to prevent or treat COVID-19.\n\nObjectivesTo find out the effective treatment as an antiviral agent for COVID-19, to determine the correlation between sociodemography with clinical outcomes and duration of treatment, and to determine the relationship between comorbidities with clinical outcomes and duration of treatment for COVID-19 patients.\n\nMethodsA prospective cohort study was conducted in this study. This study included only confirmed COVID-19 patients who were admitted to the hospital during April-May 2020. Convenience sampling was used to select 103 patients, but only 72 patients were suitable for inclusion.\n\nResultsThe survival analysis for COVID-19 patients using the Kaplan Meier method showed that patients receiving Oseltamivir + Hydroxychloroquine had an average survival rate of about 83% after undergoing treatment for about ten days. Gender (p = 0.450) and age (p = 0.226) did not have a significant correlation with the duration of treatment for COVID-19 patients. Gender (p = 0.174) and age (p = 0.065) also did not have a significant correlation with clinical outcome of COVID-19 patients. Comorbidities showed a significant correlation with duration of treatment (p = 0.002) and clinical outcome (p = 0.014) of COVID-19 patients.\n\nConclusionThe most effective antiviral agent in this study based on treatment duration was the combination of Oseltamivir + Hydroxychloroquine. The higher the patients average treatment duration, the lower the average survival rate for COVID-19 patients.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Diana Laila Ramatillah", + "author_inst": "Universitas 17 Agustus 1945 Jakarta" + }, + { + "author_name": "Suri Isnaini", + "author_inst": "Pharmacy Faculty, Universitas 17 Agustus 1945 Jakarta" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.10.20207449", "rel_title": "Recovery of monocyte exhaustion is associated with resolution of lung injury in COVID-19 convalescence.", @@ -1107813,25 +1111900,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.10.14.20212571", - "rel_title": "Novel Machine-Learned Approach for COVID-19 Resource Allocation: A Tool for EvaluatingCommunity Susceptibility", - "rel_date": "2020-10-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212571", - "rel_abs": "Despite worldwide efforts to develop an effective COVID vaccine, it is quite evident that initial supplies will be limited. Therefore, it is important to develop methods that will ensure that the COVID vaccine is allocated to the people who are at major risk until there is a sufficient global supply. Herein, I developed a machine-learning tool that could be applied to assess the risk in communities based on social, medical, and lifestyle risk factors. As a \"proof of concept,\" I modeled COVID risk in the Massachusetts communities using 29 risk factors, including the prevalence of preexisting comorbid conditions like COPD and social factors such as racial composition. Of the 29 factors, 14 were found to be significant (p < 0.1) indicators: poverty, food insecurity, lack of high school education, lack of health insurance coverage, premature mortality, population, population density, recent population growth, Asian percentage, high-occupancy housing, and preexisting prevalence of cancer, COPD, overweightness, and heart attacks. The machine-learning approach finds the 9 highest risk communities in the state of Massachusetts: Lynn, Brockton, Revere, Randolph, Lowell, New Bedford, Everett, Waltham, and Fitchburg. The 5 most at-risk counties are Suffolk, Middlesex, Bristol, Norfolk, and Plymouth. With appropriate data, the tool could evaluate risk in other communities, or even enumerate individual patient susceptibility. A ranking of communities by risk may help policymakers ensure equitable allocation of limited doses of the COVID vaccine.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Neil Kale", - "author_inst": "Massachusetts Academy of Math and Science at Worcester Polytechnic Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.14.20202531", "rel_title": "Analysis of Collective Response Reveals that COVID-19-Related Activities Start From the End of 2019 in Mainland China", @@ -1109366,6 +1113434,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.14.20090985", + "rel_title": "An attempt to optimize human resources allocation based on spatial diversity of COVID-19 cases in Poland", + "rel_date": "2020-10-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20090985", + "rel_abs": "Our task is to examine the relationship between the SARS-CoV-2 arrival and the number of confirmed COVID-19 cases in the first wave (period from March 4 to May 22, 2020 (unofficial data)), and socio-economic variables at the powiat (county) level (NUTS-4) using simple statistical techniques such as data visualization, correlation analysis, spatial clustering and multiple linear regression. We showed that immigration and the logarithm of general mobility is the best predictor of SARS-CoV-2 arrival times, while emigration, industrialization and air quality explain the most of the size of the epidemic in poviats. On the other hand, infection dynamics is driven to a lesser extent by previously postulated variables such as population size and density, income or the size of the elderly population. Our analyses could support Polish authorities in preparation for the second wave of infections and optimal management of resources as we have provided a proposition of optimal distribution of human resources between poviats.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Andrzej Jarynowski", + "author_inst": "Institute for Interdisciplinary Research" + }, + { + "author_name": "Monika Wojta-Kempa", + "author_inst": "Wroclaw Medical Universtity" + }, + { + "author_name": "Lukasz Krzowski", + "author_inst": "Military University of Technology in Warsaw" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.13.20211284", "rel_title": "Stay-at-home policy: is it a case of exception fallacy? An internet-based ecological study", @@ -1109487,53 +1113582,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.13.20212258", - "rel_title": "Development of a deep learning classifier to accurately distinguish COVID-19 from look-a-like pathology on lung ultrasound", - "rel_date": "2020-10-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20212258", - "rel_abs": "ObjectivesLung ultrasound (LUS) is a portable, low cost respiratory imaging tool but is challenged by user dependence and lack of diagnostic specificity. It is unknown whether the advantages of LUS implementation could be paired with deep learning techniques to match or exceed human-level, diagnostic specificity among similar appearing, pathological LUS images.\n\nDesignA convolutional neural network was trained on LUS images with B lines of different etiologies. CNN diagnostic performance, as validated using a 10% data holdback set was compared to surveyed LUS-competent physicians.\n\nSettingTwo tertiary Canadian hospitals.\n\nParticipants600 LUS videos (121,381 frames) of B lines from 243 distinct patients with either 1) COVID-19, Non-COVID acute respiratory distress syndrome (NCOVID) and 3) Hydrostatic pulmonary edema (HPE).\n\nResultsThe trained CNN performance on the independent dataset showed an ability to discriminate between COVID (AUC 1.0), NCOVID (AUC 0.934) and HPE (AUC 1.0) pathologies. This was significantly better than physician ability (AUCs of 0.697, 0.704, 0.967 for the COVID, NCOVID and HPE classes, respectively), p < 0.01.\n\nConclusionsA deep learning model can distinguish similar appearing LUS pathology, including COVID-19, that cannot be distinguished by humans. The performance gap between humans and the model suggests that subvisible biomarkers within ultrasound images could exist and multi-center research is merited.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Robert Arntfield", - "author_inst": "Western University" - }, - { - "author_name": "Blake VanBerlo", - "author_inst": "Western University" - }, - { - "author_name": "Thamer Alaifan", - "author_inst": "Western University" - }, - { - "author_name": "Nathan Phelps", - "author_inst": "Western University" - }, - { - "author_name": "Matthew White", - "author_inst": "Western University" - }, - { - "author_name": "Rushil Chaudhary", - "author_inst": "Western University" - }, - { - "author_name": "Jordan Ho", - "author_inst": "Western University" - }, - { - "author_name": "Derek Wu", - "author_inst": "Western University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.10.14.20212704", "rel_title": "Physical Activity Decreases the Prevalence of COVID-19-associated Hospitalization: Brazil EXTRA Study", @@ -1110900,6 +1114948,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.10.11.20211045", + "rel_title": "Understanding the Los Angeles County Coronavirus Epidemic: The Critical Role of Intrahousehold Transmission", + "rel_date": "2020-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.11.20211045", + "rel_abs": "We tracked the course of the COVID-19 epidemic among the approximately 300 communities comprising Los Angeles County. The epidemic, we found, had three distinct phases. During Phase I, from early March through about April 4, initial seeding of infection in relatively affluent areas was followed by radial geographic extension to adjoining communities. During Phase II, lasting until about July 11, COVID-19 cases continued to rise at a slower rate, and became increasingly concentrated in four geographic foci of infection across the county. Those communities with larger reductions in social mobility during April - as measured by the proportion of smartphones staying at home and number of smartphones visiting a gym - reported fewer COVID-19 cases in May. During Phase III, COVID-19 incidence only gradually declined, remaining as high as the incidence seen at the end of Phase I. Across communities, the prevalence of households at high risk for intergenerational transmission was strongly correlated with the persistence of continued COVID-19 propagation. This association was even stronger in those communities with a higher rate of gym attendance in Phase II. The map of the prevalence of at-risk households in Los Angeles County coincided strikingly with the map of cumulative COVID-19 incidence. These findings, taken together, support the critical role of household structure in the persistent propagation of COVID-19 infections in Los Angeles County. Public health policy needs to be reoriented from a focus on protecting the individual to a focus on protecting the household.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Jeffrey E Harris", + "author_inst": "Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.12.20211094", "rel_title": "Prioritisation of population groups with the most interactions for COVID-19 vaccination can substantially reduce total fatalities", @@ -1111001,33 +1115068,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.12.20211532", - "rel_title": "Early Crowdfunding Response to the COVID-19 Pandemic", - "rel_date": "2020-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.12.20211532", - "rel_abs": "BackgroundAs the number of COVID-19 cases increased precipitously in the US, policymakers and health officials marshalled their pandemic responses. As the economic impacts multiplied, anecdotal reports noted the increased use of online crowdfunding to defray these costs. We examined the online crowdfunding response in the early stage of the COVID-19 pandemic in the US.\n\nMethodsOn May 16, 2020, we extracted all available data available on US campaigns created between January 1 and May 10, 2020 on GoFundMe and identified the subset of COVID-related campaigns using keywords relevant to the COVID-19 pandemic. We explored incidence of COVID-related campaigns by geography, by category, and over time and compared campaign characteristics to non-COVID-related campaigns after March 11 when the pandemic was declared.\n\nResultsWe found that there was a substantial increase in overall GoFundMe online crowdfunding campaigns in March, largely attributable to COVID-related campaigns. However, as the COVID-19 pandemic persisted and progressed, the number of campaigns per COVID-19 cases declined more than tenfold across all states. COVID-related campaigns raised more money, had a longer narrative description, and were more likely to be shared on Facebook than other campaigns in the study period.\n\nConclusionsOnline crowdfunding appears to be a transient stopgap, predicated on the novelty of an emergency rather than the true sustained need of a community. Rather, crowdfunding activity is likely an early marker for communities in acute distress that could be used by governments and aid organizations to guide disaster relief and policy.\n\nTrial registrationN/A", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Sameh Nagui Saleh", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Christoph U. Lehmann", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Richard J. Medford", - "author_inst": "University of Texas Southwestern Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.10.12.20211656", "rel_title": "News Coverage and Drug Shortages during the COVID-19 Pandemic", @@ -1112514,6 +1116554,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.12.20211557", + "rel_title": "Nonspecific blood tests as proxies for COVID-19 hospitalization: are there plausible associations after excluding noisy predictors?", + "rel_date": "2020-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.12.20211557", + "rel_abs": "This study applied causal criteria in directed acyclic graphs for handling covariates in associations for prognosis of severe COVID-19 (Corona virus disease 19) cases. To identify nonspecific blood tests and risk factors as predictors of hospitalization due to COVID-19, one has to exclude noisy predictors by comparing the concordance statistics (AUC) for positive and negative cases of SARS-CoV-2 (acute respiratory syndrome coronavirus 2). Predictors with significant AUC at negative stratum should be either controlled for their confounders or eliminated (when confounders are unavailable). Models were classified according to the difference of AUC between strata. The framework was applied to an open database with 5644 patients from Hospital Israelita Albert Einstein in Brazil with SARS-CoV-2 RT-PCR (Reverse Transcription - Polymerase Chain Reaction) exam. C-reactive Protein (CRP) was a noisy predictor: hospitalization could have happen due to causes other than COVID-19 even when SARS-CoV-2 RT-PCR is positive and CRP is reactive, as most cases are asymptomatic to mild. Candidates of characteristic response from moderate to severe inflammation of COVID-19 were: combinations of eosinophils, monocytes and neutrophils, with age as risk factor; and creatinine, as risk factor, sharpens the odds ratio of the model with monocytes, neutrophils, and age.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Gerson Ishikawa", + "author_inst": "Universidade Tecnologica Federal do Parana" + }, + { + "author_name": "Graziela Argenti", + "author_inst": "Universidade Estadual de Ponta Grossa" + }, + { + "author_name": "Cristina Berger Fadel", + "author_inst": "Universidade Estadual de Ponta Grossa" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.13.20212118", "rel_title": "Does autism protect against COVID quarantine effects?", @@ -1112751,85 +1116818,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.13.20212035", - "rel_title": "Virus detection and identification in minutes using single-particle imaging and deep learning", - "rel_date": "2020-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20212035", - "rel_abs": "The increasing frequency and magnitude of viral outbreaks in recent decades, epitomized by the current COVID-19 pandemic, has resulted in an urgent need for rapid and sensitive diagnostic methods. Here, we present a methodology for virus detection and identification that uses a convolutional neural network to distinguish between microscopy images of single intact particles of different viruses. Our assay achieves labeling, imaging and virus identification in less than five minutes and does not require any lysis, purification or amplification steps. The trained neural network was able to differentiate SARS-CoV-2 from negative clinical samples, as well as from other common respiratory pathogens such as influenza and seasonal human coronaviruses. Additionally, we were able to differentiate closely related strains of influenza, as well as SARS-CoV-2 variants. Single-particle imaging combined with deep learning therefore offers a promising alternative to traditional viral diagnostic and genomic sequencing methods, and has the potential for significant impact.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Nicolas Shiaelis", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alexander Tometzki", - "author_inst": "University of Oxford" - }, - { - "author_name": "Leon Peto", - "author_inst": "University of Oxford" - }, - { - "author_name": "Andrew McMahon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Christof Hepp", - "author_inst": "University of Oxford" - }, - { - "author_name": "Erica Bickerton", - "author_inst": "The Pirbright Institute" - }, - { - "author_name": "Cyril Favard", - "author_inst": "IRIM-CNRS UMR9004" - }, - { - "author_name": "Delphine Muriaux", - "author_inst": "University of Montpellier" - }, - { - "author_name": "Monique Andersson", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Sarah Oakley", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Alison Vaughan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Philippa C Matthews", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nicole Stoesser", - "author_inst": "University of Oxford" - }, - { - "author_name": "Derrick Crook", - "author_inst": "NIHR Oxford Biomedical Research Centre" - }, - { - "author_name": "Achillefs N Kapanidis", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nicole C Robb", - "author_inst": "University ofWarwick" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.13.20210013", "rel_title": "Frequent testing regimen based on salivary samples for an effective COVID-19 containment strategy", @@ -1114244,6 +1118232,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.10.09.20210039", + "rel_title": "EVALUATION OF ELEVEN IMMUNOCHROMATOGRAPHIC ASSAYS FOR SARS-CoV-2 DETECTION: INVESTIGATING DENGUE CROSS-REACTION", + "rel_date": "2020-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20210039", + "rel_abs": "BackgroundCOVID-19 disease (Coronavirus disease 2019) caused by SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) is widespread worldwide, affecting more than 11 million people globally (July 6th, 2020). Diagnostic techniques have been studied in order to contain the pandemic. Immunochromatographic (IC) assays are feasible and low cost alternative for monitoring the spread of COVID-19 in the population.\n\nMethodsHere we evaluate the sensitivity and specificity of eleven different immunochromatographic tests in 98 serum samples from confirmed cases of COVID-19 through RT-PCR and 100 negative serum samples from blood donors collected in February 2019. Considering the endemic situation of Dengue in Brazil, we also evaluated the cross-reactivity with Dengue using 20 serum samples from patients with confirmed diagnosis for Dengue collected in early 2019 through four different tests.\n\nResultsOur results demonstrated agreement between immunochromatographic assays and RT-PCR, especially after 10 days since the onset of symptoms. The evaluation of IgG and IgM antibodies combined demonstrated a strong level of agreement (0.85) of IC assays and RT-PCR. It was observed cross-reactivity between Dengue and COVID-19 using four different IC assays for COVID-19 diagnosis. The specificity of IC assays to detected COVID-19 IgM antibodies using Dengue serum samples varied from 80% to 85%; the specificity of IgG detection was 100% and total antibody was 95%.\n\nConclusionsWe found high sensitivity, specificity and good agreement of IC assays, especially after 10 days onset of symptoms. However, we detected cross-reactivity between Dengue and COVID-19 mainly with IgM antibodies demonstrating the need for better studies about diagnostic techniques for these diseases.\n\nHighlightsO_LIImmunochromatographic assays demonstrated high sensitivity and specificity and good agreement with the gold-standard RT-PCR;\nC_LIO_LIIncrease in sensitivity and specificity of assays using samples collected after the 10th day of symptoms;\nC_LIO_LICross-reaction with Dengue serology in evaluation of IgM.\nC_LI", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Beatriz Araujo Oliveira", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Lea Campos de Oliveira", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Franciane Mendes de Oliveira", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Geovana Maria Pereira", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Regina Maia de Souza", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Erika Regina Manuli", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Fabricio Klerynton Marchini", + "author_inst": "Instituto Carlos Chagas, Fiocruz" + }, + { + "author_name": "Evelyn Patr\u00edcia Sanchez Espinoza", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Marcelo Park", + "author_inst": "Hospital das Cl\u00ednicas" + }, + { + "author_name": "Leandro Taniguchi", + "author_inst": "Hospital das Cl\u00ednicas" + }, + { + "author_name": "Pedro Vitale Mendes", + "author_inst": "Hospital das Cl\u00ednicas" + }, + { + "author_name": "Lucas Augusto Moyses Franco", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Ana Catharina Nastri", + "author_inst": "Hospital das Cl\u00ednicas" + }, + { + "author_name": "Maura Salaroli de Oliveira", + "author_inst": "Hospital das Cl\u00ednicas" + }, + { + "author_name": "Jos\u00e9 Mauro Vieira Junior", + "author_inst": "Hospital S\u00edrio Liban\u00eas" + }, + { + "author_name": "Esper Georges Kallas", + "author_inst": "Faculdade de Medicina da Universidade de S\u00e3o Paulo" + }, + { + "author_name": "Anna Sara Levin", + "author_inst": "Faculdade de Medicina da Universidade de S\u00e3o Paulo" + }, + { + "author_name": "Ester Cerdeira Sabino", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Silvia Figueiredo Costa", + "author_inst": "Instituto de Medicina Tropical" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.08.20209544", "rel_title": "What Specimen Urologists Should Be Most Concerned About ? A Systematic Review and Meta-Analysis", @@ -1114345,65 +1118424,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.10.20210096", - "rel_title": "Extracorporeal Blood Purification in moderate and severe COVID-19 patients: a prospective cohort study", - "rel_date": "2020-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.10.20210096", - "rel_abs": "IntroductionCOVID-19 is characterised by hyperinflammation and coagulopathy. Severe cases often develop respiratory distress, requiring mechanical ventilation and critical cases progressing to ARDS. Control of hyperinflammation has been proposed as a possible therapeutic avenue for COVID-19; extracorporeal blood purification (EBP) modalities offer an attractive mean to ameliorate maladaptive inflammation.\n\nWith this work, we describe the longitudinal variation of parameters of systemic inflammation in critically ill COVID-19 patients treated with blood purification using AN69ST (oXiris(R)) hemodiafilter.\n\nMethodsWe performed a time-series analysis of 44 consecutive COVID-19 cases treated with the AN69ST (oXiris(R)) cytokine adsorbing hemodiafilter; we visualise longitudinal results of biochemical, inflammatory, blood gas- and vital sign parameters.\n\nResultsBlood purification was indicated for suspected hyperinflammation or hypercoagulation, (= CRP [≥] 100 mg/L and/or IL-6 [≥] 40 pg/mL and/or Ferritin [≥] 500 ng/mL and/or Lactate Dehydrogenase > 365 U/L or D-dimers > 2000 ng/mL). All patients were treated with [≥] 1 cycle extracorporeal continuous venovenous hemofiltration (CVVHF) with cytokine adsorbing hemodiafilter (CAH); of these, 30 severe patients received CVVHF-CAH within 4 - 12 hours of hospitalisation. Another 14 patients admitted with mild-to-moderate symptoms progressed to severe disease and placed on EBP during the course of hospitalisation. The treatment was associated with a reduction of Ferritin, C-reactive protein, Fibrinogen, several inflammatory markers and a resolution of numerous cytopenias. The observed mortality across the cohort was 36.3% across the cohort.\n\nConclusionExtracorporeal blood purification with cytokine adsorbing hemofilter was associated with a decrease in the acute phase proteins CRP, Ferritin, and resolution of numerous cytopenias. Repetitive hemofiltration has been associated with lower levels of IL-6 in COVID-19 patients.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Rodney Rosalia", - "author_inst": "Zan Mitrev Clinic" - }, - { - "author_name": "Petar Ugurov", - "author_inst": "Zan Mitrev Clinic" - }, - { - "author_name": "Dashurie Neziri", - "author_inst": "Zan Mitrev Clinic" - }, - { - "author_name": "Simona Despotovska", - "author_inst": "Zan Mitrev Clinic" - }, - { - "author_name": "Lidija Veljanovska-Kiridjievska", - "author_inst": "Zan Mitrev Clinic" - }, - { - "author_name": "Emilija Kostoska", - "author_inst": "Zan Mitrev Clinic" - }, - { - "author_name": "Dimche Kuzmanov", - "author_inst": "Zan Mitrev Clinic" - }, - { - "author_name": "Aleksandar Trifunovski", - "author_inst": "Distantpoint" - }, - { - "author_name": "Gianluca Villa", - "author_inst": "University of Florence" - }, - { - "author_name": "Dijana Popevski", - "author_inst": "Zan Mitrev Clinic" - }, - { - "author_name": "Zan Mitrev", - "author_inst": "Zan Mitrev Clinic" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.09.20210054", "rel_title": "Maternal health care services utilization in the amid of COVID-19 pandemic in West Shoa Zone, Central Ethiopia", @@ -1116369,6 +1120389,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.08.20204750", + "rel_title": "Estimating the effect of social inequalities in the mitigation of COVID-19 across communities in Santiago de Chile", + "rel_date": "2020-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20204750", + "rel_abs": "We study the spatio-temporal spread of SARS-CoV-2 in Santiago de Chile using anonymized mobile phone data from 1.4 million users, 22% of the whole population in the area, characterizing the effects of non-pharmaceutical interventions (NPIs) on the epidemic dynamics. We integrate these data into a mechanistic epidemic model calibrated on surveillance data. As of August 1st 2020, we estimate a detection rate of 102 cases per 1,000 infections (90% CI: [95 - 112 per 1,000]). We show that the introduction of a full lockdown on May 15th, 2020, while causing a modest additional decrease in mobility and contacts with respect to previous NPIs, was decisive in bringing the epidemic under control, highlighting the importance of a timely governmental response to COVID-19 outbreaks. We find that the impact of NPIs on individuals mobility correlates with the Human Development Index of comunas in the city. Indeed, more developed and wealthier areas became more isolated after government interventions and experienced a significantly lower burden of the pandemic. The hetero-geneity of COVID-19 impact raises important issues in the implementation of NPIs and highlights the challenges that communities affected by systemic health and social inequalities face adapting their behaviors during an epidemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nicol\u00f2 Gozzi", + "author_inst": "Networks and Urban Systems Centre, University of Greenwich, London, UK" + }, + { + "author_name": "Michele Tizzoni", + "author_inst": "ISI Foundation, Turin, Italy" + }, + { + "author_name": "Matteo Chinazzi", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Leo Ferres", + "author_inst": "Data Science Institute, Universidad del Desarrollo, Santiago, Chile" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Nicola Perra", + "author_inst": "Networks and Urban Systems Centre, University of Greenwich, London, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.08.20209437", "rel_title": "Estimating the Burden of COVID-19 Symptoms Among Participants at the 2020 USA Curling Club Nationals Tournament", @@ -1116506,49 +1120565,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.08.20209684", - "rel_title": "Examining Unit Costs for COVID-19 Case Management in Kenya", - "rel_date": "2020-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20209684", - "rel_abs": "IntroductionCase management for COVID-19 patients is one of key interventions in country responses to the pandemic. Countries need information on the costs of case management to inform resource mobilization, planning and budgeting, purchasing arrangements, and assessments of the cost-effectiveness of interventions. We estimated unit costs for COVID-19 case management for patients with asymptomatic, mild to moderate, severe, and critical COVID-19 disease in Kenya.\n\nMethodsWe estimated per patient per day unit costs of COVID-19 case management for patients that are asymptomatic and those that have mild to moderate, severe, and critical symptoms. For asymptomatic and mild to moderate patients, we estimated unit costs for home-based care and institutional (hospitals and isolation centers). We used an ingredients approach, adopted a health system perspective and patient episode of care as our time horizon. We obtained data on inputs and their quantities from COVID-19 case management guidelines, home based care guidelines, and human resource guidelines, and augmented this with data provided by three public covid-19 treatment hospitals in Kenya. We obtained input prices for services from a recent costing survey of 20 hospitals in Kenya and for pharmaceuticals, non-pharmaceuticals, devices and equipment from market price databases for Kenya.\n\nResultsPer day per patient unit cost for asymptomatic patients and patients with mild to moderate COVID-19 disease under home based care are KES 1,993.01 (USD 18.89) and 1995.17 (USD 18.991) respectively. When these patients are managed in an isolation center of hospital, the same unit costs for asymptomatic patients and patients with mild to moderate disease are 7,415.28 (USD 70.29) and 7,417.44 (USD 70.31) respectively. Per day unit costs for patients with severe COVID-19 disease managed in general hospital wards and those with critical COVID-19 disease admitted in intensive care units are 12,570.75 (USD 119.16) and 59,369.42 (USD 562.79).\n\nConclusionCOVID-19 case management costs are substantial. Unit costs for asymptomatic and mild to moderate COVID-19 patients in home-based care is 4-fold lower compared institutional care of the same patients. Kenya will not only need to mobilize substantial resources to finance COVID-19 case management but also explore additional service delivery adaptations that will reduce unit costs.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Edwine Barasa", - "author_inst": "Health Economics Research Unit (HERU), KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya" - }, - { - "author_name": "Angela Kairu", - "author_inst": "Health Economics Research Unit (HERU), KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya" - }, - { - "author_name": "Wangari Nganga", - "author_inst": "Presidential Policy & Strategy Unit, Executive Office of the President, Nairobi, Kenya" - }, - { - "author_name": "Marybeth Maritim", - "author_inst": "College of Health Sciences, University of Nairobi, Kenya" - }, - { - "author_name": "Vincent Were", - "author_inst": "Health Economics Research Unit (HERU), KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya" - }, - { - "author_name": "Samuel Akech", - "author_inst": "Health Services Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya" - }, - { - "author_name": "Mercy Mwangangi", - "author_inst": "Ministry of Health, Kenya" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.10.08.20207969", "rel_title": "Mitigating the impact of COVID-19 on tuberculosis and HIV services: a cross-sectional survey of 669 health professionals in 64 low and middle-income countries", @@ -1117982,6 +1121998,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.10.20203034", + "rel_title": "Clarifying predictions for COVID-19 from testing data: the example of New-York State", + "rel_date": "2020-10-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.10.20203034", + "rel_abs": "In this article, we use testing data as an input of a new epidemic model. We get nice a concordance between the best fit the model to the reported cases data for New-York state. We also get a good concordance of the testing dynamic and the epidemics dynamic in the cumulative cases. Finally, we can investigate the effect of multiplying the number of tests by 2, 5, 10, and 100 to investigate the consequences on the reduction of the number of reported cases.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Pierre Griette", + "author_inst": "University of Bordeaux" + }, + { + "author_name": "Pierre Magal", + "author_inst": "University of Bordeaux" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.07.20208744", "rel_title": "One size fits all?: Modeling face-mask fit on population-based faces", @@ -1118087,93 +1122126,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2020.10.08.20209593", - "rel_title": "COVID-19 Susceptibility and Severity Risks in a Survey of Over 500,000 People", - "rel_date": "2020-10-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20209593", - "rel_abs": "BackgroundThe enormous toll of the COVID-19 pandemic has heightened the urgency of collecting and analyzing population-scale datasets in real time to monitor and better understand the evolving pandemic.\n\nMethodsThe AncestryDNA COVID-19 Study collected self-reported survey data on symptoms, outcomes, risk factors, and exposures for over 563,000 adult individuals in the U.S. in just under four months, including over 4,700 COVID-19 cases as measured by a self-reported positive test.\n\nResultsWe replicated previously reported associations between several risk factors and COVID-19 susceptibility and severity outcomes, and additionally found that differences in known exposures accounted for many of the susceptibility associations. A notable exception was elevated susceptibility for males even after adjusting for known exposures and age (adjusted odds ratio [aOR]=1.36, 95% confidence interval [CI] = (1.19, 1.55)). We also demonstrated that self-reported data can be used to build accurate risk models to predict individualized COVID-19 susceptibility (area under the curve [AUC]=0.84) and severity outcomes including hospitalization and critical illness (AUC=0.87 and 0.90, respectively). The risk models achieved robust discriminative performance across different age, sex, and genetic ancestry groups within the study.\n\nConclusionThe results highlight the value of self-reported epidemiological data to rapidly provide public health insights into the evolving COVID-19 pandemic.\n\nTHUMBNAILO_ST_ABSWhat is already known on this subjectC_ST_ABSO_LIThe COVID-19 pandemic has exacted a historic toll on human lives, healthcare systems and global economies, with over 83 million cases and over 1.8 million deaths worldwide as of January 2021.\nC_LIO_LICOVID-19 risk factors for susceptibility and severity have been extensively investigated by clinical and public health researchers.\nC_LIO_LISeveral groups have developed risk models to predict COVID-19 illness outcomes based on known risk factors.\nC_LI\n\nWhat this study addsO_LIWe performed association analyses for COVID-19 susceptibility and severity in a large, at-home survey and replicated much of the previous clinical literature.\nC_LIO_LIAssociations were further adjusted for known COVID-19 exposures, and we observed elevated positive test odds for males even after adjustment for these known exposures.\nC_LIO_LIWe developed risk models and evaluated them across different age, sex, and genetic ancestry cohorts, and showed robust performance across all cohorts in a holdout dataset.\nC_LIO_LIOur results establish large-scale, self-reported surveys as a potential framework for investigating and monitoring rapidly evolving pandemics.\nC_LI", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Spencer C Knight", - "author_inst": "AncestryDNA, 153 Townsend St, Suite 800, San Francisco, CA, 94107" - }, - { - "author_name": "Shannon R McCurdy", - "author_inst": "AncestryDNA, 153 Townsend St, Suite 800, San Francisco, CA, 94107" - }, - { - "author_name": "Brooke Rhead", - "author_inst": "AncestryDNA, 153 Townsend St, Suite 800, San Francisco, CA, 94107" - }, - { - "author_name": "Marie V Coignet", - "author_inst": "AncestryDNA, 153 Townsend St, Suite 800, San Francisco, CA, 94107" - }, - { - "author_name": "Danny S Park", - "author_inst": "AncestryDNA, 153 Townsend St, Suite 800, San Francisco, CA, 94107" - }, - { - "author_name": "Genevieve H L Roberts", - "author_inst": "AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043" - }, - { - "author_name": "Nathan D Berkowitz", - "author_inst": "AncestryDNA, 153 Townsend St, Suite 800, San Francisco, CA, 94107" - }, - { - "author_name": "Miao Zhang", - "author_inst": "AncestryDNA, 153 Townsend St, Suite 800, San Francisco, CA, 94107" - }, - { - "author_name": "David Turissini", - "author_inst": "AncestryDNA, 153 Townsend St, Suite 800, San Francisco, CA, 94107" - }, - { - "author_name": "Karen Delgado", - "author_inst": "AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043" - }, - { - "author_name": "Milos Pavlovic", - "author_inst": "AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043" - }, - { - "author_name": "AncestryDNA Science Team", - "author_inst": "AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043" - }, - { - "author_name": "Asher K Haug Baltzell", - "author_inst": "AncestryDNA, 1300 West Traverse Parkway, Lehi, UT 84043" - }, - { - "author_name": "Harendra Guturu", - "author_inst": "AncestryDNA, 153 Townsend St, Suite 800, San Francisco, CA, 94107" - }, - { - "author_name": "Kristin A Rand", - "author_inst": "AncestryDNA, 153 Townsend St, Suite 800, San Francisco, CA, 94107" - }, - { - "author_name": "Ahna R Girshick", - "author_inst": "AncestryDNA, 153 Townsend St, Suite 800, San Francisco, CA, 94107" - }, - { - "author_name": "Eurie L Hong", - "author_inst": "AncestryDNA, 153 Townsend St, Suite 800, San Francisco, CA, 94107" - }, - { - "author_name": "Catherine A Ball", - "author_inst": "AncestryDNA, 153 Townsend St, Suite 800, San Francisco, CA, 94107" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.10.09.20210393", "rel_title": "Physical health complaints among healthcare workers engaged in the care of critically ill COVID-19 patients: A single tertiary-care center prospective study from Japan", @@ -1119728,6 +1123680,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.10.20210328", + "rel_title": "SARS-CoV-2 infections in Italian schools: preliminary findings after one month of school opening during the second wave of the pandemic", + "rel_date": "2020-10-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.10.20210328", + "rel_abs": "IntroductionThe impact of school opening on the SARS-CoV-2 pandemic is still unknown. This study aims to provide preliminary information about the number of SARS-CoV-2 cases among students attending Italian schools.\n\nMethodsData are extracted and analysed from an open access, online dataset that monitor, on a daily basis, media news about SARS-CoV-2 infections of students attending Italian schools\n\nResultsAs of 5 October 2020, a total of 1350 cases of SARS-CoV-2 infections have been registered in the Italian territory schools (involving 1059 students, 145 teachers and 146 other school members), for a total of 1212 out of 65104 (1.8%) Italian schools involved. National schools reported only 1 case of SARS-CoV-2 infection in more than 90% of cases, and only in one high school a cluster of more than 10 cases have been described (P 0.015). The detection of one or more SARS-CoV-2 infections leaded to the closure of 192 (14.2%) entire schools, more frequently nursery/kindergartens (P<0.0005).\n\nDiscussionOur preliminary data support low transmission of SARS-CoV-2 within schools, at least among younger students. However, entire schools are frequently closed in the fear of larger outbreaks. Continuous monitoring of school settings, hopefully through daily updated open access datasets, are needed to better understand the impact of schools on the pandemic, and provide guidelines that better consider different risks within different age groups.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Danilo Buonsenso", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Cristina De Rose", + "author_inst": "Fondazione Universitaria Policlinico Gemelli, IRCSS, Rome, Italy" + }, + { + "author_name": "Rosanna Moroni", + "author_inst": "Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Piero Valentini", + "author_inst": "Fondazione Universitaria Policlinico A. Gemelli, IRCSS, Rome, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.10.07.20208389", "rel_title": "A Comparative COVID 19 Characterizations and Clinical Course Analysis between ICU and Non ICU Settings", @@ -1119877,77 +1123860,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2020.10.06.20205369", - "rel_title": "Extended laboratory panel testing in the Emergency Department for risk-stratification of patients with COVID-19: a single centre retrospective service evaluation", - "rel_date": "2020-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20205369", - "rel_abs": "BackgroundThe role of specific blood tests to predict poor prognosis in patients admitted with infection from SARS-CoV2 virus remains uncertain. During the first wave of the global pandemic, an extended laboratory testing panel was integrated into the local pathway to guide triage and healthcare resource utilisation for emergency admissions. We conducted a retrospective service evaluation to determine the utility of extended tests (D-dimer, ferritin, high-sensitivity troponin I, lactate dehydrogenase, procalcitonin) compared to the core panel (full blood count, urea & electrolytes, liver function tests, C-reactive protein).\n\nMethodsClinical outcomes for adult patients with laboratory-confirmed COVID-19 admitted between 17th March to 30st June 2020 were extracted, alongside costs estimates for individual tests. Prognostic performance was assessed using multivariable logistic regression analysis with 28-day mortality used as the primary endpoint, and a composite of 28-day intensive care escalation or mortality for secondary analysis.\n\nResultsFrom 13,500 emergency attendances we identified 391 unique adults admitted with COVID-19. Of these, 113 died (29%) and 151 (39%) reached the composite endpoint. \"Core\" test variables adjusted for age, gender and index of deprivation had a prognostic AUC of 0.79 (95% Confidence Interval, CI: 0.67 to 0.91) for mortality and 0.70 (95% CI: 0.56 to 0.84) for the composite endpoint. Addition of \"extended\" test components did not improve upon this.\n\nConclusionOur findings suggest use of the extended laboratory testing panel to risk stratify community-acquired COVID-19-positive patients on admission adds limited prognostic value. We suggest laboratory requesting should be targeted to patients with specific clinical indications.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Mark J Ponsford", - "author_inst": "Division of Infection and Immunity, School of Medicine, Cardiff University; Immunodeficiency Center for Wales, University Hospital for Wales, Cardiff, UK" - }, - { - "author_name": "Ross J Burton", - "author_inst": "Division of Infection and Immunity, School of Medicine, Cardiff University" - }, - { - "author_name": "Leitchan Smith", - "author_inst": "University Hospital of Wales, Information & Technology Team Cardiff, UK" - }, - { - "author_name": "Palwasha Khan", - "author_inst": "1. Cardiff and Vale UHB, Department of Sexual Health Cardiff, UK 2. London School of Hygiene & Tropical Medicine, Department of Clinical Research London, UK" - }, - { - "author_name": "Robert Andrews", - "author_inst": "Cardiff University, Systems Immunity Research Institute Cardiff, UK" - }, - { - "author_name": "Simone Cuff", - "author_inst": "Cardiff University, Division of Infection and Immunity, School of Medicine Cardiff, UK" - }, - { - "author_name": "Laura Tan", - "author_inst": "Cardiff and Vale UHB, Adult Critical Care Directorate Cardiff, UK" - }, - { - "author_name": "Matthias Eberl", - "author_inst": "1. Cardiff University, Division of Infection and Immunity, School of Medicine Cardiff, UK 2. Cardiff University, Systems Immunity Research Institute Cardiff, U" - }, - { - "author_name": "Ian R Humphreys", - "author_inst": "1. Cardiff University, Division of Infection and Immunity, School of Medicine Cardiff, UK 2. Cardiff University, Systems Immunity Research Institute Cardiff, U" - }, - { - "author_name": "Farbod Babolhavaeji", - "author_inst": "Cardiff and Vale UHB, Department of Emergency Medicine Cardiff, UK" - }, - { - "author_name": "Andreas Artemiou", - "author_inst": "Cardiff University, School of Mathematics Cardiff, UK" - }, - { - "author_name": "Manish Pandey", - "author_inst": "Cardiff and Vale UHB, Adult Critical Care Directorate Cardiff, UK" - }, - { - "author_name": "Stephen Jolles", - "author_inst": "University of Wales Hospital, Immunodeficiency Center for Wales Cardiff, UK" - }, - { - "author_name": "Jonathan Underwood", - "author_inst": "1. Cardiff University, Division of Infection and Immunity, School of Medicine Cardiff, UK 2. Cardiff and Vale UHB, Department of Infectious Diseases Cardiff, U" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2020.10.08.20208108", "rel_title": "Age-targeted dose allocation can halve COVID-19 vaccine requirements", @@ -1121546,6 +1125458,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.10.09.20209965", + "rel_title": "Pulmonary Embolism in Patients with COVID-19: A Systematic review and Meta-analysis", + "rel_date": "2020-10-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20209965", + "rel_abs": "BackgroundThere is an increasing evidence that COVID-19 could be complicated by coagulopathy which may lead to death; especially in severe cases. Hence, this study aimed to build concrete evidence regarding the incidence and mortality of pulmonary embolism (PE) in patients with COVID-19.\n\nMethodsWe performed a systematic search for trusted databases/search engines including PubMed, Scopus, Cochrane library and Web of Science. After screening, the relevant data were extracted and the incidences and mortality rates from the different included studies were pooled for meta-analysis.\n\nResultsTwenty studies were finally included in our study consisting of 1896 patients. The results of the meta-analysis for the all included studies showed that the incidence of PE in patients with COVID-19 was 17.6% with the 95% confidence interval (CI) of 12.7 to 22.5%. There was significant heterogeneity (I2{square}={square}91.17%). Additionally, the results of meta-analysis including 8 studies showed that the mortality in patients with both PE and COVID-19 was 43.1% with the 95% confidence interval (CI) of 19 to 67.1%. There was significant heterogeneity (I2{square}={square}86.96%).\n\nConclusionPE was highly frequent in patients with COVID-19. The mortality in patients with both COVID-19 and PE was remarkable representing almost half of the patients. Appropriate prophylaxis and management are vital for better outcomes.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Omar Hamam", + "author_inst": "Alexandria Faculty of Medicine" + }, + { + "author_name": "Ahmed Goda", + "author_inst": "Faculty of Medicine, October 6th University, Cairo, 12585 Egypt" + }, + { + "author_name": "Radwa Awad", + "author_inst": "Faculty of Medicine, Benha University, Benha, 13518 Egypt" + }, + { + "author_name": "Amr Ussama", + "author_inst": "Faculty of Medicine, Al-azhar University, Cairo, 11651 Egypt" + }, + { + "author_name": "Moustafa Eldalal", + "author_inst": "Faculty of Medicine, Alexandria University, Alexandria21131, Egypt" + }, + { + "author_name": "Ahmed Fayez", + "author_inst": "Faculty of Medicine, October 6th University, Cairo, 12585 Egypt" + }, + { + "author_name": "Karim Elyamany", + "author_inst": "Faculty of Medicine, Alexandria University, Alexandria21131, Egypt" + }, + { + "author_name": "Renu Bhandari", + "author_inst": "Department of Internal Medicine, Manipal College of Medical Sciences, Kaski, 33700 Nepal." + }, + { + "author_name": "Waleed Ikram", + "author_inst": "Lahore Medical and Dental College, Lahore, 30022 Pakistan" + }, + { + "author_name": "Abdelrhman Elbaz", + "author_inst": "Bascom Palmer Eye Institute, Miami, FL 33136 United States of America" + }, + { + "author_name": "Smarika Baral", + "author_inst": "Department of Internal Medicine, Nepalgunj Medical College, Banke, 21900 Nepal." + }, + { + "author_name": "Yomna Elbandrawy", + "author_inst": "Faculty of Medicine, Tanta University, Tanta, 31951 Egypt" + }, + { + "author_name": "Alexander Egbe", + "author_inst": "Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, 55905 United States of America." + }, + { + "author_name": "Iraida Sharina", + "author_inst": "Division of Cardiology, Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center Houston, Houston, TX 77225, Unit" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.10.07.20207845", "rel_title": "Isolation of infected people and their contacts is likely to be effective against many short-term epidemics", @@ -1121751,45 +1125734,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.07.20208819", - "rel_title": "Modelling testing and response strategies for COVID-19 outbreaks in remote Australian Aboriginal communities", - "rel_date": "2020-10-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20208819", - "rel_abs": "BackgroundRemote Australian Aboriginal and Torres Strait Islander communities have potential to be severely impacted by COVID-19, with multiple factors predisposing to increased transmission and disease severity. Our modelling aims to inform optimal public health responses.\n\nMethodsAn individual-based simulation model represented communities ranging from 100 to 3,500 people, comprised of large interconnected households. A range of strategies for case finding, quarantining of contacts, testing, and lockdown were examined, following the silent introduction of a case.\n\nResultsMultiple secondary infections are likely present by the time the first case is identified. Quarantine of close contacts, defined by extended household membership, can reduce peak infection prevalence from 60-70% to around 10%, but subsequent waves may occur when community mixing resumes. Exit testing significantly reduces ongoing transmission.\n\nConcurrent lockdown of non-quarantined households for 14 days is highly effective for epidemic control and reduces overall testing requirements; peak prevalence of the initial outbreak can be constrained to less than 5%, and the final community attack rate to less than 10% in modelled scenarios. Lockdown also mitigates the effect of a delay in the initial response. Compliance with lockdown must be at least 80-90%, however, or epidemic control will be lost.\n\nConclusionsA SARS-CoV-2 outbreak will spread rapidly in remote communities. Prompt case detection with quarantining of extended-household contacts and a 14-day lockdown for all other residents, combined with exit testing for all, is the most effective strategy for rapid containment. Compliance is crucial, underscoring the need for community supported, culturally sensitive responses.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ben B Hui", - "author_inst": "Kirby Institute, UNSW Sydney, Sydney, NSW, Australia" - }, - { - "author_name": "Damien Brown", - "author_inst": "The Peter Doherty Institute for Infection and Immunity, The Royal Melbourne Hospital and The University of Melbourne, Australia" - }, - { - "author_name": "Rebecca H Chisholm", - "author_inst": "Department of Mathematics and Statistics, School of Engineering and Mathematical Sciences, La Trobe University, Australia" - }, - { - "author_name": "Nicholas Geard", - "author_inst": "School of Computing and Information Systems, The University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Jodie McVernon", - "author_inst": "Victorian Infectious Diseases Reference Laboratory Epidemiology Unit, The Peter Doherty Institute for Infection and Immunity, The Royal Melbourne Hospital and T" - }, - { - "author_name": "David G Regan", - "author_inst": "Kirby Institute, UNSW Sydney, Sydney, NSW, Australia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.07.20208298", "rel_title": "Report on COVID-19 Verification Case Study in Nine Countries Using the SIQR model", @@ -1123107,6 +1127051,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.06.20207993", + "rel_title": "Sars-Cov-2 in Argentina: Following Virus Spreading using Granger Causality", + "rel_date": "2020-10-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20207993", + "rel_abs": "There is a debate in Argentina on how COVID-19 outbreak in one district ends up infecting its neighbor districts. This contribution aims to use tools of time series analysis for understanding processes of contagious through regions. I use VAR and Granger causality for testing neighbor spreading via sequential rate of contagion. Results show that in the case of Argentina, contagion began in the capital city of Buenos Aires and then spread to its hinterland via specific districts. Once interior districts were infected a positive feedback dynamics emerge creating regions of high reproducibility of the virus where interventions may be focus in the very near future. This specific use of time series analysis may provide a tool for tracing infectiousness along regions that may help to anticipate infection and then for intervening for reducing the problems derived by the disease.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Juan M.C. Larrosa", + "author_inst": "Universidad Nacional del Sur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.06.20208009", "rel_title": "Misinterpretation of viral load in COVID-19.", @@ -1123288,81 +1127251,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.10.07.326462", - "rel_title": "Genome-scale identification of SARS-CoV-2 and pan-coronavirus host factor networks", - "rel_date": "2020-10-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.07.326462", - "rel_abs": "The COVID-19 pandemic has claimed the lives of more than one million people worldwide. The causative agent, SARS-CoV-2, is a member of the Coronaviridae family, which are viruses that cause respiratory infections of varying severity. The cellular host factors and pathways co-opted by SARS-CoV-2 and other coronaviruses in the execution of their life cycles remain ill-defined. To develop an extensive compendium of host factors required for infection by SARS-CoV-2 and three seasonal coronaviruses (HCoV-OC43, HCoV-NL63, and HCoV-229E), we performed parallel genome-scale CRISPR knockout screens. These screens uncovered multiple host factors and pathways with pan-coronavirus and virus-specific functional roles, including major dependency on glycosaminoglycan biosynthesis, SREBP signaling, and glycosylphosphatidylinositol biosynthesis, as well as an unexpected requirement for several poorly characterized proteins. We identified an absolute requirement for the VTT-domain containing protein TMEM41B for infection by SARS-CoV-2 and all other coronaviruses. This human Coronaviridae host factor compendium represents a rich resource to develop new therapeutic strategies for acute COVID-19 and potential future coronavirus spillover events.\n\nHIGHLIGHTSGenome-wide CRISPR screens for SARS-CoV-2, HCoV-OC43, HCoV-NL63, and HCoV-229E coronavirus host factors.\n\nParallel genome-wide CRISPR screening uncovered host factors and pathways with pan-coronavirus and virus-specific functional roles.\n\nCoronaviruses co-opt multiple biological pathways, including glycosaminoglycan biosynthesis, SREBP signaling, and glycosylphosphatidylinositol biosynthesis and anchoring, among others.\n\nTMEM41B - a poorly understood factor with roles in autophagy and lipid mobilization - is a critical pan-coronavirus host factor.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "William M. Schneider", - "author_inst": "Laboratory of Virology and Infectious Disease, The Rockefeller University" - }, - { - "author_name": "Joseph M. Luna", - "author_inst": "Laboratory of Virology and Infectious Disease, The Rockefeller University" - }, - { - "author_name": "H.-Heinrich Hoffmann", - "author_inst": "Laboratory of Virology and Infectious Disease, The Rockefeller University" - }, - { - "author_name": "Francisco J. S\u00e1nchez-Rivera", - "author_inst": "Cancer Biology and Genetics, MSKCC" - }, - { - "author_name": "Andrew A. Leal", - "author_inst": "Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health" - }, - { - "author_name": "Alison W. Ashbrook", - "author_inst": "Laboratory of Virology and Infectious Disease, The Rockefeller University" - }, - { - "author_name": "J\u00e9r\u00e9mie Le Pen", - "author_inst": "Laboratory of Virology and Infectious Disease, The Rockefeller University" - }, - { - "author_name": "Eleftherios Michailidis", - "author_inst": "Laboratory of Virology and Infectious Disease, The Rockefeller University" - }, - { - "author_name": "Inna Ricardo-Lax", - "author_inst": "Laboratory of Virology and Infectious Disease, The Rockefeller University" - }, - { - "author_name": "Avery Peace", - "author_inst": "Laboratory of Virology and Infectious Disease, The Rockefeller University" - }, - { - "author_name": "Ansgar F. Stenzel", - "author_inst": "Laboratory of Virology and Infectious Disease, The Rockefeller University" - }, - { - "author_name": "Scott W. Lowe", - "author_inst": "Cancer Biology and Genetics, MSKCC" - }, - { - "author_name": "Margaret R. MacDonald", - "author_inst": "Laboratory of Virology and Infectious Disease, The Rockefeller University" - }, - { - "author_name": "Charles M. Rice", - "author_inst": "Laboratory of Virology and Infectious Disease, The Rockefeller University" - }, - { - "author_name": "John T. Poirier", - "author_inst": "Laura and Isaac Perlmutter Cancer Center, New York University Langone Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.10.08.331421", "rel_title": "Psychiatric Genomics Research During the COVID-19 Pandemic: A Survey of Psychiatric Genomics Consortium Researchers", @@ -1124929,6 +1128817,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.03.20205328", + "rel_title": "The Impact of COVID-19 on the Management of Heart Failure -A United Kingdom Patient Questionnaire Study", + "rel_date": "2020-10-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.03.20205328", + "rel_abs": "AimThe coronavirus disease 2019 (COVID-19) pandemic has created significant challenges to healthcare globally, necessitating rapid restructuring of service provision. This questionnaire survey was conducted amongst adult heart failure (HF) patients in the United Kingdom (UK), to understand the impact of COVID-19 upon HF services.\n\nMethods and ResultsThe survey was conducted by the Pumping Marvellous Foundation (PMF), a UK HF patient charity. \"Survey Monkey\" was used to disseminate the questionnaire in the PMFs online patient group and in 10 UK hospitals (out-patient hospital and community HF clinics). 1050 responses were collected (693/1050-66% women); 55% (579/1050) were aged over 60 years. Anxiety level was significantly higher regarding COVID19 (mean 7{+/-}2.5 on anxiety scale of 0 to 10) compared to anxiety regarding HF (6.1{+/-}2.4; p<0.001). Anxiety was higher amongst patients aged [≤]60 years about HF (6.3{+/-}2.2 versus 5.9{+/-}2.5 in those aged >60 years; p=0.005) and COVID-19 (7.3{+/-}2.3 versus 6.7{+/-}2.6 those aged >60 years; p<0.001). 65% respondents (686/1050) reported disruption to HF appointments (cancellation or postponement) during the lockdown period. 37% reported disruption to medication prescription services and 34% reported inability to access their HF teams promptly. 32% expressed reluctance to attend hospital (25% stated they would only attend hospital if there was no alternative and 7% stated that they would not attend hospital at all).\n\nConclusionsThe COVID-19 pandemic has caused significant anxiety amongst HF patients regarding COVID-19 and HF. Cancellation or postponement of scheduled clinic appointments, investigations, procedures, prescription and monitoring services were implicated as sources of anxiety.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Rajiv Sankaranarayanan", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Nick Hartshorne-Evans", + "author_inst": "The Pumping Marvellous Foundation" + }, + { + "author_name": "Sam Redmond-Lyon", + "author_inst": "The Pumping Marvellous Foundation" + }, + { + "author_name": "Jill Wilson", + "author_inst": "The Pumping Marvellous Foundation" + }, + { + "author_name": "Hani Essa", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Alastair Gray", + "author_inst": "Craigavon Area Hospital" + }, + { + "author_name": "Louise Clayton", + "author_inst": "University Hospitals of Leicester NHS Trust" + }, + { + "author_name": "Carys Barton", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Fozia Z Ahmed", + "author_inst": "Manchester University NHS Foundation Trust" + }, + { + "author_name": "Colin Cunnington", + "author_inst": "Manchester University NHS Foundation Trust" + }, + { + "author_name": "Duwarakan Satchithananda", + "author_inst": "University Hospital North Midlands" + }, + { + "author_name": "Clare Murphy", + "author_inst": "Royal Alexandra and Vale of Leven Hospitals" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.10.04.20206318", "rel_title": "The relationship between neighborhood poverty and COVID-19 mortality within racial/ethnic groups (Cook County, Illinois)", @@ -1125066,37 +1129017,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.03.20206185", - "rel_title": "Fractal and inertia moment analysis of SARS CoV-2 proliferation through replication", - "rel_date": "2020-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.03.20206185", - "rel_abs": "The present work proposes a surrogate method for understanding and analyzing the replication of SARS CoV-2 through fractal and inertia moment (IM) analysis of cell culture images at different stages. The fractal analysis of images of cell culture, calculated by the box-counting and power spectral density methods, reflect the stages of virus infection, leading to the replication of the virus RNA and damaging the host cell. The linear increase of IM value reveals not only the proliferation of SARS CoV-2 by replication but also damage to the host cell with time. Thus, the work shows the possibility of fractal analysis and IM measurement for understanding the dynamics of the virus infection.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "VIMAL RAJ", - "author_inst": "UNIVERSITY OF KERALA" - }, - { - "author_name": "S SREEJYOTHI", - "author_inst": "UNIVERSITY OF KERALA" - }, - { - "author_name": "M S SWAPNA", - "author_inst": "UNIVERSITY OF KERALA" - }, - { - "author_name": "S SANKARARAMAN", - "author_inst": "UNIVERSITY OF KERALA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.10.04.20206094", "rel_title": "A systematic review of the knowledge, attitudes, and practices of physicians, health workers, and the general population about Coronavirus disease 2019 (COVID-19)", @@ -1126239,6 +1130159,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.05.20207100", + "rel_title": "Updating Herd Immunity Models for the U.S. in 2020: Implications for the COVID-19 Response", + "rel_date": "2020-10-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.05.20207100", + "rel_abs": "ObjectivesTo understand what levels of herd immunity are required in the COVID-19 pandemic, given spatial population heterogeneity, to best inform policy and action.\n\nMethodsUsing a network of counties in the United States connected by transit data we considered a set of coupled differential equations for susceptible-infectious-removed populations. We calculated the classical herd immunity level plus a version reflecting the heterogeneity of connections in the network by running the model forward in time until the epidemic completed.\n\nResultsNecessary levels of herd immunity vary greatly from county to county. A population weighted average for the United States is 47.5% compared to a classically estimated level of 77.1%.\n\nConclusionsCommon thinking argues that the nation needs to achieve at least 60% herd immunity to emerge from the COVID-19 pandemic. Heterogeneity in contact structure and individual variation in infectivity, susceptibility, and resistance are key factors that reduce the disease-induced herd immunity levels to 34.2-47.5% in our models. Looking forward toward vaccination strategies, these results suggest we should consider not just who is vaccinated but where those vaccinations will do the most good.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Natalie Elizabeth Sheils", + "author_inst": "UnitedHealth Group" + }, + { + "author_name": "Gregory D Lyng", + "author_inst": "UnitedHealth Group" + }, + { + "author_name": "Ethan M Berke", + "author_inst": "UnitedHealth Group" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.03.20206359", "rel_title": "PREDICTIONS FOR EUROPE FOR THE COVID-19 PANDEMICAFTER LOCKDOWN WAS LIFTED USING AN SIR MODEL", @@ -1126356,45 +1130303,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.10.02.20206052", - "rel_title": "Vulnerability and burden of all-cause mortality associated with particulate air pollution increased during COVID-19 pandemic: a nationwide observed study in Italy", - "rel_date": "2020-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.02.20206052", - "rel_abs": "BackgroundLimited evidence is available on the health effects of particulate matter (i.e. PM2.5, particulate matter with an aerodynamic diameter < 2.5m; PM10, < 10m; PM2.5-10, 2.5-10m) during the pandemic of COVID-19 in Italy.\n\nObjectivesTo examine the associations between all-cause mortality and daily PM2.5, PM2.5-10, and PM10 in the pandemic period, and compare them to the normal periods (2015-2019) in Italy.\n\nMethodsWe collected daily data regarding all-cause (stratified by age and gender), and PM2.5, PM2.5-10, and PM10 for 107 Italian provinces from 1, January 2015 to 31, May 2020. A time-stratified case-cross design with the distributed lag non-linear model was used to examine the association between PM and all-cause mortality during the first three months of the COVID-19 outbreak (March to May in 2020) and the same months in 2015-2019. We also compared the counts and fractions of death attributable to PM in two periods.\n\nResultsOverall, Italy saw an increase in daily death counts while slight decreases in PM concentrations in 2020 pandemic period compared to same months of 2015-2019. Mortality effects were significant in lag 0-3 days for PM2.5, lag 0-2 for PM10, and lag 0-1 for PM2.5-10. Each 10 {micro}g/m3 increase in PM was associated much higher increase in daily all-cause mortality during 2020 pandemic period compared to the same months during 2015-2019 [increased mortality rate: 7.24 % (95%CI: 4.84%, 9.70%) versus 1.69% (95%CI: 1.12%, 2.25%) for PM2.5; 3.45 % (95%C: 2.58%, 4.34%) versus 1.11% (95%CI: 0.79%, 1.42%) for PM10, 4.25% (95%CI: 2.99%, 5.52%) versus 1.76% (95%CI: 1.14%, 2.38%) for PM2.5-10]. The counts and fractions of deaths attributable to PM were higher in 2020 than the normal periods for PM2.5 (attributable death counts: 20,062 in 2020 versus 3,927 per year in 2015-2019; attributable fractions: 10.2% versus 2.4%), PM10 (15,112 versus 3,999; 7.7% versus 2.5%), and PM2.5-10 (7,193 versus 2303; 3.7% versus 1.4%).\n\nConclusionsCOVID-19 pandemic increased the vulnerability and excess cases of all-cause mortality associated with short-term exposure to PM2.5, PM2.5-10 and PM10 in Italy, despite a decline in air pollution level. This suggests using historical PM-mortality association to calculate health benefits associated with reduction in PMs has big uncertainties.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Tingting Ye", - "author_inst": "Monash University" - }, - { - "author_name": "Rongbin Xu", - "author_inst": "Monash University" - }, - { - "author_name": "Wenhua Yu", - "author_inst": "Monash University" - }, - { - "author_name": "Zhaoyue Chen", - "author_inst": "Monash University" - }, - { - "author_name": "Yuming Guo", - "author_inst": "Monash University" - }, - { - "author_name": "Shanshan Li", - "author_inst": "Monash University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.03.20206177", "rel_title": "An Agent Based Model for assessing spread and health systems burden for COVID-19 using a synthetic population in Telangana state, India", @@ -1127837,6 +1131745,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.02.20200931", + "rel_title": "Association of Pre-COVID-19 Lymphocytopenia with Fatality", + "rel_date": "2020-10-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.02.20200931", + "rel_abs": "Lymphocytopenia during the COVID-19 has been associated with fatality. We tested whether pre-existing lymphocytopenia reported prior to any possible exposure to SARS-COV2 (from 2010 to 2019) was associated with fatality. Using all patients diagnosed on testing in a single regional laboratory, we identified 1137 subjects with PCR positive for SARS-COV2 and at least one available complete blood count from the decade prior to any possible exposure to the virus. Bivariate analysis indicated an association between pre-existing lymphocytopenia (defined as absolute lymphocyte count <0.9x109 /L) and fatality (18% versus 4%). Furthermore, a logistic regression model, accounting for both patient age and number of blood counts obtained, indicated the subjects with pre-existing lymphocytopenia were 1.4 times as likely to die. Because the absolute lymphocyte count is almost universally available and easily interpreted, this biomarker of the risk of fatality could be widely useful.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Richard Burack", + "author_inst": "University of Rochester" + }, + { + "author_name": "Philip Rock", + "author_inst": "University of Rochester" + }, + { + "author_name": "David Burtoon", + "author_inst": "University of Rochester" + }, + { + "author_name": "Xueya Cai", + "author_inst": "University of Rochester" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.02.20205880", "rel_title": "Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity irrespective of virus", @@ -1127962,33 +1131901,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.02.20205757", - "rel_title": "Investigating the potential benefit that requiring travellers to self-isolate on arrival may have upon the reducing of case importations during international outbreaks of influenza, SARS, Ebola virus disease and COVID-19", - "rel_date": "2020-10-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.02.20205757", - "rel_abs": "With the advent of rapid international travel, disease can now spread between nations faster than ever. As such, when outbreaks occur in foreign states, pressure mounts to reduce the risk of importing cases to the home nation. In a previous paper, we developed a model to investigate the potential effectiveness of deploying screening at airports during outbreaks of influenza, SARS, and Ebola. We also applied the model to the current COVID-19 outbreak. This model simulated the testing of travellers (assumed not to be displaying symptoms prior to boarding their flight) as they arrived at their destination. The model showed that the reduction in risk of case importation that screening alone could deliver was minimal across most scenarios considered, with outputs indicating that screening alone could detect at most 46.4%, 12.9%, and 4.0% of travellers infected with influenza, SARS and Ebola respectively, while the model also reported a detection rate of 12.0% for COVID-19. In this paper, we present a brief modification to this model allowing us to assess the added impact that quarantining incoming travelers for various periods may have on reducing the risk of case importation. Primary results show that requiring all travellers to undergo 5 days of self-isolation on arrival, after which they are tested again, has the potential to increase rates of detection to 100%, 87.6%, 81.7% and 41.3% for travellers infected with influenza, SARS, COVID-19 and Ebola respectively. Extending the period of self-isolation to 14 days increases these potential detection rates to 100%, 100%, 99.5% and 91.8% respectively.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Declan Bays", - "author_inst": "Public Health England" - }, - { - "author_name": "Emma Bennett", - "author_inst": "Public Health England" - }, - { - "author_name": "Thomas Finnie", - "author_inst": "Public Health England" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.30.20204586", "rel_title": "Benchmarking COVID-19 Mortality in the United States", @@ -1129455,6 +1133367,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.09.30.20204537", + "rel_title": "SARS-CoV-2 seroprevalence and clinical features of COVID-19 in a German liver transplant recipient cohort: a prospective serosurvey study.", + "rel_date": "2020-10-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.30.20204537", + "rel_abs": "In liver transplant (LT) recipients with severe COVID-19 fatal outcome has been reported in a substantial subset of patients. Whether LT recipients are at increased risk for severe COVID-19 compared to the general population is controversial. Here we report the first results of a SARS-CoV-2 serosurvey in a large LT recipient cohort.\n\nTaking into account known risk factors, LT recipients a priori represented a high-risk cohort for severe COVID-19 with 101/219 (46.1 %) presenting with more than 2 risk factors for severe COVID-19. Out of 219 LT recipients 8 (3.7%) were either tested positive for nasopharyngeal SARS-CoV-2 RNA or anti-SARS-CoV-2 serum IgG. 5/8 (62.5 %) did not show any clinical signs of infection, 3/8 (37.5%) had self-limited disease, none required hospitalization for COVID-19. 5/8 (67.5%) SARS-CoV-2 positive patients showed high utilization of the healthcare system. 2/8 (25 %) had known exposure to infected health care personal. A majority of 65.4 % often or always avoided outside family social contacts. Face masks were commonly worn by all patients.\n\nIn summary, LT recipients showed a SARS-CoV-2 seroconversion rate similar to the general population with a substantial percentage of unrecognized infections. The health care system can be the assumed source of infection in most of these cases.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Conrad Rauber", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Shilpa Tiwari-Heckler", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Jan Pfeiffenberger", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Arianeb Mehrabi", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Frederike Lund", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Philip Gath", + "author_inst": "Staedtisches Klinikum Ludwigshafen" + }, + { + "author_name": "Markus Mieth", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Uta Merle", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Christian Rupp", + "author_inst": "Universitaetsklinikum Heidelberg" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "transplantation" + }, { "rel_doi": "10.1101/2020.10.01.20204255", "rel_title": "COVID-19 Pandemic in University Hospital: Impact on Medical Training of Medical Interns", @@ -1129572,61 +1133535,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.10.04.325316", - "rel_title": "Efficient culture of SARS-CoV-2 in human hepatoma cells enhances viability of the virus in human lung cancer cell lines permitting the screening of antiviral compounds", - "rel_date": "2020-10-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.04.325316", - "rel_abs": "Efforts to mitigate COVID-19 include screening of existing antiviral molecules that could be re-purposed to treat SARS-CoV-2 infections. Although SARS-CoV-2 propagates efficiently in African green monkey kidney (Vero) cells, antivirals such as nucleos(t)ide analogs (nucs) often exhibit decreased activity in these cells due to inefficient metabolization. Limited SARS-CoV-2 replication and propagation occurs in human cells, which are the most relevant testing platforms. By performing serial passages of a SARS-CoV-2 isolate in the human hepatoma cell line clone Huh7.5, we selected viral populations with improved viability in human cells. Culture adaptation led to the emergence of a significant number of high frequency changes (>90% of the viral population) in the region coding for the spike glycoprotein, including a deletion of nine amino acids in the N-terminal domain and 3 amino acid changes (E484D, P812R, and Q954H). We demonstrated that the Huh7.5-adapted virus exhibited a >3-Log10 increase in infectivity titers (TCID50) in Huh7.5 cells, with titers of ~8 Log10TCID50/mL, and >2-Log10 increase in the human lung cancer cell line Calu-1, with titers of ~6 Log10TCID50/mL. Culture adaptation in Huh7.5 cells further permitted efficient infection of the otherwise SARS-CoV-2 refractory human lung cancer cell line A549, with titers of ~6 Log10TCID50/mL. The enhanced ability of the virus to replicate and propagate in human cells permitted screening of a panel of nine nucs, including broad-spectrum compounds. Remdesivir, EIDD-2801 and to a limited extent galidesivir showed antiviral effect across these human cell lines, whereas sofosbuvir, uprifosbuvir, valopicitabine, mericitabine, ribavirin, and favipiravir had no apparent activity.\n\nImportanceThe cell culture adapted variant of the SARS-CoV-2 virus obtained in the present study, showed significantly enhanced replication and propagation in various human cell lines, including lung derived cells otherwise refractory for infection with the original virus. This SARS-CoV-2 variant will be a valuable tool permitting investigations across human cell types, and studies of identified mutations could contribute to our understanding of viral pathogenesis. In particular, the adapted virus can be a good model for investigations of viral entry and cell tropism for SARS-CoV-2, in which the spike glycoprotein plays a central role. Further, as shown here with the use of remdesivir and EIDD-2801, two nucs with significant inhibitory effect against SARS-CoV-2, large differences in the antiviral activity are observed depending on the cell line. Thus, it is essential to select the most relevant target cells for pre-clinical screenings of antiviral compounds, facilitated by using a virus with broader tropism.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Santseharay Ramirez", - "author_inst": "University of Copenhagen and Hvidovre Hospital" - }, - { - "author_name": "Carlota Fernandez-Antunez", - "author_inst": "University of Copenhagen and Hvidovre Hospital" - }, - { - "author_name": "Long Van Pham", - "author_inst": "University of Copenhagen and Hvidovre Hospital" - }, - { - "author_name": "Line Abildgaard Ryberg", - "author_inst": "University of Copenhagen and Hvidovre Hospital" - }, - { - "author_name": "Shan Feng", - "author_inst": "University of Copenhagen and Hvidovre Hospital" - }, - { - "author_name": "Martin Schou Pedersen", - "author_inst": "University of Copenhagen and Hvidovre Hospital" - }, - { - "author_name": "Lotte Scheibelein Mikkelsen", - "author_inst": "University of Copenhagen and Hvidovre Hospital" - }, - { - "author_name": "Judith M Gottwein", - "author_inst": "University of Copenhagen and Hvidovre Hospital" - }, - { - "author_name": "Ulrik Fahnoe", - "author_inst": "University of Copenhagen and Hvidovre Hospital" - }, - { - "author_name": "Jens Bukh", - "author_inst": "University of Copenhagen and Hvidovre Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.10.02.20205591", "rel_title": "Risk factors associated with SARS-CoV-2 infection and outbreaks in Long Term Care Facilities in England: a national survey", @@ -1131149,6 +1135057,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.02.323915", + "rel_title": "A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion", + "rel_date": "2020-10-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.02.323915", + "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Computer simulations of complete viral particles can provide theoretical insights into large-scale viral processes including assembly, budding, egress, entry, and fusion. Detailed atomistic simulations, however, are constrained to shorter timescales and require billion-atom simulations for these processes. Here, we report the current status and on-going development of a largely \"bottom-up\" coarse-grained (CG) model of the SARS-CoV-2 virion. Structural data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. We describe how CG molecular interactions can be derived from all-atom simulations, how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG models, and how the CG models can be iteratively improved as new data becomes publicly available. Our initial CG model and the detailed methods presented are intended to serve as a resource for researchers working on COVID-19 who are interested in performing multiscale simulations of the SARS-CoV-2 virion.\n\nSignificance StatementThis study reports the construction of a molecular model for the SARS-CoV-2 virion and details our multiscale approach towards model refinement. The resulting model and methods can be applied to and enable the simulation of SARS-CoV-2 virions.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alvin Yu", + "author_inst": "University of Chicago" + }, + { + "author_name": "Alexander J Pak", + "author_inst": "University of Chicago" + }, + { + "author_name": "Peng He", + "author_inst": "University of Chicago" + }, + { + "author_name": "Viviana Monje-Galvan", + "author_inst": "University of Chicago" + }, + { + "author_name": "Lorenzo Casalino", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Zied Gaieb", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Abigail C Dommer", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Rommie E Amaro", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Gregory A Voth", + "author_inst": "University of Chicago" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.10.02.324145", "rel_title": "SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs", @@ -1131354,29 +1135313,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.10.02.323519", - "rel_title": "Transmission of SARS-COV-2 from China to Europe and West Africa: a detailed phylogenetic analysis.", - "rel_date": "2020-10-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.02.323519", - "rel_abs": "BackgroundSARS-CoV-2, the virus causing the Covid-19 pandemic emerged in December 2019 in China and raised fears that it could overwhelm healthcare systems worldwide. In June 2020, all African countries registered human infections with SARS-CoV-2.\n\nThe virus is mutating steadily and this is monitored by a well curated database of viral nucleotide sequences from samples taken from infected individual thus enabling phylogenetic analysis and phenotypic associations.\n\nMethodsWe downloaded from the GISAID database, SARS-CoV-2 sequences established from four West African countries Ghana, Gambia, Senegal and Nigeria and then performed phylogenetic analysis employing the nextstrain pipeline. Based on mutations found within the sequences we calculated and visualized statistics characterizing clades according to the GISAID nomenclature.\n\nResultsWe found country-specific patterns of viral clades: the later Europe-associated G-clades predominantly in Senegal and Gambia, and combinations of the earlier (L, S, V) and later clades in Ghana and Nigeria. Contrary to our expectations, the later Europe-associated G-clades emerged before the earlier clades. Detailed analysis of distinct samples showed that some of the earlier clades might have circulated latently and some reflect migration routes via Mali and Tunisia.\n\nConclusionsThe distinct patterns of viral clades in the West African countries point at its emergence from Europe and China via Asia and Europe. The observation that the later clades emerged before the earlier clades could be simply due to founder effects or due to latent circulation of the earlier clades. Only a marginal correlation of the G-clades associated with the D614G mutation could be identified with the relatively low case fatality (0.6-3.2).\n\nKey messagesO_LIGhana and Nigeria have a combination of earlier (L, V, S) and later Europe-associated G-clades of SARS-CoV-2, therefore pointing to multiple introductions while in Senegal and Gambia Europe-associated G-clades predominate pointing to introductions mainly from Europe.\nC_LIO_LISurprisingly, the later G-clades emerged before the earlier clades (L, V, S)\nC_LIO_LIDetailed phylogenetic analysis points at latent circulation of earlier clades before the first registered cases.\nC_LIO_LIPhylogenetic analysis of some cases points at migration routes to Europe via Tunisia, Egypt and Mali.\nC_LIO_LIA marginal correlation of r=0.28 between the percentage of the D614G mutation defining the G-clades and case-fatality can be detected.\nC_LI", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Wasco Wruck", - "author_inst": "Heinrich-Heine-University" - }, - { - "author_name": "James Adjaye", - "author_inst": "Heinrich Heine University Duesseldorf" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.10.02.324228", "rel_title": "SARS-CoV-2 proteins and anti-COVID-19 drugs induce lytic reactivation of an oncogenic virus", @@ -1132987,6 +1136923,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.29.20202416", + "rel_title": "Virus evolution affected early COVID-19 spread", + "rel_date": "2020-09-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.29.20202416", + "rel_abs": "As the SARS-Cov-2 virus spreads around the world afflicting millions of people, it has undergone divergent genetic mutations. Although most of these mutations are expected to be inconsequential, some mutations in the spike protein structure have been hypothesized to affect the critical stage at which the virus invades human cells, which could affect transmission probability and disease expression. If true, then we expect an increased growth rate of reported COVID-19 cases in regions dominated by viruses with these altered proteins. We modeled early global infection dynamics based on clade assignment along with other demographic and meteorological factors previously found to be important. Clade, but not variant D614G which has been associated with increased viral load, enhanced our ability to describe early COVID-19 growth dynamics. Including clade identity in models significantly improved predictions over earlier work based only on weather and demographic variables. In particular, higher proportions of clade 19A and 19B were negatively correlated with COVID-19 growth rate, whereas higher proportions of 20A and 20C were positively correlated with growth rate. A strong interaction between the prevalence of clade 20C and relative humidity suggests that the impact of clade identity might be more important when coupled with certain weather conditions. In particular, 20C an 20A generate the highest growth rates when coupled with low humidity. Projections based on data through April 2020 suggest that, without intervention, COVID-19 has the potential to grow more quickly in regions dominated by the 20A and 20C clades, including most of South and North America.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Derek Corcoran", + "author_inst": "University of Connecticut" + }, + { + "author_name": "Mark C Urban", + "author_inst": "University of Connecticut" + }, + { + "author_name": "Jill Wegrzyn", + "author_inst": "University of Connecticut" + }, + { + "author_name": "Cory Merow", + "author_inst": "University of Connecticut" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.30.20204644", "rel_title": "Estimation of novel coronavirus (covid-19) reproduction number and case fatality rate: a systematic review and meta-analysis", @@ -1133076,193 +1137043,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.30.20204230", - "rel_title": "Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State", - "rel_date": "2020-09-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.30.20204230", - "rel_abs": "The rapid spread of SARS-CoV-2 has gravely impacted societies around the world. Outbreaks in different parts of the globe are shaped by repeated introductions of new lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State to characterize how the spread of SARS-CoV-2 in Washington State (USA) was shaped by differences in timing of mitigation strategies across counties, as well as by repeated introductions of viral lineages into the state. Additionally, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G, but not the other variant (614D) into the state. At an individual level, we see evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we do not find any evidence that the 614G variant impacts clinical severity or patient outcomes. Overall, this suggests that at least to date, the behavior of individuals has been more important in shaping the course of the pandemic than changes in the virus.\n\nOne Sentence SummaryLocal outbreak dynamics of SARS-CoV-2 in Washington State (USA) were driven by regionally different mitigation measures and repeated introductions of unique viral variants with different viral loads.", - "rel_num_authors": 43, - "rel_authors": [ - { - "author_name": "Nicola Felix Mueller", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Cassia Wagner", - "author_inst": "University of Washington" - }, - { - "author_name": "Chris D. Frazar", - "author_inst": "University Of Washington" - }, - { - "author_name": "Pavitra Roychoudhury", - "author_inst": "University of Washington" - }, - { - "author_name": "Jover Lee", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Louise H Moncla", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Benjamin Pelle", - "author_inst": "University of Washington" - }, - { - "author_name": "Matthew Richardson", - "author_inst": "University of Washington" - }, - { - "author_name": "Erica Ryke", - "author_inst": "University of Washington" - }, - { - "author_name": "Hong Xie", - "author_inst": "University of Washington" - }, - { - "author_name": "Lasata Shrestha", - "author_inst": "University of Washington" - }, - { - "author_name": "Amin Addetia", - "author_inst": "University of Washington" - }, - { - "author_name": "Victoria M Rachleff", - "author_inst": "University of Washington" - }, - { - "author_name": "Nicole Lieberman", - "author_inst": "University of Washington" - }, - { - "author_name": "Meei-Li Huang", - "author_inst": "University of Washington" - }, - { - "author_name": "Romesh Gautom", - "author_inst": "Washington State Department of Health" - }, - { - "author_name": "Geoff Melly", - "author_inst": "Washington State Department of Health" - }, - { - "author_name": "Brian Hiatt", - "author_inst": "Washington State Department of Health" - }, - { - "author_name": "Philip Dykema", - "author_inst": "Washington State Department of Health" - }, - { - "author_name": "Amanda Adler", - "author_inst": "Seattle Childrens Research Institute" - }, - { - "author_name": "Elisabeth Brandstetter", - "author_inst": "University of Washington" - }, - { - "author_name": "Peter D. Han", - "author_inst": "University of Washington" - }, - { - "author_name": "Kairsten Fay", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Misja Ilcisin", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Kirsten Lacombe", - "author_inst": "Seattle Childrens Research Institute" - }, - { - "author_name": "Thomas R Sibley", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Melissa Truong", - "author_inst": "University of Washington" - }, - { - "author_name": "Caitlin R Wolf", - "author_inst": "University of Washington" - }, - { - "author_name": "Michael Boeckh", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Janet A Englund", - "author_inst": "Seattle Childrens Research Institute" - }, - { - "author_name": "Michael Famulare", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Barry R Lutz", - "author_inst": "University of Washington" - }, - { - "author_name": "Mark J Rieder", - "author_inst": "University of Washington" - }, - { - "author_name": "Matthew Thompson", - "author_inst": "University of Washington" - }, - { - "author_name": "Jeffrey S Duchin", - "author_inst": "University of Washington" - }, - { - "author_name": "Lea M Starita", - "author_inst": "University of Washington" - }, - { - "author_name": "Helen Y Chu", - "author_inst": "University of Washington" - }, - { - "author_name": "Jay Shendure", - "author_inst": "University of Washington" - }, - { - "author_name": "Keith R Jerome", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Scott Lindquist", - "author_inst": "Washington State Department of Health" - }, - { - "author_name": "Alex Greninger", - "author_inst": "University of Washington" - }, - { - "author_name": "Deborah A Nickerson", - "author_inst": "University of Washington" - }, - { - "author_name": "Trevor Bedford", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.29.20203554", "rel_title": "Spectrum of spinal cord involvement in COVID-19: A systematic review", @@ -1134769,6 +1138549,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2020.09.28.20200915", + "rel_title": "COVID-19 seroprevalence surveys and antibody decline - A note of caution on antibody decline", + "rel_date": "2020-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20200915", + "rel_abs": "We analyzed 21,676 residual specimens from Ontario, Canada collected between March-August, 2020 to investigate the effect of antibody decline on SARS-CoV-2 seroprevalence estimates. Testing specimens orthogonally using the Abbott (anti-nucleocapsid) and then the Ortho (anti-spike) assays, seroprevalence estimates ranged from 0.4%-1.4%, despite ongoing disease activity. The geometric mean concentration (GMC) of antibody-positive specimens decreased over time (p=0.015), and the GMC of antibody-negative specimens increased over time (p=0.0018). The association between the two tests decreased each month (p<0.001), suggesting anti-N antibody decline. Lowering the Abbott index cut-off from 1.4 to 0.7 resulted in a 16% increase in positive specimens.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Shelly Bolotin", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Vanessa Tran", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Selma Osman", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Kevin A. Brown", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Sarah A. Buchan", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Eugene Joh", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Shelley L. Deeks", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Vanessa G. Allen", + "author_inst": "Public Health Ontario" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.27.20199737", "rel_title": "High-Quality Masks Can Reduce Infections and Deaths in the US", @@ -1135042,273 +1138869,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.28.20202929", - "rel_title": "T cell assays differentiate clinical and subclinical SARS-CoV-2 infections from cross-reactive antiviral responses", - "rel_date": "2020-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20202929", - "rel_abs": "A major issue in identification of protective T cell responses against SARS-CoV-2 lies in distinguishing people infected with SARS-CoV-2 from those with cross-reactive immunity generated by exposure to other coronaviruses. We characterised SARS-CoV-2 T cell immune responses in 168 PCR-confirmed SARS-CoV-2 infected subjects and 118 seronegative subjects without known SARS-CoV-2 exposure using a range of T cell assays that differentially capture immune cell function. Strong ex vivo ELISpot and proliferation responses to multiple antigens (including M, NP and ORF3) were found in those who had been infected by SARS-CoV-2 but were rare in pre-pandemic and unexposed seronegative subjects. However, seronegative doctors with high occupational exposure and recent COVID-19 compatible illness showed patterns of T cell responses characteristic of infection, indicating that these readouts are highly sensitive. By contrast, over 90% of convalescent or unexposed people showed proliferation and cellular lactate responses to spike subunits S1/S2, indicating pre-existing cross-reactive T cell populations. The detection of T cell responses to SARS-CoV-2 is therefore critically dependent on the choice of assay and antigen. Memory responses to specific non-spike proteins provides a method to distinguish recent infection from pre-existing immunity in exposed populations.", - "rel_num_authors": 63, - "rel_authors": [ - { - "author_name": "Ane Ogbe", - "author_inst": "University of Oxford" - }, - { - "author_name": "Barbara Kronsteiner", - "author_inst": "University of Oxford" - }, - { - "author_name": "Donal T Skelly", - "author_inst": "University of Oxford" - }, - { - "author_name": "Matthew Pace", - "author_inst": "University of Oxford" - }, - { - "author_name": "Anthony Brown", - "author_inst": "University of Oxford" - }, - { - "author_name": "Emily Adland", - "author_inst": "University of Oxford" - }, - { - "author_name": "Kareena Adair", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Hossain Delowar Akhter", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mohammad Ali", - "author_inst": "University of Oxford" - }, - { - "author_name": "Serat-E Ali", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Adrienn Angyal", - "author_inst": "University of Sheffield" - }, - { - "author_name": "M. Azim Ansari", - "author_inst": "University of Oxford" - }, - { - "author_name": "Carolina V Arancibia-Carcamo", - "author_inst": "University of Oxford" - }, - { - "author_name": "Helen Brown", - "author_inst": "University of Oxford" - }, - { - "author_name": "Senthil Chinnakannan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Christopher P Conlon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Catherine de Lara", - "author_inst": "University of Oxford" - }, - { - "author_name": "Thushan de Silva", - "author_inst": "University of Sheffield" - }, - { - "author_name": "Christina Dold", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tao Dong Dong", - "author_inst": "University of Oxford" - }, - { - "author_name": "Timothy Donnison", - "author_inst": "University of Oxford" - }, - { - "author_name": "David W Eyre", - "author_inst": "University of Oxford" - }, - { - "author_name": "Amy Flaxman", - "author_inst": "University of Oxford" - }, - { - "author_name": "Helen A Fletcher", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Joshua Gardner", - "author_inst": "University of Liverpool" - }, - { - "author_name": "James T Grist", - "author_inst": "University of Oxford" - }, - { - "author_name": "Carl-Philipp Hackstein", - "author_inst": "University of Oxford" - }, - { - "author_name": "Kanoot Jaruthamsophon", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Katie Jeffrey", - "author_inst": "University of Oxford" - }, - { - "author_name": "Teresa Lambe", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lian Lee", - "author_inst": "University of Oxford" - }, - { - "author_name": "Wenqin Li", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nicholas Lim", - "author_inst": "University of Oxford" - }, - { - "author_name": "Philippa C Matthews", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alexander J Mentzer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Shona C Moore", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Dean J Naisbitt", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Monday Ogese", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Graham Ogg", - "author_inst": "University of Oxford" - }, - { - "author_name": "Peter Openshaw", - "author_inst": "Imperial College" - }, - { - "author_name": "Munir Pirmohamed", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Andrew J Pollard", - "author_inst": "University of Oxford" - }, - { - "author_name": "Narayan Ramamurthy", - "author_inst": "University of Oxford" - }, - { - "author_name": "Patpong Rongkard", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sarah Rowland-Jones", - "author_inst": "University of Oxford" - }, - { - "author_name": "Oliver L Sampson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Gavin Screaton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Lizzie Stafford", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Craig Thompson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Paul J Thomson", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Ryan Thwaites", - "author_inst": "Imperial College" - }, - { - "author_name": "Vinicius Vieira", - "author_inst": "University of Oxford" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Panagiota Zacharopoulou", - "author_inst": "University of Oxford" - }, - { - "author_name": "- Oxford Immunology Network Covid-19 Response T cell Consortium", - "author_inst": "" - }, - { - "author_name": "- Oxford Protective T cell Immunology for COVID-19 (OPTIC) Clinical team", - "author_inst": "" - }, - { - "author_name": "Lance Turtle", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Paul Klenerman", - "author_inst": "University of Oxford" - }, - { - "author_name": "Philip Goulder", - "author_inst": "University of Oxford" - }, - { - "author_name": "John Frater", - "author_inst": "University of Oxford" - }, - { - "author_name": "Eleanor Barnes", - "author_inst": "University of Oxford" - }, - { - "author_name": "Susanna Dunachie", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.28.20203067", "rel_title": "Heat-based N95 mask decontamination and reuse in a large hospital setting", @@ -1136579,6 +1140139,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.29.317289", + "rel_title": "Susceptibility of midge and mosquito vectors to SARS-CoV-2 by natural route of infection", + "rel_date": "2020-09-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.29.317289", + "rel_abs": "SARS-CoV-2 is a recently emerged, highly contagious virus and the cause of the current pandemic. It is a zoonotic virus, although its animal origin is not clear yet. Person-to-person transmission occurs by inhalation of infected droplets and aerosols, or by direct contact with contaminated fomites. Arthropods transmit numerous viral, parasitic, and bacterial diseases; however, the potential role of arthropods in SARS-CoV-2 transmission is not fully understood. Thus far, a few studies have demonstrated that SARS-CoV-2 replication is not supported in cells from certain insect species nor in certain species of mosquitoes after intrathoracic inoculation. In this study, we expanded the work of SARS-CoV-2 susceptibility to biting insects after ingesting a SARS-CoV-2infected blood meal. Species tested included Culicoides sonorensis biting midges, as well as Culex tarsalis and Culex quinquefasciatus mosquitoes, all known biological vectors for numerous RNA viruses. Arthropods were allowed to feed on SARS-CoV-2 spiked blood and at various time points post infection analyzed for the presence of viral RNA and infectious virus. Additionally, cell lines derived from C. sonorensis (W8a), Ae. aegypti (C6/36), Cx. quinquefasciatus (HSU), and Cx. tarsalis (CxTrR2) were tested for SARS-CoV-2 susceptibility. Our results indicate that none of the biting insects, nor the insect cell lines support SARS-CoV-2 replication. We conclude, that biting insect do not pose a risk for transmission of SARS-CoV-2 to humans or animals following a SARS-CoV-2 infected blood meal.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Velmurugan Balaraman", + "author_inst": "Kansas State University" + }, + { + "author_name": "Barbara S. Drolet", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Natasha N Gaudreault", + "author_inst": "Kansas State University" + }, + { + "author_name": "William C. Wilson", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Jeana Owens", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Dashzeveg Bold", + "author_inst": "Kansas State University" + }, + { + "author_name": "Dustin A Swanson", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Dane C Jasperson", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Leela E Noronha", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Juergen A Richt", + "author_inst": "Kansas State University" + }, + { + "author_name": "Dana Mitzel", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.28.317685", "rel_title": "SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo", @@ -1136736,61 +1140355,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.28.20203398", - "rel_title": "Functional immunoparalysis characterized by elevated Interleukin-10 and Interleukin-10-to-Lymphocyte Count Ratio is associated with severe disease and poor outcomes in coronavirus disease 2019 (COVID-19)", - "rel_date": "2020-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20203398", - "rel_abs": "ObjectivesSevere coronavirus disease 2019 (COVID-19) is associated with a dysregulated immune state, called cytokine storm. While research has focused on the hyperinflammation, little research has been performed on the compensatory anti-inflammatory response which if severe may lead to a state of functional immunoparalysis. The aim of this study was to evaluate the anti-inflammatory response to COVID-19, by assessing interleukin-10 (IL-10) and IL-10/lymphocyte count ratio and their association with patient outcomes.\n\nMethodsAdult patients presenting to the emergency department (ED) with laboratory-confirmed COVID-19 were recruited. The primary endpoint was peak COVID-19 severity within 30 days of index ED visit. Additional endpoints included COVID-19 severity at ED disposition, development of severe acute kidney injury (AKI) or secondary bacterial infections.\n\nResultsA total of 52 COVID-19 patients were enrolled. IL-10 and IL-10/lymphocyte count were significantly higher in patients with severe disease at both time points (all p<0.05), as well as in those who developed severe AKI and secondary bacterial infection (all p[≤]0.01). In multivariable analysis, a one-unit increase in IL-10 was associated with 42% increased odds of severe COVID-19 (p=0.031), whilst a one-unit increase IL-10/lymphocyte ratio was also associated with 32% increase in odds of severe COVID-19 (p=0.013).\n\nConclusionsThe hyperinflammatory response to COVID-19 is accompanied by a simultaneous anti-inflammatory response, which is associated with poor outcomes and may increase the risk of secondary bacterial infections. IL-10 and IL-10/lymphocyte ratio at ED presentation were independent predictors of COVID-19 severity. Functional immunoparalysis in COVID-19 requires further investigation to enable more precise immunomodulatory therapy against SARS-CoV-2.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Brandon Michael Henry", - "author_inst": "Cincinnati Children's Hospital Medical Center" - }, - { - "author_name": "Stefanie Benoit", - "author_inst": "Cincinnati Children's Hospital Medical Center" - }, - { - "author_name": "Jens Vikse", - "author_inst": "Stavanger University Hospital" - }, - { - "author_name": "Brandon Berger", - "author_inst": "University of Cincinnati" - }, - { - "author_name": "Christina Pulvino", - "author_inst": "University of Cincinnati" - }, - { - "author_name": "Jonathan Hoehn", - "author_inst": "University of Cincinnati" - }, - { - "author_name": "James Rose", - "author_inst": "Cincinnati Children's Hospital Medical Center" - }, - { - "author_name": "Maria Helena Santos de Oliveira", - "author_inst": "Federal University of Parana" - }, - { - "author_name": "Giuseppe Lippi", - "author_inst": "University of Verona" - }, - { - "author_name": "Justin Benoit", - "author_inst": "University of Cincinnati" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.29.318196", "rel_title": "Design, expression, purification and characterization of a YFP-tagged 2019-nCoV spike receptor-binding domain construct", @@ -1138273,6 +1141837,49 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.09.27.315796", + "rel_title": "A Tethered Ligand Assay to Probe the SARS-CoV-2 ACE2 Interaction under Constant Force", + "rel_date": "2020-09-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.27.315796", + "rel_abs": "The current COVID-19 pandemic has a devastating global impact and is caused by the SARS-CoV-2 virus. SARS-CoV-2 attaches to human host cells through interaction of its receptor binding domain (RBD) located on the viral Spike (S) glycoprotein with angiotensin converting enzyme-2 (ACE2) on the surface of host cells. RBD binding to ACE2 is a critical first step in SARS-CoV-2 infection. Viral attachment occurs in dynamic environments where forces act on the binding partners and multivalent interactions play central roles, creating an urgent need for assays that can quantitate SARS-CoV-2 interactions with ACE2 under mechanical load and in defined geometries. Here, we introduce a tethered ligand assay that comprises the RBD and the ACE2 ectodomain joined by a flexible peptide linker. Using specific molecular handles, we tether the fusion proteins between a functionalized flow cell surface and magnetic beads in magnetic tweezers. We observe repeated interactions of RBD and ACE2 under constant loads and can fully quantify the force dependence and kinetics of the binding interaction. Our results suggest that the SARS-CoV-2 ACE2 interaction has higher mechanical stability, a larger free energy of binding, and a lower off-rate than that of SARS-CoV-1, the causative agents of the 2002-2004 SARS outbreak. In the absence of force, the SARS-CoV-2 RBD rapidly (within [≤]1 ms) engages the ACE2 receptor if held in close proximity and remains bound to ACE2 for 400-800 s, much longer than what has been reported for other viruses engaging their cellular receptors. We anticipate that our assay will be a powerful tool investigate the roles of mutations in the RBD that might alter the infectivity of the virus and to test the modes of action of neutralizing antibodies and other agents designed to block RBD binding to ACE2 that are currently developed as potential COVID-19 therapeutics.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Magnus S. Bauer", + "author_inst": "LMU Munich" + }, + { + "author_name": "Sophia Gruber", + "author_inst": "LMU Munich" + }, + { + "author_name": "Lukas F. Milles", + "author_inst": "University of Washington, Seattle" + }, + { + "author_name": "Thomas Nicolaus", + "author_inst": "LMU Munich" + }, + { + "author_name": "Leonard C. Schendel", + "author_inst": "LMU Munich" + }, + { + "author_name": "Hermann E. Gaub", + "author_inst": "LMU Munich" + }, + { + "author_name": "Jan Lipfert", + "author_inst": "LMU Munich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.09.27.316174", "rel_title": "Discovery and Development of Human SARS-CoV-2 Neutralizing Antibodies using an Unbiased Phage Display Library Approach", @@ -1138462,33 +1142069,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.09.28.317206", - "rel_title": "Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2", - "rel_date": "2020-09-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.28.317206", - "rel_abs": "The ongoing pandemic caused by coronavirus SARS-COV-2 continues to rage with devastating consequences on human health and global economy. The spike glycoprotein on the surface of coronavirus mediates its entry into host cells and is the target of all current antibody design efforts to neutralize the virus. The glycan shield of the spike helps the virus to evade the human immune response by providing a thick sugar-coated barrier against any antibody. To study the dynamic motion of glycans in the spike protein, we performed microsecond-long MD simulation in two different states that correspond to the receptor binding domain in open or closed conformations. Analysis of this microsecond-long simulation revealed a scissoring motion on the N-terminal domain of neighboring monomers in the spike trimer. Role of multiple glycans in shielding of spike protein in different regions were uncovered by a network analysis, where the high betweenness centrality of glycans at the apex revealed their importance and function in the glycan shield. Microdomains of glycans were identified featuring a high degree of intra-communication in these microdomains. An antibody overlap analysis revealed the glycan microdomains as well as individual glycans that inhibit access to the antibody epitopes on the spike protein. Overall, the results of this study provide detailed understanding of the spike glycan shield, which may be utilized for therapeutic efforts against this crisis.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mahdi Ghorbani", - "author_inst": "University of Maryland" - }, - { - "author_name": "Bernie R Brooks", - "author_inst": "National Institutes of Health/NHLBI" - }, - { - "author_name": "Jeffery B. Klauda", - "author_inst": "University of Maryland" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.09.27.316158", "rel_title": "Hydroxychloroquine increased psychiatric-like behaviors and disrupted the expression of related genes in the mouse brain", @@ -1139679,6 +1143259,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.09.22.20195628", + "rel_title": "Public health information on COVID-19 for international travellers: Lessons learned from a rapid mixed-method evaluation in the UK containment phase", + "rel_date": "2020-09-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20195628", + "rel_abs": "Introduction In the containment phase of the response to the COVID-19 outbreak, Public Health England (PHE) delivered advice to travellers arriving at major UK ports. We aimed to rapidly evaluate the impact and effectiveness of these communication materials for passengers in the early stages of the pandemic. Methods In stage I (Patient and Public Involvement, PPI) we interviewed seven travellers who had returned from China in January and February 2020. We used these results to develop a questionnaire and topic guides for stage II, a cross-sectional survey and follow-up interviews with passengers arriving at London Heathrow Airport on scheduled flights from China and Singapore. The survey assessed passengers' knowledge of symptoms, actions to take and attitudes towards PHE COVID-19 public health information; interviews explored their views of official public health information and self-isolation. Results In stage II, 121 passengers participated in the survey and 15 in follow-up interviews. 83% of surveyed passengers correctly identified all three COVID-19 associated symptoms listed in PHE information at that time. Most could identify the recommended actions and found the advice understandable and trustworthy. Interviews revealed that passengers shared concerns about the lack of wider official action, and that passengers' knowledge had been acquired elsewhere as much from PHE. Respondents also noted their own agency in choosing to self-isolate, partially as a self-protective measure. Conclusion PHE COVID-19 public health information was perceived as clear and acceptable, but we found that passengers acquired knowledge from various sources and they saw the provision of information alone on arrival as an insufficient official response. Our study provides fresh insights into the importance of taking greater account of diverse information sources and of the need for public assurance in creating public health information materials to address global health threats. Keywords COVID-19, public health advice, government, policy, airport, international travel", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Tingting Zhang", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK" + }, + { + "author_name": "Charlotte Robin", + "author_inst": "Field Epidemiology, Field Service, National Infection Service, Public Health England, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science a" + }, + { + "author_name": "Shenghan Cai", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK" + }, + { + "author_name": "Clare Sawyer", + "author_inst": "UK Field Epidemiology Training Programme, Global Public Health Division, Public Health England, London, UK; Communicable Disease Surveillance Centre, Public Hea" + }, + { + "author_name": "Wendy Rice", + "author_inst": "Field Epidemiology, Field Service, National Infection Service, Public Health England, Bristol, UK" + }, + { + "author_name": "Louise E. Smith", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; NIHR Health Protection Research Unit in Emergency Preparedness and Resp" + }, + { + "author_name": "Richard Aml\u00f4t", + "author_inst": "NIHR Health Protection Research Unit in Behavioural Science and Evaluation, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Health Protection R" + }, + { + "author_name": "G. James Rubin", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; NIHR Health Protection Research Unit in Emergency Preparedness and Resp" + }, + { + "author_name": "Rosy Reynolds", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluati" + }, + { + "author_name": "Lucy Yardley", + "author_inst": "Health Protection Research Unit in Behavioural Science and Evaluation, Bristol Medical School, University of Bristol, Bristol, UK; School of Psychological Scien" + }, + { + "author_name": "Matthew Hickman", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluati" + }, + { + "author_name": "Isabel Oliver", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol; Field Epidemiology, Field Service, National Infection Service, Public Health England;" + }, + { + "author_name": "Helen Lambert", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluati" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.23.20200212", "rel_title": "Impact of Personal Care Habits on Post-Lockdown COVID-19 Contagion: Insights from Agent-based Simulations", @@ -1139788,97 +1143435,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.09.24.20191411", - "rel_title": "Detection of SARS-CoV-2 within the healthcare environment: a multicentre study conducted during the first wave of the COVID-19 outbreak in England", - "rel_date": "2020-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.24.20191411", - "rel_abs": "Understanding how Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is spread within the hospital setting is essential if staff are to be adequately protected, effective infection control measures are to be implemented and nosocomial transmission is to be prevented. The presence of SARS-CoV-2 in the air and on environmental surfaces around hospitalised patients, with and without respiratory symptoms, was investigated. Environmental sampling was carried out within eight hospitals in England during the first wave of the COVID-19 outbreak. Samples were analysed using reverse transcription polymerase chain reaction (RT-PCR) and virus isolation assays. SARS-CoV-2 RNA was detected on 30 (8.9%) of 336 environmental surfaces. Ct values ranged from 28.8 to 39.1 equating to 2.2 x 105 to 59 genomic copies/swab. Concomitant bacterial counts were low, suggesting the cleaning performed by nursing and domestic staff across all eight hospitals was effective. SARS-CoV-2 RNA was detected in four of 55 air samples taken < 1 m from four different patients. In all cases, the concentration of viral RNA was low and ranged from < 10 to 460 genomic copies per m3 of air. Infectious virus was not recovered from any of the PCR positive samples analysed. Effective cleaning can reduce the risk of fomite (contact) transmission but some surface types may facilitate the survival, persistence and/or dispersal of SARS-CoV-2. The presence of low or undetectable concentrations of viral RNA in the air supports current guidance on the use of specific PPE ensembles for aerosol and non-aerosol generating procedures.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Ginny Moore", - "author_inst": "Public Health England" - }, - { - "author_name": "Helen Rickard", - "author_inst": "Public Health England" - }, - { - "author_name": "David Stevenson", - "author_inst": "Public Health England" - }, - { - "author_name": "Paz Aranega Bou", - "author_inst": "Public Health England" - }, - { - "author_name": "James Pitman", - "author_inst": "Public Health England" - }, - { - "author_name": "Ant Crook", - "author_inst": "Public Health England" - }, - { - "author_name": "Katherine Davies", - "author_inst": "Public Health England" - }, - { - "author_name": "Antony Spencer", - "author_inst": "Public Health England" - }, - { - "author_name": "Chris Burton", - "author_inst": "Public Health England" - }, - { - "author_name": "Linda Easterbrook", - "author_inst": "Public Health England" - }, - { - "author_name": "Hannah E Love", - "author_inst": "Public Health England" - }, - { - "author_name": "Sian Summers", - "author_inst": "Public Health England" - }, - { - "author_name": "Stephen R Welch", - "author_inst": "Public Health England" - }, - { - "author_name": "Nadina Wand", - "author_inst": "Public Health England" - }, - { - "author_name": "Katy-Anne Thompson", - "author_inst": "Public Health England" - }, - { - "author_name": "Thomas Pottage", - "author_inst": "Public Health England" - }, - { - "author_name": "Kevin S Richards", - "author_inst": "Public Health England" - }, - { - "author_name": "Jake Dunning", - "author_inst": "Public Health England" - }, - { - "author_name": "Allan Bennett", - "author_inst": "Public Health England" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.18.20195370", "rel_title": "Diagnosis of SARS-CoV-2 infection with LamPORE, a high-throughput platform combining loop-mediated isothermal amplification and nanopore sequencing", @@ -1141421,6 +1144977,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.25.20201459", + "rel_title": "Performance of a point of care test for detecting IgM and IgG antibodies against SARS-CoV-2 and seroprevalence in blood donors and health care workers in Panama", + "rel_date": "2020-09-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20201459", + "rel_abs": "Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic, which has reached 28 million cases worldwide in eight months. The serological detection of antibodies against the virus will play a pivotal role in complementing molecular tests to improve diagnostic accuracy, contact tracing, vaccine efficacy testing and seroprevalence surveillance. Here, we aimed first to evaluate a lateral flow assays ability to identify specific IgM and IgG antibodies against SARS-CoV-2 and second, to report the seroprevalence of these antibodies among health care workers and healthy volunteer blood donors in Panama. We recruited study participants between April 30th and July 7th, 2020. For the test validation and performance evaluation, we analyzed serum samples from participants with clinical symptoms and confirmed positive RT-PCR for SARS-CoV-2, participants with other confirmed infectious diseases, and a set of pre-pandemic serum samples. We used two by two table analysis to determine the test sensitivity and specificity as well as the kappa agreement value with a 95% confidence interval. Then, we used the lateral flow assay to determine seroprevalence among serum samples from COVID-19 patients, potentially exposed health care workers, and healthy volunteer donors. Our results show this assay reached a positive percent agreement of 97.2% (95% CI 84.2-100.0%) for detecting both IgM and IgG. The assay showed a kappa of 0.898 (95%CI 0.811-0.985) and 0.918 (95% CI 0.839-0.997) for IgM and IgG, respectively. The evaluation of serum samples from hospitalized COVID-19 patients indicates a correlation between test sensitivity and the number of days since symptom onset; the highest positive percent agreement (87% (95% CI 67.0-96.3%)) was observed at [≥]15 days post-symptom onset. We found an overall antibody seroprevalence of 11.6% (95% CI 8.5-15.8%) among both health care workers and healthy blood donors. Our findings suggest this lateral flow assay could contribute significantly to implementing seroprevalence testing in locations with active community transmission of SARS-CoV-2.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Alcibiades Villarreal", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Giselle Rangel", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Xu Zhang", + "author_inst": "CAS" + }, + { + "author_name": "Digna Wong", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Carolina De La Guardia", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Gabrielle Britton", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Patricia L. Fernandez", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Carlos M Restrepo", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Ambar Perez", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Diana Oviedo", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Maria B Carreira", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Gilberto A. Eskildsen", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Dilcia Sambrano", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Yamitzel Zaldivar", + "author_inst": "GORGAS" + }, + { + "author_name": "Danilo Franco", + "author_inst": "GORGAS" + }, + { + "author_name": "Sandra Lopez Verges", + "author_inst": "GORGAS" + }, + { + "author_name": "Dexi Zhang", + "author_inst": "CAS" + }, + { + "author_name": "Fangjing Fan", + "author_inst": "CAS" + }, + { + "author_name": "Baojun Wang", + "author_inst": "KEWEI" + }, + { + "author_name": "Xavier Saez-Llorens", + "author_inst": "CEVAXIN" + }, + { + "author_name": "Rodrigo DeAntonio", + "author_inst": "CEVAXIN" + }, + { + "author_name": "Ivonne Torres-Atencio", + "author_inst": "UP" + }, + { + "author_name": "Fernando Diaz Subia", + "author_inst": "Pacifica Salud" + }, + { + "author_name": "Eduardo Ortega-Barria", + "author_inst": "GSK" + }, + { + "author_name": "Rao Kosagisharaf", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Ricardo Lleonart", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Chong Li", + "author_inst": "CAS" + }, + { + "author_name": "Amador Goodridge", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "- COVID-19 SEROLOGY COLLABORATOR GROUP", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.24.20200394", "rel_title": "Hitting the diagnostic sweet spot: Point-of-care SARS-CoV-2 salivary antigen testing with an off-the-shelf glucometer", @@ -1141570,33 +1145257,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.09.24.20197293", - "rel_title": "Poor inhibitory control and stress as risk-factors for alcohol (mis)use during the COVID-19 pandemic in the UK: a national cross-sectional study across four generations", - "rel_date": "2020-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.24.20197293", - "rel_abs": "BackgroundThe impact COVID-19 on the UK populations alcohol intake is unknown. We assessed change in alcohol-use and hazardous drinking during the first lockdown, and tested the hypothesis that variation would be predicted by stress and inhibitory-control.\n\nMethodsWe interrogated cross-sectional data from the first sweep of the COVID-19 longitudinal survey, comprising 4 national cohorts (13 453 respondents, 19-62 years). Respondents self-reported their alcohol use, stress, and inhibitory control. We regressed change in drinking and alcohol misuse on stress and inhibitory control, adjusting for covariates to account for demographics.\n\nFindings29{middle dot}08% 30-year-olds increased alcohol use post-COVID-19. Stress was a major contributing factor to increased alcohol use in 30-year olds (adjusted OR 3{middle dot}92, 95% CI 1{middle dot}17 - 13{middle dot}15), as was inhibitory control in 19-year-olds (adjusted OR 1{middle dot}14, 95% CI 1{middle dot}05 - 1{middle dot}23), 30-year-olds (adjusted OR 1{middle dot}18, 95% CI 1.05 - 1.33) and 50-year-olds (adjusted OR 1{middle dot}06, 95% CI 1{middle dot}01 - 1{middle dot}12). We identified several interactions between stress and inhibitory control in all age groups, suggesting a complex age-specific relationship between the risk factors and alcohol use and misuse during the pandemic.\n\nInterpretationIn the UK, alcohol use increased in up to 30% of the population during COVID-19, resulting from a combination of factors including poor inhibitory control and stress. It is critical in future lockdowns that clinicians and public health officials are aware of the challenges faced by different age groups, and prioritise and personalise interventions and prevention measures appropriately.\n\nFundingESRC, Foundation for Liver Research.\n\nPutting research into contextO_ST_ABSEvidence before the studyC_ST_ABSWe searched PubMed, Web of Science, EBSCO Discovery, bioRxiv, medRxiv, and PsyArXiv for articles published between Jan 1, 2020 and Sep 1, 2020, with the following keywords: \"covid-19\", \"coronavirus\", and \"alcohol\". We prioritised the selection of references based on relevance, importance, opportunity for further reading, and whether the work had been peer-reviewed. There have been several published articles that address the issue of alcohol use and misuse during COVID- 19, including a number of editorials and some limited empirical work. There were no nationally representative studies about alcohol use in the UK. In addition, all of the studies identified simply reported figures of those using alcohol during the pandemic, and to the best of our knowledge, none covered risk-factors for alcohol misuse.\n\nAdded value of this studyUsing data from the COVID-19 national longitudinal survey (first sweep), comprising data from 18 000 people across five national cohorts (aged 19-74), we tested the hypothesis that people who reported higher levels of stress, and who self-reported low impulse-control, would show higher rates of alcohol use/misuse during the pandemic lockdown. First, we show the proportion of adults across the UK that are drinking more during the pandemic, and how this differs by age and gender. Second, we show that while higher levels of stress were associated with higher levels of alcohol intake in some (e.g., 30-year-olds), we found that the relationship was complex and multifaceted. Stress-induced alcohol use and misuse was dependent on age and personality characteristics, with low impulse-control predictive of higher levels of alcohol consumption in 19-, 30- and 50-year-olds, and several stress x personality interactions.\n\nImplications of all the available evidenceStress, as well as poor inhibitory control, were risk factors for the susceptibility to increased alcohol intake and hazardous drinking during the early stages of the COVID-19 pandemic and lockdown. The government, healthcare professionals, and the global media should consider the impact of change of lifestyle and stress that might impact on alcohol consumption among at-risk individuals during any future lockdowns. Similarly, additional support for those that may go on to develop an alcohol use disorder or relapse needs to be put in place.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "James M Clay", - "author_inst": "University of Portsmouth" - }, - { - "author_name": "Lorenzo D Stafford", - "author_inst": "University of Portsmouth" - }, - { - "author_name": "Matthew O Parker", - "author_inst": "University of Portsmouth" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "addiction medicine" - }, { "rel_doi": "10.1101/2020.09.24.20197632", "rel_title": "Predictors of Incident Viral Symptoms Ascertained in the Era of Covid-19", @@ -1143143,6 +1146803,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.09.23.310565", + "rel_title": "COVID-19 CG: Tracking SARS-CoV-2 mutations by locations and dates of interest", + "rel_date": "2020-09-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.23.310565", + "rel_abs": "COVID-19 CG is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs) and lineages while filtering by location, date, gene, and mutation of interest. COVID-19 CG provides significant time, labor, and cost-saving utility to diverse projects on SARS-CoV-2 transmission, evolution, emergence, immune interactions, diagnostics, therapeutics, vaccines, and intervention tracking. Here, we describe case studies in which users can interrogate (1) SNVs in the SARS-CoV-2 Spike receptor binding domain (RBD) across different geographic regions to inform the design and testing of therapeutics, (2) SNVs that may impact the sensitivity of commonly used diagnostic primers, and (3) the recent emergence of a dominant lineage harboring an S477N RBD mutation in Australia. To accelerate COVID-19 research and public health efforts, COVID-19 CG will be continually upgraded with new features for users to quickly and reliably pinpoint mutations as the virus evolves throughout the pandemic and in response to therapeutic and public health interventions.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Albert Tian Chen", + "author_inst": "Broad Institute of MIT & Harvard" + }, + { + "author_name": "Kevin Altschuler", + "author_inst": "NA" + }, + { + "author_name": "Shing Hei Zhan", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Yujia Alina Chan", + "author_inst": "Broad Institute of MIT & Harvard" + }, + { + "author_name": "Benjamin E Deverman", + "author_inst": "Broad Institute of MIT and Harvard" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.09.24.310490", "rel_title": "Broad-spectrum, patient-adaptable inhaled niclosamide-lysozyme particles are efficacious against coronaviruses in lethal murine infection models", @@ -1143360,77 +1147055,6 @@ "type": "confirmatory results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.09.24.285940", - "rel_title": "Resveratrol And Pterostilbene Potently Inhibit SARS-CoV-2 Infection In Vitro", - "rel_date": "2020-09-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.24.285940", - "rel_abs": "The current COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has an enormous impact on human health and economy. In search for therapeutic options, researchers have proposed resveratrol, a food supplement with known antiviral, anti-inflammatory and anti-oxidant properties as an advantageous antiviral therapy for SARS-CoV-2 infection. Here, we provide evidence that both resveratrol and its metabolically more stable structural analog, pterostilbene, exhibit potent antiviral properties against SARS-CoV-2 in vitro. Resveratrol and pterostilbene showed antiviral activity in African green monkey kidney cells and in human primary bronchial epithelial cells cultured in an air-liquid interface system. Both compounds actively inhibit virus replication within infected cells as reduced virus progeny production was observed when the compound was added at post-inoculation conditions. Without replenishment of the compound, antiviral activity was observed up to roughly 5 rounds of replication, demonstrating the long-lasting effect of these compounds. Collectively, our data indicate that resveratrol and pterostilbene are promising antiviral compounds to treat SARS-CoV-2 infection. Because these results represent laboratory findings in cells, we advocate evaluation of these compounds in clinical trials before statements are made whether or not these drugs are advantageous for COVID-19 treatment.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "B. M. ter Ellen", - "author_inst": "Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, The Netherlands" - }, - { - "author_name": "N. Dinesh Kumar", - "author_inst": "Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, The Netherlands" - }, - { - "author_name": "E. M. Bouma", - "author_inst": "University Medical Center Groningen" - }, - { - "author_name": "B. Troost", - "author_inst": "Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, The Netherlands" - }, - { - "author_name": "D. P.I. van de Pol", - "author_inst": "Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, The Netherlands" - }, - { - "author_name": "H. H. van der Ende-Metselaar", - "author_inst": "Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, The Netherlands" - }, - { - "author_name": "L. Apperloo", - "author_inst": "Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, GRIAC Research Institute, The Netherlands" - }, - { - "author_name": "D. van Gosliga", - "author_inst": "Department of Pediatrics, Beatrix Childrens Hospital, University Medical Center Groningen, University of Groningen, GRIAC Research Institute, Groningen, The Net" - }, - { - "author_name": "M. van den Berge", - "author_inst": "Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, GRIAC Research Institute, Groningen, The Netherlands." - }, - { - "author_name": "M. C. Nawijn", - "author_inst": "Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, GRIAC Research Institute, 9700 RB Groningen, The Neth" - }, - { - "author_name": "P. H.J. van der Voort", - "author_inst": "Department of Critical Care, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands." - }, - { - "author_name": "J. Moser", - "author_inst": "Department of Critical Care, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands." - }, - { - "author_name": "I. A. Rodenhuis-Zybert", - "author_inst": "Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, The Netherlands" - }, - { - "author_name": "J. M. Smit", - "author_inst": "Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.09.24.311845", "rel_title": "An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic", @@ -1144889,6 +1148513,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2020.09.22.20198465", + "rel_title": "Seroprevalence of immunoglobulin M and G antibodies against SARS-CoV-2 in ophthalmic patients", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20198465", + "rel_abs": "Using serological test to estimate the prevalence and infection potential of coronavirus disease 2019 in ocular diseases patients help understand the relationship between ocular diseases and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We conducted a cross-sectional study assaying the IgG and IgM antibodies in 1331 individuals with ocular diseases by using a magnetic chemiluminescence enzyme immunoassay kit, during the period from February 2020 to May 2020. In our study, the seroposivity in total ocular disease patients was 0.83% (11/1331). The patients with different ocular diseases including xerophthalmia, keratitis, conjunctival cyst, cataract, glaucoma, refractive error, strabismus and others had seroposivity of 2.94%, 12.5%, 25%, 4.41%, 2.63%, 1.6%, 2.22% and 0%, respectively. Among that, two ocular surface disease groups (keratitis and conjunctival cyst) had higher seroprevalence compared with others. All the participants were reverse transcription polymerase chain reaction negative for SARS-CoV-2 from throat swabs. Our study evaluated the seroprevalence in patients with different ocular diseases, which will help us understand the relationship between ocular disease and SARS-CoV-2 infection. Furthermore, the serological test for the presence of IgM and/or IgG antibodies against SARS-CoV-2 might provide accurate estimate of the prevalence of SARS-CoV-2 infection in patients with ocular diseases.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "shengjie li Sr.", + "author_inst": "Fudan University" + }, + { + "author_name": "yichao qiu", + "author_inst": "fudan university" + }, + { + "author_name": "li tang", + "author_inst": "fudan university" + }, + { + "author_name": "zhujian wang", + "author_inst": "fudan university" + }, + { + "author_name": "wenjun cao", + "author_inst": "fudan university" + }, + { + "author_name": "xinghuai sun", + "author_inst": "fudan university" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.20.20198432", "rel_title": "COVID-19 dynamics across the US: A deep learning study of human mobility and social behavior", @@ -1144994,121 +1148657,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.09.22.20199455", - "rel_title": "Norwich COVID-19 Testing Initiative: feasibility project evaluation", - "rel_date": "2020-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20199455", - "rel_abs": "BackgroundThere is a high prevalence of COVID-19 in university-age students, who are returning to university campuses. There is little evidence regarding the feasibility of universal, asymptomatic testing to control outbreaks in this population. This study aimed to pilot mass COVID-19 testing on a university research park, to assess the feasibility and acceptability of scaling up to all staff and students.\n\nMethodsThis was a cross-sectional feasibility study on a university research park in the East of England. Staff and students (5,625) on the research park were eligible to participate. Polymerase chain reaction (PCR) testing was offered to all participants. Participants were offered 4 swabs, which they self-administered over a two-week period. Outcome measures included: uptake; drop-out rate; positivity rates; participant acceptability measures; laboratory processing measures.\n\nResults798/1053 (76%) of those who registered provided at least one swab and of these, 687 (86%) provided all four. 681/687 (99%) had all negative results. 6 participants had one inconclusive result. There were no positive results. 458/798 (57%) participants responded to a post-testing questionnaire. 446/458 (97.5%) of those who responded agreed that they would be interested in repeat testing in the future.\n\nConclusionsRepeated self-testing is feasible and acceptable to a university population.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Tara Berger Gillam", - "author_inst": "University of East Anglia" - }, - { - "author_name": "Jennifer Cole", - "author_inst": "University of East Anglia" - }, - { - "author_name": "Karim Gharbi", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Emily Angiolini", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Tom O Barker", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Peter Bickerton", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Thomas Brabbs", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Jeannette S Chin", - "author_inst": "University of East Anglia" - }, - { - "author_name": "Enrico Coen", - "author_inst": "John Innes Centre" - }, - { - "author_name": "Sarah Cossey", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Robert P Davey", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Rose Davidson", - "author_inst": "University of East Anglia" - }, - { - "author_name": "Alex Durrant", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Dylan Edwards", - "author_inst": "University of East Anglia" - }, - { - "author_name": "Neil Hall", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Suzanne Henderson", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Mark Hitchcock", - "author_inst": "UEA Health and Social Care Partners" - }, - { - "author_name": "Naomi Irish", - "author_inst": "Earlham Institute" - }, - { - "author_name": "James Lipscombe", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Greg Jones", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Gerard Parr", - "author_inst": "University of East Anglia" - }, - { - "author_name": "Stuart A Rushworth", - "author_inst": "University of East Anglia" - }, - { - "author_name": "Neil Shearer", - "author_inst": "Earlham Institute" - }, - { - "author_name": "Russell Smith", - "author_inst": "University of East Anglia" - }, - { - "author_name": "Nick Steel", - "author_inst": "University of East Anglia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.21.20198309", "rel_title": "Early Humoral Response Correlates with Disease Severity and Outcomes in COVID-19 Patients", @@ -1146723,6 +1150271,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.09.20.20197608", + "rel_title": "At home and online during the early months of the COVID-19 pandemic and the relationship to alcohol consumption in a national sample of U.S. adults", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.20.20197608", + "rel_abs": "ObjectiveThe current study seeks to understand the links between social media use and alcohol consumption during the early months of the COVID-19 pandemic.\n\nMethodData were from the national Understanding American Study, a probability-based Internet panel weighted to represent the U.S. population. Subjects (N=5874; 51% female) were adults, 18 years and older, who completed a March survey (wave 1) and a follow-up survey one month later (wave 3). Analyses assessed the relationship of social media use at wave 1 with wave 3 alcohol use, accounting for wave 1 alcohol use and the sociodemographic characteristics of the sample. We examined the effect of working or studying from home as a moderator.\n\nResultsTwitter and Instagram users, but not Facebook users, drank more frequently at wave 3 than non-users. For Instagram users, more frequent alcohol use at wave 3 was at least partially attributed to the frequency of drinking at wave 1. The interaction between Twitter use and working or studying from home was statistically significant. The combination of being on Twitter and working or studying from home was associated with drinking more days a week.\n\nConclusionsExposure to content about COVID-19 and increased alcohol consumption during the pandemic may contribute to more frequent alcohol use for some social media users, especially those sheltering at home. The study of public health messaging via social media to change alcohol use behaviors during traumatic events is warranted.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Karen G Chartier", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Jeanine P.D. Guidry", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Catherine A. Lee", + "author_inst": "George Mason University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "addiction medicine" + }, { "rel_doi": "10.1101/2020.09.20.20196907", "rel_title": "Microfluidic Affinity Profiling reveals a Broad Range of Target Affinities for Anti-SARS-CoV-2 Antibodies in Plasma of Covid Survivors", @@ -1146908,277 +1150483,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.18.20197228", - "rel_title": "COVeAGE-DB: A database of age-structured COVID-19 cases and deaths.", - "rel_date": "2020-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.18.20197228", - "rel_abs": "COVerAGE-DB is an open-access database including cumulative counts of confirmed COVID-19 cases, deaths, and tests by age and sex. The main goal of COVerAGE-DB is to provide a centralized, standardized, age-harmonized, and fully reproducible database of COVID-19 data. Original data and sources are provided alongside data and measures in age-harmonized formats. An international team, composed of more than 60 researchers, contributed to the collection of data and metadata in COVerAGE-DB from governmental institutions, as well as to the design and implementation of the data processing and validation pipeline. The database is still in development, and at this writing, it includes 89 countries, and 237 subnational areas. Cumulative counts of COVID-19 cases, deaths, and tests are recorded daily (when possible) since January 2020. Many time series thus fully capture the first pandemic wave and the beginning of later waves. Since collection efforts began for COVerAGE-DB several studies have used the data.", - "rel_num_authors": 64, - "rel_authors": [ - { - "author_name": "Tim Riffe", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Enrique Acosta", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Jose Manuel Aburto", - "author_inst": "University of Oxford" - }, - { - "author_name": "Diego Alburez-Gutierrez", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Anna Altov\u00e1", - "author_inst": "Charles University" - }, - { - "author_name": "Ugofilippo Basellini", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Simona Bignami", - "author_inst": "Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Didier Breton", - "author_inst": "Universit\u00e9 de Strassbourg" - }, - { - "author_name": "Eungang Choi", - "author_inst": "Ohio State University" - }, - { - "author_name": "Jorge Cimentada", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Gonzalo De Armas", - "author_inst": "Universidad de la Rep\u00fablica" - }, - { - "author_name": "Emanuele Del Fava", - "author_inst": "Max Planck Institute For Demographic Research" - }, - { - "author_name": "Alicia Delgado", - "author_inst": "Pontificia Universidad Cat\u00f3lica del Ecuador" - }, - { - "author_name": "Viorela Diaconu", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Jessica Donzowa", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Christian Dudel", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Antonia Fr\u00f6hlich", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Alain Gagnon", - "author_inst": "Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Mariana Garcia Crist\u00f3mo", - "author_inst": "Colegio de M\u00e9xico" - }, - { - "author_name": "Victor M. Garcia-Guerrero", - "author_inst": "Colegio de M\u00e9xico" - }, - { - "author_name": "Armando Gonz\u00e1lez-D\u00edaz", - "author_inst": "Colegio de M\u00e9xico" - }, - { - "author_name": "Irwin Hecker", - "author_inst": "Universit\u00e9 de Strassbourg" - }, - { - "author_name": "Dagnon Eric Koba", - "author_inst": "L'Agence Fran\u00e7aise de D\u00e9veloppement" - }, - { - "author_name": "Marina Kolobova", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Mine K\u00fchn", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "M\u00e9lanie L\u00e9pori", - "author_inst": "Universit\u00e9 de Strassbourg" - }, - { - "author_name": "Chia Liu", - "author_inst": "Saint Andrews University" - }, - { - "author_name": "Andrea Lozer", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Madalina Manea", - "author_inst": "Research Institute for the Quality of Life" - }, - { - "author_name": "Muntasir Masum", - "author_inst": "University of Texas, San Antonio" - }, - { - "author_name": "Ryohei Mogi", - "author_inst": "Centre d'estudis Demogr\u00e0fics" - }, - { - "author_name": "C\u00e9line Monicolle", - "author_inst": "Universit\u00e9 de Strassbourg" - }, - { - "author_name": "Saskia Morwinsky", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Ronald Musizvingoza", - "author_inst": "Bursa Uludag University" - }, - { - "author_name": "Mikko Myrskyl\u00e4", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Marilia R. Nepomuceno", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Michelle Nickel", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Natalie Nitsche", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Anna Oksuzyan", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Samuel Oladele", - "author_inst": "Federal University Oye Ekiti" - }, - { - "author_name": "Emmanuel Olamijuwon", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Oluwafunke Omodara", - "author_inst": "Federal University Oye Ekiti" - }, - { - "author_name": "Soumaila Ouedraogo", - "author_inst": "French Institute for Demographic Studies" - }, - { - "author_name": "Mariana Paredes", - "author_inst": "Universidad de la Rep\u00fablica" - }, - { - "author_name": "Marius Pascariu", - "author_inst": "SCOR" - }, - { - "author_name": "Manuel Piriz", - "author_inst": "Universidad de la Rep\u00fablica" - }, - { - "author_name": "Raquel Pollero", - "author_inst": "Universidad de la Rep\u00fablica" - }, - { - "author_name": "Larbi Qanni", - "author_inst": "Universit\u00e4t Rostock" - }, - { - "author_name": "Federico Rehermann", - "author_inst": "Universidad de la Rep\u00fablica" - }, - { - "author_name": "Filipe Ribeiro", - "author_inst": "Universidade de \u00c9vora" - }, - { - "author_name": "Silvia Rizzi", - "author_inst": "University of Southern Denmark" - }, - { - "author_name": "Francisco Rowe", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Isaac Sasson", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Jiaxin Shi", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Rafael Silva-Ramirez", - "author_inst": "Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Cosmo Strozza", - "author_inst": "University of Southern Denmark" - }, - { - "author_name": "Catalina Torres", - "author_inst": "Mus\u00e9um national d'histoire naturelle" - }, - { - "author_name": "Sergi Trias-Llimos", - "author_inst": "Centre d'Estudis Demogr\u00e0fics" - }, - { - "author_name": "Fumiya Uchikoshi", - "author_inst": "Princeton University" - }, - { - "author_name": "Alyson van Raalte", - "author_inst": "Max Planck Institute for Demographic Research" - }, - { - "author_name": "Paola Vazquez-Castillo", - "author_inst": "Colegio de M\u00e9xico" - }, - { - "author_name": "Estev\u00e3o Vilela", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Iv\u00e1n Williams", - "author_inst": "Universidad de Buenos Aires" - }, - { - "author_name": "Virginia Zarulli", - "author_inst": "University of Southern Denmark" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.21.20197244", "rel_title": "A simplified approach to monitoring the COVID-19 epidemiologic situation using waste water analysis and its application in Russia", @@ -1148513,6 +1151817,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.22.20199372", + "rel_title": "Limits and opportunities of SARS-CoV-2 antigen rapid Tests: an experience based perspective", + "rel_date": "2020-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20199372", + "rel_abs": "Due to the currently increasing case numbers of SARS-CoV-2 infections worldwide there is an increasing need for rapid diagnostic devices in addition to existing PCR-capacities. Therefore, rapid antigen assays including lateral flow assays are discussed as an alternative method. In comparison to an established RT-PCR protocol, however the novel lateral flow assay unfortunately lowered the expectations set in these assays.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Verena Schildgen", + "author_inst": "Kliniken der Stadt Koeln gGmbH, Klinikum der Privaten Universitaet Witten/Herdecke" + }, + { + "author_name": "Sabrina Demuth", + "author_inst": "Kliniken der Stadt Koeln" + }, + { + "author_name": "Jessica Lusebrink", + "author_inst": "Kliniken der Stadt Koeln" + }, + { + "author_name": "Oliver Schildgen", + "author_inst": "Kliniken der Stadt Koeln gGmbH, Klinikum der Privaten Universtaet Witten/Herdecke" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.21.20199133", "rel_title": "Reorganization of Substance Use Treatment and Harm Reduction Services during the COVID-19 Pandemic: A Global Survey", @@ -1148754,45 +1152089,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.22.20199430", - "rel_title": "Factors associated with drinking behaviour during COVID-19 social distancing and lockdown among adults in the UK", - "rel_date": "2020-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20199430", - "rel_abs": "AimTo assess what factors were associated with reported changes to usual alcohol drinking behaviour during the start of lockdown in the UK.\n\nDesignOnline cross-sectional survey from 21st March to 4th April 2020.\n\nSettingUK.\n\nParticipants30,375 adults aged [≥] 18y.\n\nMeasurementsChanges in drinking over the past week, sociodemographic characteristics, diagnosed or suspected COVID-19, adherence to COVID-19 protective behaviours, stress about COVID-19, finances or boredom, recent drop in household income, key worker status, and health conditions.\n\nFindingsOf 22,113 drinkers (65.7% of analytic sample), 48.1% (95% CI=47.0-49.1%) reported drinking about the same as usual, 25.7% (24.8-26.6%) reported drinking less than usual, and 26.2% (25.4-27.1%) reported drinking more than usual over the past week. Drinking less than usual was independently associated with being younger (OR=0.88 [95% CI=0.83-0.93]), male (OR=0.76 [0.68-0.84]), of an ethnic minority (OR=0.76 [0.61-0.97]), low annual household income (OR=0.74 [0.66-0.83]), having diagnosed or suspected COVID-19 (OR=2.04 [1.72-2.41]), adhering to COVID-19 protective behaviours (OR=1.58 [1.08-2.32]), being significantly stressed about becoming seriously ill from COVID-19 (OR=1.26 [1.08-1.48]) and not being a key worker (OR=0.87 [0.76-0.99]). Drinking more than usual was independently associated with being younger (OR=0.73 [0.69-0.78]), female (OR=1.36 [1.22-1.51]), post-16 qualifications (OR=1.21 [1.04-1.40]), high annual household income (OR=1.43 [1.27-1.61]), being significantly stressed about catching (OR=1.22 [1.03-1.45]) or becoming seriously ill from COVID-19 (OR=1.28 [1.10-1.48]), being significantly stressed about finances (OR=1.43 [1.24-1.66]), and having a diagnosed anxiety disorder (OR=1.24 [1.05-1.46]).\n\nConclusionsIn a representative sample of adults in the UK, about half of drinkers reported drinking the same amount of alcohol as usual during the start of the COVID-19 related lockdown, with a quarter drinking more and a quarter drinking less than usual. Drinking more than usual was associated with being younger, female, high socioeconomic position, having an anxiety disorder, and being stressed about finances or COVID-19. These groups may benefit targeted alcohol reduction support if there are further periods of lockdown.\n\nRegistrationThe analysis plan was pre-registered on Open Science Framework (https://osf.io/pnrhq/).", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Claire Garnett", - "author_inst": "University College London" - }, - { - "author_name": "Sarah E Jackson", - "author_inst": "University College London" - }, - { - "author_name": "Melissa Oldham", - "author_inst": "University College London" - }, - { - "author_name": "Jamie Brown", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Steptoe", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.20.20196899", "rel_title": "Prolonged SARS-CoV-2 replication in an immunocompromised patient", @@ -1150318,6 +1153614,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.09.20.297242", + "rel_title": "Comparative analysis reveals the species-specific genetic determinants of ACE2 required for SARS-CoV-2 entry", + "rel_date": "2020-09-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.20.297242", + "rel_abs": "Coronavirus interaction with its viral receptor is a primary genetic determinant of host range and tissue tropism. SARS-CoV-2 utilizes ACE2 as the receptor to enter host cell in a species-specific manner. We and others have previously shown that ACE2 orthologs from New World monkey, koala and mouse cannot interact with SARS-CoV-2 to mediate viral entry, and this defect can be restored by humanization of the restrictive residues in New World monkey ACE2. To better understand the genetic determinants behind the ability of ACE2 orthologs to support viral entry, we compared koala and mouse ACE2 sequences with that of human and identified the key residues in koala and mouse ACE2 that restrict viral receptor activity. Humanization of these critical residues rendered both koala and mouse ACE2 capable of binding the spike protein and facilitating viral entry. The single mutation that allowed for mouse ACE2 to serve as a viral receptor provides a potential avenue for the development of SARS-CoV-2 mouse model.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Wenlin Ren", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Gaowei Hu", + "author_inst": "Fudan University" + }, + { + "author_name": "Xiaomin Zhao", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Yuyan Wang", + "author_inst": "Fudan University" + }, + { + "author_name": "Hongyang Shi", + "author_inst": "Institut Pasteur of Shanghai, Chinese Academy of Sciences" + }, + { + "author_name": "Jun Lan", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Yunkai Zhu", + "author_inst": "Fudan University" + }, + { + "author_name": "Jianping Wu", + "author_inst": "Westlake University" + }, + { + "author_name": "Devin J. Kenney", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Douam Florian", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Yimin Tong", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Jin Zhong", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Youhua Xie", + "author_inst": "Fudan University" + }, + { + "author_name": "Xinquan Wang", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Zhenghong Yuan", + "author_inst": "Fudan University" + }, + { + "author_name": "Dongming Zhou", + "author_inst": "School of Basic Medical Sciences, Tianjin Medical University" + }, + { + "author_name": "Rong Zhang", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Qiang Ding", + "author_inst": "Tsinghua University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.21.306357", "rel_title": "Cryo-EM structure of S-Trimer, a subunit vaccine candidate for COVID-19", @@ -1150423,61 +1153806,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.18.20197590", - "rel_title": "SARS-CoV-2 antigen and antibody prevalence among UK staff working with cancer patients during the COVID-19 pandemic.", - "rel_date": "2020-09-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.18.20197590", - "rel_abs": "BackgroundInternational guidelines for testing potentially immunosuppressed cancer patients receiving non-surgical anticancer therapies for SARS-CoV-2 (COVID-19) are currently lacking. The value of routinely testing staff treating cancer patients is not known.\n\nMethodsPatient-facing oncology department staff at work during the COVID-19 pandemic consented to have a nasopharyngeal swab SARS-CoV-2 antigen test by polymerase chain reaction (PCR) and blood tests for SARS-CoV-2 antibody using a laboratory Luminex-based assay and a rapid point-of-care (POC) assay on 2 occasions 28 days apart in June and July 2020.\n\nFindings434 participants were recruited: nurses (58{middle dot}3%), doctors (21{middle dot}2%), radiographers (10{middle dot}4%) and administrators (10{middle dot}1%). 82% were female; median age 40-years (range 19-66). 26{middle dot}3% reported prior symptoms suggestive of SARS-CoV-2 infection and 1{middle dot}4% tested PCR-positive prior to June 2020. All were PCR-negative at both study day 1 and 28. 18{middle dot}4% were SARS-CoV-2 sero-positive on day 1 by Luminex, of whom 42{middle dot}5% also tested positive by POC. 47{middle dot}5% of Luminex sero-positives had antibodies to both nucleocapsid (N) and surface (S) antigens. Nurses (21{middle dot}3%) and doctors (17{middle dot}4%) had higher prevalence trends of Luminex sero-positivity compared with administrators (13{middle dot}6%) and radiographers (8{middle dot}9%) (p=0.2). 38% of sero-positive participants reported previous symptoms suggestive of SARS-CoV-2 infection, a 1{middle dot}9-fold higher odds than sero-negative participants (p=0{middle dot}01). 400 participants re-tested on day 28: 13{middle dot}3% were Luminex sero-positive of whom 92{middle dot}5% were previously positive and 7{middle dot}5% newly positive. Nurses (16{middle dot}5%) had the highest seroprevalence trend amongst staff groups (p=0{middle dot}07). 32{middle dot}5% of day 1 sero-positives became sero-negative by day 28: the majority being previously reactive to the N-antigen only (p<0{middle dot}0001).\n\nInterpretationThe high prevalence of SARS-CoV-2 IgG sero-positivity in oncology nurses, and the high decline of positivity over 4 weeks supports regular antigen and antibody testing in this staff group for SARS-CoV-2 as part of routine patient care prior to availability of a vaccine.\n\nFundingACT, NHS\n\nEvidence before this studyTo identify studies involving oncology healthcare workers and SARS-CoV-2 exposure during the COVID-19 pandemic, we searched PubMed and Medrxiv for articles published between January 1 and July 31 using the following search terms \"COVID-19\", \"SARS-CoV-2\", \"oncology staff\", \"healthcare workers\" without language restriction. To date, no large study has specifically reported and tracked patient-facing oncology staff SARS-CoV-2 exposure.\n\nAdded value of this studyTo the best of our knowledge, this is the first study specifically investigating SARS-CoV-2 exposure in UK patient-facing oncology staff who were at work during the peak of the COVID-19 pandemic between March and June 2020. 18{middle dot}4% of staff were SARS-CoV-2 antibody positive at the start of June 2020 suggesting prior SARS-CoV-2 infection, while 32{middle dot}5% of those antibody-positive cases became antibody-negative 28 days after the first sample collection. The highest seroprevalence rates at both time points were recorded in nurses.\n\nImplications of all the available evidenceThese results justify incorporating SARS-CoV-2 PCR and antibody testing of oncology nurses into international guidelines for managing cancer patients treated with non-surgical anticancer treatments prior to availability of a functional vaccine.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "David M Favara", - "author_inst": "Department of Oncology, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge UK" - }, - { - "author_name": "Karen McAdam", - "author_inst": "Department of Oncology, Peterborough City Hospital, North West Anglia NHS Foundation Trust, Peterborough" - }, - { - "author_name": "Anthony Cooke", - "author_inst": "Cambridge Clinical Laboratories, Cambridge, UK" - }, - { - "author_name": "Alex Bordessa-Kelly", - "author_inst": "School of Clinical Medicine, University of Cambridge, Cambridge, UK" - }, - { - "author_name": "Ieva Budriunaite", - "author_inst": "Tissue Typing Laboratory, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge UK" - }, - { - "author_name": "Sophie Bossingham", - "author_inst": "Tissue Typing Laboratory, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge UK" - }, - { - "author_name": "Sally Houghton", - "author_inst": "Department of Immunology, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge UK" - }, - { - "author_name": "Rainer Doffinger", - "author_inst": "Department of Immunology, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge UK" - }, - { - "author_name": "Nicola Ainsworth", - "author_inst": "Department of Oncology, The Queen Elizabeth Hospital, The Queen Elizabeth Hospital Kings Lynn NHS Foundation Trust, Kings Lynn, UK" - }, - { - "author_name": "Pippa Corrie", - "author_inst": "Department of Oncology, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2020.09.08.20190256", "rel_title": "Commercial COVID-19 serial seroconversion panel for validation of SARS-CoV-2 antibody assays", @@ -1151652,6 +1154980,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.15.20194258", + "rel_title": "COVID-19 epidemic severity is associated with timing of non-pharmaceutical interventions", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20194258", + "rel_abs": "Background: Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non-pharmaceutical interventions is still debated. International comparisons are hampered by highly variable conditions under which epidemics spread and differences in the timing and scale of interventions. Cumulative COVID-19 morbidity and mortality are functions of both the rate of epidemic growth and the duration of uninhibited growth before interventions were implemented. Incomplete and sporadic testing during the early COVID-19 epidemic makes it difficult to identify how long SARS-CoV-2 was circulating in different places. SARS-CoV-2 genetic sequences can be analyzed to provide an estimate of both the time of epidemic origin and the rate of early epidemic growth in different settings. Methods: We carried out a phylogenetic analysis of more than 29,000 publicly available whole genome SARS-CoV-2 sequences from 57 locations to estimate the time that the epidemic originated in different places. These estimates were cross-referenced with dates of the most stringent interventions in each location as well as the number of cumulative COVID-19 deaths following maximum intervention. Phylodynamic methods were used to estimate the rate of early epidemic growth and proxy estimates of epidemic size. Findings: The time elapsed between epidemic origin and maximum intervention is strongly associated with different measures of epidemic severity and explains 46% of variance in numbers infected at time of maximum intervention. The reproduction number is independently associated with epidemic severity. In multivariable regression models, epidemic severity was not associated with census population size. The time elapsed between detection of initial COVID-19 cases to interventions was not associated with epidemic severity, indicating that many locations experienced long periods of cryptic transmission. Interpretation: Locations where strong non-pharmaceutical interventions were implemented earlier experienced much less severe COVID-19 morbidity and mortality during the period of study.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Manon Ragonnet-Cronin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Olivia Boyd", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lily Geidelberg", + "author_inst": "Imperial College London" + }, + { + "author_name": "David Jorgensen", + "author_inst": "Imperial College London" + }, + { + "author_name": "Fabricia F Nascimento", + "author_inst": "Imperial College London" + }, + { + "author_name": "Igor Siveroni", + "author_inst": "Imperial College London" + }, + { + "author_name": "Robert Johnson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Marc Baguelin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Zulma M Cucunuba", + "author_inst": "Imperial College London" + }, + { + "author_name": "Elita Jauneikaite", + "author_inst": "Imperial College London" + }, + { + "author_name": "Swapnil Mishra", + "author_inst": "Imperial College London" + }, + { + "author_name": "Hayley A Thompson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver J Watson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Neil Ferguson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Christl A Donnelly", + "author_inst": "Imperial College London; University of Oxford" + }, + { + "author_name": "Erik Volz", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.14.20194589", "rel_title": "Improved estimation of time-varying reproduction numbers at low case incidence and between epidemic waves", @@ -1151785,53 +1155192,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.14.20193904", - "rel_title": "A SARS-CoV-2 Reference Standard Quantified by Multi-digital PCR Platforms for Quality Assessment of Molecular Tests", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.14.20193904", - "rel_abs": "SARS-CoV-2 is the seventh coronavirus known to infect humans and has caused an emerging and rapidly evolving global pandemic (COVID-19) with significant morbidity and mortality. To meet the urgent and massive demand for the screening and diagnosis of infected individuals, many in vitro diagnostic assays using nucleic acid tests (NATs) have been urgently authorized by regulators worldwide. The limit of detection (LoD) is a crucial feature for a diagnostic assay to detect SARS-CoV-2 in clinical samples, and a reference standard with a well-characterized concentration or titer is of the utmost importance for LoD studies. Although several reference standards of plasmids or synthetic RNA carrying specific genomic regions of SARS-CoV-2 have already been announced, a reference standard for inactivated virus particles with accurate concentration is still needed to evaluate the complete procedure including nucleic acid extraction and to accommodate customized primer-probe sets targeting different genome sequences. Here, we performed a collaborative study to estimate the NAT-detectable units as viral genomic equivalent quantity (GEQ) of an inactivated whole-virus SARS-CoV-2 reference standard candidate using digital PCR (dPCR) on multiple commercialized platforms. The median of the quantification results (4.6x105 {+/-} 6.5x104 GEQ/mL) was treated as the consensus true value of GEQ of virus particles in the reference standard. This reference standard was then used to challenge the LoDs of six officially approved diagnostic assays. Our study demonstrates that an inactivated whole virus quantified by dPCR can serve as a reference standard and provides a unified solution for assay development, quality control, and regulatory surveillance.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Haiwei Zhou", - "author_inst": "National Institutes for Food and Drug Control" - }, - { - "author_name": "Donglai Liu", - "author_inst": "National Institutes for Food and Drug Control" - }, - { - "author_name": "Liang Ma", - "author_inst": "Department of Biomedical Devices, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)" - }, - { - "author_name": "Tingting Ma", - "author_inst": "National Institutes for Food and Drug Control" - }, - { - "author_name": "Tingying Xu", - "author_inst": "National Institutes for Food and Drug Control" - }, - { - "author_name": "Lili Ren", - "author_inst": "Chinese Academy of Medical Sciences & Peking Union Medical College" - }, - { - "author_name": "Liang Li", - "author_inst": "Chinese Academy of Agricultural Sciences" - }, - { - "author_name": "Sihong Xu", - "author_inst": "National Institutes for Food and Drug Control" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.09.15.20195339", "rel_title": "Association among income loss, financial strain and depressive symptoms during COVID-19: evidence from two longitudinal studies", @@ -1153586,6 +1156946,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.09.16.20195685", + "rel_title": "Integrative Genomics Analysis Reveals a Novel 21q22.11 Locus Contributing to Susceptibility of COVID-19", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20195685", + "rel_abs": "The systematic identification of host genetic risk factors is essential for the understanding and treatment of COVID-19. By performing a meta-analysis of two independent genome-wide association (GWAS) summary datasets (N = 680,128), a novel locus at 21q22.11 was identified to be associated with COVID-19 infection (rs9976829 in IFNAR2 and upstream of IL10RB, OR = 1.16, 95% CI = 1.09 - 1.23, P = 2.57x10-6). The rs9976829 represents a strong splicing quantitative trait locus (sQTL) for both IFNAR2 and IL10RB genes, especially in lung tissue (P 1.8x10-24). Gene-based association analysis also found IFNAR2 was significantly associated with COVID-19 infection (P = 2.58x10-7). Integrative genomics analysis of combining GWAS with eQTL data showed the expression variations of IFNAR2 and IL10RB have prominent effects on COVID-19 in various types of tissues, especially in lung tissue. The majority of IFNAR2-expressing cells were dendritic cells (40%) and plasmacytoid dendritic cells (38.5%), and IL10RB-expressing cells were mainly nonclassical monocytes (29.6%). IFNAR2 and IL10RB are targeted by several interferons-related drugs. Together, our results uncover 21q22.11 as a novel susceptibility locus for COVID-19, in which individuals with G alleles of rs9976829 have a higher probability of COVID-19 susceptibility than those with non-G alleles.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Yunlong Ma", + "author_inst": "Wenzhou Medical University" + }, + { + "author_name": "Yukuan Huang", + "author_inst": "Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China" + }, + { + "author_name": "Sen Zhao", + "author_inst": "Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China" + }, + { + "author_name": "Yinghao Yao", + "author_inst": "Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325011, China" + }, + { + "author_name": "Yaru Zhang", + "author_inst": "Institute of Biomedical Big Data, School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 32" + }, + { + "author_name": "Jia Qu", + "author_inst": "Institute of Biomedical Big Data, School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 32" + }, + { + "author_name": "Nan Wu", + "author_inst": "Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China" + }, + { + "author_name": "Jianzhong Su", + "author_inst": "Institute of Biomedical Big Data, School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 32" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.09.17.20190595", "rel_title": "The \"Great Lockdown\": Inactive Workers and Mortality by Covid-19", @@ -1153715,37 +1157122,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, - { - "rel_doi": "10.1101/2020.09.17.20197020", - "rel_title": "On Topological Properties of COVID-19: Predicting and Controling Pandemic Risk with Network Statistics", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20197020", - "rel_abs": "The spread of coronavirus disease 2019 (COVID-19) has caused more than 24 million confirmed infected cases and more than 800,000 people died as of 28 August 2020. While it is essential to quantify risk and characterize transmission dynamics in closed populations using Susceptible-Infection-Recovered modeling, the investigation of the effect from worldwide pandemic cannot be neglected. This study proposes a network analysis to assess global pandemic risk by linking 164 countries in pandemic networks, where links between countries were specified by the level of 'co-movement' of newly confirmed COVID-19 cases. More countries showing increase in the COVID-19 cases simultaneously will signal the pandemic prevalent over the world. The network density, clustering coefficients, and assortativity in the pandemic networks provide early warning signals of the pandemic in late February 2020. We propose a preparedness pandemic risk score for prediction and a severity risk score for pandemic control. The preparedness risk score contributed by countries in Asia is between 25% to 50% most of the time after February and America contributes close to 50% recently. The high preparedness risk contribution implies the importance of travel restrictions between those countries. The severity risk score of America is greater than 50% after May and even exceeds 75% in July, signifying that the control of COVID-19 is still worrying in America. We can keep track of the pandemic situation in each country using an online dashboard to update the pandemic risk scores and contributions.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Mike K.P. So", - "author_inst": "The Hong Kong University of Science and Technology" - }, - { - "author_name": "Amanda M.Y. Chu", - "author_inst": "The Education University of Hong Kong" - }, - { - "author_name": "Agnes Tiwari", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Jacky N.L. Chan", - "author_inst": "The Hong Kong University of Science and Technology" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.17.20197004", "rel_title": "The Accuracy of Healthcare Worker versus Self Collected (2-in-1) Oropharyngeal and Bilateral Mid-Turbinate (OPMT) Swabs and Saliva Samples for SARS-CoV-2", @@ -1155420,6 +1158796,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.17.20195131", + "rel_title": "Seroprevalence of Antibodies to SARS-CoV-2 in US Blood Donors", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20195131", + "rel_abs": "BackgroundTo identify blood donors eligible to donate Coronavirus Disease-2019 (COVID-19) Convalescent Plasma (CCP), a large blood center began testing for antibodies to SARS-CoV-2, the etiologic agent of COVID-19. We report the seroprevalence of total immunoglobulin directed against the S1 spike protein of SARS-CoV-2 in US blood donors.\n\nMethodsUnique non-CCP donor sera from June 1-July 31, 2020 were tested with the Ortho VITROS Anti-SARS-CoV-2 total immunoglobulin assay (positive: signal-to-cutoff (S/C) [≥]1). Donor age, sex, race/ethnicity, ABO/RhD, education, and experience were compared to June and July 2019. Multivariate regressions were conducted to identify demographics associated with the presence of antibodies and with S/C values.\n\nResultsUnique donors (n=252,882) showed an overall seroprevalence of 1.83% in June (1.37%) and July (2.26%), with the highest prevalence in northern New Jersey (7.3%). In a subset of donors with demographic information (n=189,565), higher odds of antibody reactivity were associated with non-Hispanic Native American/Alaskan (NH-NAA/A) and Black (NH-B), and Hispanic (H) race/ethnicity, age 18-64, middle school or lesser education, blood Group A, and never or non-recent donor status. In positive donors (n=2,831), antibody signal was associated with male sex, race/ethnicity (NH-NAA/A, NH-B and H) and geographic location.\n\nConclusionsSeroprevalence remains low in US blood donors but varies significantly by region. Temporal trends in reactivity may be used to gauge the effectiveness of public health measures. Before generalizing these data from healthy donors to the general population however, rates must be corrected for false positive test results among low prevalence test subjects and adjusted to match the wider demography.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ralph R Vassallo", + "author_inst": "Vitalant" + }, + { + "author_name": "Marjorie D Bravo", + "author_inst": "Vitalant" + }, + { + "author_name": "Larry J Dumont", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Kelsey Hazegh", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Hany Kamel", + "author_inst": "Vitalant" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.17.20196832", "rel_title": "COVID-19 pediatric mortality rates are heterogenous between countries", @@ -1155521,37 +1158932,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.16.20195917", - "rel_title": "Meta-analysis of the clinical performance of commercial SARS-CoV-2 nucleic acid, antigen and antibody tests up to 22 August 2020", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20195917", - "rel_abs": "We reviewed the clinical performance of SARS-CoV-2 nucleic acid, viral antigen and antibody tests based on 94739 test results from 157 published studies and 20205 new test results from 12 EU/EEA Member States. Pooling the results and considering only results with 95% confidence interval width [≤]5%, we found 4 nucleic acid tests, among which 1 point of care test, and 3 antibody tests with a clinical sensitivity [≤]95% for at least one target population (hospitalised, mild or asymptomatic, or unknown). Analogously, 9 nucleic acid tests and 25 antibody tests, among which 12 point of care tests, had a clinical specificity of [≤]98%. Three antibody tests achieved both thresholds. Evidence for nucleic acid and antigen point of care tests remains scarce at present, and sensitivity varied substantially. Study heterogeneity was low for 8/14 (57.1%) sensitivity and 68/84 (81.0%) specificity results with confidence interval width [≤]5%, and lower for nucleic acid tests than antibody tests. Manufacturer reported clinical performance was significantly higher than independently assessed in 11/32 (34.4%) and 4/34 (11.8%) cases for sensitivity and specificity respectively, indicating a need for improvement in this area. Continuous monitoring of clinical performance within more clearly defined target populations is needed.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ivo Van Walle", - "author_inst": "European Centre for Disease Prevention and Control" - }, - { - "author_name": "Katrin Leitmeyer", - "author_inst": "European Centre for Disease Prevention and Control" - }, - { - "author_name": "Eeva K Broberg", - "author_inst": "European Centre for Disease Prevention and Control" - }, - { - "author_name": "- The European COVID-19 microbiological laboratories group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.18.20197202", "rel_title": "COPD in the time of COVID-19: An analysis of acute exacerbations and reported behavioural changes in patients with COPD", @@ -1157202,6 +1160582,69 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.16.300871", + "rel_title": "Distinct SARS-CoV-2 Antibody Reactivity Patterns in Coronavirus Convalescent Plasma Revealed by a Coronavirus Antigen Microarray", + "rel_date": "2020-09-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.16.300871", + "rel_abs": "A coronavirus antigen microarray (COVAM) was constructed containing 11 SARS-CoV-2, 5 SARS-1, 5 MERS, and 12 seasonal coronavirus recombinant proteins. The array is designed to measure immunoglobulin isotype and subtype levels in serum or plasma samples against each of the individual antigens printed on the array. We probed the COVAM with COVID-19 convalescent plasma (CCP) collected from 99 donors who recovered from a PCR+ confirmed SARS-CoV-2 infection. The results were analyzed using two computational approaches, a generalized linear model (glm) and Random Forest (RF) prediction model, to classify individual specimens as either Reactive or Non-Reactive against the SARS-CoV-2 antigens. A training set of 88 pre-COVID-19 specimens (PreCoV) collected in August 2019 and102 positive specimens from SARS-CoV-2 PCR+ confirmed COVID-19 cases was used for these analyses. Results compared with an FDA emergency use authorized (EUA) SARS-CoV2 S1-based total Ig chemiluminescence immunoassay (Ortho Clinical Diagnostics VITROS(R) Anti-SARS-CoV-2 Total, CoV2T) and with a SARS-CoV-2 S1-S2 spike-based pseudovirus micro neutralization assay (SARS-CoV-2 reporter viral particle neutralization titration (RVPNT) showed high concordance between the 3 assays. Three CCP specimens that were negative by the VITROS CoV2T immunoassay were also negative by both COVAM and the RVPNT assay. Concordance between VITROS CoV2T and COVAM was 96%, VITROS CoV2T and RVPNT 93%, and RVPNT and COVAM 95%. The discordances were all weakly reactive samples near the cutoff threshold of the VITROS CoV2T immunoassay. The multiplex COVAM allows CCP to be grouped according to antibody reactivity patterns against 11 SARS-CoV-2 antigens. Unsupervised K-means analysis, via the gap statistics, as well as hierarchical clustering analysis revealed 3 main clusters with distinct reactivity intensities and patterns. These patterns were not recapitulated by adjusting the VITROS CoV2T or RVPNT assay thresholds. Plasma classified according to these reactivity patterns may be better associated with CCP treatment efficacy than antibody levels alone. The use of a SARS-CoV-2 antigen array may be useful to qualify CCP for administration as a treatment for acute COVID-19 and to interrogate vaccine immunogenicity and performance in preclinical and clinical studies to understand and recapitulate antibody responses associated with protection from infection and disease.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Rafael Ramiro de Assis", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Aarti Jain", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Rie Nakajima", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Algis Jasinskas", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Saahir Khan", + "author_inst": "University of Southern California" + }, + { + "author_name": "Larry J Dumont", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Kathleen Kelly", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Graham Simmons", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Mars Stone", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Clara Di Germanio", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Michael P Busch", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Philip L Felgner", + "author_inst": "University of California, Irvine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.16.300319", "rel_title": "A soluble ACE2 microbody protein fused to a single immunoglobulin Fc domain is a potent inhibitor of SARS-CoV-2 infection in cell culture", @@ -1157611,29 +1161054,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.09.17.301861", - "rel_title": "Discovery of human ACE2 variants with altered recognition by the SARS-CoV-2 spike protein", - "rel_date": "2020-09-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.17.301861", - "rel_abs": "Understanding how human ACE2 genetic variants differ in their recognition by SARS-CoV-2 can have a major impact in leveraging ACE2 as an axis for treating and preventing COVID-19. In this work, we experimentally interrogate thousands of ACE2 mutants to identify over one hundred human single-nucleotide variants (SNVs) that are likely to have altered recognition by the virus, and make the complementary discovery that ACE2 residues distant from the spike interface can have a strong influence upon the ACE2-spike interaction. These findings illuminate new links between ACE2 sequence and spike recognition, and will find wide-ranging utility in SARS-CoV-2 fundamental research, epidemiological analyses, and clinical trial design.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Pete Heinzelman", - "author_inst": "University of Wisconsin--Madison" - }, - { - "author_name": "Philip A Romero", - "author_inst": "University of Wisconsin--Madison" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.09.17.302380", "rel_title": "Topography, spike dynamics and nanomechanics of individual native SARS-CoV-2 virions", @@ -1159020,6 +1162440,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.13.20193896", + "rel_title": "Are we there yet? An adaptive SIR model for continuous estimation of COVID-19 infection rate and reproduction number in the United States", + "rel_date": "2020-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.13.20193896", + "rel_abs": "BackgroundThe dynamics of the COVID-19 epidemic vary due to local population density and policy measures. When making decisions, policy makers consider an estimate of the effective reproduction number [R]t which is the expected number of secondary infections by a single infected individual.\n\nObjectiveWe propose a simple method for estimating the time-varying infection rate and reproduction number [R]t.\n\nMethodsWe use a sliding window approach applied to a Susceptible-Infectious-Removed model. The infection rate is estimated using the reported cases for a seven-day window to obtain continuous estimation of [R]t. The proposed adaptive SIR (aSIR) model was applied to data at the state and county levels.\n\nResultsThe aSIR model showed an excellent fit for the number of reported COVID-19 positive cases, a one-day forecast MAPE was less than 2.6% across all states. However, a seven-day forecast MAPE reached 16.2% and strongly overestimated the number of cases when the reproduction number was high and changing fast. The maximal [R]t showed a wide range of 2.0 to 4.5 across all states, with the highest values for New York (4.4) and Michigan (4.5). We demonstrate that the aSIR model can quickly adapt to an increase in the number of tests and associated increase in the reported cases of infections. Our results also suggest that intensive testing may be one of the effective methods of reducing [R]t.\n\nConclusionThe aSIR model provides a simple and accurate computational tool to obtain continuous estimation of the reproduction number and evaluate the efficacy of mitigation measures.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Mark B Shapiro", + "author_inst": "Anthem, Inc." + }, + { + "author_name": "Fazle Karim", + "author_inst": "Anthem, Inc." + }, + { + "author_name": "Guido Muscioni", + "author_inst": "Anthem, Inc." + }, + { + "author_name": "Abel Saju Augustine", + "author_inst": "Anthem, Inc." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.03.20187112", "rel_title": "Treatment with an Anti-CK2 Synthetic Peptide Improves Clinical Response in Covid-19 Patients with Pneumonia. A Randomized and Controlled Clinical Trial", @@ -1159213,129 +1162664,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.14.20191106", - "rel_title": "Impact of SARS-CoV-2 antibodies at delivery in women, partners and newborns", - "rel_date": "2020-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.14.20191106", - "rel_abs": "BackgroundOnly few studies have focused on serological testing for SARS-CoV-2 in pregnant women and no previous study has investigated the frequency in partners. The aim was to investigate the frequency and impact of SARS-CoV-2 in parturient women, their partners and newborns.\n\nMethodsFrom April 4th to July 3rd, 2020, all parturient women, their partners and newborns were invited to participate in the study. Participating women and partners had a pharyngeal swab and a blood sample taken at admission and immediately after delivery a blood sample was drawn from the umbilical cord. The swabs were analyzed for SARS-CoV-2 RNA by PCR and the blood samples were analyzed for SARS-CoV-2 antibodies. Full medical history, obstetric- and neonatal information were available.\n\nResultsA total of 1,361 parturient women, 1,236 partners and 1,342 newborns participated in the study. No associations between previous COVID-19 disease and obstetric- or neonatal complications were found. The adjusted serological prevalence was 2.9% in women and 3.8% in partners. The frequency of blood type A was significantly higher in women with antibodies compared to women without antibodies. 17 newborns had SARS-CoV-2 IgG antibodies, and none had IgM antibodies. Full serological data from 1,052 families showed an absolute risk of infection of 0.37 if the partner had antibodies. Only 55% of individuals with antibodies reported symptoms.\n\nConclusionThis large prospective cohort study reports no association between COVID-19 and obstetric- or neonatal complications. The family pattern showed a substantial increase in absolute risk for women living with a partner with antibodies.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Pia Egerup", - "author_inst": "Department of Obstetrics and Gynaecology, Hvidovre Hospital, Copenhagen University Hospital" - }, - { - "author_name": "Line Fich Olsen", - "author_inst": "Department of Obstetrics and Gynaecology, Hvidovre Hospital, Copenhagen University Hospital" - }, - { - "author_name": "Ann-Marie Hellerung Christiansen", - "author_inst": "Department of Obstetrics and Gynaecology, Hvidovre Hospital, Copenhagen University Hospital" - }, - { - "author_name": "David Westergaard", - "author_inst": "Department of Obstetrics and Gynaecology, Hvidovre Hospital, Copenhagen University Hospital and Novo Nordisk Foundation Center for Protein Research, University " - }, - { - "author_name": "Elin Rosenbek Severinsen", - "author_inst": "Department of Obstetrics and Gynaecology, Hvidovre Hospital, Copenhagen University Hospital" - }, - { - "author_name": "Kathrine Vauvert Roemmelmayer Hviid", - "author_inst": "Department of Obstetrics and Gynaecology, Hvidovre Hospital, Copenhagen University Hospital" - }, - { - "author_name": "Astrid Marie Kolte", - "author_inst": "The Recurrent Pregnancy Loss Unit, The Capital Region, Rigshospitalet, Copenhagen University Hospital and Department of Clinical Medicine, Faculty of Health and" - }, - { - "author_name": "Amalie Dyhrberg Boje", - "author_inst": "Department of Obstetrics and Gynaecology, Hvidovre Hospital, Copenhagen University Hospital" - }, - { - "author_name": "Marie-Louise Mathilde Friis Bertelsen", - "author_inst": "Department of Obstetrics and Gynaecology, Hvidovre Hospital, Copenhagen University Hospital" - }, - { - "author_name": "Lisbeth Praetorius", - "author_inst": "Department of Obstetrics and Gynaecology, The Fertility Clinic, Hvidovre, Copenhagen University Hospital" - }, - { - "author_name": "Anne Zedeler", - "author_inst": "Department of Obstetrics and Gynaecology, The Fertility Clinic, Hvidovre, Copenhagen University Hospital," - }, - { - "author_name": "Josefine Reinhardt Nielsen", - "author_inst": "Department of Obstetrics and Gynaecology, Hvidovre Hospital, Copenhagen University Hospital" - }, - { - "author_name": "Didi Bang", - "author_inst": "Department of Clinical Microbiology, Hvidovre Hospital, Copenhagen University Hospital" - }, - { - "author_name": "Sine Berntsen", - "author_inst": "Department of Obstetrics and Gynaecology, The Fertility Clinic, Hvidovre, Copenhagen University Hospital" - }, - { - "author_name": "Jeppe Ethelberg-Findsen", - "author_inst": "DNRF Center for Chromosome Stability (CCS), Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen" - }, - { - "author_name": "Ditte Marie Storm", - "author_inst": "DNRF Center for Chromosome Stability (CCS), Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen" - }, - { - "author_name": "Judith Bello-Rodriguez", - "author_inst": "DNRF Center for Chromosome Stability (CCS), Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen" - }, - { - "author_name": "Andreas Ingham", - "author_inst": "DNRF Center for Chromosome Stability (CCS), Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen" - }, - { - "author_name": "Joaquim Olle-Lopez", - "author_inst": "DNRF Center for Chromosome Stability (CCS), Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen" - }, - { - "author_name": "Eva Hoffmann", - "author_inst": "DNRF Center for Chromosome Stability (CCS), Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen" - }, - { - "author_name": "Charlotte Wilken-Jensen", - "author_inst": "Department of Obstetrics and Gynaecology, Hvidovre Hospital, Copenhagen University Hospital" - }, - { - "author_name": "Lone Krebs", - "author_inst": "Department of Obstetrics and Gynaecology, Hvidovre Hospital, Copenhagen University Hospital and Department of Clinical Medicine, Faculty of Health and Medical S" - }, - { - "author_name": "Finn Stener Joergensen", - "author_inst": "Fetal Med. Unit, Dept. of Obstetrics and Gynaecology, Copenhagen University Hospital Hvidovre and Department of Clinical Medicine, Faculty of Health and Medical" - }, - { - "author_name": "Henrik Torkil Westh", - "author_inst": "Department of Clinical Microbiology, Hvidovre Hospital, Copenhagen University Hospital and Department of Clinical Medicine, Faculty of Health and Medical Scienc" - }, - { - "author_name": "Henrik Lovendahl Jorgensen", - "author_inst": "Department of Clinical Biochemistry, Copenhagen University Hospital Hvidovre and Department of Clinical Medicine, Faculty of Health and Medical Sciences, Univer" - }, - { - "author_name": "Nina la Cour Freiesleben", - "author_inst": "Department of Obstetrics and Gynaecology, The Fertility Clinic, Hvidovre, Copenhagen University Hospital and Department of Clinical Medicine, Faculty of Health " - }, - { - "author_name": "Henriette Svarre Nielsen", - "author_inst": "Department of Obstetrics and Gynaecology, Hvidovre Hospital, Copenhagen University Hospital and Department of Clinical Medicine, Faculty of Health and Medical S" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2020.09.14.20191098", "rel_title": "Neutrophil-to-lymphocyte ratio on admission to predict the severity and mortality of COVID-19 patients: a meta-analysis", @@ -1160918,6 +1164246,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.12.20193334", + "rel_title": "Analysis of the interventions adopted due to the COVID-19 on ARI morbility for Colombia", + "rel_date": "2020-09-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.12.20193334", + "rel_abs": "Acute Respiratory Infections are among the leading causes of death globally, particularly in developing countries, and are highly correlated with the quality of health and surveillance systems and effective early interventions in high-risk age groups. According to the World Health Organization, about four million people die each year from mostly preventable respiratory tract infections, making it a public health concern. The official declaration of a pandemic in March 2020 due to the Sars-CoV-2 virus coincided with the influenza season in Colombia and with environmental alerts about low air quality that increase its incidence. The objective of this document is the application of a flexible model for the identification of the pattern and monitoring of ARI morbility for Colombia by age group that shows atypical patterns in the reported series for 5 departments and that coincide with the decisions implemented to contain the COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Alvaro Quijano-Angarita", + "author_inst": "Instituto de Evaluacion Tecnologica en Salud - IETS" + }, + { + "author_name": "Oscar Espinosa", + "author_inst": "Instituto de Evaluacion Tecnologica en Salud - IETS" + }, + { + "author_name": "Marcela M Mercado-Reyes", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Diana Walteros", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Diana Carolina Malo", + "author_inst": "Instituto Nacional de Salud" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.12.20193409", "rel_title": "Clinical characteristics and outcomes of patients with COVID-19 and ARDS admitted to a third level health institution in Mexico City", @@ -1161003,29 +1164366,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.12.20193433", - "rel_title": "The impact of natural disasters on the spread of COVID-19: a geospatial, agent based epidemiology model", - "rel_date": "2020-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.12.20193433", - "rel_abs": "Background: Natural disasters and infectious diseases are global issues, resulting in widespread disruption to human health and livelihood. At the scale of a global pandemic, the co-occurrence of natural disasters is inevitable. However, the impact of natural disasters on the spread of COVID-19 has not been extensively evaluated using agent based epidemiology models. Methods: We create an agent-based epidemiology model based on both COVID-19 clinical and epidemiological data and geographic data. We first model 35 scenarios with varying natural disaster timing and duration for a COVID-19 outbreak in a theoretical region. We then evaluate the potential effect of an eruption of Vesuvius volcano on the spread of COVID-19 in Campania, Italy. Our objective is to determine if the occurrence of a natural disaster during the COVID-19 pandemic is likely to increase infection cases and disease related fatalities. Results: In a majority of cases, the occurrence of a natural disaster increases the number of disease related fatalities. When the natural disaster occurs at the beginning of the outbreak within a given region, there is little to no increase in the progression of disease spread. However, the occurrence of a natural disaster close to the peak of infections may increase the number of fatalities by more than five-fold. In a theoretical test case, for a natural disaster that occurred fifty days after first infection case, the median increase in fatalities is 2%, 59%, and 180% for a 2, 14, and 31-day long natural disaster respectively, when compared to the no natural disaster scenario. Conclusion: We propose that the compound risk from natural disasters is greatest in the case of already widespread disease outbreak. The key risk factors for increase in spread of infection and disease related fatalities are the timing of the natural disaster relative to the peak in infections and the duration of the natural disaster.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Maximillian S Van Wyk de Vries", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Lekaashree Rambabu", - "author_inst": "National Health Service Tayside" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.13.20193730", "rel_title": "Mental health service activity during COVID-19 lockdown among individuals with Personality Disorders: South London and Maudsley data on services and mortality from January to May 2020", @@ -1162432,6 +1165772,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.09.20184143", + "rel_title": "The Effect of Early Hydroxychloroquine-based Therapy in COVID-19 Patients in Ambulatory Care Settings: A Nationwide Prospective Cohort Study", + "rel_date": "2020-09-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20184143", + "rel_abs": "ABSTRACT BACKGROUND: Currently, there is no proven effective therapy nor vaccine for the treatment of SARS-CoV-2. Evidence regarding the potential benefit of early administration of hydroxychloroquine (HCQ) therapy in symptomatic patients with Coronavirus Disease (COVID-19) is not clear. METHODS: This observational prospective cohort study took place in 238 ambulatory fever clinics in Saudi Arabia, which followed the Ministry of Health (MOH) COVID-19 treatment guideline. This guideline included multiple treatment options for COVID-19 based on the best available evidence at the time, among which was Hydroxychloroquine (HCQ). Patients with confirmed COVD-19 (by reverse transcriptase polymerase chain reaction (PCR) test) who presented to these clinics with mild to moderate symptoms during the period from 5-26 June 2020 were included in this study. Our study looked at those who received HCQ-based therapy along with supportive care (SC) and compared them to patients who received SC alone. The primary outcome was hospital admission within 28-days of presentation. The secondary outcome was a composite of intensive care admission (ICU) and/or mortality during the follow-up period. Outcome data were assessed through a follow-up telephonic questionnaire at day 28 and were further verified with national hospitalisation and mortality registries. Multiple logistic regression model was used to control for prespecified confounders. RESULTS: Of the 7,892 symptomatic PCR-confirmed COVID-19 patients who visited the ambulatory fever clinics during the study period, 5,541 had verified clinical outcomes at day 28 (1,817 patients in the HCQ group vs 3,724 in the SC group). At baseline, patients who received HCQ therapy were more likely to be males who did not have hypertension or chronic lung disease compared to the SC group. No major differences were noted regarding other comorbid conditions. All patients were presenting with active complaints; however, the HCQ groups had higher rates of symptoms compared to the SC group (fever: 84% vs 66.3, headache: 49.8 vs 37.4, cough: 44.5 vs 35.6, respectively). Early HCQ-based therapy was associated with a lower hospital admission within 28-days compared to SC alone (9.4% compared to 16.6%, RRR 43%, p-value <0.001). The composite outcome of ICU admission and/or mortality at 28-days was also lower in the HCQ group compared to the SC (1.2% compared to 2.6%, RRR 54%, p-value 0.001). Adjusting for age, gender, and major comorbid conditions, a multivariate logistic regression model showed a decrease in the odds of hospitalisation in patients who received HCQ compared to SC alone (adjusted OR 0.57 [95% CI 0.47-0.69], p-value <0.001). The composite outcome of ICU admission and/or mortality was also lower for the HCQ group compared to the SC group controlling for potential confounders (adjusted OR 0.55 [95% CI 0.34-0.91], p-value 0.019). CONCLUSION: Early intervention with HCQ-based therapy in patients with mild to moderate symptoms at presentation is associated with lower adverse clinical outcomes among COVID-19 patients, including hospital admissions, ICU admission, and/or death.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Tarek Sulaiman", + "author_inst": "King Fahad Medical City, Riyadh, Saudi Arabia" + }, + { + "author_name": "Abdulrhman Mohana", + "author_inst": "Saudi Center for Disease Prevention and Control" + }, + { + "author_name": "Laila Alawdah", + "author_inst": "King Fahad Medical City, Riyadh, Saudi Arabia" + }, + { + "author_name": "Nagla Mahmoud", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Mustafa Hassanein", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Tariq Wani", + "author_inst": "King Fahad Medical City, Riyadh, Saudi Arabia" + }, + { + "author_name": "Amel Alfaifi", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Eissa Alenazi", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Nashwa Radwan", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Nasser AlKhalifah", + "author_inst": "King Fahad Medical City, Riyadh. Saudi Arabia" + }, + { + "author_name": "Ehab Elkady", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Manwer AlAnazi", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Mohammed Alqahtani", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Khalid Abdalla", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Yousif Yousif", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Fouad AboGazalah", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Fuad Awwad", + "author_inst": "Quantitative analysis department, College of Business Administration, King Saud University, Riyadh, Saudi Arabia" + }, + { + "author_name": "Khaled AlabdulKareem", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Fahad AlGhofaili", + "author_inst": "King Fahad Medical City, Riyadh. Saudi Arabia" + }, + { + "author_name": "Ahmed AlJedai", + "author_inst": "Assistant Deputy Minister for Therapeutic Affairs, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Hani Jokhdar", + "author_inst": "Deputyship of Public Health, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Fahad Alrabiah", + "author_inst": "King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.11.20180521", "rel_title": "On Machine Learning-Based Short-Term Adjustment of Epidemiological Projections of COVID-19 in US", @@ -1162589,25 +1166032,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.08.20190876", - "rel_title": "Automatic Contact Tracing for Outbreak Detection UsingHospital Electronic Medical Record Data", - "rel_date": "2020-09-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20190876", - "rel_abs": "Contact tracing is a well-known tool for public health professionals to trace and isolate contacts of known infectious persons. During a pandemic contact tracing is critical to ending an outbreak, but the volume of cases makes tracing difficult without adequate staffing tools. Hospitals equipped with electronic medical records can utilize these databases to automatically link cases into possible transmission chains and surface potential new outbreaks. While this automatic contact tracing does not have the richness of contact tracing interviews, it does provide a way for health systems to highlight potential super-spreader events and support their local health departments. Additionally, these data provide insight into how a given infection is spreading locally. These insights can be used to inform policy at the local level.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Michael E DeWitt Jr.", - "author_inst": "Cone Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.12.20193086", "rel_title": "Impact and Correlation of Air Quality and Climate Variables with COVID-19 Morbidity and Mortality in Dhaka, Bangladesh", @@ -1164166,6 +1167590,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.10.20192195", + "rel_title": "Mathematical Modeling and a Month Ahead Forecast of the Coronavirus Disease 2019 (COVID-19) Pandemic: An Indian Scenario", + "rel_date": "2020-09-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20192195", + "rel_abs": "India, the second-most populous country in the world, has been lately witnessing a daily surge in the COVID-19 infected cases. India is currently among the worst-hit nations worldwide, due to the COVID-19 pandemic, and ranks just behind Brazil and USA. In order to prevent the further worsening of the situation, predicting the future course of the pandemic is of utmost importance. In this paper, we model the past trajectory (March 01, 2020 - July 25, 2020) and make a month-long (July 26, 2020 - August 24, 2020) forecast of the future evolution of the COVID-19 pandemic in India using an autoregressive integrated moving average (ARIMA) model. According to our forecasting results, India is likely to have 3,800,989 cumulative infected cases, 1,634,142 cumulative active cases, 2,110,697 cumulative recoveries and 56,150 cumulative deaths by August 24, 2020, if the current trend of the pandemic continues to prevail. The implications of these forecasts are that in the upcoming month the infection rate of COVID-19 in India is going to escalate, while as the rate of recovery and the case-fatality rate is likely to reduce. In order to avert these possible scenarios, the administration and health-care personnel need to formulate and implement robust control measures, while the general public needs to be more responsible and strictly adhere to the established and newly formulated guidelines to slow down the spread of the pandemic and prevent it from transforming into a catastrophe.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Suhail Ganiny", + "author_inst": "National Institute of Technology, Srinagar" + }, + { + "author_name": "Owais Nisar", + "author_inst": "SKUAST-K" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.11.20192450", "rel_title": "Impacts of the COVID-19 epidemic on the department of stomatology in a tertiary hospital: a case study in the General Hospital of the Central Theater Command, Wuhan, China", @@ -1164287,33 +1167734,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.10.20192138", - "rel_title": "Socio-economic disparities and COVID-19 in the USA", - "rel_date": "2020-09-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20192138", - "rel_abs": "COVID-19 is not a universal killer. We study the spread of COVID-19 at the county level for the United States up until the 15th of August, 2020. We show that the prevalence of the disease and the death rate are correlated with the local socio-economic conditions often going beyond local population density distributions, especially in rural areas. We correlate the COVID-19 prevalence and death rate with data from the US Census Bureau and point out how the spreading patterns of the disease show asymmetries in urban and rural areas separately and is preferentially affecting the counties where a large fraction of the population is non-white. Our findings can be used for more targeted policy building and deployment of resources for future occurrence of a pandemic due to SARS-CoV-2. Our methodology, based on interpretable machine learning and game theory, can be extended to study the spread of other diseases.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ayan Paul", - "author_inst": "DESY, Hamburg & Humboldt Universitat zu Berlin" - }, - { - "author_name": "Philipp Englert", - "author_inst": "DESY, Hamburg" - }, - { - "author_name": "Melinda Varga", - "author_inst": "2400 Elliot Ave., Seattle WA 98121, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.10.20192328", "rel_title": "On the reliability of predictions on Covid-19 dynamics: a systematic and critical review of modelling techniques", @@ -1165760,6 +1169180,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.11.20192526", + "rel_title": "Increased extravascular lung water index (EVLWI) reflects rapid inflammatory oedema and mortality in COVID-19 associated ARDS", + "rel_date": "2020-09-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20192526", + "rel_abs": "OBJECTIVENearly 5 % of the patients with COVID-19 develop an acute respiratory distress syndrome (ARDS). Extravascular lung water index (EVLWI) is a marker of pulmonary oedema which is associated with mortality in ARDS. In this study we evaluate whether EVLWI is higher in patients with COVID-19 associated ARDS as compared to controls and whether EVLWI has the potential to monitor disease progression.\n\nMETHODSFrom the day of intubation, EVLWI, cardiac function were monitored by transpulmonary thermodilution in n=25 patients with COVID-19 and compared to a control group of 49 non-COVID-19 ARDS-patients.\n\nRESULTSEVLWI in COVID-19-patients was noticeably elevated and significantly higher than in the control group (17 (11-38) vs. 11 (6-26) mL/kg; p<0.001). High pulmonary vascular permeability index values (2.9 (1.0-5.2) versus 1.9 (1.0-5.2); p=0.003) suggest inflammatory oedema. By contrast, the cardiac parameters SVI, GEF and GEDVI were comparable. High EVLWI values were associated with viral persistence, prolonged intensive care treatment and mortality (23.2{+/-}6.7% vs. 30.3{+/-}6.0%, p=0.025).\n\nCONCLUSIONSCompared to the control group, COVID-19 results in markedly elevated EVLWI-values in patients with ARDS. EVLWI reflects a non-cardiogenic pulmonary oedema in COVID-19 associated ARDS and could serve as parameter to monitor ARDS progression.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Sebastian Rasch", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Paul Schmidle", + "author_inst": "Technical University of Munich, School of Medicine, Department of Dermatology and Allergology, Biedersteiner Str. 29, 80802 Munich" + }, + { + "author_name": "Senguel Sancak", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Alexander Herner", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Christina Huberle", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Dominik Schulz", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Ulrich Mayr", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Jochen Schneider", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Christoph Spinner", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Fabian Geisler", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Roland M. Schmid", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Tobias Lahmer", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Wolfgang Huber", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.09.10.20191932", "rel_title": "Evaluating the effects of cardiometabolic exposures on circulating proteins which may contribute to SARS-CoV-2 severity", @@ -1165873,37 +1169360,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.10.20191817", - "rel_title": "COVID-19: Mechanistic model calibration subject to active and varying non-pharmaceutical interventions", - "rel_date": "2020-09-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20191817", - "rel_abs": "Mathematical models are useful in epidemiology to understand the COVID-19 contagion dynamics. Our aim is to demonstrate the effectiveness of parameter regression methods to calibrate an established epidemiological model describing COVID-19 infection rates subject to active and varying non-pharmaceutical interventions (NPIs). To do this, we assess the potential of some established chemical engineering modelling principles and practice for application to modelling of epidemiological systems. This allows us to exploit the sophisticated functionality of a commercial chemical engineering simulator capable of parameter regression with piecewise continuous integration and event and discontinuity management. Our results provide insights into the outcomes of on-going disease suppression measures, while visualisation of reported data also provides up-to-date condition monitoring of the status of the pandemic. We observe that the effective reproduction number response to NPIs is non-linear with variable response rate, magnitude and direction.\n\nHighlightsO_LIModelling COVID-19 contagion dynamics with piecewise continuous integration and event and discontinuity management\nC_LIO_LIEquivalence to kinetic model with time varying stoichiometry\nC_LIO_LIModel calibration and estimation of non-linear variation in Re\nC_LIO_LIDevelopment of prototype demonstrator algorithm for estimation of Re using data with time varying NPIs\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Mark J Willis", - "author_inst": "School of Engineering, Newcastle University" - }, - { - "author_name": "Allen R Wright", - "author_inst": "School of Engineering, Newcastle University" - }, - { - "author_name": "Victoria Bramfitt", - "author_inst": "School of Engineering, Newcastle University" - }, - { - "author_name": "Victor Hugo Grisales D\u00edaz", - "author_inst": "Grupo de investigaci\u00f3n en Microbiolog\u00eda y Biotecnolog\u00eda MICROBIOTEC, Facultad Ciencias de la Salud, Universidad Libre Seccional Pereira" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.11.20192161", "rel_title": "Early effect of the Covid-19 epidemic on vaccine coverage of major antigens in Guinea: an analysis of the interrupted time series of national immunization coverage", @@ -1167306,6 +1170762,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.09.20191700", + "rel_title": "Altered blood cell traits underlie a major genetic locus of severe COVID-19", + "rel_date": "2020-09-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20191700", + "rel_abs": "PurposeThe genetic locus 3p21.31 has been associated with severe coronavirus disease 2019 (COVID-19), but the underlying pathophysiological mechanism is unknown.\n\nMethodsTo identify intermediate traits of the COVID-19 risk variant, we performed a phenome-wide association study (PheWAS) with 923 phenotypes in 310,999 European individuals from UK Biobank. For candidate target genes, we examined associations between their expression and the polygenic score (PGS) of 1,263 complex traits in a meta-analysis of 31,684 blood samples.\n\nResultsOur PheWAS identified and replicated multiple blood cell traits to be associated with the COVID-19 risk variant, including monocyte count and percentage (p = 1.07x10-8, 4.09x10-13), eosinophil count and percentage (p = 5.73x10-3, 2.20x10-3), and neutrophil percentage (p = 3.23x10-3). The PGS analysis revealed positive associations between the expression of candidate genes and genetically predicted counts of specific blood cells: CCR3 with eosinophil and basophil (p = 5.73x10-21, 5.08x10-19); CCR2 with monocytes (p = 2.40x10-10); and CCRl with monocytes and neutrophil (p = 1.78x10-6, 7.17x10-5).\n\nConclusionsMultiple blood cell traits, especially monocyte, eosinophil, and neutrophil numbers, are associated with the COVID-19 risk variant and the expression of its candidate target genes, representing probable mechanistic links between the genetic locus 3p21.31 and severe COVID-19.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jingqi Zhou", + "author_inst": "University of Georgia" + }, + { + "author_name": "Yitang Sun", + "author_inst": "University of Georgia" + }, + { + "author_name": "Weishan Huang", + "author_inst": "Louisiana State University" + }, + { + "author_name": "Kaixiong Ye", + "author_inst": "University of Georgia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.09.08.20190884", "rel_title": "Prison population reductions and COVID-19: A latent profile analysis synthesizing recent evidence from the Texas state prison system", @@ -1167407,45 +1170894,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.03.20187526", - "rel_title": "Safety and Efficacy of Antiviral Drugs for the Treatment of Patients with SARS-CoV-2 Infection: A Systematic Review and Meta-analyses", - "rel_date": "2020-09-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187526", - "rel_abs": "ObjectiveTo systematically review the safety and efficacy outcomes of using antivirals for the treatment of COVID-19.\n\nMethodsFive databases were screened from inception to 27-Aug-2020. The effects of specific drug interventions on safety and efficacy were assessed in COVID-19 patients. Risk Ratios (RRs) with corresponding 95% confidence intervals (CIs) were pooled using random-effects models.\n\nResultsA total of 10 studies were identified which fulfill the inclusion criteria. Patients taking antivirals had 26% less risk of having a severe adverse event (SAE) compared to controls (RR, 0.74, CI:0.62 to 0.89, P=0.002). Clinical improvement at day 14 was observed among the cases treated with antivirals compared to the control group (RR 1.24, CI: 1.00 to 1.53 p=0.05).\n\nConclusionThere is evidence that Remdesivir and LPV/r reduces the hospital length of stay and that patients to which antivirals were administered had less SAE and improvement when compared to patients not prescribed with antivirals. Due to a lack of power and the quality of the studies, it was not possible to determine which antivirals have a greater risk-benefit balance, and therefore the optimal approach to antiviral treatment is still uncertain.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Zuleika Aponte Torres", - "author_inst": "Aponte Epidemiology Consultancy" - }, - { - "author_name": "Sandra Lopez-Leon", - "author_inst": "Novartis Pharmaceuticals Corporation" - }, - { - "author_name": "Thirumugam Muthuvel", - "author_inst": "Independent Researcher" - }, - { - "author_name": "Subha Manivannan", - "author_inst": "Subhag HealthTech Pvt. Ltd" - }, - { - "author_name": "Krutika Srivastava", - "author_inst": "Massachusetts College of Pharmacy and Health Science" - }, - { - "author_name": "Marco Pavesi", - "author_inst": "Data Center, European Foundation for the study of Chronic Liver Failure (EF-CLIF)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.03.20184226", "rel_title": "A New Screening Method for COVID-19 based on Ocular Feature Recognition by Machine Learning Tools", @@ -1168820,6 +1172268,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.07.20188003", + "rel_title": "The Geography of Excess Deaths in England during the Covid-19 pandemic: Longer term impacts and monthly dynamics", + "rel_date": "2020-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.07.20188003", + "rel_abs": "Physical social interaction relevant to the spread of infectious diseases occurs, by its nature, at a local level. If infection and related mortality are associated with social background, it is therefore natural to study variation in them in relation to the social composition of local areas. The first part of the paper studies the geographical impact of Covid-19 infection on age-standardised sex-specific excess death rates during the peak months of the pandemic so far, March through May 2020. The second part examines monthly mortality dynamics in relation to predictions from a spatial SIR (Susceptible, Infected, Recovered) model of infection introduced by Bisin and Moro (2020). The analysis indicates that during the peak months of the Covid-19 pandemic, a larger non-white population and higher social deprivation in an area were associated with higher excess mortality, particularly among men. Regarding dynamics, higher population density accelerated the growth in mortality during the upsurge in infection and increased its rate of decline after the peak of the epidemic, thereby producing a more peaked mortality profile. There is also evidence of a slower post-peak decline in mortality in more socially deprived areas but a more rapid decline in areas with a larger non-white population.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Richard Breen", + "author_inst": "University of Oxford" + }, + { + "author_name": "John Ermisch", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.04.20188235", "rel_title": "Trend prediction of COVID-19 based on ARIMA model in mainland of China", @@ -1168969,33 +1172440,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.07.20189449", - "rel_title": "Mitigation Strategies and Compliance in the Covid-19 Fight; How Much Compliance is Enough?", - "rel_date": "2020-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.07.20189449", - "rel_abs": "Today, with only 4% of the worlds population, the U.S. is bearing a disproportionate share of COVID-19 infections. Seeking to understand this puzzle, we investigate how mitigation strategies and compliance can work together (or in opposition) to reduce (or increase) the spread of COVID-19 infection. Drilling down to the state level, we create specific state indices suitable for the U.S. to measure the degree of strictness of public mitigation measures. In this, we build on the Oxford Stringency Index. A modified time-varying SEIRD model, incorporating this Stringency Index as well as a Compliance Indicator to reduce the transmission, is then estimated with daily data for a sample of 6 U.S. states. These are New York, New Hampshire, New Mexico, Colorado, Texas, and Arizona. We provide a simple visual policy tool to evaluate the various combinations of mitigation policies and compliance that can reduce the basic reproduction number to less than one; this is the acknowledged threshold in the epidemiological literature to control the pandemic. States successful in combating the pandemic were able to achieve a suitable combination. Understanding of this relationship by the public and policy makers is key to controlling the pandemic. This tool has the potential to be used in a real-time, dynamic fashion for flexible policy options.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Swati Mukerjee", - "author_inst": "Bentley University" - }, - { - "author_name": "Clifton Chow", - "author_inst": "Bentley University" - }, - { - "author_name": "Mingfei Li", - "author_inst": "Bentley University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.09.07.20187666", "rel_title": "Gastrointestinal involvement attenuates COVID-19 severity and mortality", @@ -1170470,6 +1173914,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.08.20190397", + "rel_title": "The impact of COVID-19 restriction measures on loneliness among older adults in Austria", + "rel_date": "2020-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20190397", + "rel_abs": "BackgroundTo halt the spread of COVID-19, Austria implemented a 7-week shut-down of public life in March/April 2020 which was followed by a gradual withdrawal of these restriction measures in May/June 2020. We expect that the ensuing reduction in social contacts led to increased loneliness among older adults (60+).\n\nMethodsWe conducted three analyses to assess the association between COVID-19 public health restriction measures and loneliness: (1) A comparison between pre-pandemic (SHARE: 2013-2017) and pandemic (May 2020) levels of loneliness (UCLA-3 scale), (2) an analysis of the correlation between being affected by COVID-19 restriction measures and loneliness based on cross-sectional survey data from early May 2020, and (3) a longitudinal analysis of weekly changes in loneliness (Corona panel data) from late March to early June 2020.\n\nResultsWe found (1) loneliness levels to have increased in 2020 in comparison with previous years, (2) an association between the number of restriction measures older adults reported to be affected from and loneliness, and (3) that loneliness was higher during shut-down compared to the subsequent re-opening phase, particularly among those who live alone.\n\nDiscussionOur results provide evidence that COVID-19 restriction measures in Austria have indeed resulted in increased levels of loneliness among older adults. However, these effects seem to be short-lived, and thus we do not expect strong negative consequences for older adults mental health downstream. Nonetheless, effects of longer and/or repeated future restriction measures aiming at social distancing should be closely monitored.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Erwin Stolz", + "author_inst": "Medical University of Graz" + }, + { + "author_name": "Hannes Mayerl", + "author_inst": "Medical University of Graz" + }, + { + "author_name": "Wolfgang Freidl", + "author_inst": "Medical University of Graz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.08.20190470", "rel_title": "Modelling the epidemic growth of preprints on COVID-19 and SARS-CoV-2", @@ -1170571,101 +1174042,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, - { - "rel_doi": "10.1101/2020.09.08.20190272", - "rel_title": "Functional myeloid-derived suppressor cells expand in blood but not airways of COVID-19 patients and predict disease severity", - "rel_date": "2020-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20190272", - "rel_abs": "The immunopathology of COVID-19 remains enigmatic, exhibiting immunodysregulation and T cell lymphopenia. Monocytic myeloid-derived suppressor cells (M-MDSC) are T cell suppressors that expand in inflammatory conditions, but their role in acute respiratory infections remains unclear. We studied blood and airways of COVID-19 patients across disease severity at multiple timepoints. M-MDSC frequencies were elevated in blood but not in nasopharyngeal or endotracheal aspirates of COVID-19 patients compared to controls. M-MDSCs isolated from COVID-19 patients suppressed T cell proliferation and IFN{gamma} production partly via an arginase-1 (Arg-1) dependent mechanism. Furthermore, patients showed increased Arg-1 and IL-6 plasma levels. COVID-19 patients had fewer T cells, and displayed downregulated expression of the CD3{zeta} chain. Ordinal regression showed that early M-MDSC frequency predicted subsequent disease severity. In conclusion, M-MDSCs expand in blood of COVID-19 patients, suppress T cells and strongly associate with disease severity, suggesting a role for M-MDSCs in the dysregulated COVID-19 immune response.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Sara Falck-Jones", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Sindhu Vangeti", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Meng Yu", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Ryan Falck-Jones", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Alberto Cagigi", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Isabella Badolati", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Bjorn Osterberg", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Maximilian Julius Lautenbach", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Eric Ahlberg", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Ang Lin", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Inga Szurgot", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Klara Lenart", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Fredrika Hellgren", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Jorgen Salde", - "author_inst": "Health Care Services Stockholm County (SLSO)" - }, - { - "author_name": "Jan Albert", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Niclas Johansson", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Max Bell", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Karin Lore", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Anna Farnert", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Anna Smed-Sorensen", - "author_inst": "Karolinska Institutet" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.07.20189415", "rel_title": "Blood neurofilament light concentration at admittance: a potential prognostic marker in COVID-19", @@ -1172440,6 +1175816,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.06.20189480", + "rel_title": "Antibody Responses to SARS-CoV-2 in Coronavirus Diseases 2019 Patients with Different Severity", + "rel_date": "2020-09-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.06.20189480", + "rel_abs": "BackgroundMore understanding of antibody responses in the SARS-CoV-2 infected population is useful for vaccine development.\n\nAimTo investigate SARS-CoV-2 IgA and IgG among COVID-19 Thai patients with different severity.\n\nMethodsWe used plasma from 118 adult patients who have confirmed SARS-CoV-2 infection and 49 patients under investigation without infection, 20 patients with other respiratory infections, and 102 healthy controls. Anti-SARS-CoV-2 IgA and IgG were performed by enzyme-linked immunosorbent assay from Euroimmun. The optical density ratio cut off for positive test was 1.1 for IgA and 0.8 for IgG. The association of antibody response with the severity of diseases and the day of symptoms was performed.\n\nResultsFrom Mar 10 to May 31, 2020, 289 participants were enrolled, and 384 samples were analyzed. Patients were categorized by clinical manifestations to mild (n = 59), moderate (n = 27) and severe (n = 32). The overall sensitivity of IgA and IgG from samples collected after day 7 is 87.9% (95% CI 79.8-93.6) and 84.8% (95% CI 76.2-91.3), respectively. The severe group had a significantly higher level of specific IgA and IgG to S1 antigen compared to the mild group. All moderate to severe patients have specific IgG while 20% of the mild group did not have any IgG detected after two weeks. Interestingly, SARS-CoV-2 IgG level was significantly higher in males compared to females among the severe group (p = 0.003).\n\nConclusionThe serologic test for SARS-CoV-2 has high sensitivity after the second week after onset of illness. Serological response differs among patients with different severity and different sex.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ekasit Kowitdamrong", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Thanyawee Puthanakit", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Watsamon Jantarabenjakul", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Eakachai Prompetchara", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Pintip Suchartlikitwong", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Opass Putcharoen", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Nattiya Hirankarn", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.05.20188821", "rel_title": "Ethnicity and clinical outcomes in COVID-19A Systematic Review and Meta-analysis", @@ -1172693,45 +1176112,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.05.20188912", - "rel_title": "Beneficial and Harmful Outcomes of Tocilizumab in Severe COVID-19: A Systematic Review and Meta-Analysis", - "rel_date": "2020-09-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.05.20188912", - "rel_abs": "BackgroundPending for randomized control trials, the use of tocilizumab (TCZ) in COVID-19 is based on observational studies and remains controversial.\n\nPurposeTo summarize evidence about the effect of TCZ to treat severe COVID-19.\n\nData sourcesPubMed (via MEDLINE), Scopus, and medRxiv repository databases from 1 January to 21 August 2020.\n\nStudy SelectionObservational studies in any language reporting efficacy and safety outcomes of TCZ use in hospitalized adults with COVID-19.\n\nData ExtractionIndependent, dually performed data extraction and quality assessments.\n\nData synthesisOf 57 eligible studies, 27 were controlled and 30 were not. The overall included patients were 8,128: 4,021 treated with TCZ, in addition to standard of care (SOC), and 4,107 only receiving SOC. The pooled mortality was lower in the TCZ-group vs. the control group, with a relative risk (RR) of 0.73 (95%CI 0.57-0.93; p = 0.010). The overall NNT to avoid one death was 20. In hospital wards, patients in the TCZ-group were transferred to intensive care unit (ICU) in a higher proportion than those in the control group; however, ICU mortality of the TCZ-group was lower than in the control group. Secondary infections occurred in a higher proportion in TCZ-treated patients. Among survivors, the length of stay was similar in both groups.\n\nLimitationsConclusions should be considered as weak evidence since they are based on observational studies, most of them retrospective. A variety of factors influencing the indication and effect of TCZ could not be evaluated in-depth.\n\nConclusionsTCZ seems beneficial in preventing in-hospital mortality in severe, non-critically ill COVID-19 patients. Conversely, patients receiving TCZ appear to be at higher risk for secondary infections, especially those admitted to ICU.\n\nFunding sourceNo funding or sponsorship was received for this study or publication of this article.\n\nThe protocol was published in the National Institute for Health Research international register of systematic reviews (PROSPERO); registration number CRD42020204934.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Manuel Rubio-Rivas", - "author_inst": "Internal Medicine Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain" - }, - { - "author_name": "Jose M. Mora-Lujan", - "author_inst": "Internal Medicine Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain" - }, - { - "author_name": "Abelardo Montero", - "author_inst": "Internal Medicine Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain" - }, - { - "author_name": "Narcis A. Homs", - "author_inst": "Internal Medicine Department, Bellvitge University Hospital, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain" - }, - { - "author_name": "Jordi Rello", - "author_inst": "Centro de Investigacion Biomedica en Red (CIBERES), Instituto de Salud Carlos III, Madrid, Spain. CRIPS, Vall Hebron Institute of Research, Barcelona, Spain. Sc" - }, - { - "author_name": "Xavier Corbella", - "author_inst": "Internal Medicine Department, Hospital Universitari de Bellvitge, Bellvitge Biomedical Research Institute-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain. Sc" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.05.20189134", "rel_title": "Characteristics of COVID-19 recurrence: a systematic review and meta-analysis", @@ -1175298,6 +1178678,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.09.04.20185645", + "rel_title": "Predicting illness trajectory and hospital resource utilization of COVID-19 hospitalized patients - a nationwide study", + "rel_date": "2020-09-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20185645", + "rel_abs": "BackgroundThe spread of COVID-19 has led to a severe strain on hospital capacity in many countries. There is a need for a model to help planners assess expected COVID-19 hospital resource utilization.\n\nMethodsRetrospective nationwide cohort study following the day-by-day clinical status of all hospitalized COVID-19 patients in Israel from March 1st to May 2nd, 2020. Patient clinical course was modelled with a machine learning approach based on a set of multistate Cox regression-based models with adjustments for right censoring, recurrent events, competing events, left truncation, and time-dependent covariates. The model predicts the patients entire disease course in terms of clinical states, from which we derive the patients hospital length-of-stay, length-of-stay in critical state, the risk of in-hospital mortality, and total and critical care hospital-bed utilization. Accuracy assessed over eight cross-validation cohorts of size 330, using per-day Mean Absolute Error (MAE) of predicted hospital utilization averaged over 64 days; and area under the receiver operating characteristics (AUROC) for individual risk of critical illness and in-hospital mortality, assessed on the first day of hospitalization. We present predicted hospital utilization under hypothetical incoming patient scenarios.\n\nFindingsDuring the study period, 2,703 confirmed COVID-19 patients were hospitalized in Israel. The per-day MAEs for total and critical-care hospital-bed utilization, were 4{middle dot}72 {+/-} 1{middle dot}07 and 1{middle dot}68 {+/-} 0{middle dot}40 respectively; the AUROCs for prediction of the probabilities of critical illness and in-hospital mortality were 0{middle dot}88 {+/-} 0{middle dot}04 and 0{middle dot}96 {+/-} 0{middle dot}04, respectively. We further present the impact of several scenarios of patient influx on healthcare system utilization, and provide an R software package for predicting hospital-bed utilization.\n\nInterpretationWe developed a model that, given basic easily obtained data as input, accurately predicts total and critical care hospital utilization. The model enables evaluating the impact of various patient influx scenarios on hospital utilization and planning ahead of hospital resource allocation.\n\nFundingThe work was funded by the Israeli Ministry of Health. M.G. received support from the U.S.-Israel Binational Science Foundation (BSF, 2016126).\n\nO_TEXTBOXResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSCOVID19 outbreaks are known to lead to severe case load in hospital systems, stretching resources, partially due to the long hospitalizations needed for some of the patients. There is a crucial need for tools helping planners assess future hospitalization load, taking into account the specific characteristics and heterogeneity of currently hospitalized COVID19 patients, as well as the characteristics of incoming patients. We searched PubMed for articles published up to September 9, 2020, containing the words \"COVID19\" and combinations of \"hospital\", \"utilization\", \"resource\", \"capacity\" and \"predict\". We found 145 studies; out of them, several included models that predict the future trend of hospitalizations using compartment models (e.g. SIR models), or by using exponential or logistic models. We discuss two of the more prominent ones, which model explicitly the passage of patients through the ICU. These models (i) do not take into account individual patient characteristics; (ii) do not consider length-of-stay heterogeneity, despite the fact that bed utilization is in part determined by a long tail of patients requiring significantly longer stays than others; (iii) do not correct for competing risks bias. We further searched for studies containing the words \"COVID19\" and \"multistate\", and \"COVID19\" and \"length\" and \"stay\". Out of 317 papers, we found two using multistate models focusing only on patients undergoing ECMO treatment.\n\nAdded value of this studyWe present the first model predicting hospital load based on the individual characteristics of hospitalized patients: age, sex, clinical state, and time already spent in-hospital. We combine this with scenarios for incoming patients, allowing for variations by age, sex and clinical state. The models precise predictions are based on a large sample of complete, day-by-day disease trajectories of patients, with a full coverage of the entire COVID-19 hospitalized population in Israel up to early May, 2020 (n =2, 703). We provide the model, as well as software for fitting such a model to local data, and an anonymized version of the dataset used to create the model.\n\nImplications of all the available evidenceAccurate predictions for hospital utilization can be made based on easy to obtain patient data: age, sex, and patient clinical state (moderate, severe or critical). The model allows hospital-and regional-level planners to allocate resources in a timely manner, preparing for different patient influx scenarios.\n\nC_TEXTBOX", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Michael Roimi", + "author_inst": "Rambam Health Care Campus" + }, + { + "author_name": "Rom Gutman", + "author_inst": "Technion - Israel Institute of Technology" + }, + { + "author_name": "Jonathan Somer", + "author_inst": "Technion - Israel Institute of Technology" + }, + { + "author_name": "Asaf Ben Arie", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Ido Calman", + "author_inst": "Independent" + }, + { + "author_name": "Yaron Bar-Lavie", + "author_inst": "Rambam Health Care Campus" + }, + { + "author_name": "Udi Gelbshtein", + "author_inst": "Israel Ministry of Health" + }, + { + "author_name": "Sigal Liverant-Taub", + "author_inst": "Israel Ministry of Health" + }, + { + "author_name": "Arnona Ziv", + "author_inst": "Gertner Institute for Epidemiology and Health Policy Research" + }, + { + "author_name": "Danny Eytan", + "author_inst": "Technion - Israel Institute of Technology and Rambam Health Care Campus" + }, + { + "author_name": "Malka Gorfine", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Uri Shalit", + "author_inst": "Technion - Israeli Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.09.04.20184523", "rel_title": "MOLECULAR EPIDEMIOLOGY TO UNDERSTAND THE SARS-CoV-2 EMERGENCE IN THE BRAZILIAN AMAZON REGION", @@ -1175583,65 +1179026,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.04.20188318", - "rel_title": "Trans-ethnic analysis reveals genetic and non-genetic associations with COVID-19 susceptibility and severity", - "rel_date": "2020-09-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20188318", - "rel_abs": "COVID-19 presents with a wide range of severity, from asymptomatic in some individuals to fatal in others. Based on a study of over one million 23andMe research participants, we report genetic and non-genetic associations with testing positive for COVID-19, respiratory symptoms, and hospitalization. Risk factors for hospitalization include advancing age, male sex, elevated body mass index, lower socio-economic status, non-European ancestry, and pre-existing cardio-metabolic and respiratory conditions. Using trans-ethnic genome-wide association studies, we identify a strong association between blood type and COVID-19 diagnosis, as well as a gene-rich locus on chr3p21.31 that is more strongly associated with outcome severity. While non-European ancestry was found to be a significant risk factor for hospitalization after adjusting for socio-demographics and pre-existing health conditions, we did not find evidence that these two primary genetic associations explain differences between populations in terms of risk for severe COVID-19 outcomes.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Janie F. Shelton", - "author_inst": "23andMe Inc., 223 N Mathilda Ave, Sunnyvale, CA 94086" - }, - { - "author_name": "Anjali J. Shastri", - "author_inst": "23andMe Inc., 223 N Mathilda Ave, Sunnyvale, CA 94086" - }, - { - "author_name": "Chelsea Ye", - "author_inst": "23andMe Inc., 223 N Mathilda Ave, Sunnyvale, CA 94086" - }, - { - "author_name": "Catherine H. Weldon", - "author_inst": "23andMe Inc., 223 N Mathilda Ave, Sunnyvale, CA 94086" - }, - { - "author_name": "Teresa Filshtein-Somnez", - "author_inst": "23andMe Inc., 223 N Mathilda Ave, Sunnyvale, CA 94086" - }, - { - "author_name": "Daniella Coker", - "author_inst": "23andMe Inc., 223 N Mathilda Ave, Sunnyvale, CA 94086" - }, - { - "author_name": "Antony Symons", - "author_inst": "23andMe Inc., 223 N Mathilda Ave, Sunnyvale, CA 94086" - }, - { - "author_name": "Jorge Esparza-Gordillo", - "author_inst": "Human genetics - R&D, GSK Medicines Research Centre, Target Sciences-R&D, Stevenage, UK" - }, - { - "author_name": "- The 23andMe COVID-19 Team", - "author_inst": "" - }, - { - "author_name": "Stella Aslibekyan", - "author_inst": "23andMe Inc., 223 N Mathilda Ave, Sunnyvale, CA 94086" - }, - { - "author_name": "Adam Auton", - "author_inst": "23andMe Inc., 223 N Mathilda Ave, Sunnyvale, CA 94086" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.04.20188771", "rel_title": "COVID-19 Preprints and Their Publishing Rate: An Improved Method", @@ -1177036,6 +1180420,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2020.09.03.20187757", + "rel_title": "The role of school reopening in the spread of COVID-19", + "rel_date": "2020-09-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187757", + "rel_abs": "Many countries chose to close schools as part of their response to the SARS-CoV2 coronavirus (COVID-19) pandemic. Whilst nations are gradually reopening schools, and many politicians advise that schools remain safe and the risks of increases in the spread of COVID-19 are low, little evidence has been presented to confirm those statements.\n\nA review of the numbers of new confirmed COVID-19 cases by country suggests that the reopening of schools is likely to be a driver in the increase of the number of new cases. This is likely exacerbated by accompanying changes and easing of restrictions. However, with the exception of China, notable for its robust test, track, trace, and isolate processes, no other countries that had significant numbers of COVID-19 cases have successfully reopened schools without an increase in cases as a consequence.\n\nWhilst reopening of schools following an initial peak and decrease in COVID-19 infections is desirable for a range of reasons, doing so without adequate controls and protections may lead to an exacerbation of spread within the school environment, which could then lead to increased community spread of disease.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Richard Beesley", + "author_inst": "Juvenile Arthritis Research" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.03.20187062", "rel_title": "College campuses and COVID-19 mitigation: clinical and economic value", @@ -1177245,25 +1180648,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.09.04.20187948", - "rel_title": "Long, thin transmission chains of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) may go undetected for several weeks at low to moderate reproductive numbers: Implications for containment and elimination strategy", - "rel_date": "2020-09-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20187948", - "rel_abs": "Especially at low to moderate reproductive numbers, the generally mild, non-specific symptomology of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) allows long, thin transmission chains to go undetected by passive surveillance over several weeks. This phenomenon has important implications: (1) Surveillance becomes less sensitive and reliable as an indicator of freedom from infection at the low reproductive numbers required to achieve elimination end points, passive surveillance systems may need to document an absence of new cases for at least a month to establish certainty of elimination. (2) Reproductive numbers should be kept as low as possible throughout such follow up periods without confirmed cases, to ensure such long, thin, undetected transmission chains all collapse before restrictions are eased and reproduction numbers are allowed to rebound. (3) While contact tracing systems may be highly effective when applied to large clusters in foci of elevated transmission where wide, rapidly expanding transmission chains are detected within two viral generations, large fractions of community transmission occurring through thinner, more extended transmission chains at lower reproductive numbers are often be too long to trace retrospectively and will be underrepresented in surveillance data. (4) Wherever surveillance systems are weak and/or younger age groups with lower rates of overt symptoms dominate transmission, containment effectiveness of contact tracing and isolation may be more severely limited, even at the higher reproduction numbers associated with larger outbreaks. While, contact tracing and isolation will remain vital for at least partially containing larger outbreaks, containment and elimination of SARS-CoV-2 will have to rely primarily upon the more burdensome and presumptive population-wide prevention measures that have proven so effective thus far against community transmission. Furthermore, these will have to be sustained at a much more stringent level and for longer periods after the last detected case than was necessary for SARS-CoV-1.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Gerry F Killeen", - "author_inst": "University College Cork" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.03.20183384", "rel_title": "Predicting the cumulative medical load of COVID-19 outbreaks after the peak in daily fatalities", @@ -1178586,6 +1181970,113 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.01.20185793", + "rel_title": "Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20185793", + "rel_abs": "ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection.\n\nMethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome.\n\nResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse outcome. C-statistics were 0.80 (95% confidence interval 0.73-0.87) for the WHO algorithm, 0.80 (0.71-0.90) for POPS, 0.76 (0.67-0.85) for COAST, and 0.71 (0.59-0.82) for SFHPC. Using pre-specified thresholds, the WHO algorithm had the highest sensitivity (0.85) and lowest specificity (0.75), but POPS and COAST could optimise sensitivity (0.96 and 0.92 respectively) at the expense of specificity (0.25 and 0.38 respectively) by using a threshold of any score above zero instead of the pre-specified threshold.\n\nConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive.\n\nRegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Katie Biggs", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Ben Thomas", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Steve Goodacre", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Ellen Lee", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Laura Sutton", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Matthew Bursnall", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Amanda Loban", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Simon Waterhouse", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Richard Simmonds", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Carl Marincowitz", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Jose Schutter", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Sarah Connelly", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Elena Sheldon", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Jamie Hall", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Emma Young", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Andrew Bentley", + "author_inst": "Manchester University NHS Foundation Trust" + }, + { + "author_name": "Kirsty Challen", + "author_inst": "Lancashire Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Chris Fitzsimmons", + "author_inst": "Sheffield Children's NHS Foundation Trust" + }, + { + "author_name": "Tim Harris", + "author_inst": "Barts Health NHS Trust" + }, + { + "author_name": "Fiona Lecky", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Andrew Lee", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Ian Maconochie", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Darren Walter", + "author_inst": "Manchester University NHS Foundation Trust" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.08.29.20184325", "rel_title": "Face-masking, an acceptable protective measure against COVID-19: Findings of Ugandan high-risk groups", @@ -1178687,53 +1182178,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.09.01.20182220", - "rel_title": "Cross-reactive antibody responses against SARS-CoV-2 and seasonal common cold coronaviruses", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20182220", - "rel_abs": "Beyond SARS-CoV-2, six more coronaviruses infect humans (hCoVs), four of which cause only mild symptoms (seasonal/common cold hCoVs) 12. Previous exposures to seasonal hCoVs may elicit immunological memory that could benefit the course of SARS-CoV-2 infections 3. While cross-reactive T cells epitopes of SARS-CoV-2 and seasonal hCoVs have been reported in individuals unexposed to SARS-CoV-2 4-6, potential antibody-based cross-reactivity is incompletely understood.\n\nHere, we have probed for high resolution antibody binding against all hCoVs represented as 1,539 peptides with a phage-displayed 7 antigen library. We detected broad serum antibody responses against peptides of seasonal hCoVs in up to 75% of individuals. Recovered COVID-19 patients exhibited distinct antibody repertoires targeting variable SARS-CoV-2 epitopes, and could be accurately classified from unexposed individuals (AUC=0.96). Up to 50% of recovered patients also mounted antibody responses against unique epitopes of seasonal hCoV-OC43, that were not detectable in unexposed individuals.\n\nThese results indicate substantial interindividual variability and antibody cross-reactivity between hCoVs from the direction of SARS-CoV-2 infections towards seasonal hCoVs. Our accurate high throughput assay allows profiling preexisting antibody responses against seasonal hCoVs cost-effectively and could inform on their protective nature against SARS-CoV-2.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Shelley Klompus", - "author_inst": "WIS" - }, - { - "author_name": "Sigal Leviatan", - "author_inst": "WIS" - }, - { - "author_name": "Thomas Vogl", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Iris Kalka", - "author_inst": "WIS" - }, - { - "author_name": "Anastasia Godneva", - "author_inst": "WIS" - }, - { - "author_name": "Eilat Shinar", - "author_inst": "Magen David Adom Blood Services, Israel" - }, - { - "author_name": "Adina Weinberger", - "author_inst": "WIS" - }, - { - "author_name": "Eran Segal", - "author_inst": "Weizmann Institute of Science" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.01.277954", "rel_title": "Angiotensin converting enzyme 2 is a novel target of the \u03b3-secretase complex", @@ -1180000,6 +1183444,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.02.20186916", + "rel_title": "Maximizing and evaluating the impact of test-trace-isolate programs", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186916", + "rel_abs": "September 2, 2020\n\nBackgroundTest-trace-isolate programs are an essential part of COVID-19 control that offer a more targeted approach than many other non-pharmaceutical interventions. Effective use of such programs requires methods to estimate their current and anticipated impact.\n\nMethods and FindingsWe present a mathematical modeling framework to evaluate the expected reductions in the reproductive number, R, from test-trace-isolate programs. This framework is implemented in a publicly available R package and an online application. We evaluated the effects of case detection, speed of isolation, contact tracing completeness and speed of quarantine using parameters consistent with COVID-19 transmission (R0 = 2.5, generation time 6.5 days). We show that R is most sensitive to changes to the proportion of infections detected in almost all scenarios, and other metrics have a reduced impact when case detection levels are low (< 30%). Although test-trace-isolate programs can contribute substantially to reducing R, exceptional performance across all metrics is needed to bring R below one through test-trace-isolate alone, highlighting the need for comprehensive control strategies. Formally framing the dynamical process also indicates that metrics used to evaluate performance of test-trace-isolate, such as the proportion of identified infections among traced contacts, may be misleading. While estimates of program performance are sensitive to assumptions about COVID-19 natural history, our qualitative findings are robust across numerous sensitivity analyses.\n\nConclusionsEffective test-trace-isolate programs first need to be strong in the \"test\" component, as case detection underlies all other program activities. Even moderately effective test-trace-isolate programs are an important tool for controlling the COVID-19 pandemic, and can alleviate the need for more restrictive social distancing measures.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kyra H Grantz", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Elizabeth C Lee", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Lucy D'Agostino McGowan", + "author_inst": "Department of Mathematics and Statistics, Wake Forest University" + }, + { + "author_name": "Kyu Han Lee", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "C. Jessica E. Metcalf", + "author_inst": "Department of Ecology and Evolutionary Biology, Princeton University; Princeton School of Public and International Affairs, Princeton University" + }, + { + "author_name": "Emily S Gurley", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Justin Lessler", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.02.20186734", "rel_title": "Could seasonal influenza vaccination influence COVID-19 risk?", @@ -1180169,173 +1183656,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.02.20185173", - "rel_title": "Characteristics and outcomes of 627 044 COVID-19 patients with and without obesity in the United States, Spain, and the United Kingdom", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20185173", - "rel_abs": "BackgroundCOVID-19 may differentially impact people with obesity. We aimed to describe and compare the demographics, comorbidities, and outcomes of obese patients with COVID-19 to those of non-obese patients with COVID-19, or obese patients with seasonal influenza.\n\nMethodsWe conducted a cohort study based on outpatient/inpatient care, and claims data from January to June 2020 from the US, Spain, and the UK. We used six databases standardized to the OMOP common data model. We defined two cohorts of patients diagnosed and/or hospitalized with COVID-19. We created corresponding cohorts for patients with influenza in 2017-2018. We followed patients from index date to 30 days or death. We report the frequency of socio-demographics, prior comorbidities, and 30-days outcomes (hospitalization, events, and death) by obesity status.\n\nFindingsWe included 627 044 COVID-19 (US: 502 650, Spain: 122 058, UK: 2336) and 4 549 568 influenza (US: 4 431 801, Spain: 115 224, UK: 2543) patients. The prevalence of obesity was higher among hospitalized COVID-19 (range: 38% to 54%) than diagnosed COVID-19 (30% to 47%), or diagnosed (15% to 47%) or hospitalized (27% to 48%) influenza patients. Obese hospitalized COVID-19 patients were more often female and younger than non-obese COVID-19 patients or obese influenza patients. Obese COVID-19 patients were more likely to have prior comorbidities, present with cardiovascular and respiratory events during hospitalization, require intensive services, or die compared to non-obese COVID-19 patients. Obese COVID-19 patients were more likely to require intensive services or die compared to obese influenza patients, despite presenting with fewer comorbidities.\n\nInterpretationWe show that obesity is more common amongst COVID-19 than influenza patients, and that obese patients present with more severe forms of COVID-19 with higher hospitalization, intensive services, and fatality than non-obese patients. These data are instrumental for guiding preventive strategies of COVID-19 infection and complications.\n\nFundingThe European Health Data & Evidence Network has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 806968. The JU receives support from the European Unions Horizon 2020 research and innovation programme and EFPIA. This research received partial support from the National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), US National Institutes of Health, US Department of Veterans Affairs, Janssen Research & Development, and IQVIA. The University of Oxford received funding related to this work from the Bill & Melinda Gates Foundation (Investment ID INV-016201 and INV-019257). APU has received funding from the Medical Research Council (MRC) [MR/K501256/1, MR/N013468/1] and Fundacion Alfonso Martin Escudero (FAME) (APU). VINCI [VA HSR RES 13-457] (SLD, MEM, KEL). JCEL has received funding from the Medical Research Council (MR/K501256/1) and Versus Arthritis (21605). No funders had a direct role in this study. The views and opinions expressed are those of the authors and do not necessarily reflect those of the Clinician Scientist Award programme, NIHR, Department of Veterans Affairs or the United States Government, NHS, or the Department of Health, England.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSPrevious evidence suggests that obese individuals are a high risk population for COVID-19 infection and complications. We searched PubMed for articles published from December 2019 until June 2020, using terms referring to SARS-CoV-2 or COVID-19 combined with terms for obesity. Few studies reported obesity and most of them were limited by small sample sizes and restricted to hospitalized patients. Further, they used different definitions for obesity (i.e. some reported together overweight and obesity, others only reported obesity with BMI>40kg/m2). To date, no study has provided detailed information on the characteristics of obese COVID-19 patients, such as the prevalence of comorbidities or COVID-19 related outcomes. In addition, despite the fact that COVID-19 has been often compared to seasonal influenza, there are no studies assessing whether obese patients with COVID-19 differ from obese patients with seasonal influenza.\n\nAdded value of this studyWe report the largest cohort of obese patients with COVID-19 and provide information on more than 29 000 aggregate characteristics publicly available. Our findings were consistent across the participating databases and countries. We found that the prevalence of obesity is higher among COVID-19 compared to seasonal influenza patients. Obese patients with COVID-19 are more commonly female and have worse outcomes than non-obese patients. Further, they have worse outcomes than obese patients with influenza, despite presenting with fewer comorbidities.\n\nImplications of all the available evidenceOur results show that individuals with obesity present more comorbidities and worse outcomes for COVID-19 than non-obese patients. These findings may be useful in guiding clinical practice and future preventative strategies for obese individuals, as well as provide useful data to support subsequent association studies focussed on obesity and COVID-19.", - "rel_num_authors": 38, - "rel_authors": [ - { - "author_name": "Martina Recalde", - "author_inst": "1. Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain 2. Universitat Autonoma de Bar" - }, - { - "author_name": "Elena Roel", - "author_inst": "Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Andrea Pistillo", - "author_inst": "Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Anthony G Sena", - "author_inst": "1. Janssen Research & Development, Titusville, NJ, USA 2. Department of Medical Informatics, Erasmus MC, Rotterdam, The Netherlands" - }, - { - "author_name": "Albert Prats-Uribe", - "author_inst": "Centre for Statistics in Medicine, NDORMS, University of Oxford" - }, - { - "author_name": "Waheed Ul-Rahman Ahmed", - "author_inst": "1. Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford 2. College of Medicine and Health, University of Exeter" - }, - { - "author_name": "Heba Alghoul", - "author_inst": "Faculty of Medicine, Islamic University of Gaza, Palestine" - }, - { - "author_name": "Thamir M Alshammari", - "author_inst": "Medication Safety Research Chair, King Saud University" - }, - { - "author_name": "Osaid Alser", - "author_inst": "Massachusetts General Hospital, Harvard Medical School, Boston, 02114, Massachusetts, USA" - }, - { - "author_name": "Carlos Areia", - "author_inst": "Nuffield Department of Clinical Neurosciences, University of Oxford" - }, - { - "author_name": "Edward Burn", - "author_inst": "1. Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain 2. Centre for Statistics in Me" - }, - { - "author_name": "Paula Casajust", - "author_inst": "Real-World Evidence, Trial Form Support, Barcelona, Spain" - }, - { - "author_name": "Dalia Dawoud", - "author_inst": "Cairo University, Faculty of Pharmacy, Cairo, Egypt" - }, - { - "author_name": "Scott L DuVall", - "author_inst": "1.VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA 2. Department of Internal Medicine, University of U" - }, - { - "author_name": "Thomas Falconer", - "author_inst": "Department of Biomedical Informatics, Columbia University, New York, NY, USA" - }, - { - "author_name": "Sergio Fernandez-Bertolin", - "author_inst": "Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Asieh Golozar", - "author_inst": "1. Department of Epidemiology, Johns Hopkins School of Public, Baltimore MD, USA 2. Pharmacoepidemiology, Regeneron Pharmaceuticals, NY, US" - }, - { - "author_name": "Mengchun Gong", - "author_inst": "DHC Technologies co, ltd., Beijing, China" - }, - { - "author_name": "Lana Yin Hui Lai", - "author_inst": "Division of Cancer Sciences, School of Medical Sciences, University of Manchester" - }, - { - "author_name": "Jennifer C.E Lane", - "author_inst": "Centre for Statistics in Medicine, NDORMS, University of Oxford" - }, - { - "author_name": "Kristine E Lynch", - "author_inst": "1.VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA 2. Department of Internal Medicine, University of U" - }, - { - "author_name": "Michael E Matheny", - "author_inst": "1. Tennessee Valley Healthcare System, Veterans Affairs Medical Center, Nashville, TN, USA 2. Department of Biomedical Informatics, Vanderbilt University Medica" - }, - { - "author_name": "Paras P Mehta", - "author_inst": "College of Medicine, The University of Arizona, Tucson, AZ, USA" - }, - { - "author_name": "Daniel R Morales", - "author_inst": "Division of Population Health and Genomics, University of Dundee, UK" - }, - { - "author_name": "Karthik Natarjan", - "author_inst": "1. Department of Biomedical Informatics, Columbia University, New York, NY, USA 2. New York-Presbyterian Hospital, New York, NY, US," - }, - { - "author_name": "Fredrik Nyberg", - "author_inst": "School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden" - }, - { - "author_name": "Jose D Posada", - "author_inst": "Department of Medicine, Stanford University, Palo Alto, California, USA" - }, - { - "author_name": "Christian G Reich", - "author_inst": "Real World Solutions, IQVIA, Cambridge, MA, USA" - }, - { - "author_name": "Lisa M Schilling", - "author_inst": "Data Science to Patient Value Program, Department of Medicine, University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Karishma Shah", - "author_inst": "Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, UK" - }, - { - "author_name": "Nigham H Shah", - "author_inst": "Department of Medicine, Stanford University, Palo Alto, California, USA" - }, - { - "author_name": "Vignesh Subbian", - "author_inst": "College of Engineering, The University of Arizona, Tucson, AZ, USA" - }, - { - "author_name": "Lin Zhang", - "author_inst": "1. School of Population Medicine and Public Health, Chinese Academy of Medical Sciences & Peking Union Medical College 2. School of Population and Global Health" - }, - { - "author_name": "Hong Zhu", - "author_inst": "1. Institute of Health Management, Southern Medical University, Guangzhou, China 2. Nanfang Hospital, Southern Medical University, Guangzhou, China" - }, - { - "author_name": "Patrick Ryan", - "author_inst": "1. Janssen Research & Development, Titusville, NJ, USA 2. Columbia University, New York, NY, U" - }, - { - "author_name": "Daniel Prieto-Alhambra", - "author_inst": "Centre for Statistics in Medicine, NDORMS, University of Oxford" - }, - { - "author_name": "Kristin Kostka", - "author_inst": "Real World Solutions, IQVIA, Cambridge, MA, USA" - }, - { - "author_name": "Talita Duarte-Salles", - "author_inst": "Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.02.20187187", "rel_title": "Computed Tomography Features of COVID-19 in Children: A Systematic Review and Meta-analysis", @@ -1181626,6 +1184946,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.01.20184101", + "rel_title": "Rapid 'mix and read' assay for scalable detection of SARS-CoV-2 antibodies in patient plasma", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20184101", + "rel_abs": "The human beta coronavirus SARS-CoV-2, causative virus of COVID-19, has infected more than 15 million people globally and continues to spread. Widespread, population level testing to detect active and past infections is critical to curb the COVID-19 pandemic. Antibody (serological) testing is the only option for detecting past infections outside the narrow window accessible to nucleic acid-based tests. However, currently available serological assays commonly lack scalability. Here, we describe the development of a rapid homogenous serological assay for the detection of antibodies to SARS-CoV-2 in patient plasma. We show that the fluorescence-based assay accurately detects seroconversion in COVID-19 patients from less than 1 L of plasma. Using a cohort of samples from COVID-19 infected or healthy individuals, we demonstrate detection with 100% sensitivity and specificity. This assay addresses an important need for a robust, low barrier to implementation, and scalable serological assay with complementary strengths to currently available serological platforms.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Hong Yue", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "Rados\u0142aw P Nowak", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "Daan Overwijn", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "N Connor Payne", + "author_inst": "Harvard University" + }, + { + "author_name": "Stephanie Fischinger", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Caroline Atyeo", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Lindsey R Baden", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Eric James Nilles", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Elizabeth W Karlson", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Xu G Yu", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Jonathan Z Li", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Ralph Mazitschek", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Eric S Fischer", + "author_inst": "Dana-Farber Cancer Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.02.20186742", "rel_title": "The role of masks in reducing the risk of new waves of COVID-19 in low transmission settings: a modeling study", @@ -1181775,25 +1185166,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2020.08.30.20184739", - "rel_title": "Test Sensitivity for Infection versus Infectiousness of SARS-CoV-2", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.30.20184739", - "rel_abs": "The most commonly used test for the presence of SARS-CoV-2 is a PCR test that is able to detect very low viral loads and inform on treatment decisions. Medical research has confirmed that many individuals might be infected with SARS-CoV-2 but not infectious. Knowing whether an individual is infectious is the critical piece of information for a decision to isolate an individual or not. This paper examines the value of different tests from an information-theoretic approach and shows that applying treatment-based approval standards for tests for infection will lower the value of those tests and likely causes decisions based on them to have too many false positives (i.e., individuals isolated who are not infectious). The conclusion is that test scoring be tailored to the decision being made.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Joshua S Gans", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.08.28.20184200", "rel_title": "Severity Prediction for COVID-19 Patients via Recurrent Neural Networks", @@ -1183332,6 +1186704,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.29.20184176", + "rel_title": "Estimating Unreported Deaths Associated with COVID-19", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.29.20184176", + "rel_abs": "Efforts to mitigate the spread of coronavirus disease 2019 (COVID-19) in the United States require an accurate understanding of how the epidemic is progressing. The National Center for Health Statistics (NCHS) releases weekly numbers of deaths attributed to a set of select causes, including deaths from COVID-19 in the entire United States (US), by state, and cumulatively for individual counties. Comparing US and state level deaths from select causes recorded in 2020 with values from 2014-2019 identifies a number of differences that exceeded 95% confidence limits on historical mean values, including three states with deaths possibly from COVID-19 in December 2019. Comparing county-level NCHS datasets with county-level data on deaths from COVID-19 compiled by four public pandemic tracking sites suggests that a large number of COVID-19 deaths have not yet been reported to the NCHS. Dividing the numbers of COVID-19 deaths counted by the public tracking sites by the percentage of COVID-19 deaths reported to the NCHS suggests that approximately 20% of all US deaths from Natural Causes, as many as 200,000, may not yet have been reported to the NCHS. Evaluating changes in the fractions of deaths attributed to COVID-19 and other specific causes or nonspecific outcomes during the epidemic, relative to 2020 totals or historical mean values, can provide a valuable perspective on the public health consequences of COVID-19.\n\nSignificance StatementEstimating total deaths from natural causes using the percentage of natural cause deaths from COVID-19 reported to the CDC and the number of COVID-19 deaths counted by public tracking sites suggests that up to 200,000 deaths from natural causes between 22 April and 15 August, 2020, around 20% of the total recorded as of 26 August, have not yet been reported to the CDC.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Benjamin Stear", + "author_inst": "The Children's Hospital of Philadelphia" + }, + { + "author_name": "Kyle Hernandez", + "author_inst": "University of Chicago," + }, + { + "author_name": "Vidya Manian", + "author_inst": "University of Puerto Rico" + }, + { + "author_name": "Som Dutta", + "author_inst": "Utah State University" + }, + { + "author_name": "Deanne Taylor", + "author_inst": "University of Pennsylvania Perelman Medical School" + }, + { + "author_name": "Catharine Conley", + "author_inst": "NASA Ames Research Center" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.30.20184804", "rel_title": "To isolate or not to isolate: The impact of changing behavior on COVID-19 transmission", @@ -1183509,29 +1186920,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.30.20184168", - "rel_title": "Suicide during the COVID-19 pandemic in Japan", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.30.20184168", - "rel_abs": "The prolonged uncertainty of the COVID-19 pandemic, fear and anxiety regarding infections, precautionary social isolation, and the resulting economic disruption could deteriorate psychological health and exacerbate the suicidal risk. Utilizing month-level suicide records covering the entire Japanese population (126 million) in 1,861 administrative units, we assessed if suicide mortality changed during the pandemic. We employed difference-in-difference estimation and found that overall suicide rate declined by 13.5% (95% CI: -17.5% to -9.5%) after the outbreak and the subsequent measures (school closure and the state of emergency). The decline is larger among males than females and among adults than children and older adults. The governments generous subsidies, reduced working hours, and fewer school sessions potentially account for its sizable decline.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Takanao Tanaka", - "author_inst": "Hong Kong University of Science and Technology" - }, - { - "author_name": "Shohei Okamoto", - "author_inst": "Tokyo Metropolitan Institute of Gerontology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.31.20185298", "rel_title": "PREDICTIVE VALUE OF SMELL AND TASTE TEST VS PCR-RT SARS-COV-2 AND RAPID DIAGNOSTIC TESTS IN THE DIAGNOSIS OF INFECTION BY COVID-19. A PROSPECTIVE MULTI-CENTRIC STUDY.", @@ -1185106,6 +1188494,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.08.31.20185314", + "rel_title": "HYDROXICLOROQUINE FOR PRE-EXPOSURE PROPHYLAXIS FOR SARS-CoV-2", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20185314", + "rel_abs": "SARS-CoV-2 infection has a high transmission level. At the present time there is not a specific treatment approved but it is known that, in vitro, chloroquine and hydroxychloroquine can inhibit the coronavirus.\n\nObjectiveverifying if patients with autoimmune diseases that are on treatment with HCQ have less incidence and severity on COVID-19.\n\nMaterial and methodsthis is a retrospective cohort study. The exposed cohort was formed by individuals with autoimmune diseases with HCQ treatment. The control cohort was randomly selected using the Health Card database. To deal with confounding variables and evaluate the effect of HCQ on the incidence and severity of SARS-CoV-2 infection, propensity score matching was used. Risk difference and paired percentage difference between exposed and non-exposed groups was estimated.\n\nResults919 individuals formed the exposed cohort and 1351 the control cohort. After matching, there were 690 patients on each group. During the time of the study, in the exposed group there were 42 (6.1%) individuals with suspected COVID-19, 12(1.7%) with confirmed COVID-19 and 3(0.4%) were hospitalized. In the control group there were 30(4.3%) individuals with suspected COVID-19, 13(1.9%) with confirmed COVID-19 and 2(0.3%) were hospitalized. The risk difference between each cohort was: 0.017(-0.05-0.04) for suspected COVID-19; -0.014(-0.015-0.012) for confirmed COVID-19 and 0.001(-0.007-0.007) for hospitalized patients. There were not significant differences.\n\nConclusionthere is no difference neither on the incidence nor on the severity of COVID-19 between patients with autoimmune diseases with HCQ treatment and patients that do not take HCQ.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Jaime Lopez de la Iglesia", + "author_inst": "GAP Leon" + }, + { + "author_name": "Naiara Cubelos", + "author_inst": "Licenciada en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Roi Naveiro", + "author_inst": "Instituto de Ciencias Matematicas. Estadistica e investigacion operativa. Consejo Superior de Investigacion Cientifica (ICMAT-CSIC)." + }, + { + "author_name": "Marina Montoro Gomez", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)" + }, + { + "author_name": "Francisco Javier Gonzalez de Haro", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Maria Ajenjo Gonzalez", + "author_inst": "Doctora en Medicina.GAP Leon (Spain)" + }, + { + "author_name": "Estefania Tobal Vicente", + "author_inst": "Doctora en Medicina. GAP Leon (Spain)" + }, + { + "author_name": "Maria Lamuedra Gil de Gomez", + "author_inst": "Graduada en Medicina. GAP Leon (Spain)" + }, + { + "author_name": "Maria Teresa Nuevo Guisado", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Isabel Torio Gomez", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Ana Penalver Andrada", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Nuria Martinez Cao", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Paula Gonzalez Figaredo", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Carlos Robles Garcia", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Lidia Anastasia Alvarado Machon", + "author_inst": "Doctora en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Angeles Lafont Alcalde", + "author_inst": "Doctora en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Jose Cesareo Naveiro Rilo", + "author_inst": "Doctor en Salud Publica y Medicina Preventiva. Unidad Docente de Medicina Familiar y Comunitaria de Leon (Spain)." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2020.09.01.20183145", "rel_title": "Impact of COVID-19 pandemic on cancer care delivery : A Real World Experience", @@ -1185231,101 +1188702,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.01.20185447", - "rel_title": "Rapid evaluation of neutralizing antibodies in COVID-19 patients", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20185447", - "rel_abs": "The ongoing coronavirus disease 2019 (COVID-19) pandemic calls for a method to rapidly and conveniently evaluate neutralizing antibody (NAb) activity in patients. Here, an up-conversion phosphor technology-based point-of-care testing (UPT-POCT) and a microneutralization assay were employed to detect total antibodies against the receptor-binding domain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein and NAb activity in COVID-19 patients sera, respectively, in order to determine if UPT-POCT could be used as a surrogate method for rapid evaluation of serum NAb activity in COVID-19 patients. In total, 519 serum samples from 213 recovered and 99 polymerase chain reaction re-positive (RP) COVID-19 patients were used in this report. We found that UPT-POCT reporting values correlated highly with NAb titers from 1:4 to 1:1024, with a correlation coefficient r = 0.9654 (P < 0.001), as well as protection rate against RP (r = 0.9886, P < 0.0001). As a significant point for reducing re-positive rate, UPT-POCT values of 4.380 {+/-} 2.677, corresponding to NAb titer of 1:64, may be appropriate as an indicator for evaluating high efficiency of protection. This study demonstrates that the quantitative lateral flow based UPT-POCT, could be used to rapidly evaluate NAb titer, which is of importance for assessing vaccine immunization efficacy, herd immunity, and screening patient plasma for high NAbs.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Pingping Zhang", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Baisheng Li", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Wei Min", - "author_inst": "Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329)" - }, - { - "author_name": "Xiaohui Wang", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Zhencui Li", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Yong Zhao", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Huan Zhang", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Min Jiang", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Huanying Zheng", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Chao Yang", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Wei Zhang", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Le Zuo", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Qi Gao", - "author_inst": "Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329)" - }, - { - "author_name": "Zhengrong Yang", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Yanzhao Li", - "author_inst": "Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329)" - }, - { - "author_name": "Tiejian Feng", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Changqing Lin", - "author_inst": "Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329)" - }, - { - "author_name": "Qinghua Hu", - "author_inst": "Shenzhen Center for Disease Control and Prevention" - }, - { - "author_name": "Tie Song", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Ruifu Yang", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.01.20185884", "rel_title": "Immune transcriptomes of highly exposed SARS-CoV-2 asymptomatic seropositive versus seronegative individuals from the Ischgl community", @@ -1187012,6 +1190388,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.08.27.20182923", + "rel_title": "Evaluation of production lots of a rapid point-of-care lateral flow serological test intended for identification of IgM and IgG against the N-terminal part of the spike protein (S1) of SARS-CoV-2", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20182923", + "rel_abs": "Background and objectivesSeveral antibody tests are available to detect SARS-CoV-2 specific antibodies, many of which address different antigens. Rapid point-of-care (POC) tests have been doubted due to an eventual risk of production errors, although it is unstudied whether such error would affect test sensitivity and/or specificity. We aimed to evaluate two separate production lots of a commercially available test intended for rapid detection of IgM and IgG against the N-terminal part of the SARS-CoV-2 spike protein (S1).\n\nMaterials and methodsSerum samples from individuals with confirmed SARS-CoV-2 infection, by RT-PCR and/or serology, and pre-COVID-19 negative control sera gathered from a biobank during 2018 were collected. The presence of anti-S1 IgM/IgG was verified by an in-house Luminex-based serological assay, serving as reference method. The index test was a commercially available rapid POC-test (the COVID-19 IgG/IgM Rapid Test Cassette [Zhejiang Orient Gene Biotech Co Ltd, Huzhou, Zhejiang, China/Healgen Scientific, LLC, U.S.A.]).\n\nResultsOne hundred samples were verified positive for anti-S1 IgG (median fluorescence intensity (MFI) [≥]900) and 74 for anti-S1 IgM (MFI [≥]700), confirmed by RT-PCR (n=90) and/or serology (n=89). None of the negative controls (n=200; MFI <300) had SARS-CoV-2 anti-S1 IgM, while one tested positive for SARS-CoV-2 anti-S1 IgG. For the two lots, the sensitivities of the rapid test were 93.2% (69/74; 95% CI: 85.1% - 97.1%) and 87.8% (65/74; 95% CI: 78.5% - 93.5%) for IgM, respectively 93.0% (93/100; 95% CI: 86.3% - 96.6%) and 100.0% for IgG (100/100; 95% CI: 96.3% - 100.0%). The specificity for both lots was 100% for IgM (200/200; 95% CI: 98.1% - 100%) and 99.5% for IgG (199/200; 95% CI: 97.2% - 99.9%). The positive predictive value was 100% for IgM and 98.9% and 99.0% for IgG. The negative predictive value was 95.7% and 97.6% for IgM, and 96.6% and 100.0% for IgG.\n\nConclusionThe rapid POC-test used in this study is suitable to assess SARS-CoV-2 anti-S1 specific IgM/IgG, as a measure of previous virus exposure on an individual level. While the specificity was not affected by production lot, external validation of separate lots of rapid POC-tests is encouraged to ensure high sensitivity before market introduction.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tove Hoffman", + "author_inst": "Uppsala University" + }, + { + "author_name": "Linda Kolstad", + "author_inst": "Uppsala University" + }, + { + "author_name": "Bengt Ronnberg", + "author_inst": "Uppsala University Hospital" + }, + { + "author_name": "Ake Lundkvist", + "author_inst": "Uppsala University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.26.20182675", "rel_title": "Epidemiological and socio-economic characteristics of the COVID-19 spring outbreak in Quebec, Canada: A population-based study", @@ -1187253,153 +1190660,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.26.20157297", - "rel_title": "Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: A guide and case study in setting up an emergency-use, laboratory-developed molecular assay", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.26.20157297", - "rel_abs": "Developing and deploying new diagnostic tests is difficult, but the need to do so in response to a rapidly emerging pandemic such as COVID-19 is crucially important for an effective response. In the early stages of a pandemic, laboratories play a key role in helping health care providers and public health authorities detect active infection, a task most commonly achieved using nucleic acid-based assays. While the landscape of diagnostics is rapidly evolving, polymerase chain reaction (PCR) remains the gold-standard of nucleic acid-based diagnostic assays, in part due to its reliability, flexibility, and wide deployment. To address a critical local shortage of testing capacity persisting during the COVID-19 outbreak, our hospital set up a molecular based laboratory developed test (LDT) to accurately and safely diagnose SARS-CoV-2. We describe here the process of developing an emergency-use LDT, in the hope that our experience will be useful to other laboratories in future outbreaks and will help to lower barriers to fast and accurate diagnostic testing in crisis conditions.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Melis N. Anahtar", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Bennett Shaw", - "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard; Massachusetts General Hospital" - }, - { - "author_name": "Damien Slater", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Elizabeth H Byrne", - "author_inst": "Broad Institute" - }, - { - "author_name": "Yolanda Botti-Lodovico", - "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard" - }, - { - "author_name": "Gordon Adams", - "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard; Massachusetts General Hospital" - }, - { - "author_name": "Stephen F. Schaffner", - "author_inst": "Broad Institute" - }, - { - "author_name": "Jacqueline S. Eversley", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Graham McGrath", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Tasos Gogakos", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Jochen Lennerz", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Hetal Desai Marble", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Lauren L. Ritterhouse", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Julie Batten", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "N. Zeke Georgantas", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Rebecca Pellerin", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Sylvia Signorelli", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Julia Thierauf", - "author_inst": "Massachusetts General Hospital; Heidelberg University Hospital" - }, - { - "author_name": "Molly Kemball", - "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard; Harvard University" - }, - { - "author_name": "Christian Happi", - "author_inst": "Redeemers University" - }, - { - "author_name": "Donald S. Grant", - "author_inst": "Kenema Government Hospital, Ministry of Health and Sanitation; University of Sierra Leone" - }, - { - "author_name": "Daouda Ndiaye", - "author_inst": "Le Dantec Hospital and Cheikh Anta Diop University" - }, - { - "author_name": "Katherine J. Siddle", - "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard; Harvard University" - }, - { - "author_name": "Samar B Mehta", - "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard; Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Jason B. Harris", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Edward T Ryan", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Virginia M. Pierce", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Regina C LaRocque", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Jacob Lemieux", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Pardis Sabeti", - "author_inst": "Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard; Massachusetts General Hospital; Harvard University; Harvard T.H. Chan School of Publ" - }, - { - "author_name": "Eric Rosenberg", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "John Branda", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Sarah E Turbett", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.08.26.20182436", "rel_title": "Previous psychopathology predicted severe COVID-19 concern, anxiety and PTSD symptoms in pregnant women during lockdown in Italy", @@ -1188614,6 +1191874,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.26.20182477", + "rel_title": "Modelling COVID-19 contagion:Risk assessment and targeted mitigation policies", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.26.20182477", + "rel_abs": "We use a spatial epidemic model with demographic and geographic heterogeneity to study the regional dynamics of COVID-19 across 133 regions in England.\n\nOur model emphasises the role of variability of regional outcomes and heterogeneity across age groups and geographic locations, and provides a framework for assessing the impact of policies targeted towards sub-populations or regions. We define a concept of efficiency for comparative analysis of epidemic control policies and show targeted mitigation policies based on local monitoring to be more efficient than country-level or non-targeted measures. In particular, our results emphasise the importance of shielding vulnerable sub-populations and show that targeted policies based on local monitoring can considerably lower fatality forecasts and, in many cases, prevent the emergence of second waves which may occur under centralised policies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rama Cont", + "author_inst": "University of Oxford" + }, + { + "author_name": "RenYuan Xu", + "author_inst": "University of Oxford" + }, + { + "author_name": "Artur Kotlicki", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.26.20181990", "rel_title": "Empowering the crowd: Feasible strategies to minimize the spread of COVID-19 in high-density informal settlements", @@ -1188715,41 +1192002,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.08.28.20183814", - "rel_title": "Host-to-Host Airborne Transmission As a Multiphase Flow Problem For Science-Based Social Distance Guidelines", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.28.20183814", - "rel_abs": "COVID-19 pandemic has strikingly demonstrated how important it is to develop fundamental knowledge related to generation, transport and inhalation of pathogen-laden droplets and their subsequent possible fate as airborne particles, or aerosols, in the context of human to human transmission. It is also increasingly clear that airborne transmission is an important contributor to rapid spreading of the disease. In this paper, we discuss the processes of droplet generation by exhalation, their potential transformation into airborne particles by evaporation, transport over long distances by the exhaled puff and by ambient air turbulence, and final inhalation by the receiving host as interconnected multiphase flow processes. A simple model for the time evolution of droplet/aerosol concentration is presented based on a theoretical analysis of the relevant physical processes. The modeling framework along with detailed experiments and simulations can be used to study a wide variety of scenarios involving breathing, talking, coughing and sneezing and in a number of environmental conditions, as humid or dry atmosphere, confined or open environment. Although a number of questions remain open on the physics of evaporation and coupling with persistence of the virus, it is clear that with a more reliable understanding of the underlying flow physics of virus transmission one can set the foundation for an improved methodology in designing case-specific social distancing and infection control guidelines.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "S Balachandar", - "author_inst": "University of Florida" - }, - { - "author_name": "Stephane Zaleski", - "author_inst": "Sorbonne" - }, - { - "author_name": "Alfredo Soldati", - "author_inst": "TU Wien" - }, - { - "author_name": "Goodarz Ahmadi", - "author_inst": "Clarkson University" - }, - { - "author_name": "Lydia Bourouiba", - "author_inst": "MIT" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.27.20183202", "rel_title": "Data-Driven Inference of COVID-19 Clinical Prognosis", @@ -1190292,6 +1193544,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.08.29.20126201", + "rel_title": "Sex-based clinical and immunological differences in COVID-19", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.29.20126201", + "rel_abs": "BackgroundMales and females differ in their immunological responses to foreign pathogens. However, most of the current COVID-19 clinical practices and trials do not take sex as consideration.\n\nMethodsWe performed an unbiased sex-based comparative analysis for the clinical outcomes, peripheral immune cells, and SARS-CoV-2 specific antibody levels of 1,558 males and 1,499 females COVID-19 patients from a single center. The lymphocyte subgroups were measured by Flow cytometry. Total antibody, Spike protein (S)-, receptor binding domain (RBD)-, and nucleoprotein (N)-specific IgM and IgG levels were measured by chemiluminescence.\n\nResultsWe found that the mortality and ICU admission rates were approximately 2-fold higher in males than that in females (P<0.005). Survival analysis revealed that sex is an independent prognostic factor for COVID-19 (Hazard ratio=2.2, P=0.003). The concentration of inflammatory factors in peripheral blood was significantly higher in males. Besides, the renal and hepatic abnormality induced by COVID-19 was more common in males during the hospitalization. The analysis of lymphocyte subsets revealed that the percentage of CD19+ B cell and CD4+ T cell was significantly higher in females (P<0.001) during hospitalization, indicating the stronger humoral immunity in females than males. Notably, the protective IgG sharply increased and reached a peak in the fourth week after symptom onset in females, while gradually increased and reached a peak in the seventh week in males.\n\nConclusionsThe unfavorable prognosis of male COVID-19 patients may result from the weak humoral immunity and indolent antibody responses during SARS-CoV-2 infection and recovery. Early medical intervention and close monitoring are important, especially for male COVID-19 patients. Hormonal or convalescent plasma therapy may help improve the immunity of males to fight against SARS-CoV-2 infection.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Kening Li", + "author_inst": "COVID-19 Research Center, Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine" + }, + { + "author_name": "Bin Huang", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Yun Cai", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Zhihua Wang", + "author_inst": "Department of Laboratory Medicine & Blood Transfusion, the 907th Hospital" + }, + { + "author_name": "Lu Li", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Lingxiang Wu", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Mengyan Zhu", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Jie Li", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Ziyu Wang", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Min Wu", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Wanlin Li", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Wei Wu", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Lishen Zhang", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Xinyi Xia", + "author_inst": "COVID-19 Research Center, Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine" + }, + { + "author_name": "Shukui Wang", + "author_inst": "Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University" + }, + { + "author_name": "Qianghu Wang", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.27.20183616", "rel_title": "A Comparison of Covid-19 Patient Characteristics Before versus After Partial Lockdown in Vietnam", @@ -1190421,37 +1193752,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.28.20183921", - "rel_title": "The importance of saturating density dependence for predicting SARS-CoV-2 resurgence", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.28.20183921", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is transmitted more effectively in densely populated areas and omitting this phenomenon from epidemiological models may substantially affect projections of spread and control. Adjusting for deprivation, proportion of ethnic minority population and proportion of key workers among the working population, mortality data from England show good evidence for an increasing trend with population density until a saturating level. Projections from a mathematical model that accounts for this observation deviate markedly from the current status quo for SARS-CoV-2 models which either assume linearity between density and transmission (30% of models) or no relationship at all (70%). Respectively, these standard model structures over- and under-estimate the delay in infection resurgence following the release of lockdown. Models have had a prominent role in SARS-CoV-2 intervention strategy; identifying saturation points for given populations and including transmission terms that account for this feature will improve model utility.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Emily Nightingale", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Oliver J Brady", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "- CMMID Covid-19 working group", - "author_inst": "" - }, - { - "author_name": "Laith Yakob", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.26.20182444", "rel_title": "Convalescent Plasma for COVID-19: A multicenter, randomized clinical trial", @@ -1192166,6 +1195466,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.25.20181487", + "rel_title": "Risk of COVID-19 hospitalisation rises exponentially with age, inversely proportional to T-cell production", + "rel_date": "2020-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20181487", + "rel_abs": "Here we report that COVID-19 hospitalisation rates follow an exponential relationship with age, doubling for every 16 years of age or equivalently increasing by 4.5% per year of life (R2=0.98). This mirrors the well studied exponential decline of both thymus volume and T-cell production, which halve every 16 years. COVID-19 can therefore be added to the list of other diseases with this property, including those caused by MRSA, MERS-CoV, West Nile virus, Streptococcus Pneumonia and certain cancers, such as chronic myeloid leukemia and brain cancers. In addition, incidence of severe disease and mortality due to COVID-19 are both higher in men, consistent with the degree to which thymic involution (and the decrease in T-cell production with age) is more severe in men compared to women. Since these properties are shared with some non-contagious diseases, we hypothesised that the age-dependence does not come from social-mixing patterns, i.e. that the probability of hospitalisation given infection rises exponentially, doubling every 16 years. A Bayesian analysis of daily hospitalisations, incorporating contact matrices, found that this relationship holds for every age group except for the under 20s. While older adults have less contacts than young adults, our analysis suggests that there is an approximate cancellation between the effects of less contacts for the elderly and higher infectiousness due to a higher probability of developing severe disease. Our model fitting suggests under 20s have 49-75% additional immune protection beyond that predicted by strong thymus function alone, consistent with increased juvenile cross-immunity from other viruses. We found no evidence for differences between age groups in susceptibility to infection or infectiousness to others (given disease state), i.e. the only important factor in the age-dependence of hospitalisation rates is the probability of hospitalisation given infection. These findings suggest the existence of a T-cell exhaustion threshold, proportional to thymic output, and that clonal expansion of peripheral T-cells does not affect disease risk. The strikingly simple inverse relationship between risk and thymic T-cell output adds to the evidence that thymic involution is an important factor in the decline of the immune system with age and may also be an important clue in understanding disease progression, not just for COVID-19 but other diseases as well.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sam Palmer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nik Cunniffe", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ruairi Donnelly", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.25.20154252", "rel_title": "SARS-CoV-2-RNA viremia is associated to hypercytokinemia and critical illness in COVID-19", @@ -1192627,45 +1195954,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.08.25.20181792", - "rel_title": "Mortality & COVID-19: A Snapshot of a Tertiary Care Facility in Pakistan", - "rel_date": "2020-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20181792", - "rel_abs": "IntroductionEver since Sars CoV-2 infection has started from China and has taken the shape of pandemic the mortality associated with this disease has been under discussion and hypercoagubility, acute severe respiratory syndrome and sepsis with multi organ failure have been accursed as possible reasons of deaths in cases infected with novel Corona virus. We conducted a retrospective analysis of the cases admitted in our high dependency and Intensive care unit and tried to pinpoint the major cause of mortality in our cases.\n\nMethodsThis is a single center retrospective study carried out at Bahria International Hospital Lahore over a 3 month period (May 10th to July 10th 2020) in which we analyzed the clinical and biochemical profiles of the COVID-19 patients who died during this period.\n\nResultsA total of 108 patients were admitted during this period out of which 11 patients died. 7 of them were men and 4 women. Majority of them had sudden cardiac arrest due to acute coronary syndrome followed by multiorgan dysfunction syndrome and acute respiratory distress syndrome.\n\nConclusionAcute coronary syndrome due to hypercoagubility was the leading cause of death in our patients.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Muhammad Asim Rana", - "author_inst": "Bahria International Hospital, Lahore" - }, - { - "author_name": "Ahad Qayyum", - "author_inst": "Bahria International Hospital, Lahore, Pakistan" - }, - { - "author_name": "Mubashar Sultan Hashmi", - "author_inst": "Bahria International Hospital, Lahore, Pakistan" - }, - { - "author_name": "Muhammad Muneeb Ullah Saif", - "author_inst": "Bahria International Hospital, Lahore, Pakistan" - }, - { - "author_name": "Muhammad Faisal Munir", - "author_inst": "Bahria International Hospital, Lahore, Pakistan" - }, - { - "author_name": "Muhammad Mansoor Hafeez", - "author_inst": "Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore, Pakistan, Lahore, PAK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.08.24.20180067", "rel_title": "Evaluation of the comparative risk of aerosol generation by tracheal intubation and extubation in the operating theatre", @@ -1194300,6 +1197588,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.29.272864", + "rel_title": "A simplified cell-based assay to identify coronavirus 3CL protease inhibitors", + "rel_date": "2020-08-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.29.272864", + "rel_abs": "We describe a mammalian cell-based assay capable of identifying coronavirus 3CL protease (3CLpro) inhibitors without requiring the use of live virus. By enabling the facile testing of compounds across a range of coronavirus 3CLpro enzymes, including the one from SARS-CoV-2, we are able to quickly identify compounds with broad or narrow spectra of activity. We further demonstrate the utility of our approach by performing a curated compound screen along with structure-activity profiling of a series of small molecules to identify compounds with antiviral activity. Throughout these studies, we observed concordance between data emerging from this assay and from live virus assays. By democratizing the testing of 3CL inhibitors to enable screening in the majority of laboratories rather than the few with extensive biosafety infrastructure, we hope to expedite the search for coronavirus 3CL protease inhibitors, to address the current epidemic and future ones that will inevitably arise.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Samuel J Resnick", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Sho Iketani", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Seo Jung Hong", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Arie Zask", + "author_inst": "Columbia University" + }, + { + "author_name": "Hengrui Liu", + "author_inst": "Columbia University" + }, + { + "author_name": "Sungsoo Kim", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Schuyler Melore", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Manoj S Nair", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Yaoxing Huang", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Nicholas E S Tay", + "author_inst": "Columbia University" + }, + { + "author_name": "Tomislav Rovis", + "author_inst": "Columbia University" + }, + { + "author_name": "Hee Won Yang", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Brent R Stockwell", + "author_inst": "Columbia University" + }, + { + "author_name": "David D Ho", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Alejandro Chavez", + "author_inst": "Columbia University Irving Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.29.257360", "rel_title": "The SARS-CoV-2 ORF10 is not essential in vitro or in vivo in humans.", @@ -1194477,145 +1197840,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.08.28.272955", - "rel_title": "Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms", - "rel_date": "2020-08-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.28.272955", - "rel_abs": "The worldwide SARS-CoV-2 outbreak poses a serious challenge to human societies and economies. SARS-CoV-2 proteins orchestrate complex pathogenic mechanisms that underlie COVID-19 disease. Thus, understanding how viral polypeptides rewire host protein networks enables better-founded therapeutic research. In complement to existing proteomic studies, in this study we define the first proximal interaction network of SARS-CoV-2 proteins, at the whole proteome level in human cells. Applying a proximity-dependent biotinylation (BioID)-based approach greatly expanded the current knowledge by detecting interactions within poorly soluble compartments, transient, and/or of weak affinity in living cells. Our BioID study was complemented by a stringent filtering and uncovered 2,128 unique cellular targets (1,717 not previously associated with SARS-CoV-1 or 2 proteins) connected to the N- and C-ter BioID-tagged 28 SARS-CoV-2 proteins by a total of 5,415 (5,236 new) proximal interactions. In order to facilitate data exploitation, an innovative interactive 3D web interface was developed to allow customized analysis and exploration of the landscape of interactions (accessible at http://www.sars-cov-2-interactome.org/). Interestingly, 342 membrane proteins including interferon and interleukin pathways factors, were associated with specific viral proteins. We uncovered ORF7a and ORF7b protein proximal partners that could be related to anosmia and ageusia symptoms. Moreover, comparing proximal interactomes in basal and infection-mimicking conditions (poly(I:C) treatment) allowed us to detect novel links with major antiviral response pathway components, such as ORF9b with MAVS and ISG20; N with PKR and TARB2; NSP2 with RIG-I and STAT1; NSP16 with PARP9-DTX3L. Altogether, our study provides an unprecedented comprehensive resource for understanding how SARS-CoV-2 proteins orchestrate host proteome remodeling and innate immune response evasion, which can inform development of targeted therapeutic strategies.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Estelle MN Laurent", - "author_inst": "Univ. Lille, Inserm, CHU Lille, U1192 - Proteomique Reponse Inflammatoire Spectrometrie de Masse - PRISM, F-59000 Lille, France" - }, - { - "author_name": "Yorgos Sofianatos", - "author_inst": "Institute for Fundamental Biomedical Research, BSRC \"Alexander Fleming\", 34 Fleming Street, 16672, Vari, Greece" - }, - { - "author_name": "Anastassia Komarova", - "author_inst": "Departement de Virologie, Unite de Genetique Moleculaire des Virus a ARN (GMVR), Institut Pasteur, UMR3569, Centre National de la Recherche Scientifique (CNRS)," - }, - { - "author_name": "Jean-Pascal Gimeno", - "author_inst": "Univ. Lille, Inserm, CHU Lille, U1192 - Proteomique Reponse Inflammatoire Spectrometrie de Masse - PRISM, F-59000 Lille, France" - }, - { - "author_name": "Payman Samavarchi Tehrani", - "author_inst": "Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada" - }, - { - "author_name": "Dae-Kyum Kim", - "author_inst": "Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto and Lunenfeld-Tanenbaum Research Institute, Sinai Health Syste" - }, - { - "author_name": "Hala Abdouni", - "author_inst": "Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada" - }, - { - "author_name": "Marie Duhamel", - "author_inst": "Univ. Lille, Inserm, CHU Lille, U1192 - Proteomique Reponse Inflammatoire Spectrometrie de Masse - PRISM, F-59000 Lille, France" - }, - { - "author_name": "Patricia Cassonnet", - "author_inst": "Departement de Virologie, Unite de Genetique Moleculaire des Virus a ARN (GMVR), Institut Pasteur, UMR3569, Centre National de la Recherche Scientifique (CNRS)," - }, - { - "author_name": "Jennifer J Knapp", - "author_inst": "Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto and Lunenfeld-Tanenbaum Research Institute, Sinai Health Syste" - }, - { - "author_name": "Da Kuang", - "author_inst": "Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto and Lunenfeld-Tanenbaum Research Institute, Sinai Health Syste" - }, - { - "author_name": "Aditya Chawla", - "author_inst": "Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto and Lunenfeld-Tanenbaum Research Institute, Sinai Health Syste" - }, - { - "author_name": "Dayag Sheykhkarimli", - "author_inst": "Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto and Lunenfeld-Tanenbaum Research Institute, Sinai Health Syste" - }, - { - "author_name": "Ashyad Rayhan", - "author_inst": "Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto and Lunenfeld-Tanenbaum Research Institute, Sinai Health Syste" - }, - { - "author_name": "Roujia Li", - "author_inst": "Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto and Lunenfeld-Tanenbaum Research Institute, Sinai Health Syste" - }, - { - "author_name": "Oxana Pogoutse", - "author_inst": "Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto and Lunenfeld-Tanenbaum Research Institute, Sinai Health Syste" - }, - { - "author_name": "David E Hill", - "author_inst": "Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatni" - }, - { - "author_name": "Mike E Calderwood", - "author_inst": "Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatni" - }, - { - "author_name": "Pascal Falter-Braun", - "author_inst": "Institute of Network Biology (INET), Helmholtz Center Munich, German Research Center for Environmental Health, Munich-Neuherberg, Germany and Microbe-Host Inter" - }, - { - "author_name": "Patrick Aloy", - "author_inst": "Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08020 Barcelona, Catalonia, Spai" - }, - { - "author_name": "Ulrich Stelzl", - "author_inst": "Department of Pharmaceutical Chemistry, Institute of Pharmaceutical Sciences, University of Graz and BioTechMed-Graz, Graz, Austria" - }, - { - "author_name": "Marc Vidal", - "author_inst": "Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Genetics, Blavatni" - }, - { - "author_name": "Anne-Claude Gingras", - "author_inst": "Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada" - }, - { - "author_name": "Georgios A Pavlopoulos", - "author_inst": "Institute for Fundamental Biomedical Research, BSRC \"Alexander Fleming\", 34 Fleming Street, 16672, Vari, Greece" - }, - { - "author_name": "Sylvie Van Der Werf", - "author_inst": "Departement de Virologie, Unite de Genetique Moleculaire des Virus a ARN (GMVR), Institut Pasteur, UMR3569, Centre National de la Recherche Scientifique (CNRS)," - }, - { - "author_name": "Isabelle Fournier", - "author_inst": "Univ. Lille, Inserm, CHU Lille, U1192 - Proteomique Reponse Inflammatoire Spectrometrie de Masse - PRISM, F-59000 Lille, France" - }, - { - "author_name": "Frederick P Roth", - "author_inst": "Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto and Lunenfeld-Tanenbaum Research Institute, Sinai Health Syste" - }, - { - "author_name": "Michel Salzet", - "author_inst": "Univ. Lille, Inserm, CHU Lille, U1192 - Proteomique Reponse Inflammatoire Spectrometrie de Masse - PRISM, F-59000 Lille, France" - }, - { - "author_name": "Caroline Demeret", - "author_inst": "Departement de Virologie, Unite de Genetique Moleculaire des Virus a ARN (GMVR), Institut Pasteur, UMR3569, Centre National de la Recherche Scientifique (CNRS)," - }, - { - "author_name": "Yves Jacob", - "author_inst": "Departement de Virologie, Unite de Genetique Moleculaire des Virus a ARN (GMVR), Institut Pasteur, UMR3569, Centre National de la Recherche Scientifique (CNRS)," - }, - { - "author_name": "Etienne Coyaud", - "author_inst": "Univ. Lille, Inserm, CHU Lille, U1192 - Proteomique Reponse Inflammatoire Spectrometrie de Masse - PRISM, F-59000 Lille, France" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.08.29.271015", "rel_title": "Silicon Nitride Inactivates SARS-CoV-2 in vitro", @@ -1196049,6 +1199273,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.27.270637", + "rel_title": "Structure of SARS-CoV-2 ORF8, a rapidly evolving coronavirus protein implicated in immune evasion", + "rel_date": "2020-08-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.27.270637", + "rel_abs": "The molecular basis for the severity and rapid spread of the COVID-19 disease caused by SARS-CoV-2 is largely unknown. ORF8 is a rapidly evolving accessory protein that has been proposed to interfere with immune responses. The crystal structure of SARS-CoV-2 ORF8 was determined at 2.04 [A] resolution by x-ray crystallography. The structure reveals a ~60 residue core similar to SARS-CoV ORF7a with the addition of two dimerization interfaces unique to SARS-CoV-2 ORF8. A covalent disulfide-linked dimer is formed through an N-terminal sequence specific to SARS-CoV-2, while a separate non-covalent interface is formed by another SARS-CoV-2-specific sequence, 73YIDI76. Together the presence of these interfaces shows how SARS-CoV-2 ORF8 can form unique large-scale assemblies not possible for SARS-CoV, potentially mediating unique immune suppression and evasion activities.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Thomas G Flower", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Cosmo Z Buffalo", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Richard M Hooy", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Marc Allaire", + "author_inst": "Lawrence Berkeley National Laboratory" + }, + { + "author_name": "Xuefeng Ren", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "James H Hurley", + "author_inst": "UC Berkeley" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.08.26.267781", "rel_title": "Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades", @@ -1196186,53 +1199449,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2020.08.24.20180729", - "rel_title": "Convalescent Plasma in treatment of COVID-19: A review of evidence for a living systematic benefit-risk assessment", - "rel_date": "2020-08-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.24.20180729", - "rel_abs": "ObjectivesWe aimed to review the evidence for a living systematic benefit risk assessment for convalescent plasma use amongst patients with severe COVID-19 disease, based on currently available data.\n\nMethodsThe assessment used the Benefit-Risk Action Team (BRAT) framework. Convalescent plasma treatment in severe COVID-19 was compared to standard of care, placebo or other treatments. A literature search was conducted to identify published papers from January 1st, 2019 until July 8th, 2020. A value tree was constructed which included ranked key benefits and risks.\n\nResultsWe screened 396 papers from PubMed and 127 papers from Embase. Four studies were eligible for inclusion as they contained comparative data. Results from a randomised controlled trial revealed a non-statistically significant shortening of time to clinical improvement of 2.15 days (95% CI, -5.28 to 0.99 days) in the intervention group compared with the control group, with a possible signal of increased efficacy amongst a small subset of patients with severe disease (but not life threatening disease), however this study may have been underpowered. Interpretation of findings amongst the three controlled non-randomised studies were limited by small patient numbers, lack of randomisation, and confounding by co-administration of other treatments. Limited data availability at the current time precluded construction of a data summary table and further quantitative analysis.\n\nConclusionsThere was insufficient evidence from controlled studies to complete a data summary table for a systematic benefit-risk assessment of the use of CP for severe COVID-19 disease at the current time, and as such a benefit-risk conclusion could not be made. Whilst uncontrolled case series have suggested positive findings with CP, results from these studies are very difficult to interpret. We provide a framework which can be updated when further data that have an impact on the benefit-risk become available.\n\nArticle SummaryStrengths and limitations of this study\n\nO_LIprovides a living systematic benefit risk assessment based on currently available data for the use of convalescent plasma in patients with severe COVID-19 disease\nC_LIO_LIestablishes a framework inclusive of ranked key benefits and risks for convalescent plasma in severe COVID-19 disease, into which additional data can be added as this becomes available facilitating re-assessment of the benefit risk profile\nC_LIO_LIuses a transparent framework (BRAT framework) which can be applied to other potential treatment options in this disease context\nC_LIO_LIinsufficient data available at the current time from comparative studies to form a benefit risk conclusion\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Miranda Davies", - "author_inst": "Drug Safety Research Unit, Southampton, UK" - }, - { - "author_name": "Samantha Lane", - "author_inst": "Drug Safety Research Unit, Southampton, UK" - }, - { - "author_name": "Alison Evans", - "author_inst": "Drug Safety Research Unit, Southampton, UK" - }, - { - "author_name": "Jacqueline Denyer", - "author_inst": "Drug Safety Research Unit, Southampton, UK" - }, - { - "author_name": "Sandeep Dhanda", - "author_inst": "Drug Safety Research Unit, Southampton, UK" - }, - { - "author_name": "Debabrata Roy", - "author_inst": "Drug Safety Research Unit, Southampton, UK" - }, - { - "author_name": "Vicki Osborne", - "author_inst": "Drug Safety Research Unit, Southampton, UK" - }, - { - "author_name": "Saad AW Shakir", - "author_inst": "Drug Safety Research Unit, Southampton, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.24.20180810", "rel_title": "Mutational landscape and dominant lineages in the SARS-CoV-2 infections in the state of Telangana, India", @@ -1197663,6 +1200879,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.26.266825", + "rel_title": "Multi-species ELISA for the detection of antibodies against SARS-CoV-2 in animals", + "rel_date": "2020-08-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.26.266825", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic with millions of infected humans and hundreds of thousands of fatalities. As the novel disease - referred to as COVID-19 - unfolded, occasional anthropozoonotic infections of animals by owners or caretakers were reported in dogs, felid species and farmed mink. Further species were shown to be susceptible under experimental conditions. The extent of natural infections of animals, however, is still largely unknown. Serological methods will be useful tools for tracing SARS-CoV-2 infections in animals once test systems are validated for use in different species. Here, we developed an indirect multi-species ELISA based on the receptor-binding domain (RBD) of SARS-CoV-2. The newly established ELISA was validated using 59 sera of infected or vaccinated animals including ferrets, raccoon dogs, hamsters, rabbits, chickens, cattle and a cat, and a total of 220 antibody-negative sera of the same animal species. Overall, a diagnostic specificity of 100.0% and sensitivity of 98.31% was achieved, and the functionality with every species included in this study could be demonstrated. Hence, a versatile and reliable ELISA protocol was established that enables high-throughput antibody detection in a broad range of animal species, which may be used for outbreak investigations, to assess the seroprevalence in susceptible species or to screen for reservoir or intermediate hosts.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Kerstin Wernike", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Andrea Aebischer", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Anna Michelitsch", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Donata Hoffmann", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Conrad Freuling", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Anne Balkema-Buschmann", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Annika Graaf", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Thomas Mueller", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Nikolaus Osterrieder", + "author_inst": "Freie Universitaet Berlin" + }, + { + "author_name": "Melanie Rissmann", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Dennis Rubbenstroth", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Jacob Schoen", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Claudia Schulz", + "author_inst": "University of Veterinary Medicine Hannover" + }, + { + "author_name": "Jakob Trimpert", + "author_inst": "Freie Universitaet Berlin" + }, + { + "author_name": "Lorenz Ulrich", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Asisa Volz", + "author_inst": "University of Veterinary Medicine Hannover" + }, + { + "author_name": "Thomas Mettenleiter", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Martin Beer", + "author_inst": "Friedrich-Loeffler-Institut" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.25.267328", "rel_title": "A unique view of SARS-CoV-2 through the lens of ORF8 protein", @@ -1197948,33 +1201251,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.08.26.267724", - "rel_title": "Epitopes targeted by T cells in convalescent COVID-19 patients", - "rel_date": "2020-08-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.26.267724", - "rel_abs": "Knowledge of the epitopes of SARS-CoV-2 that are targeted by T cells in convalescent patients is important for understanding T cell immunity against COVID-19. This information can aid the design, development and assessment of COVID-19 vaccines, and inform novel diagnostic technologies. Here we provide a unified description and meta-analysis of emerging data of SARS-CoV-2 T cell epitopes compiled from 15 independent studies of cohorts of convalescent COVID-19 patients. Our analysis demonstrates the broad diversity of T cell epitopes that have been collectively recorded for SARS-CoV-2, while also identifying a selected set of immunoprevalent epitopes that induced consistent T cell responses in multiple cohorts and in a large fraction of tested patients. The landscape of SARS-CoV-2 T cell epitopes that we describe can help guide future immunological studies, including those related to vaccines and diagnostics. A web-based platform has been developed to help complement these efforts.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ahmed A. Quadeer", - "author_inst": "The Hong Kong University of Science and Technology" - }, - { - "author_name": "Syed Faraz Ahmed", - "author_inst": "The Hong Kong University of Science and Technology" - }, - { - "author_name": "Matthew R. McKay", - "author_inst": "The Hong Kong University of Science and Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.25.267500", "rel_title": "The SARS-CoV-2 Spike mutation D614G increases entry fitness across a range of ACE2 levels, directly outcompetes the wild type, and is preferentially incorporated into trimers", @@ -1199609,6 +1202885,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.23.20180307", + "rel_title": "Hesitant or not? A global survey of potential acceptance of a COVID-19 vaccine", + "rel_date": "2020-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.23.20180307", + "rel_abs": "A number of COVID-19 vaccines are under development, with one or more possibly becoming available in 2021. We conducted a global survey in June 2020 of 13,426 people in 19 countries to determine potential acceptance rates of a COVID-19 vaccine and factors influencing acceptance. We ran univariate logistic regressions to examine the associations with demographic variables. 71.5% reported they would be very or somewhat likely to take a COVID-19 vaccine; 61.4% reported they would accept their employers recommendation to take a COVID-19 vaccine. Differences in acceptance across countries ranged from almost 9 in 10 (China) to fewer than 6 in 10 (Russia). Respondents reporting higher levels of trust in information from government sources were more likely to accept a vaccine, and take their employers advice to do so. Targeted interventions addressing age, sex, income, and education level are required to increase and sustain public acceptance of a COVID-19 vaccine.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jeffrey V Lazarus", + "author_inst": "Barcelona Institute for Global Health (ISGlobal)" + }, + { + "author_name": "Scott Ratzan", + "author_inst": "City University of New York (CUNY) Graduate School of Public Health & Health Policy, New York, USA" + }, + { + "author_name": "Adam Palayew", + "author_inst": "Barcelona Institute for Global Health (ISGlobal)" + }, + { + "author_name": "Lawrence O Gostin", + "author_inst": "Georgetown University, Washington, DC, USA" + }, + { + "author_name": "Heidi J Larson", + "author_inst": "London School of Hygiene and Tropical Medicine, London, United Kingdom" + }, + { + "author_name": "Kenneth Rabin", + "author_inst": "City University of New York (CUNY) Graduate School of Public Health & Health Policy, New York, USA" + }, + { + "author_name": "Spencer Kimball", + "author_inst": "Emerson College, Boston, Mass, USA" + }, + { + "author_name": "Ayman El-Mohandes", + "author_inst": "City University of New York (CUNY) Graduate School of Public Health & Health Policy, New York, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.23.20180513", "rel_title": "3D Printed N95 Equivalent for PPE Shortages: The Kansas City Mask", @@ -1199694,29 +1203017,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.08.23.20180497", - "rel_title": "Bayesian Estimation of the Seroprevalence of Antibodies to SARS-CoV-2", - "rel_date": "2020-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.23.20180497", - "rel_abs": "Accurately estimating the seroprevalence of antibodies to SARS-CoV-2 requires the use of appropriate methods. Bayesian statistics provides a natural framework for considering the variabilities of specificity and sensitivity of the antibody tests, as well as for incorporating prior knowledge of viral infection prevalence. We present a full Bayesian approach for this purpose, and we demonstrate the utility of our approach using a recently published large-scale dataset from the U.S. CDC.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Qunfeng Dong", - "author_inst": "Loyola University Chicago" - }, - { - "author_name": "Xiang Gao", - "author_inst": "Loyola University Chicago" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.08.23.20180554", "rel_title": "An examination of COVID-19 mitigation efficiency among 23 countries", @@ -1201370,6 +1204670,57 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.08.24.264077", + "rel_title": "An hACE2 peptide mimic blocks SARS-CoV-2 Pulmonary Cell Infection", + "rel_date": "2020-08-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.24.264077", + "rel_abs": "In the light of the recent accumulated knowledge on SARS-CoV-2 and its mode of human cells invasion, the binding of viral spike glycoprotein to human Angiotensin Converting Enzyme 2 (hACE2) receptor plays a central role in cell entry. We designed a series of peptides mimicking the N-terminal helix of hACE2 protein which contains most of the contacting residues at the binding site and have a high helical folding propensity in aqueous solution. Our best peptide mimics bind to the virus spike protein with high affinity and are able to block SARS-CoV-2 human pulmonary cell infection with an inhibitory concentration (IC50) in the nanomolar range. These first in class blocking peptide mimics represent powerful tools that might be used in prophylactic and therapeutic approaches to fight the coronavirus disease 2019 (COVID-19).", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Philippe Karoyan", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Vincent Vieillard", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Estelle Odile", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Alexis Denis", + "author_inst": "Oncodesign" + }, + { + "author_name": "amelie guihot", + "author_inst": "Assistance Publique Hopitaux de Paris Hopital Pitie Salpetriere Service de Medecine Intensive Reanimation Institut de Cardiologie 75013, Paris, France" + }, + { + "author_name": "charles edouard luyt", + "author_inst": "Assistance Publique Hopitaux de Paris, Hopital Pitie Salpetriere, Service de Medecine Intensive Reanimation, Institut de Cardiologie 75013 Paris France" + }, + { + "author_name": "Luis Gomes-Morales", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Pascal Grondin", + "author_inst": "Oncodesign" + }, + { + "author_name": "Olivier Lequin", + "author_inst": "Sorbonne Universite" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.08.24.264630", "rel_title": "SARS-CoV-2 neutralizing human antibodies protect against lower respiratory tract disease in a hamster model", @@ -1201571,49 +1204922,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.08.24.265090", - "rel_title": "Induction of SARS-CoV-2 protein S-specific CD8+ T cells in the lungs of gp96-Ig-S vaccinated mice", - "rel_date": "2020-08-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.24.265090", - "rel_abs": "Given the aggressive spread of COVID-19-related deaths, there is an urgent public health need to support the development of vaccine candidates to rapidly improve the available control measures against SARS-CoV-2. To meet this need, we are leveraging our existing vaccine platform to target SARS-CoV-2. Here, we generated cellular heat shock chaperone protein, glycoprotein 96 (gp96), to deliver SARS-CoV-2 protein S (spike) to the immune system and to induce cell-mediated immune responses. We showed that our vaccine platform effectively stimulates a robust cellular immune response against protein S. Moreover, we confirmed that gp96-Ig, secreted from allogeneic cells expressing full-length protein S, generates powerful, protein S polyepitope-specific CD4+ and CD8+ T cell responses in both lung interstitium and airways. These findings were further strengthened by the observation that protein-S -specific CD8+ T cells were induced in human leukocyte antigen (HLA)-A2-02-01 transgenic mice thus providing encouraging translational data that the vaccine is likely to work in humans, in the context of SARS-CoV-2 antigen presentation.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Eva Fisher", - "author_inst": "Univesrity of Miami" - }, - { - "author_name": "Laura Padula", - "author_inst": "University of Miami" - }, - { - "author_name": "Krisitn Podack", - "author_inst": "University of Miami" - }, - { - "author_name": "Matthew M Seavey", - "author_inst": "Heat Biologics" - }, - { - "author_name": "Padmini Jayaraman", - "author_inst": "Heat Biologics" - }, - { - "author_name": "Rahul Jasuja", - "author_inst": "Heat Biologics" - }, - { - "author_name": "Natasa Strbo", - "author_inst": "University of Miami" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.24.264895", "rel_title": "The influence of major S protein mutations of SARS-CoV-2 on the potential B cell epitopes", @@ -1202956,6 +1206264,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.23.255364", + "rel_title": "Antiviral activity of lambda-carrageenan against influenza viruses in mice and severe acute respiratory syndrome coronavirus 2 in vitro", + "rel_date": "2020-08-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.23.255364", + "rel_abs": "Influenza virus and coronavirus, belonging to enveloped RNA viruses, are major causes of human respiratory diseases. The aim of this study was to investigate the broad spectrum antiviral activity of a naturally existing sulfated polysaccharide, lambda-carrageenan ({lambda}-CGN), purified from marine red algae. Cell culture-based assays revealed that the macromolecule efficiently inhibited both influenza A and B viruses, as well as currently circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with EC50 values ranging from 0.3-1.4 g/ml. No toxicity to host cells was observed at concentrations up to 300 g/ml. Plaque titration and western blot analysis verified that {lambda}-CGN reduced expression of viral proteins in cell lysates and suppressed progeny virus production in culture supernatants in a dose-dependent manner. This polyanionic compound exerts antiviral activity by targeting viral attachment to cell surface receptors and preventing entry. Moreover, intranasal administration to mice during influenza A viral challenge not only alleviated infection-mediated reductions in body weight but also protected 60% of mice from virus-induced mortality. Thus, {lambda}-CGN could be a promising antiviral agent for preventing infection by several respiratory viruses.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ye Jin Jang", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Heegwon Shin", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Myoung Kyu Lee", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Oh Seung Kwon", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Jin Soo Shin", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Yongil Kim", + "author_inst": "Hanmi Pharmaceutical Co." + }, + { + "author_name": "Meehyein Kim", + "author_inst": "Korea Research Institute of Chemical Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.20.20178723", "rel_title": "Automatic analysis system of COVID-19 radiographic lung images (XrayCoviDetector)", @@ -1203109,61 +1206460,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.20.20178699", - "rel_title": "Systematic review and patient-level meta-analysis of SARS-CoV-2 viral dynamics to model response to antiviral therapies", - "rel_date": "2020-08-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.20.20178699", - "rel_abs": "SARS-CoV-2 viral loads change rapidly following symptom onset so to assess antivirals it is important to understand the natural history and patient factors influencing this. We undertook an individual patient-level meta-analysis of SARS-CoV-2 viral dynamics in humans to describe viral dynamics and estimate the effects of antivirals used to-date. This systematic review identified case reports, case series and clinical trial data from publications between 1/1/2020 and 31/5/2020 following PRISMA guidelines. A multivariable Cox proportional hazards regression model (Cox-PH) of time to viral clearance was fitted to respiratory and stool samples. A simplified four parameter nonlinear mixed-effects (NLME) model was fitted to viral load trajectories in all sampling sites and covariate modelling of respiratory viral dynamics was performed to quantify time dependent drug effects. Patient-level data from 645 individuals (age 1 month-100 years) with 6316 viral loads were extracted. Model-based simulations of viral load trajectories in samples from the upper and lower respiratory tract, stool, blood, urine, ocular secretions and breast milk were generated. Cox-PH modelling showed longer time to viral clearance in older patients, males and those with more severe disease. Remdesivir was associated with faster viral clearance (adjusted hazard ratio (AHR) = 9.19, p<0.001), as well as interferon, particularly when combined with ribavirin (AHR = 2.2, p=0.015; AHR = 6.04, p = 0.006). Combination therapy should be further investigated. A viral dynamic dataset and NLME model for designing and analysing antiviral trials has been established.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Silke Gastine", - "author_inst": "University College London Institute of Child Health" - }, - { - "author_name": "Juanita Pang", - "author_inst": "University College London" - }, - { - "author_name": "Florencia A.T. Boshier", - "author_inst": "University College London" - }, - { - "author_name": "Simon J Carter", - "author_inst": "University College London" - }, - { - "author_name": "Dagan O. Lonsdale", - "author_inst": "St Georges University of London" - }, - { - "author_name": "Mario Cortina-Borja", - "author_inst": "University College London" - }, - { - "author_name": "Ivan F.N. Hung", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Judith Breuer", - "author_inst": "University College London" - }, - { - "author_name": "Frank Kloprogge", - "author_inst": "University College London" - }, - { - "author_name": "Joseph F. Standing", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.20.20144014", "rel_title": "The active lung microbiota landscape of COVID-19 patients", @@ -1204642,6 +1207938,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.19.20178129", + "rel_title": "Epidemic Analysis of COVID-19 in Egypt, Qatar and Saudi Arabia using the Generalized SEIR Model", + "rel_date": "2020-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20178129", + "rel_abs": "BackgroundSince its emergence in late December 2019 and its declaration as a global pandemic by World Health Organization (WHO) on March 11, 2020, the novel coronavirus disease known as (COVID-19) has attracted global attention. The process of modeling and predicting the pandemic behavior became crucial as the different states needed accurate predictions to be able to adopt suitable policies to minimize the pressure on their health care systems. Researchers have employed modified variants of classical SIR/SEIR models to describe the dynamics of this pandemic. In this paper, after proven effective in numerous countries, a modified variant of SEIR is implemented to predict the behavior of COVID-19 in Egypt and other countries in the Middle East and North Africa region (MENA).\n\nMethodsWe built MATLAB simulations to fit the real data of COVID-19 Active, recovered and death Cases in Egypt, Qatar and Saudi Arabia to the modified SEIR model via Nelder-Mead algorithm to be able to estimate the future dynamics of the pandemic.\n\nFindingsWe estimate several characteristics of COVID-19 future dynamics in Egypt, Qatar and Saudi Arabia. We also estimate that the pandemic will resolve in the countries under investigation in February 2021, January 2021 and 28th August 2020 With total death cases of 9,742, 5,600, 185 and total cases of 187,600, 490,000, 120,000, respectively.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ahmed E Fahmy", + "author_inst": "Zewail University of Science and Technology" + }, + { + "author_name": "Mohammed M Eldesouky", + "author_inst": "Zewail University of Science and Technology" + }, + { + "author_name": "Ahmed S.A. Mohamed", + "author_inst": "Zewail University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.19.20177956", "rel_title": "Disparities in COVID-19 Hospitalizations and Mortality among Black and Hispanic Patients: Cross-Sectional Analysis from the Greater Houston Metropolitan Area", @@ -1204779,25 +1208102,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.19.20178228", - "rel_title": "COVID19 epidemic growth rates have declined since early March in U.S. regions with active hospitalized case surveillance", - "rel_date": "2020-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20178228", - "rel_abs": "IntroductionOptimal pandemic monitoring and management requires unbiased and regionally specific estimates of disease incidence and epidemic growth.\n\nMethodsI estimated growth rates and doubling times across a 22-week period of the SARS-COV-2 pandemic using hospital admissions incidence data collected through the US CDC COVID-NET surveillance program which operates in 98 U.S. counties located in 13 states. I cross validated the growth measures using mortality incidence data for the same regions and time periods.\n\nResultsBetween March 1 and August 8, 2020, two distinct waves of epidemic activity occurred. During the first wave in the COVID-NET monitoring regions, the harmonic mean of the maximum weekly growth rate was 534% (Median: 575; Range: 250 to 2250) and this maximum occurred in the second or third week of March in different regions. The harmonic mean of the minimum doubling time occurred with maximum growth rate and was 0.35 weeks (Median 0.36 weeks; Range: 0.22 to 0.55 weeks). The harmonic mean of the maximum incidence rate during the first wave of the epidemic was 8.5 hospital admissions per 100,000 people per week (Median: 9.2, Range: 4 to 40.5) and the peak of epidemic infection transmission associated with this maximum occurred on or before March 27, 2020 in eight of the 13 regions. Dividing the 22-week observed period into four intervals, the harmonic mean of the weekly hospitalization incidence rate was highest during the second interval (4.6 hospitalizations per week per 100,000), then fell during the third and fourth intervals. Growth rates declined from 101 percent per week in the first interval to 2.5 percent per week in the last. Doubling time have lengthened from 3/5th of a week in the first interval to 12.5 weeks in the last. Period by period, the cumulative incidence has grown primarily in a linear mode. The mean cumulative incidence of hospitalizations on Aug 8th, 2020 in the COVID-NET regions is 96 hospitalizations per 100,000. Regions which experienced the highest maximum weekly incidence rates or greatest cumulative incidence rates in the first wave, generally, but not uniformly, observed the lower incidence rates in the second wave. Growth measures calculated based on mortality incidence data corroborate these findings.\n\nConclusionsDeclining epidemic growth rates of SARS-COV-2 infection appeared in early March in the first observations of nationwide hospital admissions surveillance program in multiple U.S. regions. A sizable fraction of the U.S. population may have been infected in a cryptic February epidemic acceleration phase. To more accurately monitor epidemic trends and inform pandemic mitigation planning going forward, the US CDC needs measures of epidemic disease incidence that better reflect clinical disease and account for large variations in case ascertainment strategies over time.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Rajiv Bhatia", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.19.20178111", "rel_title": "Effective Reproduction Number and Dispersion under Contact Tracing and Lockdown on COVID-19 in Karnataka", @@ -1206164,6 +1209468,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.17.20176735", + "rel_title": "Comparing the Fit of N95, KN95, Surgical, and Cloth Face Masks and Assessing the Accuracy of Fit Checking", + "rel_date": "2020-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20176735", + "rel_abs": "IntroductionThe COVID-19 pandemic has made well-fitting face masks a critical piece of protective equipment for healthcare workers and civilians. While the importance of wearing face masks has been acknowledged, there remains a lack of understanding about the role of good fit in rendering protective equipment useful. In addition, supply chain constraints have caused some organizations to abandon traditional quantitative or qualitative fit testing, and instead, have implemented subjective fit checking. Our study seeks to quantitatively evaluate the level of fit offered by various types of masks, and most importantly, assess the accuracy of implementing fit checks by comparing fit check results to quantitative fit testing results.\n\nMethodsSeven participants first evaluated N95 and KN95 masks by performing a fit check. Participants then underwent quantitative fit testing wearing five N95 masks, a KN95 mask, a surgical mask, and fabric masks.\n\nResultsN95 masks offered higher degrees of protection than the other categories of masks tested; however, it should be noted that most N95 masks failed to fit the participants adequately. Fit check responses had poor correlation with quantitative fit scores. All non-N95 masks achieved low fit scores.\n\nConclusionFit is critical to the level of protection offered by masks. For an N95 mask to provide the promised protection, it must fit the participant. Performing a fit check was an unreliable way of determining fit.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Eugenia O'Kelly", + "author_inst": "Cambridge University" + }, + { + "author_name": "Anmol Arora", + "author_inst": "Cambridge University" + }, + { + "author_name": "Sophia Pirog", + "author_inst": "Northwestern University" + }, + { + "author_name": "James Ward", + "author_inst": "Cambridge University" + }, + { + "author_name": "P John Clarkson", + "author_inst": "Cambridge University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.17.20175117", "rel_title": "Real-time spatial health surveillance: mapping the UK COVID-19 epidemic", @@ -1206273,65 +1209612,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.08.18.20167270", - "rel_title": "Keep calm and carry on: safety, feasibility and early outcomes of head and neck cancer treatment during the COVID-19 pandemic", - "rel_date": "2020-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20167270", - "rel_abs": "BackgroundPatients with cancer are considered at higher risk of COVID-19 infection and increased severity of infection. Anti-cancer treatment may further increase those risks.\n\nThe aim of this work is to report early outcomes in patients with head and neck cancer (HNC) treated during the pandemic.\n\nMaterials and MethodsA retrospective cohort study in a UK tertiary level oncology centre between 1st March and 23 June 2020, including patients with HNC who were either newly diagnosed, had developed new recurrent/metastatic disease, or were already scheduled to receive treatment during that period.\n\nResults200 patients were evaluated. Median age was 64 years, 65.5% had multiple co-morbidities, 77.5% were current or ex-smokers and 59.5% lived in areas of deprivation. 99 patients were treated with 6 weeks of radical (chemo) radiotherapy. Systemic anti-cancer treatment was delivered to 40 patients.\n\n2 (1.0%) patients with HNC had confirmed COVID-19 infection; 1 patient prior to primary radical RT - no delay to treatment was required and RT was completed as planned, 1 patient acquired COVID-19 after primary surgery but recovered well and started adjuvant RT 9.7 weeks after surgery.\n\nThe proportion of patients receiving supportive care only (19.5%) was in keeping with that pre-COVID-19. The proportion of patients not completing (chemo) radiotherapy (3.4%) or with gaps in treatment (14.1%) was similar to pre-COVID-19. 30-day mortality after radical (chemo)radiotherapy was 2.3%, no higher than in previous years.\n\nConclusionsIt is feasible and safe to deliver standard treatment for patients with HNC during the COVID-19 pandemic.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Sara Walker", - "author_inst": "Beatson West of Scotland Cancer Centre" - }, - { - "author_name": "Maureen C Thomson", - "author_inst": "Beatson West of Scotland Cancer Centre" - }, - { - "author_name": "Frances Campbell", - "author_inst": "Beatson West of Scotland Cancer Centre" - }, - { - "author_name": "Lisa K Hay", - "author_inst": "Beatson West of Scotland Cancer Centre" - }, - { - "author_name": "Derek Grose", - "author_inst": "Beatson West of Scotland Cancer Centre" - }, - { - "author_name": "Allan James", - "author_inst": "Beatson West of Scotland Cancer Centre" - }, - { - "author_name": "Carolynn Lamb", - "author_inst": "Beatson West of Scotland Cancer Centre" - }, - { - "author_name": "Ioanna Nixon", - "author_inst": "Beatson West of Scotland Cancer Centre" - }, - { - "author_name": "Stefano Schipani", - "author_inst": "Beatson West of Scotland Cancer Centre" - }, - { - "author_name": "Christina Wilson", - "author_inst": "Beatson West of Scotland Cancer Centre" - }, - { - "author_name": "Claire Paterson", - "author_inst": "Beatson West of Scotland Cancer Centre" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2020.08.18.20176776", "rel_title": "Accurately Differentiating COVID-19, Other Viral Infection, and Healthy Individuals Using Multimodal Features via Late Fusion Learning", @@ -1207802,6 +1211082,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.20.260190", + "rel_title": "Astodrimer sodium, dendrimer antiviral, inhibits replication of SARS-CoV-2 in vitro", + "rel_date": "2020-08-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.20.260190", + "rel_abs": "An effective response to the ongoing coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will involve a range of complementary preventive modalities. The current studies were conducted to evaluate the in vitro SARS-CoV-2 antiviral and virucidal activity of astodrimer sodium, a dendrimer with broad spectrum antimicrobial activity, including against enveloped viruses in in vitro and in vivo models, that is marketed for antiviral and antibacterial applications. We report that astodrimer sodium inhibits replication of SARS-CoV-2 in Vero E6 and Calu-3 cells, with 50% effective concentrations (EC50) for i) reducing virus-induced cytopathic effect of 0.002 to 0.012 mg/mL in Vero E6 cells, and ii) infectious virus release by plaque assay of 0.019 to 0.031 mg/mL in Vero E6 cells and 0.031 to 0.045 mg/mL in Calu-3 cells. The selectivity index (SI) in these assays was as high as 2197. Astodrimer sodium was also virucidal, reducing SARS-CoV-2 infectivity by >99.9% (>3 log10) within 1 minute of exposure, and up to >99.999% (>5 log10) shown at astodrimer sodium concentrations of 10 to 30 mg/mL in Vero E6 and Calu-3 cell lines. Astodrimer sodium also inhibited infection in a primary human airway epithelial cell line. The data were similar for all investigations and were consistent with the potent antiviral and virucidal activity of astodrimer sodium being due to inhibition of virus-host cell interactions, as previously demonstrated for other viruses. Further studies will confirm if astodrimer sodium binds to SARS-CoV-2 spike protein and physically blocks initial attachment of the virus to the host cell. Given the in vitro effectiveness and significantly high SI, astodrimer sodium warrants further investigation for potential as a nasally administered or inhaled antiviral agent for SARS-CoV-2 prevention and treatment applications.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jeremy R.A. Paull", + "author_inst": "Starpharma Pty Ltd" + }, + { + "author_name": "Graham P. Heery", + "author_inst": "Starpharma Pty Ltd" + }, + { + "author_name": "Michael D Bobardt", + "author_inst": "Scripps Research Institute" + }, + { + "author_name": "Alex Castellarnau", + "author_inst": "Starpharma Pty Ltd" + }, + { + "author_name": "Carolyn A. Luscombe", + "author_inst": "Starpharma Pty Ltd" + }, + { + "author_name": "Jacinth K. Fairley", + "author_inst": "Starpharma Pty Ltd" + }, + { + "author_name": "Philippe A Gallay", + "author_inst": "Scripps Research Institute" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.21.261289", "rel_title": "Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses", @@ -1207971,97 +1211294,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.17.20176925", - "rel_title": "Engineering luminescent biosensors for point-of-care SARS-CoV-2 antibody detection", - "rel_date": "2020-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20176925", - "rel_abs": "Current serology tests for SARS-CoV-2 antibodies mainly take the form of enzyme-linked immunosorbent assays or lateral flow assays, with the former being laborious and the latter being expensive and often lacking sufficient sensitivity and scalability. Here we present the development and validation of a rapid, low-cost solution-based assay to detect antibodies in serum, plasma, whole blood, and saliva, using rationally designed split luciferase antibody biosensors (spLUC). This new assay, which generates quantitative results in as short as 5 minutes, substantially reduces the complexity and improves the scalability of COVID-19 antibody tests for point-of-care and broad population testing.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Susanna K. Elledge", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Xin X. Zhou", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "James R. Byrnes", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Alexander J. Martinko", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Irene Lui", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Katarina Pance", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Shion A. Lim", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jeff E. Glasgow", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Anum A. Glasgow", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Keirstinne Turcios", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Nikita Iyer", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Leonel Torres", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Michael J. Peluso", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Timothy J. Henrich", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Taia T. Wang", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Cristina M. Tato", - "author_inst": "Chan Zuckerberg Biohub" - }, - { - "author_name": "Kevin K. Leung", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Bryan Greenhouse", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "James A. Wells", - "author_inst": "University of California, San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.18.20177428", "rel_title": "Comprehensive Surveillance of SARS-CoV-2 Spread Using Wastewater-based Epidemiology Studies", @@ -1209532,6 +1212764,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.16.20175901", + "rel_title": "Air pollution, SARS-CoV-2 transmission, and COVID-19 outcomes: A state-of-the-science review of a rapidly evolving research area", + "rel_date": "2020-08-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.16.20175901", + "rel_abs": "BackgroundAs the coronavirus pandemic rages on, 692,000 (August 7, 2020) human lives and counting have been lost worldwide to COVID-19. Understanding the relationship between short- and long-term exposure to air pollution and adverse COVID-19 health outcomes is crucial for developing solutions to this global crisis.\n\nObjectivesTo conduct a scoping review of epidemiologic research on the link between short- and long-term exposure to air pollution and COVID-19 health outcomes.\n\nMethodWe searched PubMed, Web of Science, Embase, Cochrane, MedRxiv, and BioRxiv for preliminary epidemiological studies of the association between air pollution and COVID-19 health outcomes. 28 papers were finally selected after applying our inclusion/exclusion criteria; we categorized these studies as long-term studies, short-term time-series studies, or short-term cross-sectional studies. One study included both short-term time-series and a cross-sectional study design.\n\nResults27 studies of the 28 reported evidence of statistically significant positive associations between air pollutant exposure and adverse COVID-19 health outcomes; 11 of 12 long-term studies and all 16 short-term studies reported statistically significant positive associations. The 28 identified studies included various confounders, spatial and temporal resolutions of pollution concentrations, and COVID-19 health outcomes.\n\nDiscussionWe discuss methodological challenges and highlight additional research areas based on our findings. Challenges include data quality issues, ecological study design limitations, improved adjustment for confounders, exposure errors related to spatial resolution, geographic variability in testing, mitigation measures and pandemic stage, clustering of health outcomes, and a lack of publicly available data and code.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anushka Bhaskar", + "author_inst": "Harvard University" + }, + { + "author_name": "Jay Chandra", + "author_inst": "Harvard University" + }, + { + "author_name": "Danielle Braun", + "author_inst": "Harvard TH Chan School of Public Health" + }, + { + "author_name": "Jacqueline Cellini", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Francesca Dominici", + "author_inst": "Harvard TH Chan School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.08.19.257493", "rel_title": "Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2", @@ -1209709,85 +1212976,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.08.19.258244", - "rel_title": "An effective, safe and cost-effective cell-based chimeric vaccine against SARS-CoV2", - "rel_date": "2020-08-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.19.258244", - "rel_abs": "More than one hundred vaccines against SARS-CoV-2 have been developed and some of them have entered clinical trials, but the latest results revealed that these vaccines still face great challenges. Here, we developed a novel cell-based gp96-Ig-secreting chimeric vaccine which is composed of two viral antigens, the RBD of spike protein, and a truncated nucleocapsid protein that could induce epitope-specific cytotoxic T lymphocytes but low antibody response. Syrian hamsters immunized with the cell-based vaccine produced high level of SARS-CoV-2 specific NAbs and specific T cell immunity which could eliminate RBD-truncated N-expressing cells, without the induction of antibody against N protein and other observed toxicity. This study provides a proof of concept for clinical testing of this safe, effective and cost-effective vaccine against SARS-CoV2 infection.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "zhenguo Cheng", - "author_inst": "zhengzhou university" - }, - { - "author_name": "Danhua Zhang", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Jinxin Miao", - "author_inst": "zhengzhou university" - }, - { - "author_name": "Jiaoyao wang", - "author_inst": "zhengzhou university" - }, - { - "author_name": "Haoran Guo", - "author_inst": "zhengzhou university" - }, - { - "author_name": "Wenli Yan", - "author_inst": "zhengzhou university" - }, - { - "author_name": "Zhe Zhang", - "author_inst": "zhengzhou university" - }, - { - "author_name": "Shuangshuang Lu", - "author_inst": "zhengzhou university" - }, - { - "author_name": "Na Zhang", - "author_inst": "zhengzhou university" - }, - { - "author_name": "Jingjing Wang", - "author_inst": "zhengzhou university" - }, - { - "author_name": "Zhongxian Zhang", - "author_inst": "zhengzhou university" - }, - { - "author_name": "Yi Zhang", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Lirong Zhang", - "author_inst": "zhengzhou university" - }, - { - "author_name": "Jianzeng Dong", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Nicholas R Lemoine", - "author_inst": "zhengzhou university" - }, - { - "author_name": "Yaohe Wang", - "author_inst": "zhengzhou university" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.20.258129", "rel_title": "Development of a high-throughput homogeneous AlphaLISA drug screening assay for the detection of SARS-CoV-2 Nucleocapsid", @@ -1211478,6 +1214666,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.17.20174821", + "rel_title": "Quantifying the efficiency of non-pharmaceutical interventions against SARS-COV-2 transmission in Europe", + "rel_date": "2020-08-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20174821", + "rel_abs": "Since the emergence of SARS-CoV-2, governments around the World have implemented a combination of public health responses based on non-pharmaceutical interventions (NPIs), with significant social and economic consequences. Though most European countries have overcome the first epidemic wave, it remains of high priority to quantify the efficiency of different NPIs to inform preparedness for an impending second wave. In this study, combining capture-recapture methods with Bayesian inference in an age-structured mathematical model, we use a unique European dataset compiled by the European Centre for Disease Control (ECDC) to quantify the efficiency of 24 NPIs and their combinations (referred to as public health responses, PHR) in reducing SARS-Cov-2 transmission rates in 32 European countries. Of 166 unique PHR tested, we found that median decrease in viral transmission was 74%, which is enough to suppress the epidemic. PHR efficiency was positively associated with the number of NPIs implemented. We found that bans on mass gatherings had the largest effect among NPIs, followed by school closures, teleworking, and stay home orders. Partial implementation of most NPIs resulted in lower than average response efficiency. This first large-scale estimation of NPI and PHR efficiency against SARS-COV-2 transmission in Europe suggests that a combination of NPIs targeting different population groups should be favored to control future epidemic waves.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Andres Garchitorena", + "author_inst": "Institut de Recherche pour le Developpement" + }, + { + "author_name": "Hugo Gruson", + "author_inst": "IRD" + }, + { + "author_name": "Bernard Cazelles", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Tommi Karki", + "author_inst": "European Centre for Disease Control" + }, + { + "author_name": "Bertrand Sudre", + "author_inst": "European Centre for Disese Control" + }, + { + "author_name": "Benjamin ROCHE", + "author_inst": "IRD" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.17.20176552", "rel_title": "SARS-CoV-2 antibody responses in children with MIS-C and mild and severe COVID-19", @@ -1211655,45 +1214882,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.16.20176081", - "rel_title": "Protection Level and Reusability of a Modified Full-Face Snorkel Mask as Alternative Personal Protective Equipment for Healthcare Workers During the COVID-19 Pandemic", - "rel_date": "2020-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.16.20176081", - "rel_abs": "The worldwide outbreak of the COVID-19 drastically increased pressure on medical resources and highlighted the need for rapidly available, large-scale and low-cost personal protective equipment (PPE). In this work, an alternative full-face mask is adapted from a modified snorkel mask to be used as PPE with two medical grade filters and a 3D-printed adapter. As the mask covers the eyes, mouth and nose, it acts as a full-face shield, providing additional protection to healthcare workers. The filtration efficiency of different medical filters is measured for particles below 300 nm to cover the size of the SARS-CoV-2 and small virus-laden droplets. The filtration performance of the adapted full-face mask is characterized using NaCl particles below 500 nm and different fitting scenarios. The mask is compared to a commercial respirator and characterized according to the EN 149 standard, demonstrating that the protection fulfills the requirements for the FFP2 level (filtering face-piece 2, stopping at least 94% of airborne particles). The device shows a good resistance to several cycles of decontamination (autoclaving and ethanol immersion), is easy to be produced locally at low cost and helps addressing the shortage in FFP2 masks and face shields by providing adequate protection to healthcare workers against particles below 500 nm.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jean Schmitt", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Lewis S. Jones", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Elise A. Aeby", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Christian Gloor", - "author_inst": "Swiss Federal Office of Civil Protection" - }, - { - "author_name": "Berthold Moser", - "author_inst": "Medical University of Innsbruck" - }, - { - "author_name": "Jing Wang", - "author_inst": "ETH Zurich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.08.16.20176107", "rel_title": "Longitudinal SARS-CoV-2 serosurveillance of over ten thousand health care workers in the Providence Oregon cohort.", @@ -1213340,6 +1216528,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.15.20175513", + "rel_title": "Behavioral preventive measures and the use of medicines and herbal products among the public in response to Covid-19 in Bangladesh: A cross-sectional study", + "rel_date": "2020-08-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.15.20175513", + "rel_abs": "The present study was conducted to assess the behavioral preventive measures and the use of medicines and herbal foods/products among the public in response to Covid-19. A cross-sectional survey was conducted from 27 June to 20 July 2020, and 1222 people participated. Kruskal-Wallis test was used to identify the differences in behavioral preventive practices across different demographic categories. To identify the factors associated with the use of preventive medicines and herbal foods/products, multivariable logistic regression was performed. Most participants adopted the recommended preventive practices such as washing hands more frequently (87.5%), staying home more often (85.5%), avoiding crowds (86%), and wearing masks (91.6%). About half of the smokers reported a decreased rate of smoking during the pandemic. Also, 14.8% and 57.6% of the participants took medicines and herbal foods/products as preventive measures against Covid-19. Arsenicum album and Zinc supplements were the most commonly used preventive medicines. Gender, age, and fear of Covid-19 were significantly associated with the use of both preventive medicines and herbal products. For the management of Covid-19 related symptoms, Paracetamols, Fexofenadine, and Zinc supplements were used most often. Most participants sought information from non-medical sources while using medicines and herbal products. Moreover, potentially inappropriate and unnecessary use of drugs were identified.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Iftekhar Ahmed", + "author_inst": "Department of Pharmacy, Jahangirnagar University, Dhaka, Bangladesh" + }, + { + "author_name": "Maruf Hasan", + "author_inst": "Department of Pharmacy, Jahangirnagar University, Dhaka, Bangladesh" + }, + { + "author_name": "Rahima Akter", + "author_inst": "Department of Pharmacy, World University of Bangladesh, Dhaka, Bangladesh" + }, + { + "author_name": "Bidduth Kumar Sarkar", + "author_inst": "Department of Pharmacy, Ranada Prasad Shaha University, Narayanganj, Bangladesh" + }, + { + "author_name": "Marufa Rahman", + "author_inst": "Department of Pharmacy, Jahangirnagar University, Savar, Dhaka, Bangladesh" + }, + { + "author_name": "Md Samun Sarker", + "author_inst": "Bangladesh Livestock Research Institute (BLRI), Savar, Dhaka, Bangladesh" + }, + { + "author_name": "Mohammed A. Samad", + "author_inst": "Bangladesh Livestock Research Institute (BLRI), Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.15.20175786", "rel_title": "Universal PCR and antibody testing demonstrate little to no transmission of SARS-CoV-2 in a rural community", @@ -1213597,61 +1216828,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.15.20172080", - "rel_title": "Evaluation of commercially available immuno-magnetic agglutination and enzyme-linked immunosorbent assays for rapid point-of-care diagnostics of COVID-19", - "rel_date": "2020-08-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.15.20172080", - "rel_abs": "IntroductionCoronavirus Disease 2019 (COVID-19) is caused by severe acute respiratory coronavirus-2 (SARS-CoV-2). Fast, accurate and simple blood-based assays for quantification of anti-SARS-CoV-2 antibodies are urgently needed to identify infected individuals and keep track of the spread of disease.\n\nMethodsThe study included 35 plasma samples from 22 individuals with confirmed COVID-19 by real time reverse-transcriptase-polymerase-chain-reaction and 40 non-COVID-19 plasma samples. Anti-SARS-CoV-2 IgM/lgA or IgG antibodies were detected by a microfluidic quantitative immunomagnetic assay (IMA) (ViroTrack Sero COVID IgM+lgA /IgG Ab, Blusense Diagnostics, Denmark) and by enzyme-linked immunosorbent assay ((ELISA) (Eurolmmun Medizinische Labordiagnostika, Germany).\n\nResultsOf the 35 plasma samples from the COVID-19 patients, 29 (82.9%) were positive for IgA/IgM or IgG by IMA and 29 samples (82.9%) were positive by ELISA. Sensitivity for only one sample per patient was 68% for IgA+IgM and 73% IgG by IMA and 73% by ELISA. For samples collected 14 days after symptom onset, the sensitivity of both IMA and ELISA was around 90%. Specificity of the IMA reached 100% compared to 95% for ELISA IgA and 97.5% for ELISA IgG.\n\nConclusionIMA for COVID-19 is a rapid simple-to-use point of care test with sensitivity and specificity similar to a commercial ELISA.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Maria Engel Moeller", - "author_inst": "Department of Infectious Diseases, Copenhagen University Hospital, Amager and Hvidovre" - }, - { - "author_name": "Jeppe Fock", - "author_inst": "BluSense Diagnostics" - }, - { - "author_name": "Pearlyn Pah", - "author_inst": "BluSense Diagnostics" - }, - { - "author_name": "Antia De La Campa Veras", - "author_inst": "BluSense Diagnostics" - }, - { - "author_name": "Melanie Bade", - "author_inst": "BluSense Diagnostics" - }, - { - "author_name": "Marco Donolato", - "author_inst": "BluSense Diagnostics" - }, - { - "author_name": "Simone Bastrup Israelsen", - "author_inst": "Department of Infectious Diseases, Copenhagen University Hospital, Amager and Hvidovre" - }, - { - "author_name": "Jesper Eugen-Olsen", - "author_inst": "Department of Clinical Research, Copenhagen University Hospital, Amager and Hvidovre" - }, - { - "author_name": "Thomas Benfield", - "author_inst": "Department of Infectious Diseases, Copenhagen University Hospital, Amager and Hvidovre" - }, - { - "author_name": "Frederik Neess Engsig", - "author_inst": "Department of Infectious Diseases, Copenhagen University Hospital, Amager and Hvidovre" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.15.20175455", "rel_title": "Specific Dynamic Variations in the Peripheral Blood Lymphocyte Subsets in COVID-19 and Severe Influenza A Patients: A Retrospective Observational Study", @@ -1215022,6 +1218198,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.14.20170878", + "rel_title": "Estimating the epidemic growth dynamics within the first week", + "rel_date": "2020-08-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20170878", + "rel_abs": "Information about the early growth of infectious outbreaks are indispensable to estimate the epidemic spreading. A large number of mathematical tools have been developed to this end, facing as much large number of different dynamic evolutions, ranging from sub-linear to super-exponential growth. Of course, the crucial point is that we do not have enough data during the initial outbreak phase to make reliable inferences. Here we propose a methodology to estimate the epidemic growth dynamics from the infected cumulative data of just a week, provided a surveillance system is available over the whole territory. The methodology, based on the Newcomb-Benford Law, is applied to Italian covid 19 case-study. Results show that it is possible to discriminate the epidemic dynamics using the first seven data points collected over fifty Italian cities. Moreover, the form of the most probable approximating function of the growth, within a six weeks epidemic scenario, is identified.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "VINCENZO FIORITI", + "author_inst": "ENEA" + }, + { + "author_name": "IVAN ROSELLI", + "author_inst": "ENEA" + }, + { + "author_name": "MARTA CHINNICI", + "author_inst": "ENEA" + }, + { + "author_name": "ANDREA ARBORE", + "author_inst": "ICT CONSULTANT" + }, + { + "author_name": "NICOLA SIGISMONDI", + "author_inst": "ICT CONSULTANT" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.14.20175190", "rel_title": "Bidirectional associations between COVID-19 and psychiatric disorder: a study of 62,354 COVID-19 cases", @@ -1215199,49 +1218410,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.14.20174649", - "rel_title": "Widespread testing, case isolation and contact tracing may allow safe school reopening with continued moderate physical distancing: a modeling analysis of King County, WA data", - "rel_date": "2020-08-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20174649", - "rel_abs": "BackgroundIn late March 2020, a \"Stay Home, Stay Healthy\" order was issued in Washington State in response to the COVID-19 pandemic. On May 1, a 4-phase reopening plan began. If implemented without interruptions, all types of public interactions were planned to resume by July 15. We investigated whether adjunctive prevention strategies would allow less restrictive physical distancing to avoid second epidemic waves and secure safe school reopening.\n\nMethodsWe developed a mathematical model, stratifying the population by age (0-19 years, 20-49 years, 50-69 years, and 70+ years), infection status (susceptible, exposed, asymptomatic, pre-symptomatic, symptomatic, recovered) and treatment status (undiagnosed, diagnosed, hospitalized) to project SARS-CoV-2 transmission during and after the reopening period. The model was parameterized with demographic and contact data from King County, WA and calibrated to confirmed cases, deaths (overall and by age) and epidemic peak timing. Adjunctive prevention interventions were simulated assuming different levels of pre-COVID physical interactions (pC_PI) restored. We made several predictions related to adjunctive interventions or changes in pC_PI.\n\nResultsThe best model fit estimated ~35% pC_PI under lockdown. Gradually restoring 75% pC_PI for all age groups between May 15-July 15 resulted in ~350 daily deaths by early September 2020. Maintaining less than 45% pC_PI was required with current testing practices to ensure low levels of daily infections and deaths. If widespread community transmission persisted, isolating the elderly does not lower daily death rates significantly. Increased testing, isolation of symptomatic infections, and contact tracing permitted 60% pC_PI without significant increases in daily deaths before September, although this strategy may not be sufficient to eliminate community transmission. This combination strategy also allowed opening of schools with <15 daily deaths. Inpatient antiviral treatment reduces deaths significantly without lowering cases or hospitalizations.\n\nConclusionsWe predict that widespread implementation of \"test and isolate\" policy alone is insufficient to prevent the rapid re-emergence of SARS CoV-2 without moderate physical distancing. However, widespread testing, contact tracing and case isolation would allow relaxation of physical distancing, as well as opening of schools, without a surge in local cases and deaths.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Chloe Bracis", - "author_inst": "Ifremer, France" - }, - { - "author_name": "Eileen Burns", - "author_inst": "Independent Researcher, Seattle, WA" - }, - { - "author_name": "Mia Moore", - "author_inst": "Fred Hutchinson Cancer Research Center; Seattle, WA" - }, - { - "author_name": "David Swan", - "author_inst": "Fred Hutchinson Cancer Research Center; Seattle, WA" - }, - { - "author_name": "Daniel B Reeves", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Joshua T Schiffer", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Dobromir T Dimitrov", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.14.20168088", "rel_title": "Robust, reproducible clinical patterns in hospitalised patients with COVID-19", @@ -1217032,6 +1220200,97 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.08.14.248880", + "rel_title": "In plain sight: the role of alpha-1-antitrypsin in COVID-19 pathogenesis and therapeutics.", + "rel_date": "2020-08-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.14.248880", + "rel_abs": "RationaleSARS-CoV-2 entry into host cells is facilitated by endogenous and exogenous proteases that proteolytically activate the spike glycoprotein and antiproteases inhibiting this process. Understanding the key actors in viral entry is crucial for advancing knowledge of virus tropism, pathogenesis, and potential therapeutic targets.\n\nObjectivesWe aimed to investigate the role of naive serum and alpha-1-antitrypsin (AAT) in inhibiting protease-mediated SARS-CoV-2 entry and explore the implications of AAT deficiency on susceptibility to different SARS-CoV-2 variants.\n\nFindingsOur study demonstrates that naive serum exhibits significant inhibition of SARS-CoV-2 entry, with AAT identified as the major serum protease inhibitor potently restricting entry. Using pseudoparticles, replication-competent pseudoviruses, and authentic SARS-CoV-2, we show that AAT inhibition occurs at low concentrations compared with those in serum and bronchoalveolar tissues, suggesting physiological relevance. Furthermore, sera from subjects with an AAT-deficient genotype show reduced ability to inhibit entry of both Wuhan-Hu-1 (WT) and B.1.617.2 (Delta) but exhibit no difference in inhibiting B.1.1.529 (Omicron) entry.\n\nConclusionsAAT may have a variant-dependent therapeutic potential against SARS-CoV-2. Our findings highlight the importance of further investigating the complex interplay between proteases, antiproteases, and spike glycoprotein activation in SARS-CoV-2 and other respiratory viruses to identify potential therapeutic targets and improve understanding of disease pathogenesis.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Christian S Stevens", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kasopefoluwa Y Oguntuyo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Shreyas Kowdle", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Aditya Gowlikar", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Mohammed NA Siddiquey", + "author_inst": "Louisiana State University Health Sciences Center Shreveport" + }, + { + "author_name": "Joshua A Acklin", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Griffin Haas", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Robert M Schilke", + "author_inst": "Louisiana State University Health Sciences Center Shreveport" + }, + { + "author_name": "Matthew D Woolard", + "author_inst": "Louisiana State University Health Sciences Center-Shreveport" + }, + { + "author_name": "Hongbo Zhang", + "author_inst": "Louisiana State University Health Sciences Center-Shreveport" + }, + { + "author_name": "Luca Brambilla", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Satoshi Ikegame", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Chuan-tien Hung", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jean K Lim", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Robert W Cross", + "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" + }, + { + "author_name": "Thomas W Geisbert", + "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" + }, + { + "author_name": "Stanimir S Ivanov", + "author_inst": "Louisiana State University Health Sciences Center-Shreveport" + }, + { + "author_name": "Jeremy P Kamil", + "author_inst": "Louisiana State University Health Sciences Center Shreveport" + }, + { + "author_name": "Benhur Lee", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.13.20174508", "rel_title": "Data Mining Approach to Analyze Covid19 Dataset of Brazilian Patients", @@ -1217225,57 +1220484,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.13.20174524", - "rel_title": "Mortality Associated With Intubation and Mechanical Ventilation in Patients with COVID-19", - "rel_date": "2020-08-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174524", - "rel_abs": "ObjectiveThe need for critical care, hemodynamic support, renal replacement therapy, and mechanical ventilation have emerged as key features of the SARS-nCoV-2 (COVID-19) pandemic. The primary aim of this study was to determine the in-hospital mortality rate of mechanically ventilated patients. We also sought to determine the risk of in-hospital mortality by age, gender, race, ethnicity, and body mass index.\n\nMethodsWe performed a retrospective cohort study to determine the mortality rate among inpatient adults with COVID-19 on mechanical ventilation in the Nuvance Health system between March 1, 2020 and July 17, 2020. Patients were included if they were 18 years or older, had a laboratory confirmed COVID-19 diagnosis, were admitted to hospitals within the Nuvance Health network (7 hospitals), and were on mechanical ventilation at any time during their inpatient stay.\n\nResultsOverall mortality in our cohort of 304 patients was 53.3%. Multivariable logistic regression including age, gender, race, ethnicity, and BMI demonstrated patients over 71 years old had greater risk of mortality compared to patients ages 61-70, and females had half the risk compared to males. There was no significant difference in risk of mortality given race, ethnicity, or BMI.\n\nConclusionsIn adult patients with confirmed COVID-19 infection requiring mechanical ventilation and intensive care, advanced age (>71 years old) and male gender are associated with increased risk of mortality. This information contributes to a collective body of evidence to support ongoing planning and decision-making among clinicians and for directed infection prevention programming.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Patrick Zimmerman", - "author_inst": "Division of Surgery, Nuvance Health" - }, - { - "author_name": "Stephanie Stroever", - "author_inst": "Department of Innovation and Research, Nuvance Health" - }, - { - "author_name": "Timothy Burton", - "author_inst": "Department of Surgery, Nuvance Health" - }, - { - "author_name": "Karri Hester", - "author_inst": "Department of Surgery, Nuvance Health" - }, - { - "author_name": "Minha Kim", - "author_inst": "Department of Surgery, Nuvance Health" - }, - { - "author_name": "Ryan Fahy", - "author_inst": "Department of Surgery, Nuvance Health" - }, - { - "author_name": "Kimberly Corbitt", - "author_inst": "Department of Surgery, Nuvance Health" - }, - { - "author_name": "Joann Petrini", - "author_inst": "Department of Innovation and Research, Nuvance Health" - }, - { - "author_name": "Jeffrey Nicastro", - "author_inst": "Department of Surgery, Nuvance Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.08.13.20174631", "rel_title": "Forecasting United States COVID-19 Cases and Deaths Through Machine Learning", @@ -1218534,6 +1221742,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.11.20145086", + "rel_title": "Face Coverings and Respiratory Tract Droplet Dispersion", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20145086", + "rel_abs": "Respiratory droplets are the primary transmission route for SARS-CoV-2. Evidence suggests that virus transmission can be reduced by face coverings, but robust evidence for how mask usage might affect safe distancing parameters is lacking. Accordingly, we investigate the effectiveness of surgical masks and single-layer cotton masks on mitigating dispersion of large respiratory droplets (i.e. non aerosol). We tested a manikin ejecting fluorescent droplets and human volunteers in speaking and coughing conditions. We quantified the number of droplets in flight using laser sheet illumination and UV-light for those that had landed at table height at up to 2m. For human volunteers, expiratory droplets were caught on a microscope slide 5cm from the mouth. Whether manikin or human, wearing a face covering decreased the number of projected droplets by >1000-fold. We estimated that a person standing 2m from someone coughing without a mask is exposed to over 1000 times more respiratory droplets than from someone standing 5 cm away wearing a basic single layer mask. Our results indicate that face coverings show consistent efficacy at blocking respiratory droplets. If aerosol transmission is later determined to be a significant driver of infection, then our findings may overestimate the effectiveness of face coverings.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Lucia Bandiera", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Geethanjali Pavar", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Gabriele Pisetta", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Shuji Otomo", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Enzo Mangano", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Jonathan R. Seckl", + "author_inst": "Queen`s Medical Research Institute, University of Edinburgh" + }, + { + "author_name": "Paul Digard", + "author_inst": "The Roslin Institute, University of Edinburgh" + }, + { + "author_name": "Emanuela Molinari", + "author_inst": "School of Informatics, University of Edinburgh" + }, + { + "author_name": "Filippo Menolascina", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Ignazio Maria Viola", + "author_inst": "School of Engineering, University of Edinburgh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.11.20173062", "rel_title": "Quantitative analysis of SARS-CoV-2 RNA from wastewater solids in communities with low COVID-19 incidence and prevalence", @@ -1218687,85 +1221950,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.08.11.20171967", - "rel_title": "Lower respiratory tract myeloid cells harbor SARS-CoV-2 and display an inflammatory phenotype", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20171967", - "rel_abs": "SARS-CoV-2 pneumonia may induce an aberrant immune response with brisk recruitment of myeloid cells into the lower respiratory tract, which may contribute to morbidity and mortality. We describe endotracheal aspirate samples from seven patients with SARS-CoV-2 pneumonia requiring mechanical ventilation. We note SARS-CoV-2 virions within lower respiratory tract myeloid cells shown by electron tomography, immunofluorescence confocal imaging, and immuno-electron microscopy. Endotracheal aspirates are primarily composed of mononuclear and polymorphonuclear leukocytes. These myeloid cells that harbor virus are frequently positive for CD14 and/or CD16 and most display an inflammatory phenotype marked by expression of IL-6 and tissue factor mRNA transcript and protein expression.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "William Bain", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Hernan F. Penaloza", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Mark S. Ladinsky", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Rick van der Geest", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Mara Sullivan", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Mark Ross", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Georgios D Kitsios", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Barbara Methe", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Bryan J. McVerry", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Alison Morris", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Alan M. Watson", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Simon C. Watkins", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Claudette M. St. Croix", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Donna B. Stolz", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Pamela J. Bjorkman", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Janet S. Lee", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.08.12.20173385", "rel_title": "Influence of nursing staff working hours on the stress level during the COVID-19 pandemic: a cross-sectional online survey", @@ -1220304,6 +1223488,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.13.20174060", + "rel_title": "Comprehensive Systematic Review to Identify putative COVID-19 Treatments: Roles for Immunomodulator and Antiviral Treatments", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174060", + "rel_abs": "ObjectivesTo identify putative COVID-19 treatments and identify the roles of immunomodulators and antivirals in disease management.\n\nDesignSystematic review.\n\nData sourcesPubMed, bioRxiv.org and medRxiv.org were searched for studies suggestive of effective treatments for COVID-19. Additional studies were identified via a snowballing method applied to the references of retrieved papers as well as a subsequent targeted search for drug names.\n\nReview methodsInclusion criteria included any case series or randomised control trials in any language that were published from 18th December 2019 to 18th April 2020 and described COVID-19 treatment. Of an initial 2140 studies identified from the initial search, 29 studies were found to meet the inclusion criteria and included in this comprehensive systematic review.\n\nResults19 studies of antiviral treatments for COVID-19 have been reported and seven studies for immunomodulatory treatments. Six randomised controlled trials have been published with one positive trial for Hydroxychloroquine. This small study consisted of 31 patients though subsequent studies showed contradictory findings. All the remaining studies were observational studies, retrospective case reviews or non-randomised trials and these results are difficult to interpret due to methodological issues.\n\nConclusionsTo date, an impressive number of studies have been performed in a short space of time, indicative of a resilient clinical trials infrastructure. However, there is a lack of high quality evidence to support any novel treatments for COVID-19 to be incorporated into the current standard of care. The majority of the studies of treatments for COVID-19 could only be found in pre-print servers. Future clinical reviews should therefore be Comprehensive Systematic Reviews involving pre-print studies to prevent potential unnecessary replications of clinical studies.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Thomas Hill", + "author_inst": "Department of Oncology, Queen Elizabeth Hospital Birmingham, Mindelsohn Way, Edgbaston, B152GW" + }, + { + "author_name": "Mark Baker", + "author_inst": "Birmingham Medical School, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT" + }, + { + "author_name": "Lawrence Isherwood", + "author_inst": "Birmingham Medical School, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT" + }, + { + "author_name": "Lennard YW Lee", + "author_inst": "Department of Oncology, Queen Elizabeth Hospital Birmingham, Mindelsohn Way, Edgbaston B15 2GW, United Kingdom. Institute of Cancer and Genomic Sciences, Univer" + } + ], + "version": "1", + "license": "cc0_ng", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.12.20173104", "rel_title": "First report of tocilizumab use in a cohort of Latin American patients hospitalized for severe COVID-19 pneumonia", @@ -1220417,77 +1223632,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.12.20173849", - "rel_title": "Obesity and Smoking as Risk Factors for Invasive Mechanical Ventilation in COVID-19: a Retrospective, Observational Cohort Study", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20173849", - "rel_abs": "PurposeTo describe the trajectory of respiratory failure in COVID-19 and explore factors associated with risk of invasive mechanical ventilation (IMV).\n\nMaterials and MethodsA retrospective, observational cohort study of 112 inpatient adults diagnosed with COVID-19 between March 12 and April 16, 2020. Data were manually extracted from electronic medical records. Multivariable and Univariable regression were used to evaluate association between baseline characteristics, initial serum markers and the outcome of IMV.\n\nResultsOur cohort had median age of 61 (IQR 45-74) and was 66% male. In-hospital mortality was 6% (7/112). ICU mortality was 12.8% (6/47), and 18% (5/28) for those requiring IMV. Obesity (OR 5.82, CI 1.74-19.48), former (OR 8.06, CI 1.51-43.06) and current smoking status (OR 10.33, CI 1.43-74.67) were associated with IMV after adjusting for age, sex, and high prevalence comorbidities by multivariable analysis. Initial absolute lymphocyte count (OR 0.33, CI 0.11-0.96), procalcitonin (OR 1.27, CI 1.02-1.57), IL-6 (OR 1.17, CI 1.03-1.33), ferritin (OR 1.05, CI 1.005-1.11), LDH (OR 1.57, 95% CI 1.13-2.17) and CRP (OR 1.13, CI 1.06-1.21), were associated with IMV by univariate analysis.\n\nConclusionsObesity, smoking history, and elevated inflammatory markers were associated with increased need for IMV in patients with COVID-19.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Ana Carolina Costa Monteiro", - "author_inst": "UCLA Ronald Reagan" - }, - { - "author_name": "Rajat Suri", - "author_inst": "UCLA Ronald Reagan" - }, - { - "author_name": "Ileanacho Obi Emeruwa", - "author_inst": "UCLA Ronald Reagan" - }, - { - "author_name": "Robert J Stretch", - "author_inst": "UCLA Ronald Reagan" - }, - { - "author_name": "Roxana Y Cortes Lopez", - "author_inst": "UCLA Ronald Reagan" - }, - { - "author_name": "Alexander Sherman", - "author_inst": "UCLA Ronald Reagan" - }, - { - "author_name": "Catherine C Lindsay", - "author_inst": "UCLA Ronald Reagan" - }, - { - "author_name": "Jennifer A Fulcher", - "author_inst": "UCLA Ronald Reagan" - }, - { - "author_name": "David Goodman-Meza", - "author_inst": "UCLA Ronald Reagan" - }, - { - "author_name": "Anil Sapru", - "author_inst": "UCLA Ronald Reagan" - }, - { - "author_name": "Russell G Buhr", - "author_inst": "UCLA Ronald Reagan" - }, - { - "author_name": "Steven Y Chang", - "author_inst": "UCLA Ronald Reagan" - }, - { - "author_name": "Tisha Wang", - "author_inst": "UCLA Ronald Reagan" - }, - { - "author_name": "Nida Qadir", - "author_inst": "UCLA Ronald Reagan" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.08.12.20173450", "rel_title": "Analysing air particle quantity in a dental primary care setting", @@ -1221666,6 +1224810,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.12.20172726", + "rel_title": "Testing of Healthcare Workers Exposed to COVID19 with Rapid Antigen Detection", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20172726", + "rel_abs": "There is a need to develop safe and cost-effective ways to test healthcare workers for COVID19. Here we describe a rapid antigen testing strategy in a cohort of 497 Healthcare workers exposed to SARS-CoV-2 that can be applied by systems facing a surge of COVID19 cases, increased number of exposures in their workforce and limited RT-PCR availability. Our findings support an expanded use for antigen testing beyond its current indication and highlights the importance of further evaluating this modality for the diagnosis of COVID19 on asymptomatic individuals.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Victor Herrera", + "author_inst": "Adventhealth" + }, + { + "author_name": "Vincent Hsu", + "author_inst": "AdventHealth" + }, + { + "author_name": "Ademola Adewale", + "author_inst": "Adventhealth" + }, + { + "author_name": "Timothy Hendrix", + "author_inst": "AdventHealth" + }, + { + "author_name": "Lee Johnson", + "author_inst": "Adventhealth" + }, + { + "author_name": "Jeffrey Kuhlman", + "author_inst": "Adventhealth" + }, + { + "author_name": "Neil Finkler", + "author_inst": "Adventhealth" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.13.20170068", "rel_title": "A novel approach for evaluating contact patterns and risk mitigation strategies for COVID-19 in English Primary Schools with application of Structured Expert Judgement", @@ -1221771,53 +1224958,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.13.20174045", - "rel_title": "COVID-19 vaccination intention in the UK: Results from the COVID-19 Vaccination Acceptability Study (CoVAccS), a nationally representative cross-sectional survey", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174045", - "rel_abs": "AimTo investigate factors associated with intention to be vaccinated against COVID-19.\n\nMethodsOnline cross-sectional survey of 1,500 UK adults, recruited from an existing online research panel. Data were collected between 14th and 17th July 2020. We used linear regression analyses to investigate associations between intention to be vaccinated for COVID-19 \"when a vaccine becomes available to you\" and socio-demographic factors, previous influenza vaccination, general vaccine attitudes and beliefs, attitudes and beliefs about COVID-19, and attitudes and beliefs about a COVID-19 vaccination.\n\nResults64% of participants reported being likely to be vaccinated against COVID-19; 27% were unsure and 9% reported being unlikely to be vaccinated. Personal and clinical characteristics, previous influenza vaccination, general vaccination beliefs, and beliefs and attitudes about COVID-19 and a COVID-19 vaccination explained 77% of the variance in vaccination intention. Intention to be vaccinated was associated with more positive general COVID-19 vaccination beliefs and attitudes, weaker beliefs that the vaccination would cause side effects or be unsafe, greater perceived information sufficiency to make an informed decision about COVID-19 vaccination, greater perceived risk of COVID-19 to others but not oneself, older age, and having been vaccinated for influenza last winter (2019/20).\n\nConclusionsDespite uncertainty around the details of a COVID-19 vaccination, most participants reported intending to be vaccinated for COVID-19. Actual uptake will likely be lower. Vaccination intention reflects general vaccine beliefs and attitudes. Campaigns and messaging about a COVID-19 vaccination should emphasize the risk of COVID-19 to others and necessity for everyone to be vaccinated.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Susan Mary Sherman", - "author_inst": "Keele University" - }, - { - "author_name": "Louise E. Smith", - "author_inst": "King's College London" - }, - { - "author_name": "Julius Sim", - "author_inst": "Keele University" - }, - { - "author_name": "Richard Aml\u00f4t", - "author_inst": "Public Health England" - }, - { - "author_name": "Megan Cutts", - "author_inst": "Keele University" - }, - { - "author_name": "Hannah Dasch", - "author_inst": "Kings College London" - }, - { - "author_name": "G James Rubin", - "author_inst": "Kings College London" - }, - { - "author_name": "Nick Sevdalis", - "author_inst": "Kings College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.14.250928", "rel_title": "SARS-CoV-2 Infection And Longitudinal Fecal Screening In Malayan Tigers (Panthera tigris jacksoni), Amur Tigers (Panthera tigris altaica), And African Lions (Panthera leo krugeri) At The Bronx Zoo, New York, USA", @@ -1223440,6 +1226580,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.07.20166868", + "rel_title": "Factors Associated with Disease Severity and Mortality among Patients with Coronavirus Disease 2019: A Systematic Review and Meta-Analysis", + "rel_date": "2020-08-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20166868", + "rel_abs": "BackgroundUnderstanding the factors associated with disease severity and mortality in Coronavirus disease (COVID-19) is imperative to effectively triage patients. We performed a systematic review to determine the demographic, clinical, laboratory and radiological factors associated with severity and mortality in COVID-19.\n\nMethodsWe searched PubMed, Embase and WHO database for English language articles from inception until May 8, 2020. We included Observational studies with direct comparison of clinical characteristics between a) patients who died and those who survived or b) patients with severe disease and those without severe disease. Data extraction and quality assessment were performed by two authors independently.\n\nResultsAmong 15680 articles from the literature search, 109 articles were included in the analysis. The risk of mortality was higher in patients with increasing age, male gender (RR 1.45, 95%CI 1.23-1.71), dyspnea (RR 2.55, 95%CI 1.88-2.46), diabetes (RR 1.59, 95%CI 1.41-1.78), hypertension (RR 1.90, 95%CI 1.69-2.15). Congestive heart failure (OR 4.76, 95%CI 1.34-16.97), hilar lymphadenopathy (OR 8.34, 95%CI 2.57-27.08), bilateral lung involvement (OR 4.86, 95%CI 3.19-7.39) and reticular pattern (OR 5.54, 95%CI 1.24-24.67) were associated with severe disease. Clinically relevant cut-offs for leukocytosis(>10.0 x109/L), lymphopenia(< 1.1 x109/L), elevated C-reactive protein(>100mg/L), LDH(>250U/L) and D-dimer(>1mg/L) had higher odds of severe disease and greater risk of mortality.\n\nConclusionKnowledge of the factors associated of disease severity and mortality identified in our study may assist in clinical decision-making and critical-care resource allocation for patients with COVID-19.\n\nPrimary Funding SourceNone.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Vignesh Chidambaram", + "author_inst": "Johns Hopkins Bloomberg school of Public health" + }, + { + "author_name": "Nyan Lynn Tun", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Waqas Haque", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Marie Gilbert Majella", + "author_inst": "Department of Preventive and Social Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India" + }, + { + "author_name": "Ranjith Kumar Sivakumar", + "author_inst": "Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China" + }, + { + "author_name": "Amudha Kumar", + "author_inst": "Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA" + }, + { + "author_name": "Angela Ting-Wei Hsu", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Izza Ishak", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Aqsha Nur", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Samuel Ayeh", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Emmanuella Salia", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Ahsan Zil-E-Ali", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Muhammad Saeed", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Ayu Sarena", + "author_inst": "Bhayangkara Setukpa Hospital, Sukabumi, Indonesia" + }, + { + "author_name": "Bhavna Seth", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Muzzammil Ahmadzada", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Eman Haque", + "author_inst": "Southern Methodist University, Dallas, TX, USA" + }, + { + "author_name": "Pranita Neupane", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Kuang-Heng Wang", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Tzu-Miao Pu", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Syed Ali", + "author_inst": "Fatima Memorial Hospital, Lahore, Pakistan" + }, + { + "author_name": "Muhammad Arshad", + "author_inst": "Nishtar Hospital, Multan, Pakistan" + }, + { + "author_name": "Lin Wang", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Sheriza Baksh", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Petros Karakousis", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Panagis Galiatsatos", + "author_inst": "Johns Hopkins School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.26.20162008", "rel_title": "COVID-19 mild cases determination from correlating COVID-line calls to reported cases", @@ -1223569,41 +1226828,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.10.20167247", - "rel_title": "Fine-tuned Forecasting Techniques for COVID-19 Prediction in India", - "rel_date": "2020-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20167247", - "rel_abs": "Estimation of statistical quantities plays a cardinal role in handling of convoluted situations such as COVID-19 pandemic and forecasting the number of affected people and fatalities is a major component for such estimations. Past researches have shown that simplistic numerical models fare much better than the complex stochastic and regression-based models when predicting for countries such as India, United States and Brazil where there is no indication of a peak anytime soon. In this research work, we present two models which give most accurate results when compared with other forecasting techniques. We performed both short-term and long-term forecasting based on these models and present the results for two discrete durations.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Abhinav Gola", - "author_inst": "National Institute of Technology Delhi" - }, - { - "author_name": "Ravi Kumar Arya", - "author_inst": "National Institute of Technology Delhi" - }, - { - "author_name": "Animesh Animesh", - "author_inst": "National Institute of Technology Delhi" - }, - { - "author_name": "Ravi Dugh", - "author_inst": "The University of Rochester" - }, - { - "author_name": "Zuber Khan", - "author_inst": "National Institute of Technology Delhi" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.09.20171264", "rel_title": "Estimating the Impact of COVID-19 on the Individual Lifespan:A Conceptual Detour and an Empirical Shortcut", @@ -1224946,6 +1228170,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.10.20171371", + "rel_title": "Impaired cellular immunity to SARS-CoV-2 in severe COVID-19 patients", + "rel_date": "2020-08-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20171371", + "rel_abs": "The World Health Organization has declared SARS-CoV-2 virus outbreak a world-wide pandemic. Individuals infected by the virus exhibited different degrees of symptoms, the basis of which remains largely unclear. Currently, though convalescent individuals have been shown with both cellular and humoral immune responses, there is very limited understanding on the immune responses, especially adaptive immune responses, in patients with severe COVID-19. Here, we examined 10 blood samples from COVID-19 patients with acute respiratory distress syndrome (ARDS). The majority of them (70%) mounted SARS-CoV-2-specific humoral immunity with production of neutralizing antibodies. However, compared to healthy controls, the percentages and absolute numbers of both NK cells and CD8+ T cells were significantly reduced, accompanied with decreased IFN{gamma} expression in CD4+ T cells in peripheral blood from severe patients. Most notably, we failed in detecting SARS-CoV-2-specific IFN{gamma} production by peripheral blood lymphocytes from these patients. Our work thus indicates that COVID-19 patients with severe symptoms are associated with defective cellular immunity, which not only provides insights on understanding the pathogenesis of COVID-19, but also has implications in developing an effective vaccine to SARS-CoV-2.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Ling Ni", + "author_inst": "Institute for Immunology and School of Medicine,Tsinghua University" + }, + { + "author_name": "Meng-Li Cheng", + "author_inst": "College of Basic Medical Science, Jilin University" + }, + { + "author_name": "Hui Zhao", + "author_inst": "Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" + }, + { + "author_name": "Yu Feng", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Jingyuan Liu", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging Infectious Diseases," + }, + { + "author_name": "Fang Ye", + "author_inst": "Department of Hematology, Chui Yang Liu Hospital affiliated to Tsinghua University" + }, + { + "author_name": "Qing Ye", + "author_inst": "Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences," + }, + { + "author_name": "Gengzhen Zhu", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Xiaoli Li", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Pengzhi Wang", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Jing Shao", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Yong-qiang Deng", + "author_inst": "Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" + }, + { + "author_name": "Peng Wei", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Fang Chen", + "author_inst": "Department of Cardiology, Chui Yang Liu Hospital affiliated to Tsinghua University" + }, + { + "author_name": "Cheng-feng Qin", + "author_inst": "Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" + }, + { + "author_name": "Guoqing Wang", + "author_inst": "College of Basic Medical Science, Jilin University" + }, + { + "author_name": "Fan Li", + "author_inst": "College of Basic Medical Science, Jilin University" + }, + { + "author_name": "Hui Zeng", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging Infectious Diseases" + }, + { + "author_name": "Chen Dong", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2020.08.10.20171439", "rel_title": "Extended SEIQR type model for COVID-19 epidemic and data analysis", @@ -1225063,61 +1228378,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.11.20173005", - "rel_title": "Histopathology of Third Trimester Placenta from SARS-CoV-2-Positive Women", - "rel_date": "2020-08-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20173005", - "rel_abs": "BackgroundThis study aims to investigate whether maternal SARS-CoV-2 status affect placental pathology.\n\nMethodsA retrospective case-control study was conducted by reviewing charts and slides of placentas between April 1 to July 24, 2020. Clinical history of \"COVID-19\" were searched in Pathology Database (CoPath). Controls were matched with SARS-CoV-2-negative women with singleton deliveries in the 3rd-trimester. Individual and group, pathological features were extracted from placental pathology reports.\n\nResultsTwenty-one 3rd-trimester, placentas from SARS-CoV-2-positive women were identified and compared to 20 placentas from SARS-CoV-2-negative women. There were no significant differences in individual or group gross or microscopic pathological features between the groups. Within the SARS-CoV-2+ group, there are no differences between symptomatic and asymptomatic women.\n\nConclusionPlacentas from SARS-CoV-2-positive women do not demonstrate a specific pathological pattern. Pregnancy complicated with COVID-19 during the 3rd trimester does not have a demonstrable effect on placental structure and pathology.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Mai He", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "Priya Skaria", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "Kasey Kreutz", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "Ling Chen", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "Ian Hagemann", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "Ebony B Carter", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "Indira U Mysorekar", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "D Michael Nelson", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "John Pfeifer", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "Louis P Dehner", - "author_inst": "Washington University in St. Louis School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.08.10.20169912", "rel_title": "Seroprevalence of anti-SARS-CoV-2 IgG antibodies in children with household exposition to adults with COVID-19: preliminary findings", @@ -1226764,6 +1230024,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.07.20161737", + "rel_title": "LamPORE: rapid, accurate and highly scalable molecular screening for SARS-CoV-2 infection, based on nanopore sequencing", + "rel_date": "2020-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20161737", + "rel_abs": "LamPORE is a rapid way of testing/screening large numbers of samples for the presence or absence of SARS-CoV-2, the virus causing COVID-19. It combines barcoded multi-target amplification, 15-minute barcoded library preparation and real-time nanopore sequencing. Starting with extracted RNA, results can be obtained from 12 samples in approximately an hour and from 96 samples in under 2 hours. High scalability is achieved by combinatorial barcoding. Performance characteristics are currently being established and regulatory clearance to market is underway.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Phillip James", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "David Stoddart", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "Eoghan D Harrington", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "John Beaulaurier", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "Lynn Ly", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "Stuart Reid", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "Daniel J Turner", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "Sissel Juul", + "author_inst": "Oxford Nanopore Technologies" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.07.20170407", "rel_title": "Model-based projections for COVID-19 outbreak size and student-days lost to closure in Ontario childcare centres and primary schools", @@ -1226905,125 +1230212,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.07.20160275", - "rel_title": "Severe COVID-19 and Diabetes: A Retrospective Cohort Study from Three London Teaching Hospitals", - "rel_date": "2020-08-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20160275", - "rel_abs": "Patients with diabetes mellitus admitted to hospital with COVID-19 caused by infection with the novel coronavirus (SARS-CoV-2) have poorer outcomes. However, the drivers for this are not fully elucidated. We performed a retrospective cohort study, including detailed pre-hospital and presenting clinical and biochemical factors of 889 patients diagnosed with COVID-19 in three constituent hospitals of a large London NHS Trust. 62% of patients with severe COVID-19 were of non-White ethnic backgrounds and the prevalence of diabetes was 38%. 323 (36%) patients met the primary outcome of death or admission to the intensive care unit (ICU) within 30 days of diagnosis. Male gender, advancing age and the Clinical Frailty Scale, an established measure of multimorbidity, independently predicted poor outcomes on multivariate analysis. Diabetes did not confer an independent risk for adverse outcomes in COVID-19, although patients with diabetes and ischaemic heart disease were at particular risk. Additional risk factors which significantly and independently associated with poorer outcomes in patients with diabetes were age, male gender and lower platelet count. Antiplatelet medication was associated with a lower risk of death/ICU admission and should be evaluated in randomised clinical trials amongst high risk patient groups.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Chioma Izzi-Engbeaya", - "author_inst": "Imperial College London and Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Walter Distaso", - "author_inst": "Imperial College London" - }, - { - "author_name": "Anjali Amin", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Wei Yang", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Oluwagbemiga Idowu", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Julia S Kenkre", - "author_inst": "Imperial College London and Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Ronak J Shah", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Evelina Woin", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Christine Shi", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Nael Alavi", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Hala Bedri", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Niamh Brady", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Sophie Blackburn", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Martina Leczycka", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Sanya Patel", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Elizaveta Sokol", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Edward Toke-Bjolgerud", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Ambreen Qayum", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Mariana Abdel-Malek", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "David C D Hope", - "author_inst": "Imperial College London and Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Nick S Oliver", - "author_inst": "Imperial College London and Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Vasiliki Bravis", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Shivani Misra", - "author_inst": "Imperial College London and Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Tricia M Tan", - "author_inst": "Imperial College London and Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Neil Hill", - "author_inst": "Imperial College London and Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Victoria Salem", - "author_inst": "Imperial College London and Imperial College Healthcare NHS Trust" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2020.08.07.20170555", "rel_title": "Compound risks of hurricane evacuation amid the COVID-19 pandemic in the United States", @@ -1228546,6 +1231734,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.10.20172155", + "rel_title": "EPIDEMIC ANALYSIS OF COVID-19 IN ALGERIA BY A GENERALIZED SEIR MODEL", + "rel_date": "2020-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20172155", + "rel_abs": "The novel coronavirus diseases 2019 (COVID-19) in Wuhan is continuing to impress the world by its fast spread and the number of affected persons attracting an unprecedented attention. In this article, we used the classical SEIR model and a generalized SEIR model called SEIRDP model inspired in a model previously used during the outbreak in China to predict the evolution of COVID-19 in Algeria for a future period of 100 days using official reported data from early April to early August, 2020. Initial evaluation showed that thetwo models had a net correspondence with the reported data during this period for cumulative infected cases but the number of cumulative deaths was underestimated with the classical SEIR model. Model prediction with the SEIRDP concluded that the number of cumulative infected cases will increase in the next days reaching a number of about 60 k in middle November with a median of about 300 daily cases. Also, the number of estimated deaths will be around 2k. These results suggest that the COVID-19 is ongoing to infect more persons which may push national authorities to carefully act in the probable leaving of containment.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Mohamed LOUNIS Sr.", + "author_inst": "University of Ziane Achour Djelfa" + }, + { + "author_name": "Juarez dos Santos AZEVEDO Sr.", + "author_inst": "Universidade Federal da Bahia (UFBA)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.10.20172189", "rel_title": "Janus Kinase-Inhibitor and Type I Interferon Ability to Produce Favorable Clinical Outcomes in COVID-19 Patients: A Systematic Review and Meta-Analysis", @@ -1228687,85 +1231898,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, - { - "rel_doi": "10.1101/2020.08.11.244863", - "rel_title": "Cryo-EM Structures of the SARS-CoV-2 Endoribonuclease Nsp15", - "rel_date": "2020-08-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.11.244863", - "rel_abs": "New therapeutics are urgently needed to inhibit SARS-CoV-2, the virus responsible for the on-going Covid-19 pandemic. Nsp15, a uridine-specific endoribonuclease found in all coronaviruses, processes viral RNA to evade detection by RNA-activated host defense systems, making it a promising drug target. Previous work with SARS-CoV-1 established that Nsp15 is active as a hexamer, yet how Nsp15 recognizes and processes viral RNA remains unknown. Here we report a series of cryo-EM reconstructions of SARS-CoV-2 Nsp15. The UTP-bound cryo-EM reconstruction at 3.36 [A] resolution provides molecular details into how critical residues within the Nsp15 active site recognize uridine and facilitate catalysis of the phosphodiester bond, whereas the apo-states reveal active site conformational heterogeneity. We further demonstrate the specificity and mechanism of nuclease activity by analyzing Nsp15 products using mass spectrometry. Collectively, these findings advance understanding of how Nsp15 processes viral RNA and provide a structural framework for the development of new therapeutics.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Monica C Pillon", - "author_inst": "NIEHS/NIH" - }, - { - "author_name": "Meredith N Frazier", - "author_inst": "NIEHS/NIH" - }, - { - "author_name": "Lucas Dillard", - "author_inst": "NIEHS/NIH" - }, - { - "author_name": "Jason G Williams", - "author_inst": "NIEHS/NIH" - }, - { - "author_name": "Seda Kocaman", - "author_inst": "NIEHS/NIH" - }, - { - "author_name": "Juno M Krahn", - "author_inst": "NIEHS/NIH" - }, - { - "author_name": "Lalith Perera", - "author_inst": "NIEHS/NIH" - }, - { - "author_name": "Cassandra K Hayne", - "author_inst": "NIEHS/NIH" - }, - { - "author_name": "Jacob Gordon", - "author_inst": "NIEHS/NIH" - }, - { - "author_name": "Zachary D Stewart", - "author_inst": "NIEHS/NIH" - }, - { - "author_name": "Mack Sobhany", - "author_inst": "NIEHS/NIH" - }, - { - "author_name": "Leesa J Deterding", - "author_inst": "NIEHS/NIH" - }, - { - "author_name": "Allen L. Hsu", - "author_inst": "NIEHS/NIH" - }, - { - "author_name": "Venkata P Dandey", - "author_inst": "NIEHS/NIH" - }, - { - "author_name": "Mario J. Borgnia", - "author_inst": "NIEHS/NIH" - }, - { - "author_name": "Robin E Stanley", - "author_inst": "NIEHS/NIH" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.08.11.232520", "rel_title": "A Comprehensive Classification of Coronaviruses and Inferred Cross-Host Transmissions", @@ -1230692,6 +1233824,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.09.242867", + "rel_title": "A potent neutralizing nanobody against SARS-CoV-2 with inhaled delivery potential", + "rel_date": "2020-08-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.09.242867", + "rel_abs": "The outbreak of COVID-19 has emerged as a global pandemic. The unprecedented scale and severity call for rapid development of effective prophylactics or therapeutics. We here reported Nanobody (Nb) phage display libraries derived from four camels immunized with the SARS-CoV-2 spike receptor-binding domain (RBD), from which 381 Nbs were identified to recognize SARS-CoV-2-RBD. Furthermore, seven Nbs were shown to block interaction of human angiotensin converting enzyme 2 (ACE2) with SARS-CoV-2-RBD-variants, bat-SL-CoV-WIV1-RBD and SARS-CoV-1-RBD. Among the seven candidates, Nb11-59 exhibited the highest activity against authentic SARS-CoV-2 with ND50 of 0.55 g/mL. Nb11-59 can be produced on a large-scale in Pichia pastoris, with 20 g/L titer and 99.36% purity. It also showed good stability profile, and nebulization did not impact its stability. Overall, Nb11-59 might be a promising prophylactic and therapeutic molecule against COVID-19, especially through inhalation delivery.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC=\"FIGDIR/small/242867v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (42K):\norg.highwire.dtl.DTLVardef@e4434org.highwire.dtl.DTLVardef@9fee79org.highwire.dtl.DTLVardef@1e15bb1org.highwire.dtl.DTLVardef@4adb0c_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Junwei Gai", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Linlin Ma", + "author_inst": "Shanghai University of Medicine and Health Sciences" + }, + { + "author_name": "Guanghui Li", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Min Zhu", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Peng Qiao", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Xiaofei Li", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Haiwei Zhang", + "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Yanmin Zhang", + "author_inst": "School of Science, China Pharmaceutical University" + }, + { + "author_name": "Yadong Chen", + "author_inst": "School of Science, China Pharmaceutical University" + }, + { + "author_name": "Weiwei Ji", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Hao Zhang", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Huanhuan Cao", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Xionghui Li", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Rui Gong", + "author_inst": "Wuhan Institute of Virology Chinese Academy of Sciences" + }, + { + "author_name": "Yakun Wan", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2020.08.04.20168054", "rel_title": "SARS-CoV-2 and the Role of Orofecal Transmission: Systematic Review", @@ -1230845,69 +1234052,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.07.241653", - "rel_title": "Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France", - "rel_date": "2020-08-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.07.241653", - "rel_abs": "Through routine genomic surveillance of the novel SARS-CoV-2 virus (n=229 whole genome sequences), 2 different frameshifting deletions were newly detected in the open reading frame (ORF) 6, starting at the same position (27267). While the 26-nucleotide deletion variant was only found in one sample in March 2020, the 34-nucleotide deletion variant was found within a single geriatric hospital unit in 5/9 patients sequenced and one health care worker with samples collected between April 2nd and 9th, 2020. Both the presence of the 34-nucleotide deletion variant limited to this unit and the clustering of the corresponding whole genome sequences by phylogeny analysis strongly suggested a nosocomial transmission between patients. Interestingly, prolonged viral excretion of the 34-nucleotide deletion variant was identified in a stool sample 14 days after initial diagnosis for one patient. Clinical data revealed no significant difference in disease severity between patients harboring the wild-type or the 34-nucleotide deletion variants. The in vitro infection of the two deletion variants on primate endothelial kidney cells (BGM) and human lung adenocarcinoma cells (Calu-3) yielded comparable replication kinetics with the wild-type strain. Furthermore, high viral loads were found in vivo regardless of the presence or absence of the ORF6 deletion. Our study highlights the transmission and replication capacity of two newly described deletion variants in the same ORF6 region.\n\nImportanceWhile the SARS-CoV-2 genome has remained relatively stable since its emergence in the human population, genomic deletions are an evolutionary pattern previously described for the related SARS-CoV. Real-time genomic monitoring of the circulating variants is paramount to detect strain prevalence and transmission dynamics. Given the role of ORF6 in interferon modulation, further characterization, such as mechanistic interactions and interferon monitoring in patients, is crucial in understanding the viral-host factors driving disease evolution.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Gregory Queromes", - "author_inst": "CIRI (Centre International de Recherche en Infectiologie)" - }, - { - "author_name": "Gregory Destras", - "author_inst": "Infectious Agents Institute" - }, - { - "author_name": "Antonin Bal", - "author_inst": "Infectious Agents Institute" - }, - { - "author_name": "Hadrien Regue", - "author_inst": "Infectious Agents Institute" - }, - { - "author_name": "Gwendolyne Burfin", - "author_inst": "Infectious Agents Institute" - }, - { - "author_name": "Solenne Brun", - "author_inst": "Infectious Agents Institute" - }, - { - "author_name": "Remi Fanget", - "author_inst": "Infectious Agents Institute" - }, - { - "author_name": "Florence Morfin", - "author_inst": "Infectious Agents Institute" - }, - { - "author_name": "Martine Valette", - "author_inst": "Infectious Agents Institute" - }, - { - "author_name": "Bruno Lina", - "author_inst": "Infectious Agents Institute" - }, - { - "author_name": "Emilie Frobert", - "author_inst": "Infectious Agents Institute" - }, - { - "author_name": "Laurence Josset", - "author_inst": "Infectious Agents Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.04.20161067", "rel_title": "A Long-Lasting Sanitizing Skin Protectant based on CAGE, a Choline and Geranic Acid Eutectic", @@ -1232506,6 +1235650,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.07.20169961", + "rel_title": "Neutralizing antibody response in non-hospitalized SARS-CoV-2 patients", + "rel_date": "2020-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20169961", + "rel_abs": "The majority of infections with SARS-CoV-2 are asymptomatic or mild without the necessity of hospitalization. It is of importance to reveal if these patients develop an antibody response against SARS-CoV-2 and to define which antibodies confer virus neutralization. We conducted a comprehensive serological survey of 49 patients with a mild course of disease and quantified neutralizing antibody responses against a clinical SARS-CoV-2 isolate employing human cells as targets.\n\nFour patients (8%), even though symptomatic, did not develop antibodies against SARS-CoV-2 and two other patients (4%) were only positive in one of the six serological assays employed. For the remainder, antibody response against the S-protein correlated with serum neutralization whereas antibodies against the nucleocapsid were poor predictors of virus neutralization. Regarding neutralization, only six patients (12%) could be classified as highly neutralizers. Furthermore, sera from several individuals with fairly high antibody levels had only poor neutralizing activity. In addition, employing a novel serological Western blot system to characterize antibody responses against seasonal coronaviruses, we found that antibodies against the seasonal coronavirus 229E might contribute to SARS-CoV-2 neutralization.\n\nAltogether, we show that there is a wide breadth of antibody responses against SARS-CoV-2 in patients that differentially correlate with virus neutralization. This highlights the difficulty to define reliable surrogate markers for immunity against SARS-CoV-2.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Natalia Ruetalo", + "author_inst": "Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen" + }, + { + "author_name": "Ramona Businger", + "author_inst": "Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen" + }, + { + "author_name": "Karina Althaus", + "author_inst": "Institute for Transfusion Medicine, University Hospital Tuebingen" + }, + { + "author_name": "Simon Fink", + "author_inst": "NMI, Reutlingen" + }, + { + "author_name": "Felix Ruoff", + "author_inst": "NMI, Reutlingen" + }, + { + "author_name": "Klaus Hamprecht", + "author_inst": "Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen" + }, + { + "author_name": "Bertram Flehmig", + "author_inst": "Mediagnost GmbH, Reutlingen" + }, + { + "author_name": "Tamam Bakchoul", + "author_inst": "Institute for Transfusion Medicine, University Hospital Tuebingen" + }, + { + "author_name": "Markus F Templin", + "author_inst": "NMI, Reutlingen" + }, + { + "author_name": "Michael Schindler", + "author_inst": "University Hospital Tuebingen" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.05.20168476", "rel_title": "Specificity and Performance of Nucleocapsid and Spike-based SARS-CoV-2 Serologic Assays", @@ -1232723,77 +1235922,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.08.06.20169797", - "rel_title": "The effect of school closures and reopening strategies on COVID-19 infection dynamics in the San Francisco Bay Area: a cross-sectional survey and modeling analysis", - "rel_date": "2020-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169797", - "rel_abs": "BackgroundLarge-scale school closures have been implemented worldwide to curb the spread of COVID-19. However, the impact of school closures and re-opening on epidemic dynamics remains unclear.\n\nMethodsWe simulated COVID-19 transmission dynamics using an individual-based stochastic model, incorporating social-contact data of school-aged children during shelter-in-place orders derived from Bay Area (California) household surveys. We simulated transmission under observed conditions and counterfactual intervention scenarios between March 17-June 1, and evaluated various fall 2020 K-12 reopening strategies.\n\nFindingsBetween March 17-June 1, assuming children <10 were half as susceptible to infection as older children and adults, we estimated school closures averted a similar number of infections (13,842 cases; 95% CI: 6,290, 23,040) as workplace closures (15,813; 95% CI: 9,963, 22,617) and social distancing measures (7,030; 95% CI: 3,118, 11,676). School closure effects were driven by high school and middle school closures. Under assumptions of moderate community transmission, we estimate that fall 2020 school reopenings will increase symptomatic illness among high school teachers (an additional 40.7% expected to experience symptomatic infection, 95% CI: 1.9, 61.1), middle school teachers (37.2%, 95% CI: 4.6, 58.1), and elementary school teachers (4.1%, 95% CI: -1.7, 12.0). Results are highly dependent on uncertain parameters, notably the relative susceptibility and infectiousness of children, and extent of community transmission amid re-opening. The school-based interventions needed to reduce the risk to fewer than an additional 1% of teachers infected varies by grade level. A hybrid-learning approach with halved class sizes of 10 students may be needed in high schools, while maintaining small cohorts of 20 students may be needed for elementary schools.\n\nInterpretationMultiple in-school intervention strategies and community transmission reductions, beyond the extent achieved to date, will be necessary to avoid undue excess risk associated with school reopening. Policymakers must urgently enact policies that curb community transmission and implement within-school control measures to simultaneously address the tandem health crises posed by COVID-19 and adverse child health and development consequences of long-term school closures.\n\nFundingJVR, JRH, QC, PAC, SP, AKH, CMH, and KC were supported in part by National Science Foundation grant no. 2032210, National Institutes of Health grants nos. R01AI125842, R01TW010286 and R01AI148336, and by the University of California Multicampus Research Programs and Initiatives award # 17-446315. JAL received support from the Berkeley Population Center (grant number P2CHD073964 from the National Institute of Child Health & Human Development, National Institutes of Health).\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSGiven the urgent need to enact quick public health interventions to curb transmission of SARS-CoV-2, large-scale school closures were implemented globally. We searched the terms \"school\", \"children\", \"closure\", \"coronavirus\", and \"COVID-19\" in PubMed to assess the current evidence evaluating the role of school closures in mitigating SARS-CoV-2 transmission. Data motivating the decision to close schools remained largely limited to experiences with influenza outbreaks, where children are highly susceptible to infection, are key drivers of transmission, and experience severe outcomes. At the time of writing, no modeling studies to our knowledge have quantified the net impact of COVID-19 related school closures in the United States, and observational studies that documented decreases in COVID-19 incidence associated with statewide school closures are subject to confounding by other concurrently implemented non-pharmaceutical interventions. Further, the scientific consensus remains fragmented in its understanding of key epidemiological parameters, namely the relative susceptibility and infectiousness of children compared to adults, exacerbating uncertainties around the risks of opening schools. As policymakers weigh the negative consequences of school closures on child health and development against the risks of reopening, it becomes critical to discern the range of potential impacts of school reopenings on the COVID-19 epidemic accounting for uncertainty in epidemiological parameters and plausible strategies for risk mitigation.\n\nAdded value of this studyThis study uses an individual-based transmission model parameterized with contact patterns we derived from a web-based contact survey administered to Bay Area (California) households with children during school closures to advance the understanding of the relative impact of Bay Area spring 2020 school closures compared to other non-pharmaceutical interventions, and projects the potential impact of school reopening strategies in the fall 2020 semester. Within the context of our model, we found that school closures averted a similar number of cases as workplace closures in spring 2020, with most of the averted cases attributable to high school closures. We found that COVID-19 risks associated with reopening schools in fall 2020 are highly dependent on the relative susceptibility of children and the level of community transmission at the time of reopening. Strategies necessary to reduce school transmission such that fewer than an additional 1% of teachers would be infected varied across school divisions. Safely reopening high schools may require combining multiple strict contact reduction measures, including staggering school days, halving class sizes, or maintaining small, stable cohorts, while safely reopening elementary schools may be achieved with a more limited set of interventions, including use of stable cohorts and masks.\n\nImplications of all the available evidenceUnder plausible assumptions regarding the susceptibility and infectiousness of school-aged children and teenagers, this study highlights heterogeneity of COVID-19 risks, and necessary mitigation strategies, associated with reopening across levels of schooling. It also highlights the urgency of resolving uncertain parameters, especially those pertaining to the relative susceptibility and infectiousness of children. Research is needed to quantify the role of children in transmission of COVID-19 in schools or similar settings to enumerate the risk of school-based outbreaks, particularly as transmission remains high in many regions of the United States. To balance both the adverse long-term consequence of school closures on child development and concerns about safe reopening, policy makers must quickly devote resources to ensure schools that choose to reopen amid uncertain evidence can adopt and adhere to strict infection, prevention, and control strategies that are critical to ensuring students, teachers, and community members remain healthy.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jennifer R Head", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Kristin Andrejko", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Qu Cheng", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Philip A Collender", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Sophie Phillips", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Anna Boser", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Alexandra K Heaney", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Christopher M Hoover", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Sean L Wu", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Graham R Northrup", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Karen Click", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Robert Harrison", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Joseph A Lewnard", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Justin V Remais", - "author_inst": "University of California Berkeley" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.07.20169847", "rel_title": "Pre-pandemic psychiatric disorders and risk of COVID-19: a cohort analysis in the UK Biobank", @@ -1234248,6 +1237376,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.05.20168799", + "rel_title": "COVID-19 Test & Trace Success Determinants: Modeling On A Network", + "rel_date": "2020-08-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20168799", + "rel_abs": "What determines the success of a COVID-19 Test & Trace policy? We use an SEIR agent-based model on a graph, with realistic epidemiological parameters. Simulating variations in certain parameters of Testing & Tracing, we find that important determinants of successful containment are: (i) the time from symptom onset until a patient is self-isolated and tested, and (ii) the share of contacts of a positive patient who are successfully traced. Comparatively less important is (iii) the time of test analysis and contact tracing. When the share of contacts successfully traced is higher, the Test & Trace Time rises somewhat in importance. These results are robust to a wide range of values for how infectious presymptomatic patients are, to the amount of asymptomatic patients, to the network degree distribution and to base epidemic growth rate. We also provide mathematical arguments for why these simulation results hold in more general settings. Since real world Test & Trace systems and policies could affect all three parameters, Symptom Onset to Test Time should be considered, alongside test turnaround time and contact tracing coverage, as a key determinant of Test & Trace success.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ofir Reich", + "author_inst": "Google" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.04.20168518", "rel_title": "Phylodynamics reveals the role of human travel and contact tracing in controlling COVID-19 in four island nations", @@ -1234445,57 +1237592,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.05.20168682", - "rel_title": "The Trend of Neutralizing Antibody Response Against SARS-CoV-2 and the Cytokine/Chemokine Release in Patients with Differing Severities of COVID-19: All Individuals Infected with SARS-CoV-2 Obtained Neutralizing Antibody", - "rel_date": "2020-08-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20168682", - "rel_abs": "BackgroundCOVID-19 patients show a wide clinical spectrum ranging from mild respiratory symptoms to severe and fatal disease, and older individuals are known to be affected more severely. Neutralizing antibody for viruses is critical for their elimination, and increased cytokine/chemokine levels are thought to be related to COVID-19 severity. However, the trend of the neutralizing antibody production and cytokine/chemokine levels during the clinical course of COVID-19 patients with differing levels of severity has not been established.\n\nMethodsWe serially collected 45 blood samples from 12 patients with different levels of COVID-19 severity, and investigated the trend of neutralizing antibody production using authentic SARS-CoV-2 and cytokine/chemokine release in the patients clinical courses.\n\nResultsAll 12 individuals infected with SARS-CoV-2 had the neutralizing antibody against it, and the antibodies were induced at approx. 4-10 days after the patients onsets. The antibodies in the critical and severe cases showed high neutralizing activity in all clinical courses. Most cytokine/chemokine levels were clearly high in the critical patients compared to those with milder symptoms.\n\nConclusionNeutralizing antibodies against SARS-CoV-2 were induced at a high level in the severe COVID-19 patients, indicating that abundant virus replication occurred. Cytokines/chemokines were expressed more in the critical patients, indicating that high productions of cytokines/chemokines have roles in the disease severity. These results may indicate that plasma or neutralizing antibody therapy could be a first-line treatment for older patients to eliminate the virus, and corticosteroid therapy could be effective to suppress the cytokine storm after the viral genomes disappearance.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Lidya Handayani Tjan", - "author_inst": "Kobe University" - }, - { - "author_name": "Tatsuya Nagano", - "author_inst": "Kobe University" - }, - { - "author_name": "Koichi Furukawa", - "author_inst": "Kobe University" - }, - { - "author_name": "Mitsuhiro Nishimura", - "author_inst": "Kobe University" - }, - { - "author_name": "Jun Arii", - "author_inst": "Kobe University" - }, - { - "author_name": "Sayo Fujinaka", - "author_inst": "Hyogo Prefectural Kakogawa Medical Center" - }, - { - "author_name": "Sachiyo Iwata", - "author_inst": "Hyogo Prefectural Kakogawa Medical Center" - }, - { - "author_name": "Yoshihiro Nishimura", - "author_inst": "Kobe University" - }, - { - "author_name": "Yasuko Mori", - "author_inst": "Kobe University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.04.20168617", "rel_title": "Rapid, reliable, and cheap point-of-care bulk testing for SARS-CoV-2 by combining hybridization capture with improved colorimetric LAMP (Cap-iLAMP)", @@ -1236218,6 +1239314,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.06.239798", + "rel_title": "IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection", + "rel_date": "2020-08-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.06.239798", + "rel_abs": "The novel virus SARS-CoV-2 has infected more than 14 million people worldwide resulting in the Coronavirus disease 2019 (COVID-19). Limited information on the underlying immune mechanisms that drive disease or protection during COVID-19 severely hamper development of therapeutics and vaccines. Thus, the establishment of relevant animal models that mimic the pathobiology of the disease is urgent. Rhesus macaques infected with SARS-CoV-2 exhibit disease pathobiology similar to human COVID-19, thus serving as a relevant animal model. In the current study, we have characterized the transcriptional signatures induced in the lungs of juvenile and old rhesus macaques following SARS-CoV-2 infection. We show that genes associated with Interferon (IFN) signaling, neutrophil degranulation and innate immune pathways are significantly induced in macaque infected lungs, while pathways associated with collagen formation are downregulated. In COVID-19, increasing age is a significant risk factor for poor prognosis and increased mortality. We demonstrate that Type I IFN and Notch signaling pathways are significantly upregulated in lungs of juvenile infected macaques when compared with old infected macaques. These results are corroborated with increased peripheral neutrophil counts and neutrophil lymphocyte ratio in older individuals with COVID-19 disease. In contrast, pathways involving VEGF are downregulated in lungs of old infected macaques. Using samples from humans with SARS-CoV-2 infection and COVID-19, we validate a subset of our findings. Finally, neutrophil degranulation, innate immune system and IFN gamma signaling pathways are upregulated in both tuberculosis and COVID-19, two pulmonary diseases where neutrophils are associated with increased severity. Together, our transcriptomic studies have delineated disease pathways to improve our understanding of the immunopathogenesis of COVID-19 to facilitate the design of new therapeutics for COVID-19.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Bruce A. Rosa", + "author_inst": "Washington University in Saint Louis School of Medicine" + }, + { + "author_name": "Mushtaq Ahmed", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Dhiraj K. Singh", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jose Alberto Choreno-Parra", + "author_inst": "Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias" + }, + { + "author_name": "Journey Cole", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Luis Armando Jimenez-Alvarez", + "author_inst": "Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias" + }, + { + "author_name": "Tatiana Sofia Rodriguez-Reyna", + "author_inst": "Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Medicas y Nutricion" + }, + { + "author_name": "Bindu Singh", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Olga Golzalez", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Ricardo Carrion", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Larry S. Schlesinger", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "John Martin", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Joaquin Zuniga", + "author_inst": "Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional" + }, + { + "author_name": "Makedonka Mitreva", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Shabaana A Khader", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Deepak Kaushal", + "author_inst": "Texas Biomedical Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.08.06.240333", "rel_title": "Computational Hot-Spot Analysis of the SARS-CoV-2 Receptor Binding Domain / ACE2 Complex", @@ -1236375,93 +1239550,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.08.06.234674", - "rel_title": "Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate", - "rel_date": "2020-08-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.06.234674", - "rel_abs": "Vaccine efforts against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for the current COVID-19 pandemic are focused on SARS-CoV-2 spike glycoprotein, the primary target for neutralizing antibodies. Here, we performed cryo-EM and site-specific glycan analysis of one of the leading subunit vaccine candidates from Novavax based on a full-length spike protein formulated in polysorbate 80 (PS 80) detergent. Our studies reveal a stable prefusion conformation of the spike immunogen with slight differences in the S1 subunit compared to published spike ectodomain structures. Interestingly, we also observed novel interactions between the spike trimers allowing formation of higher order spike complexes. This study confirms the structural integrity of the full-length spike protein immunogen and provides a basis for interpreting immune responses to this multivalent nanoparticle immunogen.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Sandhya Bangaru", - "author_inst": "Scripps Research" - }, - { - "author_name": "Gabriel Ozorowski", - "author_inst": "Scripps Research Institute" - }, - { - "author_name": "Hannah L Turner", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Aleksandar Antanasijevic", - "author_inst": "Scripps Research" - }, - { - "author_name": "Deli Huang", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Xiaoning Wang", - "author_inst": "Scripps Research" - }, - { - "author_name": "Jonathan L Torres", - "author_inst": "Scripps Research" - }, - { - "author_name": "Jolene K Diedrich", - "author_inst": "The Scripps Research Institute and The Salk Institute for Biological Studies" - }, - { - "author_name": "Jing-Hui Tian", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Alyse D. Portnoff", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Nita Patel", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Michael J. Massare", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "John Robert Yates III", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "David Nemazee", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "James C. Paulson", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Greg Glenn", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Gale Smith", - "author_inst": "Novavax, Inc." - }, - { - "author_name": "Andrew B. Ward", - "author_inst": "The Scripps Research Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.07.30.20164939", "rel_title": "Evaluating the impact of non-pharmaceutical interventions for SARS-CoV-2 on a global scale", @@ -1238140,6 +1241228,177 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.31.20163055", + "rel_title": "SARS-CoV-2 Seroprevalence Across a Diverse Cohort of Healthcare Workers", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20163055", + "rel_abs": "ImportanceAntibody testing is important for understanding patterns of exposure and potential immunity to SARS-CoV-2. Prior data on seroprevalence have been subject to variations in selection of individuals and nature as well as timing of testing in relation to exposures.\n\nObjectiveWe sought to determine the extent of SARS-CoV-2 seroprevalance and the factors associated with seroprevelance across a diverse cohort of healthcare workers.\n\nDesignObservational cohort study of healthcare workers, including SARS-CoV-2 serology testing and participant questionaires.\n\nParticipantsA diverse and unselected population of adults (n=6,062) employed in a multi-site healthcare delivery system located in Los Angeles County, including individuals with direct patient contact and others with non-patient-oriented work functions.\n\nExposureExposure and infection with the SARS-CoV-2 virus, as determined by seropositivity.\n\nMain OutcomesUsing Bayesian and multi-variate analyses, we estimated seroprevalence and factors associated with seropositivity and antibody titers, including pre-existing demographic and clinical characteristics; potential Covid-19 illness related exposures; and, symptoms consistent with Covid-19 infection.\n\nResultsWe observed a seroprevalence rate of 4.1%, with anosmia as the most prominently associated self-reported symptom in addition to fever, dry cough, anorexia, and myalgias. After adjusting for potential confounders, pre-existing medical conditions were not associated with antibody positivity. However, seroprevalence was associated with younger age, Hispanic ethnicity, and African-American race, as well as presence of either a personal or household member having a prior diagnosis of Covid-19. Importantly, African American race and Hispanic ethnicity were associated with antibody positivity even after adjusting for personal Covid-19 diagnosis status, suggesting the contribution of unmeasured structural or societally factors. Notably, number of people, or children, in the home was not associated with antibody positivity.\n\nConclusion and RelevanceThe demographic factors associated with SARS-CoV-2 seroprevalence among our healthcare workers underscore the importance of exposure sources beyond the workplace. The size and diversity of our study population, combined with robust survey and modeling techniques, provide a vibrant picture of the demographic factors, exposures, and symptoms that can identify individuals with susceptibility as well as potential to mount an immune response to Covid-19.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat is the SARS-CoV-2 IgG seroprevalence rate across a large and diverse healthcare worker population, and which clinical, envionrmental, and symptom-based measures are associated with seropositivity?\n\nFindingsWe observed a seroprevalence rate of 4.1%. Adjusting for potential confounders, seropositivity was associated with younger age, Hispanic ethnicity, African-American race, and the symptom of anosmia, while not significantly associated with any pre-existing medical conditions.\n\nMeaningFactors associated with SARS-CoV-2 seroprevalence among our healthcare workers underscore the importance of exposure sources beyond the workplace.", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Joseph Ebinger", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Gregory J. Botwin", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Christine M. Albert", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Mona Alotaibi", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Moshe Arditi", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Anders H. Berg", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Aleksandra Binek", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Patrick G. Botting", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Justyna Fert-Bober", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Jane C. Figueiredo", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Jonathan D. Grein", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Wohaib Hasan", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Mir Henglin", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Shehnaz K. Hussain", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Mohit Jain", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Sandy Joung", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Michael Karin", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Elizabeth H Kim", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Dalin Li", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Yunxian Liu", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Eric Luong", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Dermot P.B. McGovern", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Akil Merchant", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Noah M. Merin", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Peggy B. Miles", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Margo Minissian", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Trevor-Trung Nguyen", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Koen Raedschelders", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Mohamad A. Rashid", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Celine E. Riera", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Richard V. Riggs", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Sonia Sharma", + "author_inst": "La Jolla Institute" + }, + { + "author_name": "Sarah Sternbach", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Nancy Sun", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Warren G. Tourtellotte", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Jennifer E. Van Eyk", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Kimia Sobhani", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Jonathan G. Braun", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Susan Cheng", + "author_inst": "Cedars-Sinai Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.31.20165738", "rel_title": "Early clinical characteristics of Covid-19: scoping review", @@ -1238473,45 +1241732,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.30.20165563", - "rel_title": "Making cotton face masks extra-protective by use of impervious cloth as the front layer to restrict flow of aerosols and droplets", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20165563", - "rel_abs": "IntroductionOne of the important measures to prevent spread of COVID-19 in community is use of face mask. Though the debate is going on regarding the airborne transmission of SARS-CoV-2 it makes reasonable point for universal use of face masks. A large variety of face masks are available in the market or people can make their own using household items. The efficacy of masks depends upon the type of cloth and number of layers of the cloth.\n\nMaterial and methodsWe have created an innovative mask with two layers of cotton and an impervious layer. The impervious layer made from polypropylene coated with polyurethane was applied on the outer side in the middle half of the mask in front of mouth and nose. The efficacy of this test mask was measured against N95FFR (reference standard), triple layer surgical masks and single layer cotton mask. A manikin was used wearing these masks/respirator and aerosols/droplets of diluted red coloured carbol fuchsin and fluorescent Auramine O were sprayed from distance of 1m and 2m. We also tested use of face shield. Both macroscopic and microscopic examination of the dissected masks and respirator was performed.\n\nResultsThe N95FFR was able to block the aerosols/droplets by its front layer. One triple layer surgical mask showed microscopic presence of stain in its innermost layer while the other blocked it with middle layer. The single layer cotton mask was not able to protect as we observed stain on the face itself. The test mask blocked most of the stain on impervious layer and also on the front cotton layer on lateral sides, where impervious layer was absent. When fluorescent stain was used, ultraviolet examination demonstrated that the whole area covered by test mask was clean while the other non covered area was fluorescent.\n\nConclusionWe believe that our innovation can be used in the community as well as in general areas of the hospital like, offices, labs, etc. and can be a better alternative to single use triple layer surgical masks. Further testing may be done by other organizations to rule out bias in our study.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Priyanka L Shahane-Kapse", - "author_inst": "Mahatma Gandhi Institute of Medical Sciences, Sevagram, Wardha, Maharashtra, India" - }, - { - "author_name": "Moreshwar R Shende", - "author_inst": "Mahatma Gandhi Institute of Medical Sciences, Sevagram, Wardha, Maharashtra, India" - }, - { - "author_name": "Sumit Kar", - "author_inst": "Mahatma Gandhi Institute of Medical Sciences, Sevagram, Wardha, Maharashtra, India" - }, - { - "author_name": "Pradeep Deshmukh", - "author_inst": "All India Institute of Medical Sciences, Nagpur, Maharashtra, India" - }, - { - "author_name": "Dhiraj Bhandari", - "author_inst": "Mahatma Gandhi Institute of Medical Sciences, Sevagram, Wardha, Maharashtra, India" - }, - { - "author_name": "Rahul Narang", - "author_inst": "Mahatma Gandhi Institute of Medical Sciences, Sevagram, Wardha, Maharashtra, India" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.30.20160069", "rel_title": "Genomic heterogeneity and clinical characterization of SARS-CoV-2 in Oregon", @@ -1239870,6 +1243090,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, + { + "rel_doi": "10.1101/2020.08.03.20167320", + "rel_title": "Retrospective SARS-CoV-2 Real-Time PCR Testing of Stored Bronchoalveolar Lavage Samples from February 2020", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20167320", + "rel_abs": "Bronchoalveolar lavage samples (n=34) collected in February, 2020 prior to the wide availability of molecular testing for SARS-CoV-2 were retrospectively assayed for presence of viral RNA. None of these patients qualified for SARS-CoV-2 testing based on Centers for Disease Control criteria at the time. None of the samples tested positive for SARS-CoV-2, suggesting that the virus was not yet widespread in Minnesota at the time these samples were obtained.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Douglas W Challener", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Aditya Shah", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Matthew Binnicker", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew Badley", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "John O'Horo", + "author_inst": "Mayo Clinic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.02.20166256", "rel_title": "Clinical characteristics and antibody response to SARS-CoV-2 spike 1 protein using the VITROS Anti-SARS-CoV-2 antibody tests in COVID-19 patients in Japan", @@ -1240035,53 +1243290,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.01.20166595", - "rel_title": "Implication of backward contact tracing in the presence of overdispersed transmission in COVID-19 outbreak", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.01.20166595", - "rel_abs": "Unlike forward contact tracing, backward contact tracing identifies the source of newly detected cases. This approach is particularly valuable when there is high individual-level variation in the number of secondary transmissions. By using a simple branching process model, we explored the potential of combining backward contact tracing with more conventional forward contact tracing for control of COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Akira Endo", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "- Centre for the Mathematical Modelling of Infectious Diseases (CMMID) COVID-19 Working Group", - "author_inst": "" - }, - { - "author_name": "Quentin J Leclerc", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Gwenan M Knight", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Graham F Medley", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Katherine E Atkins", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Sebastian Funk", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Adam J Kucharski", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.01.20166397", "rel_title": "Sensitivity of nasopharyngeal, oropharyngeal and nasal washes specimens for SARS-CoV-2 detection in the setting of sampling device shortage", @@ -1241432,6 +1244640,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.03.20165233", + "rel_title": "Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20165233", + "rel_abs": "Most currently approved strategies for the collection of saliva for COVID-19 diagnostics require specialized tubes containing buffers promoted for the stabilization of SARS-CoV-2 RNA and virus inactivation. Yet many of these are expensive, in limited supply, and not necessarily validated specifically for viral RNA. While saliva is a promising sample type as it can be reliably self-collected for the sensitive detection of SARS-CoV-2, the expense and availability of these collection tubes are prohibitive to mass testing efforts. Therefore, we investigated the stability of SARS-CoV-2 RNA and infectious virus detection from saliva without supplementation. We tested RNA stability over extended periods of time (2-25 days) and at temperatures representing at-home storage and elevated temperatures which might be experienced when cold chain transport may be unavailable. We found SARS-CoV-2 RNA in saliva from infected individuals is stable at 4{degrees}C, room temperature ([~]19{degrees}C), and 30{degrees}C for prolonged periods and found limited evidence for viral replication in stored saliva samples. This work demonstrates that expensive saliva collection options involving RNA stabilization and virus inactivation buffers are not always needed, permitting the use of cheaper collection options. Affordable testing methods are urgently needed to meet current testing demands and for continued surveillance in reopening strategies.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Isabel M Ott", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Madison S Strine", + "author_inst": "Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Anne E Watkins", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Maikel Boot", + "author_inst": "Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Chaney C Kalinich", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Christina A Harden", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Chantal B.F. Vogels", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Arnau Casanovas-Massana", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Adam J Moore", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "M. Catherine Muenker", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Maura Nakahata", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Maria Tokuyama", + "author_inst": "Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Allison Nelson", + "author_inst": "Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "John Fournier", + "author_inst": "Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Santos Bermejo", + "author_inst": "Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Melissa Campbell", + "author_inst": "Department of Pediatrics, Division of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Rupak Datta", + "author_inst": "Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "- the Yale IMPACT Research team", + "author_inst": "" + }, + { + "author_name": "Charles S Dela Cruz", + "author_inst": "Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Shelli F Farhadian", + "author_inst": "Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Albert I Ko", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA; Department of Medicine, Section of Infectious Diseases" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA; Howard Hughes Medical Institute, New Haven, CT 06510, USA" + }, + { + "author_name": "Nathan D Grubaugh", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Craig B Wilen", + "author_inst": "Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Anne Louise Wyllie", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.03.20167304", "rel_title": "Correlation between daily infections and fatality rate due to Covid-19 in Germany", @@ -1241565,69 +1244888,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.03.20167122", - "rel_title": "Ethnic minority groups in England and Wales - factors affecting the size and timing of elevated COVID-19 mortality: a retrospective cohort study linking Census and death records", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20167122", - "rel_abs": "ObjectivesTo estimate population-level associations between ethnicity and coronavirus disease 2019 (COVID-19) mortality, and to investigate how ethnicity-specific mortality risk evolved over the course of the pandemic.\n\nDesignRetrospective cohort study using linked administrative data.\n\nSettingEngland and Wales, deaths occurring 2 March to 15 May 2020.\n\nParticipantsRespondents to the 2011 Census of England and Wales aged [≤]100 years and enumerated in private households, linked to death registrations and adjusted to account for emigration before the outcome period, who were alive on 1 March 2020 (n=47,872,412).\n\nMain outcome measureDeath related to COVID-19, registered by 29 May 2020.\n\nStatistical methodsWe estimated hazard ratios (HRs) for ethnic minority groups compared with the White population using Cox regression models, controlling for geographical, demographic, socio-economic, occupational, and self-reported health factors. HRs were estimated on the full outcome period and separately for pre- and post-lockdown periods in the UK.\n\nResultsIn the age-adjusted models, people from all ethnic minority groups were at elevated risk of COVID-19 mortality; the HRs for Black males and females were 3.13 [95% confidence interval: 2.93 to 3.34] and 2.40 [2.20 to 2.61] respectively. However, in the fully adjusted model for females, the HRs were close to unity for all ethnic groups except Black (1.29 [1.18 to 1.42]). For males, COVID-19 mortality risk remained elevated for the Black (1.76 [1.63 to 1.90]), Bangladeshi/Pakistani (1.35 [1.21 to 1.49]) and Indian (1.30 [1.19 to 1.43]) groups. The HRs decreased after lockdown for all ethnic groups, particularly Black and Bangladeshi/Pakistani females.\n\nConclusionsDifferences in COVID-19 mortality between ethnic groups were largely attenuated by geographical and socio-economic factors, although some residual differences remained. Lockdown was associated with reductions in excess mortality risk in ethnic minority populations, which has major implications for a second wave of infection or local spikes. Further research is needed to understand the causal mechanisms underpinning observed differences in COVID-19 mortality between ethnic groups.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Daniel Ayoubkhani", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Vahe Nafilyan", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Chris White", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Peter Goldblatt", - "author_inst": "UCL Institute for Health Equity" - }, - { - "author_name": "Charlotte Gaughan", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Louisa Blackwell", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Nicky Rogers", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Amitava Banerjee", - "author_inst": "Institute of Health Informatics, University College London" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "Diabetes Research Centre, University of Leicester" - }, - { - "author_name": "Myer Glickman", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Ben Humberstone", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Ian Diamond", - "author_inst": "Office for National Statistics" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.03.20167254", "rel_title": "Review of Forecasting Models for Coronavirus (COVID-19) Pandemic in India during Country-wise Lockdown", @@ -1243274,6 +1246534,20 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.04.234880", + "rel_title": "SCV-2000bp: a primer panel for SARS-CoV-2 full-genome sequencing", + "rel_date": "2020-08-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.04.234880", + "rel_abs": "Here we provide technical data for amplifying the complete genome of SARS-CoV-2 from clinical samples using only seventeen pairs of primers. We demonstrate that the [C]V2000bp primer panel successfully produces genomes when used with the residual total RNA extracts from positive clinical samples following diagnostic RT-PCRs (with Ct in the range from 13 to 20). The library preparation method reported here includes genome amplification of ~1750-2000 bp fragments followed by ultrasonic fragmentation combined with the introduction of Illumina compatible adapters. Using the SCV2000bp panel, 25 complete SARS-CoV-2 virus genome sequences were sequenced from clinical samples of COVID-19 patients from Moscow obtained in late March - early April.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_by_nc_nd", + "type": "confirmatory results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.08.04.236653", "rel_title": "Pathogenetic Perspective of Missense Mutations of ORF3a Protein of SARS-CoV2", @@ -1243431,77 +1246705,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.04.234153", - "rel_title": "SARS-CoV-2 genome analysis of strains in Pakistan reveals GH, S and L clade strains at the start of the pandemic", - "rel_date": "2020-08-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.04.234153", - "rel_abs": "ObjectivesPakistan has a high infectious disease burden with about 265,000 reported cases of COVID-19. We investigated the genomic diversity of SARS-CoV-2 strains and present the first data on viruses circulating in the country.\n\nMethodsWe performed whole-genome sequencing and data analysis of SARS-CoV-2 eleven strains isolated in March and May.\n\nResultsStrains from travelers clustered with those from China, Saudi Arabia, India, USA and Australia. Five of eight SARS-CoV-2 strains were GH clade with Spike glycoprotein D614G, Ns3 gene Q57H, and RNA dependent RNA polymerase (RdRp) P4715L mutations. Two were S (ORF8 L84S and N S202N) and three were L clade and one was an I clade strain. One GH and one L strain each displayed Orf1ab L3606F indicating further evolutionary transitions.\n\nConclusionsThis data reveals SARS-CoV-2 strains of L, G, S and I have been circulating in Pakistan from March, at the start of the pandemic. It indicates viral diversity regarding infection in this populous region. Continuing molecular genomic surveillance of SARS-CoV-2 in the context of disease severity will be important to understand virus transmission patterns and host related determinants of COVID-19 in Pakistan.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Najia K Ghanchi", - "author_inst": "The Aga Khan University" - }, - { - "author_name": "Kiran I Masood", - "author_inst": "The Aga Khan University" - }, - { - "author_name": "Asghar Nasir", - "author_inst": "The Aga Khan University" - }, - { - "author_name": "Waqasuddin Khan", - "author_inst": "The Aga Khan University" - }, - { - "author_name": "Syed H Abidi", - "author_inst": "The Aga Khan University" - }, - { - "author_name": "Saba Shahid", - "author_inst": "The Aga Khan University" - }, - { - "author_name": "Syed F Mahmood", - "author_inst": "The Aga Khan University" - }, - { - "author_name": "Akbar R Kanji", - "author_inst": "The Aga Khan University" - }, - { - "author_name": "Safina A Razzak", - "author_inst": "The Aga Khan University" - }, - { - "author_name": "Zeeshan Ansar", - "author_inst": "The Aga Khan University" - }, - { - "author_name": "Nazneen Islam", - "author_inst": "The Aga Khan University" - }, - { - "author_name": "Mohammad B Dharejo", - "author_inst": "Govt. of Sindh" - }, - { - "author_name": "Zahra Hasan", - "author_inst": "The Aga Khan University" - }, - { - "author_name": "Rumina Hasan", - "author_inst": "The Aga Khan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.08.04.235689", "rel_title": "Cold-adapted live attenuated SARS-CoV-2 vaccine completely protects human ACE2 transgenic mice from SARS-CoV-2 infection", @@ -1245444,6 +1248647,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.30.20163824", + "rel_title": "Clinical Utility of a Highly Sensitive Lateral Flow Immunoassay as determined by Titer Analysis for the Detection of anti-SARS-CoV-2 Antibodies at the Point-of-Care", + "rel_date": "2020-08-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20163824", + "rel_abs": "Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), became a pandemic in early 2020. Lateral flow immunoassays for antibody testing have been viewed as a cheap and rapidly deployable method for determining previous infection with SARS-CoV-2; however, these assays have shown unacceptably low sensitivity. We report on nine lateral flow immunoassays currently available and compare their titer sensitivity in serum to a best-practice enzyme-linked immunosorbent assay (ELISA) and viral neutralization assay. For a small group of PCR-positive, we found two lateral flow immunoassay devices with titer sensitivity roughly equal to the ELISA; these devices were positive for all PCR-positive patients harboring SARS-CoV-2 neutralizing antibodies. One of these devices was deployed in Northern Italy to test its sensitivity and specificity in a real-world clinical setting. Using the device with fingerstick blood on a cohort of 27 hospitalized PCR-positive patients and seven hospitalized controls, ROC curve analysis gave AUC values of 0.7646 for IgG. For comparison, this assay was also tested with saliva from the same patient population and showed reduced discrimination between cases and controls with AUC values of 0.6841 for IgG. Furthermore, during viral neutralization testing, one patient was discovered to harbor autoantibodies to ACE2, with implications for how immune responses are profiled. We show here through a proof-of-concept study that these lateral flow devices can be as analytically sensitive as ELISAs and adopted into hospital protocols; however, additional improvements to these devices remain necessary before their clinical deployment.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Amanda Haymond", + "author_inst": "George Mason University" + }, + { + "author_name": "Claudius Mueller", + "author_inst": "George Mason University" + }, + { + "author_name": "Hannah Steinberg", + "author_inst": "University of Illinois, Chicago" + }, + { + "author_name": "K. Alex Hodge", + "author_inst": "George Mason University" + }, + { + "author_name": "Caitlin W Lehman", + "author_inst": "George Mason University" + }, + { + "author_name": "Shih-Chao Lin", + "author_inst": "George Mason University" + }, + { + "author_name": "Lucia Collini", + "author_inst": "Santa Chiara Hospital" + }, + { + "author_name": "Heather Branscome", + "author_inst": "George Mason University" + }, + { + "author_name": "Tuong Vi Nguyen", + "author_inst": "George Mason University" + }, + { + "author_name": "Sally Rucker", + "author_inst": "George Mason University" + }, + { + "author_name": "Lauren Panny", + "author_inst": "George Mason University" + }, + { + "author_name": "Rafaela Flor", + "author_inst": "George Mason University" + }, + { + "author_name": "Raouf Guirguis", + "author_inst": "George Mason University" + }, + { + "author_name": "Richard Hoefer", + "author_inst": "Sentara Dorothy G. Hoefer Comprehensive Breast Center" + }, + { + "author_name": "Giovanni Lorenzin", + "author_inst": "Santa Chiara Hospital" + }, + { + "author_name": "Emanuel Petricoin", + "author_inst": "George Mason University" + }, + { + "author_name": "Fatah Kashanchi", + "author_inst": "George Mason University" + }, + { + "author_name": "Kylene Kehn-Hall", + "author_inst": "George Mason University" + }, + { + "author_name": "Paolo Lanzafame", + "author_inst": "Santa Chiara Hospital" + }, + { + "author_name": "Lance Liotta", + "author_inst": "George Mason University" + }, + { + "author_name": "Alessandra Luchini", + "author_inst": "George Mason University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.30.20114959", "rel_title": "Impact of tocilizumab administration on mortality in severe COVID-19", @@ -1245585,53 +1248887,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.08.02.233023", - "rel_title": "A Systemic and Molecular Study of Subcellular Localization of SARS-CoV-2 Proteins", - "rel_date": "2020-08-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.02.233023", - "rel_abs": "Coronavirus possesses the largest RNA genome among all the RNA viruses. Its genome encodes about 29 proteins. Most of the viral proteins are non-structural proteins (NSP) except envelop (E), membrane (M), nucleocapsid (N) and Spike (S) proteins that constitute the viral nucleocapsid, envelop and surface. We have recently cloned all the 29 SARS-CoV-2 genes into vectors for their expressions in mammalian cells except NSP11 that has only 14 amino acids (aa). We are able to express all the 28 cloned SARS-CoV-2 genes in human cells to characterize their subcellular distributions. The proteins of SARS-CoV-2 are mostly cytoplasmic but some are both cytoplasmic and nuclear. Those punctate staining proteins were further investigated by immunofluorescent assay (IFA) using specific antibodies or by co-transfection with an organelle marker-expressing plasmid. As a result, we found that NSP15, ORF6, M and ORF7a are related to Golgi apparatus, and that ORF7b, ORF8 and ORF10 colocalize with endoplasmic reticulum (ER). Interestingly, ORF3a distributes in cell membrane, early endosome, endosome, late endosome and lysosome, which suggests that ORF3a might help the infected virus to usurp endosome and lysosome for viral use. Furthermore, we revealed that NSP13 colocalized with SC35, a protein standing for splicing compartments in the nucleus. Our studies for the first time visualized the subcellular locations of SARS-CoV-2 proteins and might provide novel insights into the viral proteins biological functions.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jing Zhang", - "author_inst": "Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China" - }, - { - "author_name": "Ruth Cruz-cosme", - "author_inst": "Howard University College of Medicine, 520 W Street NW, Washington, DC 20059" - }, - { - "author_name": "Meng-Wei Zhuang", - "author_inst": "Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China" - }, - { - "author_name": "Dongxiao Liu", - "author_inst": "Howard University College of Medicine, 520 W Street NW, Washington, DC 20059" - }, - { - "author_name": "Yuan Liu", - "author_inst": "Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA" - }, - { - "author_name": "Shaolei Teng", - "author_inst": "Department of Biology, Howard University, 415 College St. NW, Washington, DC 20059" - }, - { - "author_name": "Pei-Hui Wang", - "author_inst": "Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China" - }, - { - "author_name": "Qiyi Tang", - "author_inst": "Howard University College of Medicine, 520 W Street NW, Washington, DC 20059" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.02.232892", "rel_title": "A New Model of SARS-CoV-2 Infection Based on (Hydroxy)Chloroquine Activity", @@ -1247118,6 +1250373,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2020.07.31.231746", + "rel_title": "Engineered ACE2 receptor traps potently neutralize SARS-CoV-2", + "rel_date": "2020-08-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.31.231746", + "rel_abs": "An essential mechanism for SARS-CoV-1 and -2 infection begins with the viral spike protein binding to the human receptor protein angiotensin-converting enzyme II (ACE2). Here we describe a stepwise engineering approach to generate a set of affinity optimized, enzymatically inactivated ACE2 variants that potently block SARS-CoV-2 infection of cells. These optimized receptor traps tightly bind the receptor binding domain (RBD) of the viral spike protein and prevent entry into host cells. We first computationally designed the ACE2-RBD interface using a two-stage flexible protein backbone design process that improved affinity for the RBD by up to 12-fold. These designed receptor variants were affinity matured an additional 14-fold by random mutagenesis and selection using yeast surface display. The highest affinity variant contained seven amino acid changes and bound to the RBD 170-fold more tightly than wild-type ACE2. With the addition of the natural ACE2 collectrin domain and fusion to a human Fc domain for increased stabilization and avidity, the most optimal ACE2 receptor traps neutralized SARS-CoV-2 pseudotyped lentivirus and authentic SARS-CoV-2 virus with half-maximal inhibitory concentrations (IC50) in the 10-100 ng/ml range. Engineered ACE2 receptor traps offer a promising route to fighting infections by SARS-CoV-2 and other ACE2-utilizing coronaviruses, with the key advantage that viral resistance would also likely impair viral entry. Moreover, such traps can be pre-designed for viruses with known entry receptors for faster therapeutic response without the need for neutralizing antibodies isolated or generated from convalescent patients.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Anum Glasgow", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jeff Edward Glasgow", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Daniel Limonta", + "author_inst": "University of Alberta" + }, + { + "author_name": "Paige Solomon", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Irene Lui", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Yang Zhang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Matthew A Nix", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Nicholas J Rettko", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Shion A Lim", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Shoshana Zha", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Rachel Yamin", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Kevin Kao", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Oren S Rosenberg", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jeffrey V Ravetch", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Arun P Wiita", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kevin K Leung", + "author_inst": "UCSF" + }, + { + "author_name": "Xin X Zhou", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Tom C Hobman", + "author_inst": "University of Alberta" + }, + { + "author_name": "Tanja K Kortemme", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "James A. Wells", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2020.07.31.190454", "rel_title": "Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy", @@ -1247331,85 +1250681,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.30.20164921", - "rel_title": "Estrogen and COVID-19 symptoms: associations in women from the COVID Symptom Study", - "rel_date": "2020-08-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20164921", - "rel_abs": "BackgroundMen and older women have been shown to be at higher risk of adverse COVID-19 outcomes. Animal model studies of SARS-CoV and MERS suggest that the age and sex difference in COVID-19 symptom severity may be due to a protective effect of the female sex hormone estrogen. Females have shown an ability to mount a stronger immune response to a variety of viral infections because of more robust humoral and cellular immune responses.\n\nObjectivesWe sought to determine whether COVID-19 positivity increases in women entering menopause. We also aimed to identify whether premenopausal women taking exogenous hormones in the form of the combined oral contraceptive pill (COCP) and post-menopausal women taking hormone replacement therapy (HRT) have lower predicted rates of COVID-19, using our published symptom-based model.\n\nDesignThe COVID Symptom Study developed by Kings College London and Zoe Global Limited was launched in the UK on 24th March 2020. It captured self-reported information related to COVID-19 symptoms. Data used for this study included records collected between 7th May - 15th June 2020.\n\nMain outcome measuresWe investigated links between COVID-19 rates and 1) menopausal status, 2) COCP use and 3) HRT use, using symptom-based predicted COVID-19, tested COVID-19, and disease severity based on requirement for hospital attendance or respiratory support.\n\nParticipantsFemale users of the COVID Symptom Tracker Application in the UK, including 152,637 women for menopause status, 295,689 for COCP use, and 151,193 for HRT use. Analyses were adjusted for age, smoking and BMI.\n\nResultsPost-menopausal women aged 40-60 years had a higher rate of predicted COVID (P=0.003) and a corresponding range of symptoms, with consistent, but not significant trends observed for tested COVID-19 and disease severity. Women aged 18-45 years taking COCP had a significantly lower predicted COVID-19 (P=8.03E-05), with a reduction in hospital attendance (P=0.023). Post-menopausal women using HRT or hormonal therapies did not exhibit consistent associations, including increased rates of predicted COVID-19 (P=2.22E-05) for HRT users alone.\n\nConclusionsOur findings support a protective effect of estrogen on COVID-19, based on positive association between predicted COVID-19 and menopausal status, and a negative association with COCP use. HRT use was positively associated with COVID-19 symptoms; however, the results should be considered with caution due to lack of data on HRT type, route of administration, duration of treatment, and potential comorbidities.\n\nTrial registrationThe App Ethics has been approved by KCL ethics Committee REMAS ID 18210, review reference LRs-19/20-18210", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Ricardo Costeira", - "author_inst": "King's College London" - }, - { - "author_name": "Karla A Lee", - "author_inst": "Department of Twin Research and Genetic Epidemiology" - }, - { - "author_name": "Benjamin Murray", - "author_inst": "King's College London" - }, - { - "author_name": "Colette Christiansen", - "author_inst": "King's College London" - }, - { - "author_name": "Juan Castillo-Fernandez", - "author_inst": "King's College London" - }, - { - "author_name": "Mary Ni Lochlainn", - "author_inst": "King's College London" - }, - { - "author_name": "Joan Capdevila Pujol", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Iain Buchan", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Louise C Kenny", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Jonathan Wolf", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Janice Rymer", - "author_inst": "King's College London" - }, - { - "author_name": "Sebastien Ourselin", - "author_inst": "King's College London" - }, - { - "author_name": "Claire Steves", - "author_inst": "King's College London" - }, - { - "author_name": "Timothy Spector", - "author_inst": "King's College London" - }, - { - "author_name": "Louise Newson", - "author_inst": "Newson HealthMenopause & Wellbeing Centre" - }, - { - "author_name": "Jordana Bell", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2020.07.30.20165134", "rel_title": "Improving COVID-19 critical care mortality over time in England: A national cohort study, March to June 2020", @@ -1248800,6 +1252071,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.31.231472", + "rel_title": "New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release", + "rel_date": "2020-07-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.31.231472", + "rel_abs": "The massive worldwide spread of the SARS-CoV-2 virus is fueling the COVID-19 pandemic. Since the first whole-genome sequence was published in January 2020, a growing database of tens of thousands of viral genomes has been constructed. This offers opportunities to study pathways of molecular change in the expanding viral population that can help identify molecular culprits of virulence and virus spread. Here we investigate the genomic accumulation of mutations at various time points of the early pandemic to identify changes in mutationally highly active genomic regions that are occurring worldwide. We used the Wuhan NC_045512.2 sequence as a reference and sampled 15,342 indexed sequences from GISAID, translating them into proteins and grouping them by month of deposition. The per-position amino acid frequencies and Shannon entropies of the coding sequences were calculated for each month, and a map of intrinsic disorder regions and binding sites was generated. The analysis revealed dominant variants, most of which were located in loop regions and on the surface of the proteins. Mutation entropy decreased between March and April of 2020 after steady increases at several sites, including the D614G mutation site of the spike (S) protein that was previously found associated with higher case fatality rates and at sites of the NSP 12 polymerase and the NSP13 helicase proteins. Notable expanding mutations include R203K and G204R of the nucleocapsid (N) protein inter-domain linker region and G251V of the viroporin encoded by ORF3a between March and April. The regions spanning these mutations exhibited significant intrinsic disorder, which was enhanced and decreased by the N-protein and viroporin 3a protein mutations, respectively. These results predict an ongoing mutational shift from the spike and replication complex to other regions, especially to encoded molecules known to represent major {beta}-interferon antagonists. The study provides valuable information for therapeutics and vaccine design, as well as insight into mutation tendencies that could facilitate preventive control.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tre Tomaszewski", + "author_inst": "University of Illinois" + }, + { + "author_name": "Ryan S DeVries", + "author_inst": "University of Illinois" + }, + { + "author_name": "Mengyi Dong", + "author_inst": "University of Illinois" + }, + { + "author_name": "Gitanshu Bhatia", + "author_inst": "University of Illinois" + }, + { + "author_name": "Miles D Norsworthy", + "author_inst": "University of Illinois" + }, + { + "author_name": "Xuying Zheng", + "author_inst": "University of Illinois" + }, + { + "author_name": "Gustavo Caetano-Anolles", + "author_inst": "University of Illinois" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.31.230730", "rel_title": "Biomechanical Characterization of SARS-CoV-2 Spike RBD and Human ACE2 Protein-Protein Interaction", @@ -1249005,41 +1252319,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.28.20163915", - "rel_title": "Converting Microwave Ovens into Plasma-Generating Decontamination Units for N-95 Respirators", - "rel_date": "2020-07-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20163915", - "rel_abs": "We show how a common microwave oven, a coat-hanger and a coffee cup can be used to decontaminate N-95 respirators in 30 seconds. Tulane virus in artificial saliva was reduced by >3 log and Geobacillus stearothermophilus spores were reduced by >6 log. Respirators maintained filtration and fitting after 10 cycles.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "David N. Ruzic", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Chamteut Oh", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Joseph V. Puthussery", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Vishal Verma", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Thanh H. Nguyen", - "author_inst": "University of Illinois at Urbana-Champaign" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.31.20165811", "rel_title": "COVID-19 case-fatality rate and demographic and socioeconomic influencers: a worldwide spatial regression analysis based on country-level data", @@ -1250478,6 +1253757,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.28.20163816", + "rel_title": "Multimorbidity patterns among COVID-19 deaths: considerations for a better medical practice", + "rel_date": "2020-07-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20163816", + "rel_abs": "Medical care of individuals diagnosed with severe COVID-19 is complex, especially when patients are older adults with multimorbidity. The objective of this study was to describe patterns of multimorbidity among fatal cases of COVID-19. Data of Colombian confirmed deaths of COVID-19 until June 11, 2020, were included in this analysis (1488 deaths). Relationships between COVID-19, combinations of health conditions and age were explored using locally weighted polynomial regressions. Some multimorbidity patterns increase probability of death among older individuals, whereas other patterns are not age-related, or decreases the probability of death among older people. Consider multimorbidity in the medical management of COVID-19 patients is important to determine the more adequate medical interventions. In addition to the co-occurrence of COVID-19 with diseases of high prevalence in the world, in Colombia there are cases more complex with COVID-19 co-occur with endemic and orphan tropical diseases. In these cases, although its occurrence may be low, clinical management requires adjusting to its complex clinical condition.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Julian Alfredo Fernandez-Nino", + "author_inst": "Fundacion Universidad del Norte" + }, + { + "author_name": "Jhon A Guerra-Gomez", + "author_inst": "Northeastern University, Silicon Valle" + }, + { + "author_name": "Alvaro Javier Idrovo-Velandia", + "author_inst": "Universidad Industrial de Santander" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.28.20163980", "rel_title": "Stochastic modelling of the effects of human-mobility restriction and viral infection characteristics on the spread of COVID-19", @@ -1250567,49 +1253873,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.29.20164152", - "rel_title": "The Role of Weather Conditions in COVID-19 Transmission: A Study of a Global Panel of 1236 Regions", - "rel_date": "2020-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20164152", - "rel_abs": "Weather condition may impact COVID-19 transmission. The effects of temperature and humidity on COVID-19 transmission are not clear due to the difficulties in separating impacts of social distancing. We collected COVID-19 data and social-economic features of 1236 regions in the world (1112 regions at the provincial level and 124 countries with small land area). Moreover, a large-scale satellite data was combined with these data with a regression analysis model to explore effects of temperature and relative humidity on COVID-19 spreading, as well as the possible transmission risk due to temperature change driven by seasonal cycles. The result showed every degree Celsius increase in average temperature appears to cause a 2.88% decrease in the fraction of new daily cases 6 days later and a 0.62 percent point decrease in the reproductive number (R0). Every percentage point increase in relative humidity is found to lead to a 0.19% decrease in the fraction of new daily cases and a 0.02 percent point decrease in R0 6 days later. Further, the effect of temperature and humidity is near to linear based on our samples. Government intervention (e.g. lockdown policies) and lower population movement contributed to the decrease the new daily case ratio. The conclusions withstand several robustness checks, such as observation scales and maximum/minimum temperature. The conclusion indicates air temperature and relative humidity are shown to be negatively correlated with COVID-19 transmission throughout the world. Given the diversity in both climate and social-economic conditions, the risk of transmission varies globally and possibly amplifies existing global health inequalities. Weather conditions are not the decisive factor in COVID-19 transmission, in that government intervention as well as public awareness, could contribute to the mitigation of the spreading of the virus.\n\nJEL codesI18, Q01, Q56", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Chen Zhang", - "author_inst": "Environmental and Health Research Group, Center for Energy and Environmental Policy Research, Beijing Institute of Technology" - }, - { - "author_name": "Hua Liao", - "author_inst": "Environmental and Health Research Group, Center for Energy and Environmental Policy Research, Beijing Institute of Technology" - }, - { - "author_name": "Eric Strol", - "author_inst": "Department of Economics, University of Bern" - }, - { - "author_name": "Hui Li", - "author_inst": "Environmental and Health Research Group, Center for Energy and Environmental Policy Research, Beijing Institute of Technology" - }, - { - "author_name": "Ru Li", - "author_inst": "Environmental and Health Research Group, Center for Energy and Environmental Policy Research, Beijing Institute of Technology" - }, - { - "author_name": "Steen Solvang Jensen", - "author_inst": "Department of Environmental Science, Aarhus University" - }, - { - "author_name": "Ying Zhang", - "author_inst": "Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.28.20160630", "rel_title": "Nicotine-replacement therapy, as a surrogate of smoking, and the risk of hospitalization with Covid-19 and all-cause mortality: a nationwide, observational cohort study in France", @@ -1252208,6 +1255471,45 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2020.07.17.20156463", + "rel_title": "SARS-CoV-2 Infection and Stroke: Coincident or Causal?", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20156463", + "rel_abs": "Neurological manifestations of SARS-CoV-2 infection described in isolated case reports and single institutions do not accurately reflect the clinical spectrum of disease across all geographies in a global pandemic. Data collected during peak of the Covid-19 pandemic from stroke centers in five states reveal few similarities to what has recently been published. Given the diversity in phenotype, we caution policymakers and health care providers when considering cerebrovascular complications from SARS-CoV-2 infection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Melanie Walker", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Christopher C. Young", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Malveeka Sharma", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Michael R Levitt", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "David L Tirschwell", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "- WWAMI Stroke Investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.07.23.20160887", "rel_title": "Divide in Vaccine Belief in COVID-19 Conversations: Implications for Immunization Plans", @@ -1252357,57 +1255659,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.21.20158337", - "rel_title": "Endpoint PCR Detection of Sars-CoV-2 RNA", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20158337", - "rel_abs": "Quantitative real-time PCR methods have been used to perform approximately 278 million tests for COVID-19 up to mid-July 2020. Real-time PCR involves a rate limiting step where the samples are measured in situ during each PCR amplification cycle. This creates a bottleneck limiting scalability and as a consequence reducing access to inexpensive reliable testing at national and international scales. We investigated endpoint PCR for the qualitative detection of SARS-CoV-2 sequences on synthetic RNA standards and hospital patient samples. The endpoint PCR detection limit is constrained only by the stochastics of low copy numbers and reliably detected single copies of synthetic RNA standards. On a set of 30 patient samples, endpoint PCR found one additional positive sample and was able to confirm an indeterminate sample as negative. These results were found using 4 l reagent and 1 l of sample representing an 80% reduction in required RNA extract input and PCR reagent volumes relative to the NHS protocol (20 l reagent and 5 l sample). These results indicate that endpoint PCR should be the method of choice for large scale testing programmes. Based on the experience from ultra-high throughput genotyping efforts a single workflow using 384-well plates has similar PCR capacity (250 Million) to that required for all testing done worldwide during the first 7 month of the pandemic.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Samuel Elliot Moses", - "author_inst": "East Kent Hospitals University NHS Foundation Trust" - }, - { - "author_name": "Claire Warren", - "author_inst": "East Kent Hospitals University NHS Foundation Trust" - }, - { - "author_name": "Phil Robinson", - "author_inst": "Independent Researcher" - }, - { - "author_name": "Jon Curtis", - "author_inst": "Independent Researcher" - }, - { - "author_name": "Steve Asquith", - "author_inst": "3CR Bioscience, Unit 10, West Point Business Park, Harlow CM20 2BU" - }, - { - "author_name": "John Holme", - "author_inst": "3CR Bioscience, Unit 10, West Point Business Park, Harlow CM20 2BU" - }, - { - "author_name": "Nisha Jain", - "author_inst": "3CR Bioscience, Unit 10, West Point Business Park, Harlow CM20 2BU" - }, - { - "author_name": "Keeley J Brookes", - "author_inst": "Nottingham Trent University" - }, - { - "author_name": "Quentin S Hanley", - "author_inst": "Nottingham Trent University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.17.20156265", "rel_title": "Descriptive epidemiology of 16,780 hospitalized COVID-19 patients in the United States", @@ -1253758,6 +1257009,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.27.20149757", + "rel_title": "Children with COVID-19 like symptoms in Italian Pediatric Surgeries: the dark side of the coin", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20149757", + "rel_abs": "BackgroundSymptoms of SARS-CoV-2 infection in children are nonspecific and shared with other common acute viral illnesses (fever, respiratory or gastrointestinal symptoms, and cutaneous signs), thus making clinical differential diagnosis tricky. In Italy, first line management of pediatric care is handed over to Primary Care Pediatricians (PCPs), who were not allowed to directly perform diagnostic tests during the recent COVID-19 outbreak. Without a confirmatory diagnosis, PCPs could only collect information on \"COVID-19 like symptoms\" rather than identify typical COVID-19 symptoms.\n\nAimTo evaluate the prevalence of COVID-19 like symptoms in outpatient children, during Italian lockdown. To provide PCPs a risk score to be used in clinical practice during the differential diagnosis process.\n\nMethodsA survey was submitted to 50 PCPs (assisting 47,500 children) from 7 different Italian regions between the 4th of March and the 23rd of May 2020 (total and partial lockdown period). COVID-19 like symptoms in the assisted children were recorded, as well as presence of confirmed/suspected cases in childrens families, which was taken as proxy of COVID-19. Multivariable logistic regression was accomplished to estimate the risk of having suspected/confirmed cases in families, considering symptoms as potential determinants.\n\nResults2,300 children (4.8% of overall survey population) fell ill with COVID-19 like symptoms, 3.1% and 1.7% during total and partial lockdown period respectively. The concurrent presence of fatigue, cough, and diarrhea in children, in absence of sore throat/earache and abnormal skin signs, represents the maximum risk level of having a suspected/confirmed case of COVID-19 at home.\n\nConclusionsThe percentage of children presenting COVID-19 like symptoms at home has been remarkable also during the total lockdown period. The present study identified a pattern of symptoms which could help, in a cost-effective perspective, PCPs in daily clinical practice to define priorities in addressing children to the proper diagnostic procedure.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Gianfranco Trapani", + "author_inst": "Alfred Nobel's Friends International Association Study Center and Primary Care Pediatrician, Sanremo (IM), Italy" + }, + { + "author_name": "Vassilios Fanos", + "author_inst": "Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Cagliari, Italy" + }, + { + "author_name": "Enrico Bertino", + "author_inst": "Neonatal Care Unit, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy" + }, + { + "author_name": "Giulia Maiocco", + "author_inst": "Neonatal Care Unit, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy" + }, + { + "author_name": "Osama Al Jamal", + "author_inst": "Alfred Nobel's Friends International Association Study Center and Primary Care Pediatrician, Cagliari, Italy" + }, + { + "author_name": "Michele Fiore", + "author_inst": "Primary Care Pediatrician, Genoa, Italy" + }, + { + "author_name": "VIncenzo Bembo", + "author_inst": "Primary Care Pediatrician, Frosinone, Italy" + }, + { + "author_name": "Domenico Careddu", + "author_inst": "Alfred Nobel's Friends International Association Study Center and Primary Care Pediatrician, Novara, Italy" + }, + { + "author_name": "Lando Barberio", + "author_inst": "Primary Care Pediatrician, Taggia (IM), Italy" + }, + { + "author_name": "Luisella Zanino", + "author_inst": "Alfred Nobel's Friends International Association Study Center and Primary Care Pediatrician, Turin, Italy" + }, + { + "author_name": "Giuseppe Verlato", + "author_inst": "Unit of Epidemiology and Medical Statistics, Department of Diagnostics & Public Health, University of Verona, Verona, Italy" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.07.27.20162057", "rel_title": "Predicting PPE use, post-traumatic stress, and physical symptoms during the early weeks of COVID-19 lockdowns in the USA", @@ -1253867,193 +1257177,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, - { - "rel_doi": "10.1101/2020.07.27.20163147", - "rel_title": "High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20163147", - "rel_abs": "During COVID19 and other viral pandemics, rapid generation of host and pathogen genomic data is critical to tracking infection and informing therapies. There is an urgent need for efficient approaches to this data generation at scale. We have developed a scalable, high throughput approach to generate high fidelity low pass whole genome and HLA sequencing, viral genomes, and representation of human transcriptome from single nasopharyngeal swabs of COVID19 patients.", - "rel_num_authors": 43, - "rel_authors": [ - { - "author_name": "John E Gorzynski", - "author_inst": "Department of Genetics, Stanford University, Stanford CA" - }, - { - "author_name": "Hannah N De Jong", - "author_inst": "Department of Genetics, Stanford University, Stanford CA" - }, - { - "author_name": "David Amar", - "author_inst": "Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Chris R Hughes", - "author_inst": "Department of Genetics, Stanford University, Stanford CA" - }, - { - "author_name": "Alexander Ioannidis", - "author_inst": "Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Rob Bierman", - "author_inst": "Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Darren Liu", - "author_inst": "Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Yosuke Tanigawa", - "author_inst": "Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Amy Kistler", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA" - }, - { - "author_name": "Jack Kamm", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA" - }, - { - "author_name": "Jaehee Kim", - "author_inst": "Department of Biology, Stanford University, Stanford, CA" - }, - { - "author_name": "Lorenzo Cappello", - "author_inst": "Department of Statistics, Stanford University, Stanford, CA" - }, - { - "author_name": "Norma F. Neff", - "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA" - }, - { - "author_name": "Simone Rubinacci", - "author_inst": "Swiss Institure of Bioinformatics" - }, - { - "author_name": "Olivier Delaneau", - "author_inst": "Swiss Institute of BioInformatics" - }, - { - "author_name": "Massa J. Shoura", - "author_inst": "Department of Genetics, Stanford University, Stanford, CA, Department of Pathology, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Kinya Seo", - "author_inst": "Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Anna Kirillova", - "author_inst": "Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Archana Raja", - "author_inst": "Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Shirley Sutton", - "author_inst": "Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "ChunHong Huang", - "author_inst": "Department of Pathology, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Malaya Kumar Sahoo", - "author_inst": "Department of Pathology, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Kalyan C. Mallempati", - "author_inst": "Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA" - }, - { - "author_name": "Gonzalo Montero-Martin", - "author_inst": "Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA" - }, - { - "author_name": "Kazutoyo Osoegawa", - "author_inst": "Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA" - }, - { - "author_name": "David Jimenez-Morales", - "author_inst": "Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Nathaniel Watson", - "author_inst": "Clinical Genomics Program, Stanford Medicine, Palo Alto, CA" - }, - { - "author_name": "Nathan Hammond", - "author_inst": "Clinical Genomics Program, Stanford Medicine, Palo Alto, CA" - }, - { - "author_name": "Ruchi Joshi", - "author_inst": "Clinical Genomics Program, Stanford Medicine, Palo Alto, CA" - }, - { - "author_name": "Marcelo Fernandez-Vina", - "author_inst": "Department of Statistics, Stanford University, Department of Pathology, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Jeffrey W. Christle", - "author_inst": "Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Matthew T. Wheeler", - "author_inst": "Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Phil Febbo", - "author_inst": "Illumina, San Dieg, CA" - }, - { - "author_name": "Kyle Farh", - "author_inst": "Illumina, San Diego, C" - }, - { - "author_name": "Gary Schroth", - "author_inst": "Illumina, Inc., San Diego, CA" - }, - { - "author_name": "F Desouza", - "author_inst": "Illumina, San Diego, CA" - }, - { - "author_name": "Julia Palacios", - "author_inst": "Biomedical Data Science, Stanford University, Stanford, CA, Department of Statistics, Stanford University" - }, - { - "author_name": "Julia Salzman", - "author_inst": "Biomedical Data Science, Stanford University, Stanford, CA" - }, - { - "author_name": "Benjamin A. Pinsky", - "author_inst": "Department of Pathology, Stanford University School of Medicine, Stanford, CA, Department of Medicine, Division of Infectious Diseases and Geographic Medicine, " - }, - { - "author_name": "Manuel A Rivas", - "author_inst": "Biomedical Data Science, Stanford University, Stanford, CA" - }, - { - "author_name": "Carlos D. Bustamante", - "author_inst": "Department of Genetics, Stanford University, Stanford CA, Biomedical Data Science, Stanford University, Stanford, CA" - }, - { - "author_name": "Euan A. Ashley", - "author_inst": "Department of Genetics, Stanford University, Stanford CA, Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, S" - }, - { - "author_name": "Victoria N. Parikh", - "author_inst": "Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.07.28.20163451", "rel_title": "Serial population based serosurvey of antibodies to SARS-CoV-2 in a low and high transmission area of Karachi, Pakistan", @@ -1255800,6 +1258923,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.28.225581", + "rel_title": "Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis", + "rel_date": "2020-07-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.28.225581", + "rel_abs": "The novel betacoronavirus named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused a worldwide pandemic (COVID-19) after initially emerging in Wuhan, China. Here we applied a novel, comprehensive bioinformatic strategy to public RNA sequencing and viral genome sequencing data, to better understand how SARS-CoV-2 interacts with human cells. To our knowledge, this is the first meta-analysis to predict host factors that play a specific role in SARS-CoV-2 pathogenesis, distinct from other respiratory viruses. We identified differentially expressed genes, isoforms and transposable element families specifically altered in SARS-CoV-2 infected cells. Well-known immunoregulators including CSF2, IL-32, IL-6 and SERPINA3 were differentially expressed, while immunoregulatory transposable element families were overexpressed. We predicted conserved interactions between the SARS-CoV-2 genome and human RNA-binding proteins such as hnRNPA1, PABPC1 and eIF4b, which may play important roles in the viral life cycle. We also detected four viral sequence variants in the spike, polymerase, and nonstructural proteins that correlate with severity of COVID-19. The host factors we identified likely represent important mechanisms in the disease profile of this pathogen, and could be targeted by prophylactics and/or therapeutics against SARS-CoV-2.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC=\"FIGDIR/small/225581v3_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@15ca5a6org.highwire.dtl.DTLVardef@17f455forg.highwire.dtl.DTLVardef@a39f50org.highwire.dtl.DTLVardef@306ec1_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Mariana G. Ferrarini", + "author_inst": "University of Lyon, INSA-Lyon, INRAE, BF2I" + }, + { + "author_name": "Avantika Lal", + "author_inst": "NVIDIA" + }, + { + "author_name": "Rita Rebollo", + "author_inst": "University of Lyon, INSA-Lyon, INRAE, BF2I" + }, + { + "author_name": "Andreas Gruber", + "author_inst": "Oxford Big Data Institute, Nuffield Department of Medicine, University of Oxford" + }, + { + "author_name": "Andrea Guarracino", + "author_inst": "Centre for Molecular Bioinformatics, Department of Biology, University Of Rome Tor Vergata" + }, + { + "author_name": "Itziar Martinez Gonzalez", + "author_inst": "Netherlands\tAmsterdam UMC" + }, + { + "author_name": "Taylor Floyd", + "author_inst": "Center for Neurogenetics, Weill Cornell Medicine, Cornell University" + }, + { + "author_name": "Daniel Siqueira de Oliveira", + "author_inst": "Laboratoire de Biometrie et Biologie Evolutive, Universite de Lyon, CNRS" + }, + { + "author_name": "Justin Shanklin", + "author_inst": "Brigham Young University" + }, + { + "author_name": "Ethan Beausoleil", + "author_inst": "Brigham Young University" + }, + { + "author_name": "Taneli Pusa", + "author_inst": "Luxembourg Centre for Systems Biomedicine" + }, + { + "author_name": "Brett Pickett", + "author_inst": "Brigham Young University" + }, + { + "author_name": "Vanessa Aguiar-Pulido", + "author_inst": "Center for Neurogenetics, Weill Cornell Medicine, Cornell University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.29.227389", "rel_title": "On the molecular mechanism of SARS-CoV-2 retention in the upper respiratory tract", @@ -1255917,29 +1259107,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.07.25.20162016", - "rel_title": "Capping Mobility to Control COVID-19: A Collision-based Infectious Disease Transmission Model", - "rel_date": "2020-07-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.25.20162016", - "rel_abs": "We developed a mobility-informed disease-transmission model for COVID-19, inspired by collision theory in gas-phase chemistry. This simple kinetic model leads to a closed-form infectious population as a function of time and cumulative mobility. This model uses fatality data from Johns Hopkins to infer the infectious population in the past, and mobility data from Google, without social-distancing policy, geological or demographic inputs. It was found that the model appears to be valid for twenty hardest hit counties in the United States. Based on this model, the number of infected people grows (shrinks) exponentially once the relative mobility exceeds (falls below) a critical value ([~]30% for New York City and [~]60% for all other counties, relative to a median mobility from January 3 to February 6, 2020). A simple mobility cap can be used by government at different levels to control COVID-19 transmission in reopening or imposing another shutdown.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Yunfeng Shi", - "author_inst": "Rensselaer Polytechnic Institute" - }, - { - "author_name": "Xuegang Ban", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.25.20162024", "rel_title": "Public Reactions towards the COVID-19 Pandemic on Twitter in the United Kingdom and the United States", @@ -1257382,6 +1260549,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.28.224386", + "rel_title": "Comparative Analysis of Human Coronaviruses Focusing on Nucleotide Variability and Synonymous Codon Usage Pattern", + "rel_date": "2020-07-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.28.224386", + "rel_abs": "Prevailing pandemic across the world due to SARSCoV-2 drawing great attention towards discovering its evolutionary origin. We perform an exploratory study to understand the variability of the whole coding region of possible proximal evolutionary neighbours of SARSCoV-2. We consider seven (07) human coronavirus strains from six different species as a candidate for our study.\n\nFirst, we observe a good variability of nucleotides across candidate strains. We did not find a significant variation of GC content across the strains for codon position first and second. However, we interestingly see huge variability of GC-content in codon position 3rd (GC3), and pairwise mean GC-content (SARSCoV, MERSCoV), and (SARSCoV-2, hCoV229E) are quite closer. While observing the relative abundance of dinucleotide feature, we find a shared typical genetic pattern, i.e., high usage of GC and CT nucleotide pair at the first two positions (P12) of codons and the last two positions (P23) of codons, respectively. We also observe a low abundance of CG pair that might help in their evolution bio-process. Secondly, Considering RSCU score, we find a substantial similarity for mild class coronaviruses, i.e., hCoVOC43, hCoVHKU1, and hCoVNL63 based on their codon hit with high RSCU value ([≥] 1.5), and minim number of codons hit (count-9) is observed for MERSCoV. We see seven codons ATT, ACT, TCT, CCT, GTT, GCT and GGT with high RSCU value, which are common in all seven strains. These codons are mostly from Aliphatic and Hydroxyl amino acid group. A phylogenetic tree built using RSCU feature reveals proximity among hCoVOC43 and hCoV229E (mild). Thirdly, we perform linear regression analysis among GC content in different codon position and ENC value. We observe a strong correlation (significant p-value) between GC2 and GC3 for SARSCoV-2, hCoV229E and hCoVNL63, and between GC1 and GC3 for hCoV229E, hCoVNL63, SARSCoV. We believe that our findings will help in understanding the mechanism of human coronavirus.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Jayanta Das", + "author_inst": "Johns Hopkins University, MD-21205, USA" + }, + { + "author_name": "Swarup Roy", + "author_inst": "Sikkim University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.07.22.20154542", "rel_title": "Prophylaxis with tetracyclines in ARDS: Potential therapy for COVID-19-induced ARDS?", @@ -1257499,33 +1260689,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.07.23.20160481", - "rel_title": "Why (and how) COVID-19 could move us closer to the \"health information for all\" goal", - "rel_date": "2020-07-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.23.20160481", - "rel_abs": "In this manuscript, we present an analysis of open access (OA) rates of papers concerning COVID-19 and other important human diseases, whose results helped develop an evidence-based scalable strategy aimed at increasing the full and timely access to medical literature. We show that COVID-19 papers are much more openly available (OA rate of 89.5%) than those concerning the four most recent viral outbreaks (Avian influenza, Middle East Respiratory Syndrome, Severe Acute Respiratory Syndrome, Swine influenza; OA rates (from 26.2% to 51.3%) and the ten non COVID-19 disease categories responsible for the highest number of deaths worldwide (OA rates from 44.0% for \"Maternal and neonatal disorders\" to 58.9% for \"Respiratory infections and tuberculosis\"). This evidence confronts us with an inevitable question: how can we bridge the gap between OA rates for COVID-19 and other high-impact human diseases? Based on empirical data and projections, we show that it is possible to increase substantially immediate OA to publicly-funded research and complement more demanding initiatives for access to medical literature in developing countries working on the sharing of post-prints at individual, group and multi stakeholder partnership level. However, to make our plan effective in bringing us closer to the \"health information for all\" goal a more widespread culture of cooperation is fundamental. We argue that the lesson taught by COVID-19 is a unique opportunity to raise awareness among researchers and stakeholders about the importance of open science for human health and to demonstrate that a real change is now possible.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Marco Capocasa", - "author_inst": "Istituto Italiano di Antropologia" - }, - { - "author_name": "Giovanni Destro Bisol", - "author_inst": "University of Rome \"La Sapienza\"" - }, - { - "author_name": "Paolo Anagnostou", - "author_inst": "University of Rome La Sapienza" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2020.07.24.20155192", "rel_title": "Predicting Critical State after COVID-19 Diagnosis Using Real-World Data from 20152 Confirmed US Cases", @@ -1259180,6 +1262343,105 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.27.223495", + "rel_title": "Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals", + "rel_date": "2020-07-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.27.223495", + "rel_abs": "The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Harsha Vardhan Doddapaneni", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Sara Javornik Cregeen", + "author_inst": "Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Richard Sucgang", + "author_inst": "Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Qingchang Meng", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Xiang Qing", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Vasanthi Avadhanula", + "author_inst": "Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Hsu Chao", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Vipin Menon", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Erin Nicholson", + "author_inst": "Department of Molecular Virology and Microbiology, and Pediatrics , Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "David Henke", + "author_inst": "Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Felipe-Andres Piedra", + "author_inst": "Department of Molecular Virology and Microbiology , Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Anubama Rajan", + "author_inst": "Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Zeineen Momin", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Kavya Kottapalli", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Kristi L. Hoffman", + "author_inst": "Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Fritz J Sedlazeck", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Ginger Metcalf", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Pedro A Piedra", + "author_inst": "Department of Molecular Virology and Microbiology and Pediatrics , Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Donna M Muzny", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Joseph F Petrosino", + "author_inst": "Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Richard A Gibbs", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.07.27.222836", "rel_title": "Targeting the endolysosomal host-SARS-CoV-2 interface by the clinically licensed antidepressant fluoxetine", @@ -1259289,57 +1262551,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.07.26.222208", - "rel_title": "CAR Macrophages for SARS-CoV-2 Immunotherapy", - "rel_date": "2020-07-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.26.222208", - "rel_abs": "Targeted therapeutics for the treatment of coronavirus disease 2019 (COVID-19), especially severe cases, are currently lacking. As macrophages have unique effector functions as a first-line defense against invading pathogens, we genetically armed human macrophages with chimeric antigen receptors (CARs) to reprogram their phagocytic activity against SARS-CoV-2. After investigation of CAR constructs with different intracellular receptor domains, we found that although cytosolic domains from MERTK (CARMERTK) did not trigger antigen-specific cellular phagocytosis or killing effects, unlike those from MEGF10, FcR{gamma} and CD3{zeta} did, these CARs all mediated similar SARS-CoV-2 clearance in vitro. Notably, we showed that CARMERTK macrophages reduced the virion load without upregulation of proinflammatory cytokine expression. These results suggest that CARMERTK drives an immunologically silent scavenger effect in macrophages and pave the way for further investigation of CARs for the treatment of individuals with COVID-19, particularly those with severe cases at a high risk of hyperinflammation.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Wenyan Fu", - "author_inst": "Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Changhai Lei", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Kewen Qian", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Zetong Ma", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Tian Li", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Wei Zhang", - "author_inst": "Department of Respiratory and Critical Care Medicine, First affiliated hospital, the Second Military Medical University; Guanggu District, the Maternal and Chil" - }, - { - "author_name": "Fangxing Lin", - "author_inst": "Second Military Medical University" - }, - { - "author_name": "Jian Zhao", - "author_inst": "KOCHKOR Biotech, Inc" - }, - { - "author_name": "Shi Hu", - "author_inst": "Second Military Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.07.27.222943", "rel_title": "Epitope-resolved profiling of the SARS-CoV-2 antibody response identifies cross-reactivity with an endemic human CoV", @@ -1260918,6 +1264129,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2020.07.21.20156711", + "rel_title": "Healthcare Workers' Mental Health and Wellbeing During the COVID-19 Pandemic in the UK: Contrasting Guidelines with Experiences in Practice", + "rel_date": "2020-07-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20156711", + "rel_abs": "BackgroundSubstantial evidence has highlighted the importance of considering healthcare workers (HCW) mental health during the COVID-19 pandemic, and several organisations have issued guidelines with recommendations. However, the definition of wellbeing and the evidence-base behind such guidelines remains unclear.\n\nObjectivesAssessing the applicability of wellbeing guidelines in practice; identifying unaddressed HCWs needs; and providing recommendations for supporting frontline staff during the current and future pandemics.\n\nMethods and DesignThis paper discusses the findings of a qualitative study based on interviews with frontline healthcare staff in the UK and examines them in relation to a rapid review of wellbeing guidelines developed in response to the COVID-19 pandemic.\n\nResults14 guidelines were included in the rapid review and 33 interviews with HCWs were conducted in the qualitative study. As a whole, the guidelines placed greater emphasis on wellbeing at an individual level, while HCWs placed greater emphasis on structural conditions at work, such as understaffing and the invaluable support of the community. This in turn had implications for the focus of wellbeing intervention strategies; staff reported an increased availability of formal mental health support, however, understaffing or clashing schedules prevented them from participating in these activities.\n\nConclusionHCWs expressed wellbeing needs which align with social-ecological conceptualisations of wellbeing related to quality of life. This approach to wellbeing has been highlighted in literature about HCWs support in previous health emergencies, yet it has not been monitored during this pandemic. Wellbeing guidelines should explore staffs needs and contextual characteristics affecting the implementation of recommendations.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Norha Vera San Juan", + "author_inst": "Insitute of Psychiatry, Psychology and Neuroscience. King's College London" + }, + { + "author_name": "David Aceituno", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience. King's College London" + }, + { + "author_name": "Nehla Djellouli", + "author_inst": "Institute for Global Health. University College London" + }, + { + "author_name": "Kirsi Sumray", + "author_inst": "Institute of Epidemiology and Health Care. University College London" + }, + { + "author_name": "Nina Regenold", + "author_inst": "Institute of Epidemiology and Health Care. University College London" + }, + { + "author_name": "Aron Syversen", + "author_inst": "Institute of Epidemiology and Health Care. University College London" + }, + { + "author_name": "Sophie Mulcahy Symmons", + "author_inst": "Institute of Epidemiology and Health Care. University College London" + }, + { + "author_name": "Anna Dowrick", + "author_inst": "Institute of Population Health and Science. Queen Mary University of London" + }, + { + "author_name": "Lucy Mitchinson", + "author_inst": "Marie Cuerie Pallatieve Care Research Department. University College London" + }, + { + "author_name": "Georgina Singleton", + "author_inst": "Health Services Research Centre. University College London" + }, + { + "author_name": "Cecilia Vindrola-Padros", + "author_inst": "Rapid Research, Evaluation and Appraisal Lab. University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.07.20.20157149", "rel_title": "Association of contact to small children with mild course of COVID-19", @@ -1261279,537 +1264549,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.22.20157263", - "rel_title": "Recent smell loss is the best predictor of COVID-19: a preregistered, cross-sectional study", - "rel_date": "2020-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20157263", - "rel_abs": "BackgroundCOVID-19 has heterogeneous manifestations, though one of the most common symptoms is a sudden loss of smell (anosmia or hyposmia). We investigated whether olfactory loss is a reliable predictor of COVID-19.\n\nMethodsThis preregistered, cross-sectional study used a crowdsourced questionnaire in 23 languages to assess symptoms in individuals self-reporting recent respiratory illness. We quantified changes in chemosensory abilities during the course of the respiratory illness using 0-100 visual analog scales (VAS) for participants reporting a positive (C19+; n=4148) or negative (C19-; n=546) COVID-19 laboratory test outcome. Logistic regression models identified singular and cumulative predictors of COVID-19 status and post-COVID-19 olfactory recovery.\n\nResultsBoth C19+ and C19-groups exhibited smell loss, but it was significantly larger in C19+ participants (mean{+/-}SD, C19+: -82.5{+/-}27.2 points; C19-: -59.8{+/-}37.7). Smell loss during illness was the best predictor of COVID-19 in both single and cumulative feature models (ROC AUC=0.72), with additional features providing negligible model improvement. VAS ratings of smell loss were more predictive than binary chemosensory yes/no-questions or other cardinal symptoms, such as fever or cough. Olfactory recovery within 40 days was reported for [~]50% of participants and was best predicted by time since illness onset.\n\nConclusionsAs smell loss is the best predictor of COVID-19, we developed the ODoR-19 tool, a 0-10 scale to screen for recent olfactory loss. Numeric ratings [≤]2 indicate high odds of symptomatic COVID-19 (460 years and coronary artery disease were independent predictors of mortality in multivariate analysis. Cox Proportional Hazards modeling for time to death demonstrated a significantly high ratio for COPD/Asthma, and favorable effects on outcomes for pre-admission ACE inhibitors and ARBs. CRP (180, 283 mg/L), LDH (551, 638 U/L), glucose (182, 163 mg/dL), procalcitonin (1.03, 1.68 ng/mL), and neutrophil / lymphocyte ratio (8.5, 10.0) were predictive of mortality on admission and at 48-96 hrs. Of the 496 inpatients, 48% died, one third of patients died within the first three days of admission. 54/488 patients received invasive mechanical ventilation, of which 87% died and of the remaining patients, 32% died.\n\nCONCLUSIONSCOVID-19 patients in our predominantly Black neighborhood had higher mortality, likely due to higher prevalence of comorbidities. Early dialysis and pre-admission intake of ACE inhibitors/ARBs improved patient outcomes. Early escalation of care based on comorbidities and key laboratory indicators is critical for improving outcomes in African-American patients.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Raavi Gupta", + "author_inst": "State University of New York, Downstate Medical Center" + }, + { + "author_name": "Raag Agrawal", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Zaheer Bukhari", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Absia Jabbar", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Donghai Wang", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "John Diks", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Mohamed Alshal", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Dokpe Yvonne Emechebe", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "F. Charles Brunicardi", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Jason M Lazar", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Robert Chamberlain", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Aaliya Burza", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "M. A. Haseeb", + "author_inst": "SUNY Downstate Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.15.20154971", "rel_title": "Time-dependent dynamic transmission potential and instantaneous reproduction number of COVID-19 pandemic in India.", @@ -1283537,33 +1286451,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.15.20154476", - "rel_title": "Causal analysis of COVID-19 observational data in German districts reveals effects of mobility, awareness, and temperature", - "rel_date": "2020-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154476", - "rel_abs": "Mobility, awareness, and weather are suspected to be causal drivers for new cases of COVID-19 infection. Correcting for possible confounders, we estimated their causal effects on reported case numbers. To this end, we used a directed acyclic graph (DAG) as a graphical representation of the hypothesized causal effects of the aforementioned determinants on new reported cases of COVID-19. Based on this, we computed valid adjustment sets of the possible confounding factors. We collected data for Germany from publicly available sources (e.g. Robert Koch Institute, Germanys National Meteorological Service, Google) for 401 German districts over the period of 15 February to 8 July 2020, and estimated total causal effects based on our DAG analysis by negative binomial regression. Our analysis revealed favorable causal effects of increasing temperature, increased public mobility for essential shopping (grocery and pharmacy), and awareness measured by COVID-19 burden, all of them reducing the outcome of newly reported COVID-19 cases. Conversely, we saw adverse effects of public mobility in retail and recreational areas, awareness measured by searches for \"corona\" in Google, and higher rainfall, leading to an increase in new COVID-19 cases. This comprehensive causal analysis of a variety of determinants affecting COVID-19 progression gives strong evidence for the driving forces of mobility, public awareness, and temperature, whose implications need to be taken into account for future decisions regarding pandemic management.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Edgar Steiger", - "author_inst": "Central Research Institute of Ambulatory Health Care in Germany (Zi)" - }, - { - "author_name": "Tobias Mussgnug", - "author_inst": "Central Research Institute of Ambulatory Health Care in Germany (Zi)" - }, - { - "author_name": "Lars Eric Kroll", - "author_inst": "Central Research Institute of Ambulatory Health Care in Germany (Zi)" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.15.20154617", "rel_title": "Inference of COVID-19 epidemiological distributions from Brazilian hospital data", @@ -1284882,6 +1287769,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.07.13.20152231", + "rel_title": "A Quantitative Lung Computed Tomography Image Feature for Multi-Center Severity Assessment of COVID-19", + "rel_date": "2020-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152231", + "rel_abs": "The COVID-19 pandemic has affected millions and congested healthcare systems globally. Hence an objective severity assessment is crucial in making therapeutic decisions judiciously. Computed Tomography (CT)-scans can provide demarcating features to identify severity of pneumonia --commonly associated with COVID-19--in the affected lungs. Here, a quantitative severity assessing chest CT image feature is demonstrated for COVID-19 patients. An open-source multi-center Italian database1 was used, among which 60 cases were incorporated in the study (age 27-86, 71% males) from 27 CT imaging centers. Lesions in the form of opacifications, crazy-paving patterns, and consolidations were segmented. The severity determining feature --Lnorm was quantified and established to be statistically distinct for the three --mild, moderate, and severe classes (p-value<0.0001). The thresholds of Lnorm for a 3-class classification were determined based on the optimum sensitivity/specificity combination from Receiver Operating Characteristic (ROC) analyses. The feature Lnorm classified the cases in the three severity categories with 86.88% accuracy. Substantial to almost-perfect intra-rater and inter-rater agreements were achieved involving expert and non-expert based evaluations ({kappa}-score 0.79-0.97). We trained machine learning based classification models and showed Lnorm alone has a superior diagnostic accuracy over standard image intensity and texture features. Classification accuracy was further increased when Lnorm was used for 2-class classification i.e. to delineate the severe cases from non-severe ones with a high sensitivity (97.7%), and specificity (97.49%). Therefore, key highlights of this severity assessment feature are accuracy, lower dependency on expert availability, and wide utility across different imaging centers.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Biswajoy Ghosh", + "author_inst": "Indian Institute of Technology Kharagpur" + }, + { + "author_name": "Nikhil Kumar", + "author_inst": "Indian Institute of Technology Kharagpur" + }, + { + "author_name": "Nitisha Singh", + "author_inst": "National Institute of Technology Durgapur" + }, + { + "author_name": "Anup K Sadhu", + "author_inst": "EKO CT and MRI Scan Centre, Medical College and Hospitals Campus, Kolkata" + }, + { + "author_name": "Nirmalya Ghosh", + "author_inst": "Indian Institute of Technology Kharagur" + }, + { + "author_name": "Pabitra Mitra", + "author_inst": "Indian Institute of Technology Kharagur" + }, + { + "author_name": "Jyotirmoy Chatterjee", + "author_inst": "Indian Institute of Technology Kharagur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.07.13.20153130", "rel_title": "Asthma in COVID-19: An extra chain fitting around the neck?", @@ -1285027,57 +1287957,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.13.20152207", - "rel_title": "Clinical Electroencephalography Findings and Considerations in Hospitalized Patients with Coronavirus SARS-CoV-2", - "rel_date": "2020-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152207", - "rel_abs": "Background and PurposeReports have suggested that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes neurologic manifestations including encephalopathy and seizures. However, there has been relatively limited electrophysiology data to contextualize these specific concerns and to understand their associated clinical factors. Our objective was to identify EEG abnormalities present in patients with SARS-CoV-2, and to determine whether they reflect new or preexisting brain pathology.\n\nMethodsWe studied a consecutive series of hospitalized patients with SARS-CoV-2 who received an EEG, obtained using tailored safety protocols. Data from EEG reports and clinical records were analyzed to identify EEG abnormalities and possible clinical associations, including neurologic symptoms, new or preexisting brain pathology, and sedation practices.\n\nResultsWe identified 37 patients with SARS-CoV-2 who underwent EEG, of whom 14 had epileptiform findings (38%). Patients with epileptiform findings were more likely to have preexisting brain pathology (6/14, 43%) than patients without epileptiform findings (2/23, 9%; p=0.042). There were no clear differences in rates of acute brain pathology. One case of nonconvulsive status epilepticus was captured, but was not clearly a direct consequence of SARS-CoV-2.\n\nAbnormalities of background rhythms were common, and patients recently sedated were more likely to lack a posterior dominant rhythm (p=0.022).\n\nConclusionsEpileptiform abnormalities were common in patients with SARS-CoV-2 referred for EEG, but particularly in the context of preexisting brain pathology and sedation. These findings suggest that neurologic manifestations during SARS-CoV-2 infection may not solely relate to the infection itself, but rather may also reflect patients broader, preexisting neurologic vulnerabilities.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Neishay Ayub", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Joseph Cohen", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Jin Jing", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Aayushee Jain", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Ryan Tesh", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Shibani S. Mukerji", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Sahar F. Zafar", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "M. Brandon Westover", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Eyal Y Kimchi", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2020.07.13.20152397", "rel_title": "Women in power: Female leadership and public health outcomes during the COVID-19 pandemic", @@ -1286464,6 +1289343,33 @@ "type": "confirmatory results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.15.176933", + "rel_title": "Alignment-free machine learning approaches for the lethality prediction of potential novel human-adapted coronavirus using genomic nucleotide", + "rel_date": "2020-07-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.15.176933", + "rel_abs": "A newly emerging novel coronavirus appeared and rapidly spread worldwide and World Health Organization declared a pandemic on March 11, 2020. The roles and characteristics of coronavirus have captured much attention due to its power of causing a wide variety of infectious diseases, from mild to severe on humans. The detection of the lethality of human coronavirus is key to estimate the viral toxicity and provide perspective for treatment. We developed alignment-free machine learning approaches for an ultra-fast and highly accurate prediction of the lethality of potential human-adapted coronavirus using genomic nucleotide. We performed extensive experiments through six different feature transformation and machine learning algorithms in combination with digital signal processing to infer the lethality of possible future novel coronaviruses using previous existing strains. The results tested on SARS-CoV, MERS-Cov and SARS-CoV-2 datasets show an average 96.7% prediction accuracy. We also provide preliminary analysis validating the effectiveness of our models through other human coronaviruses. Our study achieves high levels of prediction performance based on raw RNA sequences alone without genome annotations and specialized biological knowledge. The results demonstrate that, for any novel human coronavirus strains, this alignment-free machine learning-based approach can offer a reliable real-time estimation for its viral lethality.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rui YIN", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Zihan Luo", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Chee Keong Kwoh", + "author_inst": "Nanyang Technological University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.14.203463", "rel_title": "Comprehensive analysis of genomic diversity of SARS-CoV-2 in different geographic regions of India: An endeavour to classify Indian SARS-CoV-2 strains on the basis of co-existing mutations", @@ -1286673,133 +1289579,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.15.205211", - "rel_title": "An Antioxidant Enzyme Therapeutic for COVID-19", - "rel_date": "2020-07-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.15.205211", - "rel_abs": "The COVID-19 pandemic has taken a significant toll on people worldwide, and there are currently no specific antivirus drugs or vaccines. We report herein a therapeutic based on catalase, an antioxidant enzyme that can effectively breakdown hydrogen peroxide and minimize the downstream reactive oxygen species, which are excessively produced resulting from the infection and inflammatory process. Catalase assists to regulate production of cytokines, protect oxidative injury, and repress replication of SARS-CoV-2, as demonstrated in human leukocytes and alveolar epithelial cells, and rhesus macaques, without noticeable toxicity. Such a therapeutic can be readily manufactured at low cost as a potential treatment for COVID-19.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Meng Qin", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Zheng Cao", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Jing Wen", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Qingsong Yu", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Chaoyong Liu", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Fang Wang", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Fengmei Yang", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Yanyan Li", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Gregory A. Fishbein", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Sen Yan", - "author_inst": "Jinan University" - }, - { - "author_name": "Bin Xu", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Yi Hou", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Zhenbo Ning", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Kaili Nie", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Ni Jiang", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Zhen Liu", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Jun Wu", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Yanting Yu", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Heng Li", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Huiwen Zheng", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Jing Li", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Weihua Jin", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences" - }, - { - "author_name": "Sheng Pan", - "author_inst": "Vivibaba, Inc." - }, - { - "author_name": "Shuai Wang", - "author_inst": "Vivibaba Inc." - }, - { - "author_name": "Jianfeng Chen", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Zhihua Gan", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Zhanlong He", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences," - }, - { - "author_name": "Yunfeng Lu", - "author_inst": "University of California, Los Angeles" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.07.14.201947", "rel_title": "Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation", @@ -1288266,6 +1291045,73 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.07.14.202549", + "rel_title": "Targeting heparan sulfate proteoglycan-assisted endocytosis as a COVID-19 therapeutic option", + "rel_date": "2020-07-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.14.202549", + "rel_abs": "The cell entry of SARS-CoV-2 has emerged as an attractive drug repurposing target for COVID-19. Here we combine genetics and chemical perturbation to demonstrate that ACE2-mediated entry of SARS-CoV and CoV-2 requires the cell surface heparan sulfate (HS) as an assisting cofactor: ablation of genes involved in HS biosynthesis or incubating cells with a HS mimetic both inhibit Spike-mediated viral entry. We show that heparin/HS binds to Spike directly, facilitates the attachment of viral particles to the cell surface to promote cell entry. We screened approved drugs and identified two classes of inhibitors that act via distinct mechanisms to target this entry pathway. Among the drugs characterized, Mitoxantrone is a potent HS inhibitor, while Sunitinib and BNTX disrupt the actin network to indirectly abrogate HS-assisted viral entry. We further show that drugs of the two classes can be combined to generate a synergized activity against SARS-CoV-2-induced cytopathic effect. Altogether, our study establishes HS as an attachment factor that assists SARS coronavirus cell entry, and reveals drugs capable of targeting this important step in the viral life cycle.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Qi Zhang", + "author_inst": "NIH" + }, + { + "author_name": "Catherine Chen", + "author_inst": "NIH" + }, + { + "author_name": "Manju Swaroop", + "author_inst": "NIH" + }, + { + "author_name": "Miao Xu", + "author_inst": "NIH" + }, + { + "author_name": "Lihui Wang", + "author_inst": "NIH" + }, + { + "author_name": "Juhyung Lee", + "author_inst": "NIH" + }, + { + "author_name": "Manisha Pradhan", + "author_inst": "NIH" + }, + { + "author_name": "Min Shen", + "author_inst": "NIH" + }, + { + "author_name": "Zhiji Luo", + "author_inst": "NIH" + }, + { + "author_name": "Yue Xu", + "author_inst": "NIH" + }, + { + "author_name": "Wenwei Huang", + "author_inst": "NIH" + }, + { + "author_name": "Wei Zheng", + "author_inst": "NIH" + }, + { + "author_name": "Yihong Ye", + "author_inst": "NIH" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2020.07.13.20152793", "rel_title": "At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR based tests?: A systematic review of individual participant data", @@ -1288435,41 +1291281,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.10.20150698", - "rel_title": "Subsequent waves of viral pandemics, a hint for the future course of the SARS-CoV-2 pandemic.", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20150698", - "rel_abs": "BackgroundIt is unknown if the SARS-CoV-2 pandemic will have a second wave. We analysed published data of five influenza pandemics (such as the Spanish Flu and the Swine Flu) and the SARS-CoV-1 pandemic to describe whether there were subsequent waves and how they differed.\n\nMethodsWe reanalysed literature and WHO reports on SARS-CoV-1 and literature on five influenza pandemics. We report frequencies of second and third waves, wave heights, wavelengths and time between subsequent waves. From this, we estimated peak-to-peak ratios to compare the wave heights, and wave-length-to-wave-length ratios to compare the wavelengths differences in days. Furthermore, we analysed the seasonality of the wave peaks and the time between the peak values of two waves.\n\nResultsSecond waves, the Spanish Flu excluded, were usually about the same height and length as first waves and were observed in 93% of the 57 described epidemic events of influenza pandemics and in 42% of the 19 epidemic events of the SARS-CoV-1 pandemic. Third waves occurred in 54% of the 28 influenza and in 11% of the 19 SARS-CoV-1 epidemic events. Third waves, the Spanish Flu excluded, usually peaked higher than second waves with a peak-to-peak ratio of 0.5.\n\nConclusionWhile influenza epidemics are usually accompanied by 2nd waves, this is only the case in the minority of SARS-Cov1 epidemics.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Fabian Standl", - "author_inst": "University of Duisburg-Essen, medical faculty" - }, - { - "author_name": "Karl-Heinz Joeckel", - "author_inst": "University of Duisburg-Essen, medical faculty" - }, - { - "author_name": "Bernd Kowall", - "author_inst": "University of Duisburg-Essen, medical faculty" - }, - { - "author_name": "Boerge Schmidt", - "author_inst": "University of Duisburg-Essen, medical faculty" - }, - { - "author_name": "Andreas Stang", - "author_inst": "University Hospital of Essen, medical faculty" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.13.20152686", "rel_title": "Two New Models for Epidemics with Application to the COVID-19 Pandemic in the United States, Italy, and the United Kingdom", @@ -1289844,6 +1292655,233 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.07.13.20152355", + "rel_title": "State-level tracking of COVID-19 in the United States", + "rel_date": "2020-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152355", + "rel_abs": "As of 1st June 2020, the US Centers for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths reported in the next most severely impacted country. We jointly modelled the US epidemic at the state-level, using publicly available death data within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate the number of individuals that have been infected, the number of individuals that are currently infectious and the time-varying reproduction number (the average number of secondary infections caused by an infected person). We used changes in mobility to capture the impact that non-pharmaceutical interventions and other behaviour changes have on the rate of transmission of SARS-CoV-2. Nationally, we estimated 3.7% [3.4%-4.0%] of the population had been infected by 1st June 2020, with wide variation between states, and approximately 0.01% of the population was infectious. We also demonstrated that good model forecasts of deaths for the next 3 weeks with low error and good coverage of our credible intervals.", + "rel_num_authors": 53, + "rel_authors": [ + { + "author_name": "H Juliette T Unwin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Swapnil Mishra", + "author_inst": "Imperial College London" + }, + { + "author_name": "Valerie C Bradley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Axel Gandy", + "author_inst": "Imperial College London" + }, + { + "author_name": "Thomas A Mellan", + "author_inst": "Imperial College" + }, + { + "author_name": "Helen Coupland", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jonathan Ish-Horowicz", + "author_inst": "Imperial College London" + }, + { + "author_name": "Michaela Andrea Christine Vollmer", + "author_inst": "Imperial College London" + }, + { + "author_name": "Charles Whittaker", + "author_inst": "Imperial College London" + }, + { + "author_name": "Sarah L Filippi", + "author_inst": "Imperial College London" + }, + { + "author_name": "Xiaoyue Xi", + "author_inst": "Imperial College London" + }, + { + "author_name": "M\u00e9lodie Monod", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver Ratmann", + "author_inst": "Imperial College London" + }, + { + "author_name": "Michael Hutchinson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Fabian Valka", + "author_inst": "None" + }, + { + "author_name": "Harrison Zhu", + "author_inst": "Imperial College London" + }, + { + "author_name": "Iwona Hawryluk", + "author_inst": "Imperial College London" + }, + { + "author_name": "Philip Milton", + "author_inst": "Imperial College London" + }, + { + "author_name": "Kylie E C Ainslie", + "author_inst": "Imperial College London" + }, + { + "author_name": "Marc Baguelin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Adhiratha Boonyasiri", + "author_inst": "Imperial College London" + }, + { + "author_name": "Nick F Brazeau", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lorenzo Cattarino", + "author_inst": "Imperial College London" + }, + { + "author_name": "Zulma M Cucunub\u00e1", + "author_inst": "Imperial College London" + }, + { + "author_name": "Gina Cuomo-Dannenburg", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ilaria Dorigatti", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver D Eales", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jeffrey W Eaton", + "author_inst": "Imperial College London" + }, + { + "author_name": "Sabinee L van Elsland", + "author_inst": "Imperial College London" + }, + { + "author_name": "Richard G FitzJohn", + "author_inst": "Imperial College London" + }, + { + "author_name": "Katy A M Gaythorpe", + "author_inst": "Imperial College London" + }, + { + "author_name": "William Green", + "author_inst": "Imperial College London" + }, + { + "author_name": "Wes Hinsley", + "author_inst": "Imperial College London" + }, + { + "author_name": "Benjamin Jeffrey", + "author_inst": "Imperial College London" + }, + { + "author_name": "Edward Knock", + "author_inst": "Imperial College London" + }, + { + "author_name": "Daniel J Laydon", + "author_inst": "Imperial College London" + }, + { + "author_name": "John Lees", + "author_inst": "Imperial College London" + }, + { + "author_name": "Gemma Nedjati-Gilani", + "author_inst": "Imperial College London" + }, + { + "author_name": "Pierre Nouvellet", + "author_inst": "University of Sussex" + }, + { + "author_name": "Lucy C Okell", + "author_inst": "Imperial College London" + }, + { + "author_name": "Kris V Parag", + "author_inst": "Imperial College London" + }, + { + "author_name": "Igor Siveroni", + "author_inst": "Imperial College London" + }, + { + "author_name": "Hayley A Thompson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Patrick Walker", + "author_inst": "Imperial College London" + }, + { + "author_name": "Caroline E Walters", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver J Watson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lilith K Whittles", + "author_inst": "Imperial College London" + }, + { + "author_name": "Azra Ghani", + "author_inst": "Imperial College London" + }, + { + "author_name": "Neil M Ferguson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Steven Riley", + "author_inst": "Dept Inf Dis Epi, Imperial College" + }, + { + "author_name": "Christl A. Donnelly", + "author_inst": "Imperial College London" + }, + { + "author_name": "Samir Bhatt", + "author_inst": "Imperial College London" + }, + { + "author_name": "Seth Flaxman", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.12.20152157", "rel_title": "Quantifying Respiratory Airborne Particle Dispersion Control Through Improvised Reusable Masks", @@ -1289965,41 +1293003,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.07.12.20152124", - "rel_title": "Assessing required SARS-CoV-2 blanket testing rates for possible control of the outbreak in the epicentre Lusaka province of Zambia with consideration for asymptomatic individuals: a simple mathematical modelling study.", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.12.20152124", - "rel_abs": "IntroductionThe novel Coronavirus disease (COVID-19), caused by the severe acute respiratory syndrome coronavirus - 2 (SARS-CoV-2), in Africa is characterised by a more substantial proportion of asymptomatic (or mildly symptomatic) individuals thought to be playing a role in the spread of the infection. The exact proportion and degree of infectiousness of asymptomatic individuals remains unclear. Studies however indicate that their management is crucial for control of SARS-CoV-2 transmission.\n\nMethodologyWe developed a simplified deterministic susceptible-exposed-infectious-removed (SEIR) mathematical model to assess the effect of active isolation of SARS-CoV-2 infected but asymptomatic individuals through blanket testing for control of the outbreak in Lusaka Province of Zambia. Here we modelled two scenarios; (1) assuming asymptomatic individuals comprised 70% of all COVID-19 cases and (2) asymptomatic individuals comprised only 50% of the cases. For contrast, the model was assessed first under the assumption that asymptomatic individuals are equally as infectious as symptomatic individuals and then secondly, and more likely, assuming asymptomatic individuals are only half as infectious as symptomatic individuals.\n\nResultsFor the model assuming 70% asymptomatic cases, a minimum sustained blanket testing rate of [≥] 7911 tests/100000 population was sufficient to control the outbreak if asymptomatic individuals are only half as infectious while if equal infectiousness was assumed then a testing rate of [≥] 10028 tests/ 100000 population would be required. For 50% asymptomatic, minimum blanket testing rates of [≥] 4540 tests/ 100000 population was sufficient to control the outbreak at both assumed levels of infectiousness for asymptomatic individuals relative to symptomatic individuals.\n\nDiscussion and conclusionOur model predicts that the current testing rates of {approx} 150/100,000 population are inadequate to control transmission of SARS-Cov-2 in Lusaka. Active isolation of COVID-19 cases including asymptomatic individuals through blanket testing can be used as a possible measure for control of the SARS-Cov-2 transmission in Lusaka, Zambia.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Joseph Sichone", - "author_inst": "Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia / Department of Biomedical Sciences, School of Health Science" - }, - { - "author_name": "Musalula Sinkala", - "author_inst": "Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia" - }, - { - "author_name": "Mervis Kikonko", - "author_inst": "Department of Mathematics and Statistics, School of Natural Sciences, University of Zambia, Lusaka, Zambia" - }, - { - "author_name": "Sody Munsaka", - "author_inst": "Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia" - }, - { - "author_name": "Martin Simuunza", - "author_inst": "Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia /Africa Centre of Excellence for Infectious Diseases of Human" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.13.20151795", "rel_title": "Longitudinal symptom dynamics of COVID-19 infection in primary care", @@ -1291290,6 +1294293,33 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2020.07.12.199364", + "rel_title": "Flexibility and mobility of SARS-CoV-2-related protein structures", + "rel_date": "2020-07-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.12.199364", + "rel_abs": "The worldwide CoVid-19 pandemic has led to an unprecedented push across the whole of the scientific community to develop a potent antiviral drug and vaccine as soon as possible. Existing academic, governmental and industrial institutions and companies have engaged in large-scale screening of existing drugs, in vitro, in vivo and in silico. Here, we are using in silico modelling of SARS-CoV-2 drug targets, i.e. SARS-CoV-2 protein structures as deposited on the Protein Databank (PDB). We study their flexibility, rigidity and mobility, an important first step in trying to ascertain their dynamics for further drug-related docking studies. We are using a recent protein flexibility modelling approach, combining protein structural rigidity with possible motion consistent with chemical bonds and sterics. For example, for the SARS-CoV-2 spike protein in the open configuration, our method identifies a possible further opening and closing of the S1 subunit through movement of SB domain. With full structural information of this process available, docking studies with possible drug structures are then possible in silico. In our study, we present full results for the more than 200 thus far published SARS-CoV-2-related protein structures in the PDB.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rudolf A Roemer", + "author_inst": "University of Warwick" + }, + { + "author_name": "Navodya Sophie Roemer", + "author_inst": "University of Lincoln" + }, + { + "author_name": "Anne Katrine Wallis", + "author_inst": "University of Warwick" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.07.10.20150045", "rel_title": "Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka", @@ -1291447,61 +1294477,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.10.20150375", - "rel_title": "Poor correlation between antibody titers and neutralizing activity in sera from SARS-CoV-2 infected subjects", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20150375", - "rel_abs": "Plenty of serologic tests for SARS-CoV-2 have been developed so far, thus documenting the importance of evaluating the relevant features of the immune response to this viral agent. The performance of these assays is currently under investigation. Amongst them, LIAISON(R) SARS-CoV-2 S1/S2 IgG by DiaSorin and Elecsys Anti-SARS-CoV-2 cobas(R) by Roche are currently used by laboratory medicine hospital departments in Italy and many other countries. In the present study, we have firstly compared two serologic tests on serum samples collected at two different time points from forty-six laboratory-confirmed COVID-19 subjects. Secondly, eighty-five negative serum samples collected before the SARS-CoV-2 pandemic were analyzed. Thirdly, possible correlations between antibody levels and the resulting neutralizing activity against a clinical isolate of SARS-CoV-2 were evaluated. Results revealed that both tests are endowed with low sensitivity on the day of hospital admission, which increased to 97.8 and 100% for samples collected after 15 days for DiaSorin and Roche tests, respectively. The specificity of the two tests ranges from 96.5 to 100%, respectively. Importantly, a poor direct correlation between antibody titers and neutralizing activity levels was evidenced in the present study.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Elena Criscuolo", - "author_inst": "Vita-Salute San Raffaele University" - }, - { - "author_name": "Roberta A Diotti", - "author_inst": "Vita-Salute San Raffaele University" - }, - { - "author_name": "Marta Strollo", - "author_inst": "IRCCS San Raffaele Hospital" - }, - { - "author_name": "Serena Rolla", - "author_inst": "IRCCS San Raffaele Hospital" - }, - { - "author_name": "Alessandro Ambrosi", - "author_inst": "Vita-Salute San Raffaele University" - }, - { - "author_name": "Massimo Locatelli", - "author_inst": "IRCCS San Raffaele Hospital" - }, - { - "author_name": "Roberto Burioni", - "author_inst": "Vita-Salute San Raffaele University" - }, - { - "author_name": "Nicasio Mancini", - "author_inst": "Vita-Salute San Raffaele University; IRCCS San Raffaele Hospital" - }, - { - "author_name": "Massimo Clementi", - "author_inst": "Vita-Salute San Raffaele University; IRCCS San Raffaele Hospital" - }, - { - "author_name": "Nicola Clementi", - "author_inst": "Vita-Salute San Raffaele University; IRCCS San Raffaele Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.10.20150524", "rel_title": "Community prevalence of SARS-CoV-2 virus in England during May 2020: REACT study", @@ -1292820,6 +1295795,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.11.20151365", + "rel_title": "Decreased serum levels of inflammaging marker miR-146a are associated with clinical response to tocilizumab in COVID-19 patients", + "rel_date": "2020-07-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.11.20151365", + "rel_abs": "BackgroundCurrent COVID-19 pandemic poses an unprecedented threat to global health and healthcare systems. At least in western countries, the most amount of the death toll is accounted by old people affected by age-related diseases. In this regard, we proposed that COVID-19 severity may be tightly related to inflammaging, i.e. the age-related onset of inflammation, which is responsible for age-related diseases. It has been reported that systemic hyper-inflammation may turn to be detrimental in COVID-19 patients.\n\nObjectiveHere, we exploited a recently closed clinical trial (NCT04315480) on the anti-IL-6 drug tocilizumab to assess whether microRNAs regulating inflammaging can be assessed as biomarkers of drug response and outcome.\n\nMethodsSerum levels of miR-146a-5p, -21-5p, and -126-3p were quantified by RT-PCR and Droplet Digital PCR by two independent laboratories on 30 patients with virologically confirmed COVID-19, characterized by multifocal interstitial pneumonia confirmed by CT-scan and requiring oxygen therapy, and 29 age- and gender-matched healthy control subjects. COVID-19 patients were treated with a single-dose intravenous infusion of 8 mg/kg tocilizumab and categorized into responders and non-responders.\n\nResultsWe showed that COVID-19 patients who did not respond to tocilizumab have lower serum levels of miR-146a-5p after the treatment (p=0.007). Moreover, among non-responders, those with the lowest serum levels of miR-146a-5p experienced the most adverse outcome (p=0.008).\n\nConclusionOur data show that blood-based biomarkers, such as miR-146a-5p, can provide a molecular link between inflammaging and COVID-19 clinical course, thus allowing to enlarge the drug armory against this worldwide health threat.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Jacopo Sabbatinelli", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Angelica Giuliani", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Giulia Matacchione", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Silvia Latini", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Noemi Laprovitera", + "author_inst": "University of Bologna" + }, + { + "author_name": "Giovanni Pomponio", + "author_inst": "Azienda Ospedaliera \"Ospedali Riuniti\" di Ancona" + }, + { + "author_name": "Alessia Ferrarini", + "author_inst": "Azienda Ospedaliera \"Ospedali Riuniti\" di Ancona" + }, + { + "author_name": "Silvia Svegliati Baroni", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Marianna Pavani", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Marco Moretti", + "author_inst": "Azienda Ospedaliera \"Ospedali Riuniti\" di Ancona" + }, + { + "author_name": "Armando Gabrielli", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Antonio Domenico Procopio", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Manuela Ferracin", + "author_inst": "University of Bologna" + }, + { + "author_name": "Massimiliano Bonaf\u00e8", + "author_inst": "University of Bologna" + }, + { + "author_name": "Fabiola Olivieri", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.10.20150904", "rel_title": "Serological Tests for SARS-CoV-2 Coronavirus by Commercially Available Point-of-Care and Laboratory Diagnostics in Pre-COVID-19 Samples in Japan", @@ -1292913,41 +1295963,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.10.20150607", - "rel_title": "Wastewater SARS-CoV-2 Concentration and Loading Variability from Grab and 24-Hour Composite Samples", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20150607", - "rel_abs": "The ongoing COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires a significant, coordinated public health response. Assessing case density and spread of infection is critical and relies largely on clinical testing data. However, clinical testing suffers from known limitations, including test availability and a bias towards enumerating only symptomatic individuals. Wastewater-based epidemiology (WBE) has gained widespread support as a potential complement to clinical testing for assessing COVID-19 infections at the community scale. The efficacy of WBE hinges on the ability to accurately characterize SARS-CoV-2 RNA concentrations in wastewater. To date, a variety of sampling schemes have been used without consensus around the appropriateness of grab or composite sampling. Here we address a key WBE knowledge gap by examining the variability of SARS-CoV-2 RNA concentrations in wastewater grab samples collected every 2 hours for 72 hours compared with three corresponding 24-hour flow-weighted composite samples collected over the same period. Results show relatively low variability (respective means for N1, N2, N3 assays = 608, 847.9, 768.4 copies 100 mL-1, standard deviations = 501.4, 500.3, 505.8 copies 100 mL-1) for grab sample concentrations, and good agreement between most grab samples and their respective composite (mean deviation from composite = 159 copies 100 mL-1). When SARS-CoV-2 RNA concentrations are used to calculate viral load (RNA concentration * total influent flow the sample day), the discrepancy between grabs (log10 range for all grabs = 11.9) or a grab and its associated 24-hour composite (log10 difference = 11.6) are amplified. A similar effect is seen when estimating carrier prevalence in a catchment population with median estimates based on grabs ranging 63-1885 carriers. Findings suggest that grab samples may be sufficient to characterize SARS-CoV-2 RNA concentrations, but additional calculations using these data may be sensitive to grab sample variability and warrant the use of flow-weighted composite sampling. These data inform future WBE work by helping determine the most appropriate sampling scheme and facilitate sharing of datasets between studies via consistent methodology.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Kyle Curtis", - "author_inst": "Hampton Roads Sanitation District" - }, - { - "author_name": "David Keeling", - "author_inst": "Hampton Roads Sanitation District" - }, - { - "author_name": "Kathleen Yetka", - "author_inst": "Hampton Roads Sanitation District" - }, - { - "author_name": "Allison Larson", - "author_inst": "Hampton Roads Sanitation District" - }, - { - "author_name": "Raul Gonzalez", - "author_inst": "Hampton Roads Sanitation District" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.10.20150656", "rel_title": "Diagnostic value of skin manifestation of SARS-CoV-2 infection", @@ -1294474,6 +1297489,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.11.198770", + "rel_title": "ACE2-expressing endothelial cells in aging mouse brain", + "rel_date": "2020-07-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.11.198770", + "rel_abs": "Angiotensin-converting enzyme 2 (ACE2) is a key receptor mediating the entry of SARS-CoV-2 into the host cell. Through a systematic analysis of publicly available mouse brain sc/snRNA-seq data, we found that ACE2 is specifically expressed in small sub-populations of endothelial cells and mural cells, namely pericytes and vascular smooth muscle cells. Further, functional changes in viral mRNA transcription and replication, and impaired blood-brain barrier regulation were most prominently implicated in the aged, ACE2-expressing endothelial cells, when compared to the young adult mouse brains. Concordant EC transcriptomic changes were further found in normal aged human brains. Overall, this work reveals an outline of ACE2 distribution in the mouse brain and identify putative brain host cells that may underlie the selective susceptibility of the aging brain to viral infection.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "SU Bin Lim", + "author_inst": "Johns Hopkins University, School of Medicine" + }, + { + "author_name": "Valina L. Dawson", + "author_inst": "Johns Hopkins University, School of Medicine" + }, + { + "author_name": "Ted M. Dawson", + "author_inst": "Johns Hopkins University, School of Medicine" + }, + { + "author_name": "Sung-Ung Kang", + "author_inst": "Johns Hopkins University, School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2020.07.06.20147827", "rel_title": "Clinical Features of Hemodialysis (HD) patients confirmed with Coronavirus Disease 2019 (COVID-19): a Retrospective Case-Control Study", @@ -1294651,25 +1297697,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.07.08.20148924", - "rel_title": "A Holistic Approach to Identification of Covid-19 Patients from Chest X-Ray Images utilizing Transfer Based Learning", - "rel_date": "2020-07-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.08.20148924", - "rel_abs": "Novel coronavirus likewise called COVID-19 began in Wuhan, China in December 2019 and has now outspread over the world. Around 8 millions of individuals previously got influenced by novel coronavirus and it causes at any rate 500,000 deaths. There are just about 90,000 individuals contaminated by COVID-19 in Bangladesh too. As it is an exceptionally new pandemic infection, its diagnosis is challenging for the medical community. In regular cases, it is hard for lower incoming countries to test cases easily. RT-PCR test is the most generally utilized analysis framework for COVID-19 patient detection. However, by utilizing X-ray image based programmed recognition can diminish the expense and testing time. So according to handling this test, it is important to program and effective recognition to forestall transmission to others. In this paper, we attempt to distinguish COVID-19 patients by chest X-ray images. We execute different pre-trained deep neural system models, for example, Sequential, DenseNet121, ResNet152 and EfficientNetB4 to assess the most productive outcome. And aims to utilize transfer-based learning. We assess this outcome by AUC, where EfficientNetB4 has 0.997 AUC, ResNet50 has 0.967 AUC, DenseNet121 has 0.874 AUC and the Sequential model has 0.762 AUC individually. And EfficientNetB4 has achieved 98.86% accuracy.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Taki Hasan Rafi", - "author_inst": "Ahsanullah University of Science and Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2020.07.09.20148056", "rel_title": "IL-33 expression in response to SARS-CoV-2 correlates with seropositivity in COVID-19 convalescent individuals", @@ -1296384,6 +1299411,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.08.20149146", + "rel_title": "Recurrent Neural Reinforcement Learning for Counterfactual Evaluation of Public Health Interventions on the Spread of Covid-19 in the world", + "rel_date": "2020-07-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.08.20149146", + "rel_abs": "As the Covid-19 pandemic soars around the world, there is urgent need to forecast the expected number of cases worldwide and the length of the pandemic before receding and implement public health interventions for significantly stopping the spread of Covid-19. Widely used statistical and computer methods for modeling and forecasting the trajectory of Covid-19 are epidemiological models. Although these epidemiological models are useful for estimating the dynamics of transmission of epidemics, their prediction accuracies are quite low. Alternative to the epidemiological models, the reinforcement learning (RL) and causal inference emerge as a powerful tool to select optimal interventions for worldwide containment of Covid-19. Therefore, we formulated real-time forecasting and evaluation of multiple public health intervention problems into off-policy evaluation (OPE) and counterfactual outcome forecasting problems and integrated RL and recurrent neural network (RNN) for exploring public health intervention strategies to slow down the spread of Covid-19 worldwide, given the historical data that may have been generated by different public health intervention policies. We applied the developed methods to real data collected from January 22, 2020 to July 30, 2020 for real-time forecasting the confirmed cases of Covid-19 across the world. We observed that the number of new cases of Covid-19 worldwide reached a peak (407,205) on July 24, 2020 and forecasted that the number of laboratory-confirmed cumulative cases of Covid-19 will pass 20 million as of August 22, 2020. The results showed that outbreak of Covid-19 worldwide has peaked and is on the decline", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Qiyang Ge", + "author_inst": "Fudan University" + }, + { + "author_name": "Zixin Hu", + "author_inst": "fudan University" + }, + { + "author_name": "Kai Zhang", + "author_inst": "University of Texas School of Public Health" + }, + { + "author_name": "Shudi Li", + "author_inst": "University of Texas School of Public Health" + }, + { + "author_name": "Wei Lin", + "author_inst": "Fudan University" + }, + { + "author_name": "Li Jin", + "author_inst": "Fudan University" + }, + { + "author_name": "Momiao Xiong", + "author_inst": "University of Texas School of Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.08.20148742", "rel_title": "Disproportionate incidence of COVID-19 in African Americans correlates with dynamic segregation", @@ -1296533,53 +1299603,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.09.196618", - "rel_title": "A Strategy to Treat COVID-19 Disease with Targeted Delivery of Inhalable Liposomal Hydroxychloroquine: A Non-clinical Pharmacokinetic Study", - "rel_date": "2020-07-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.09.196618", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a newly identified pathogen causing coronavirus disease 2019 (COVID-19) pandemic. Hydroxychloroquine (HCQ), an antimalarial and anti-inflammatory drug, has been shown to inhibit SARS-CoV-2 infection in vitro and tested in clinical studies. However, lung concentration (6.7 {micro}g/mL) to predict the in vivo antiviral efficacy might not be achievable with the currently proposed oral dosing regimen. Further, a high cumulative doses of HCQ may raise concerns of systemic toxicity, including cardiotoxicity. Here, we described a non-clinical study to investigate the pharmacokinetics of a novel formulation of liposomal HCQ administrated by intratracheal (IT) instillation in Sprague-Dawley (SD) rats which achieved 129.4 {micro}g/g (Cmax) in the lung. Compared to unformulated HCQ administered intravenous (IV), liposomal HCQ with normalized dose showed higher ([~]30-fold) lung exposure, longer ([~]2.5-fold) half-life in lung, but lower blood exposure with [~]20% of Cmax and 74% of AUC and lower heart exposure with 24% of Cmax and 58% of AUC. In conclusion, the pharmacokinetics results in an animal model demonstrate the proof of concept that inhalable liposomal HCQ may provide clinical benefit and serve as a potential treatment for COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Tien-Tzu Tai", - "author_inst": "Taiwan Liposome Company" - }, - { - "author_name": "Tzung-Ju Wu", - "author_inst": "Taiwan Liposome Company" - }, - { - "author_name": "Huey-Dong Wu", - "author_inst": "National Taiwan University Hospital" - }, - { - "author_name": "Yi-Chen Tsai", - "author_inst": "Taiwan Liposome Company" - }, - { - "author_name": "Hui-Ting Wang", - "author_inst": "Taiwan Liposome Company" - }, - { - "author_name": "An-Min Wang", - "author_inst": "Taiwan Liposome Company" - }, - { - "author_name": "Sheue-Fang Shih", - "author_inst": "Taiwan Liposome Company" - }, - { - "author_name": "Yee-Chun Chen", - "author_inst": "National Taiwan University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.07.08.194613", "rel_title": "Inactivation analysis of SARS-CoV-2 by specimen transport media, nucleic acid extraction reagents, detergents and fixatives", @@ -1298530,6 +1301553,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.09.194639", + "rel_title": "Decline of humoral responses against SARS-CoV-2 Spike in convalescent individuals", + "rel_date": "2020-07-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.09.194639", + "rel_abs": "In the absence of effective vaccines and with limited therapeutic options, convalescent plasma is being collected across the globe for potential transfusion to COVID-19 patients. The therapy has been deemed safe and several clinical trials assessing its efficacy are ongoing. While it remains to be formally proven, the presence of neutralizing antibodies is thought to play a positive role in the efficacy of this treatment. Indeed, neutralizing titers of [≥]1:160 have been recommended in some convalescent plasma trials for inclusion. Here we performed repeated analyses at one-month interval on 31 convalescent individuals to evaluate how the humoral responses against the SARS-CoV-2 Spike, including neutralization, evolve over time. We observed that receptor-binding domain (RBD)-specific IgG slightly decreased between six and ten weeks after symptoms onset but RBD-specific IgM decreased much more abruptly. Similarly, we observed a significant decrease in the capacity of convalescent plasma to neutralize pseudoparticles bearing SARS-CoV-2 S wild-type or its D614G variant. If neutralization activity proves to be an important factor in the clinical efficacy of convalescent plasma transfer, our results suggest that plasma from convalescent donors should be recovered rapidly after symptoms resolution.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Guillaume Beaudoin-Bussi\u00e8res", + "author_inst": "CRCHUM" + }, + { + "author_name": "Annemarie Laumaea", + "author_inst": "Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Sai Priya Anand", + "author_inst": "CRCHUM / McGill" + }, + { + "author_name": "J\u00e9r\u00e9mie Pr\u00e9vost", + "author_inst": "CRCHUM / Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Romain Gasser", + "author_inst": "Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Guillaume Goyette", + "author_inst": "CRCHUM" + }, + { + "author_name": "Halima Medjahed", + "author_inst": "CRCHUM" + }, + { + "author_name": "Jos\u00e9ee Perreault", + "author_inst": "H\u00e9ma-Qu\u00e9bec" + }, + { + "author_name": "Tony Tremblay", + "author_inst": "H\u00e9ma-Qu\u00e9bec" + }, + { + "author_name": "Antoine Lewin", + "author_inst": "H\u00e9ma-Qu\u00e9bec" + }, + { + "author_name": "Laurie Gokool", + "author_inst": "CRCHUM" + }, + { + "author_name": "Chantal Morrisseau", + "author_inst": "CRCHUM" + }, + { + "author_name": "Philippe B\u00e9gin", + "author_inst": "CHU Ste-Justine" + }, + { + "author_name": "Cecile Tremblay", + "author_inst": "CRCHUM" + }, + { + "author_name": "Val\u00e9rie Martel-Laferri\u00e8re", + "author_inst": "CRCHUM" + }, + { + "author_name": "Jonathan Richard", + "author_inst": "Centre de Recherche du CHUM" + }, + { + "author_name": "Ren\u00e9e Bazin", + "author_inst": "H\u00e9ma-Qu\u00e9bec" + }, + { + "author_name": "Andr\u00e9s Finzi", + "author_inst": "CRCHUM, Universit\u00e9 de Montr\u00e9al" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.07.08.194456", "rel_title": "Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2", @@ -1298743,20 +1301853,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.07.09.193722", - "rel_title": "Comprehensive variant and haplotype landscapes of 50,500 global SARS-CoV-2 isolates and accelerating accumulation of country-private variant profiles", - "rel_date": "2020-07-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.09.193722", - "rel_abs": "Understanding the genetic etiology of COVID-19 requires a comprehensive understanding of the variant and haplotype landscape of all reported genomes of SARS-COV-2, the causative virus of the disease. Country-, state/region- and possibly even city-private variant profiles may contribute to varied disease exemplifications and fatality rates observed across the globe along with host factors such as age, ethnicity and comorbidity. The Childrens Hospital of Los Angeles (CHLA) COVID-19 Analysis Research Database (CARD) captures up-to-date fulllength SARS-CoV-2 sequences of ~50,500 isolates from GISAID, GenBank, CHLA Center for Personalized Medicine, and other sources (as of June 18, 2020). Among which, 49,637 isolates carry at least one variation from the reference genome NC_045512, a total of 6,070 variants and 2,513 haplotypes were detected in at least three isolates independently. Together, they constituted the most likely SARS-CoV-2 variant and haplotype landscapes world-wide currently.\n\nEvidence supporting positive (orf3a, orf8, S genes) and purifying (M gene) selections were detected, which warrants further investigation. Most interestingly, we identified 1,583 countryprivate variants from 10,238 isolates (20.6% overall) reported in 48 countries. 807 countryprivate haplotypes, defined as a haplotype shared by at least 5 isolates all of which came from the same country, were identified in in 8,656 isolates from 39 countries. United Kingdom, USA, and Australia had 464, 166 and 32 private haplotypes respectively, comprising 22.4%, 16.6% and 16.4% of the isolates from each country. Together with their descendent and private haplotypes with fewer members, 22,171 (45.8%) isolates carried country-private haplotypes globally. The percentage were 28.2-29.6% in January to March, and rapidly increased to 46.4% and 59.6% in April and May, co-occurring with global travel restrictions. The localization of the variant profiles appeared to be similarly accelerating from 14.2% in March and 28.4% in April to over 40% isolates carrying the country-private variants around May.\n\nIn summary, a common pattern is seen world-wide in COVID-19 in which at the onset of disease there appeared to be a significant number of SARS-CoV-2 variants that accumulate quickly and then begin to rapidly coalesce into distinct haplotypes. This may be the result of localized outbreaks due to factors such as multiple points viral introduction, geographic separation and the introduction of policies such as travel restriction, social distancing and quarantine, resulting in the emergence of country-private haplotypes.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.07.09.195008", "rel_title": "Air and surface contamination in non-health care settings among 641 environmental specimens of 39 COVID-19 cases", @@ -1300451,6 +1303547,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2020.07.07.20148304", + "rel_title": "COVID-19 Mortality Risk Assessment: An International Multi-Center Study", + "rel_date": "2020-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20148304", + "rel_abs": "BackgroundTimely identification of COVID-19 patients at high risk of mortality can significantly improve patient management and resource allocation within hospitals. This study seeks to develop and validate a data-driven personalized mortality risk calculator for hospitalized COVID-19 patients.\n\nMethodsDe-identified data was obtained for 3,927 COVID-19 positive patients from six independent centers, comprising 33 different hospitals. Demographic, clinical, and laboratory variables were collected at hospital admission. The COVID-19 Mortality Risk (CMR) tool was developed using the XGBoost algorithm to predict mortality. Its discrimination performance was subsequently evaluated on three validation cohorts.\n\nFindingsThe derivation cohort of 3,062 patients has an observed mortality rate of 26.84%. Increased age, decreased oxygen saturation ([≤] 93%), elevated levels of C-reactive protein ([≥] 130 mg/L), blood urea nitrogen ([≥] 18 mg/dL), and blood creatinine ([≥] 1.2 mg/dL) were identified as primary risk factors, validating clinical findings. The model obtains out-of-sample AUCs of 0.90 (95% CI, 0.87-0.94) on the derivation cohort. In the validation cohorts, the model obtains AUCs of 0.92 (95% CI, 0.88-0.95) on Seville patients, 0.87 (95% CI, 0.84-0.91) on Hellenic COVID-19 Study Group patients, and 0.81 (95% CI, 0.76-0.85) on Hartford Hospital patients. The CMR tool is available as an online application at covidanalytics.io/mortality_calculator and is currently in clinical use.\n\nInterpretationThe CMR model leverages machine learning to generate accurate mortality predictions using commonly available clinical features. This is the first risk score trained and validated on a cohort of COVID-19 patients from Europe and the United States.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, BioRxiv, MedRxiv, arXiv, and SSRN for peer-reviewed articles, preprints, and research reports in English from inception to March 25th, 2020 focusing on disease severity and mortality risk scores for patients that had been infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Earlier investigations showed promise at predicting COVID-19 disease severity using data at admission. However, existing work was limited by its data scope, either relying on a single center with rich clinical information or broader cohort with sparse clinical information. No analysis has leveraged Electronic Health Records data from an international multi-center cohort from both Europe and the United States.\n\nAdded value of this studyWe present the first multi-center COVID-19 mortality risk study that uses Electronic Health Records data from 3,062 patients across four different countries, including Greece, Italy, Spain, and the United States, encompassing 33 hospitals. We employed state-of-the-art machine learning techniques to develop a personalized COVID-19 mortality risk (CMR) score for hospitalized patients upon admission based on clinical features including vitals, lab results, and comorbidities. The model validates clinical findings of mortality risk factors and exhibits strong performance, with AUCs ranging from 0.81 to 0.92 across external validation cohorts. The model identifies increased age as a primary mortality predictor, consistent with observed disease trends and subsequent public health guidelines. Additionally, among the vital and lab values collected at admission, decreased oxygen saturation ([≤] 93%) and elevated levels of C-reactive protein ([≥] 130 mg/L), blood urea nitrogen ([≥] 18 mg/dL), blood creatinine ([≥] 1.2 mg/dL), and blood glucose ([≥]180 mg/dL) are highlighted as key biomarkers of mortality risk. These findings corroborate previous studies that link COVID-19 severity to hypoxemia, impaired kidney function, and diabetes. These features are also consistent with risk factors used in severity risk scores for related respiratory conditions such as community-acquired pneumonia.\n\nImplications of all the available evidenceOur work presents the development and validation of a personalized mortality risk score. We take a data-driven approach to derive insights from Electronic Health Records data spanning Europe and the United States. While many existing papers on COVID-19 clinical characteristics and risk factors are based on Chinese hospital data, the similarities in our findings suggest consistency in the disease characteristics across international cohorts. Additionally, our machine learning model offers a novel approach to understanding the disease and its risk factors. By creating a single comprehensive risk score that integrates various admission data components, the calculator offers a streamlined way of evaluating COVID-19 patients upon admission to augment clinical expertise. The CMR model provides a valuable clinical decision support tool for patient triage and care management, improving risk estimation early within admission, that can significantly affect the daily practice of physicians.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Dimitris Bertsimas", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Galit Lukin", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Luca Mingardi", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Omid Nohadani", + "author_inst": "Benefits Science Technologies" + }, + { + "author_name": "Agni Orfanoudaki", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Bartolomeo Stellato", + "author_inst": "Princeton University" + }, + { + "author_name": "Holly Wiberg", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Sara Gonzalez-Garcia", + "author_inst": "Institute of Biomedicine of Seville (IBIS), Virgen del Rocio University Hospital, CSIC, University of Seville" + }, + { + "author_name": "Carlos Luis Parra-Calderon", + "author_inst": "Institute of Biomedicine of Seville (IBIS), Virgen del Rocio University Hospital, CSIC, University of Seville" + }, + { + "author_name": "- The Hellenic COVID-19 Study Group", + "author_inst": "" + }, + { + "author_name": "Kenneth Robinson", + "author_inst": "Hartford HealthCare" + }, + { + "author_name": "Michelle Schneider", + "author_inst": "Hartford HealthCare" + }, + { + "author_name": "Barry Stein", + "author_inst": "Hartford HealthCare" + }, + { + "author_name": "Alberto Estirado", + "author_inst": "HM Hospitals" + }, + { + "author_name": "Lia a Beccara", + "author_inst": "Azienda Socio-Sanitaria Territoriale di Cremona" + }, + { + "author_name": "Rosario Canino", + "author_inst": "Azienda Socio-Sanitaria Territoriale di Cremona" + }, + { + "author_name": "Martina Dal Bello", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Federica Pezzetti", + "author_inst": "Azienda Socio-Sanitaria Territoriale di Cremona" + }, + { + "author_name": "Angelo Pan", + "author_inst": "Azienda Socio-Sanitaria Territoriale di Cremona" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.07.20148213", "rel_title": "No evidence of viral polymorphisms associated with Paediatric Inflammatory Multisystem Syndrome Temporally Associated With SARS-CoV-2 (PIMS-TS).", @@ -1300624,37 +1303811,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.07.20146902", - "rel_title": "Joint Detection of Serum IgM/IgG Antibody is An Important Key to Clinical Diagnosis of SARS-COV-2 Infection", - "rel_date": "2020-07-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20146902", - "rel_abs": "BackgroundThis study was aimed to investigate the application of SARS- COV-2 IgM and IgG antibodies in diagnosis of COVID-19 infection.\n\nMethodThis study enrolled a total of 178 patients at Huangshi Central Hospital from January to February, 2020. Among them, 68 patients were SARS-COV-2 infected confirmed with nucleic acid test (NAT) and CT imaging. 9 patients were in the suspected group (NAT negative) with fever and other respiratory symptoms. 101 patients were in the control group with other diseases and negative to SARS-COV-2 infection. After serum samples were collected, SARS-COV-2 IgG and IgM antibodies were tested by chemiluminescence immunoassay (CLIA) for all patients.\n\nResultsThe specificity of serum IgM and IgG antibodies to SARS-COV-2 were 99.01% (100/101) and 96.04% (97/101) respectively, and the sensitivity were 88.24% (60/68) and 97.06% (66/68) respectively. The combined detection rate of SARS-COV-2 IgM and IgG antibodies were 98.53% (67/68).\n\nConclusionCombined detection of serum SARS-COV-2 IgM and IgG antibodies had better sensitivity compared with single IgM or IgG test, which can be used as an important diagnostic tool for SARS-COV-2 infection and a screening tool of potential SARS-COV-2 carriers in clinics, hospitals and accredited scientific laboratory.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Fang Hu", - "author_inst": "Department of Clinical Laboratory, Huangshi Central Hospital, Edong Healthcare Group (Affiliated Hospital of Hubei Polytechnic University)" - }, - { - "author_name": "Xiaoling Shang", - "author_inst": "Department of Clinical Laboratory, Huangshi Central Hospital, Edong Healthcare Group (Affiliated Hospital of Hubei Polytechnic University)" - }, - { - "author_name": "Meizhou Chen", - "author_inst": "Department of Clinical Laboratory, Huangshi Central Hospital, Edong Healthcare Group (Affiliated Hospital of Hubei Polytechnic University)" - }, - { - "author_name": "Changliang Zhang", - "author_inst": "Department of Clinical Laboratory, Huangshi Central Hospital, Edong Healthcare Group (Affiliated Hospital of Hubei Polytechnic University)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.07.20148106", "rel_title": "Novel SARS-CoV-2 specific antibody and neutralization assays reveal wide range of humoral immune response during COVID-19", @@ -1302109,6 +1305265,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.06.182972", + "rel_title": "Unique transcriptional changes in coagulation cascade genes in SARS-CoV-2-infected lung epithelial cells: A potential factor in COVID-19 coagulopathies", + "rel_date": "2020-07-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.06.182972", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a global pandemic. In addition to the acute pulmonary symptoms of COVID-19 (the disease associated with SARS-CoV-2 infection), pulmonary and distal coagulopathies have caused morbidity and mortality in many patients. Currently, the molecular pathogenesis underlying COVID-19 associated coagulopathies are unknown. While there are many theories for the cause of this pathology, including hyper inflammation and excess tissue damage, the cellular and molecular underpinnings are not yet clear. By analyzing transcriptomic data sets from experimental and clinical research teams, we determined that changes in the gene expression of genes important in the extrinsic coagulation cascade in the lung epithelium may be important triggers for COVID-19 coagulopathy. This regulation of the extrinsic blood coagulation cascade is not seen with influenza A virus (IAV)-infected NHBEs suggesting that the lung epithelial derived coagulopathies are specific to SARS-Cov-2 infection. This study is the first to identify potential lung epithelial cell derived factors contributing to COVID-19 associated coagulopathy.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC=\"FIGDIR/small/182972v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (42K):\norg.highwire.dtl.DTLVardef@93cfb7org.highwire.dtl.DTLVardef@2a23c9org.highwire.dtl.DTLVardef@93623borg.highwire.dtl.DTLVardef@161e25_HPS_FORMAT_FIGEXP M_FIG C_FIG AUTHOR SUMMARYO_ST_ABSWhy was this study done?C_ST_ABSO_LISevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a global pandemic.\nC_LIO_LIIn addition to the acute pulmonary symptoms of COVID-19 (the disease associated with SARS-CoV-2 infection), pulmonary and distal coagulopathies have caused morbidity and mortality in many patients.\nC_LIO_LICurrently, the molecular pathogenesis underlying COVID-19 associated coagulopathies are unknown. Understanding the molecular basis of dysregulated blood coagulation during SARS-CoV-2 infection may help promote new therapeutic strategies to mitigate these complications in COVID-19 patients.\nC_LI\n\nWhat did the researchers do and find?O_LIWe analyzed three publicly available RNA sequencing datasets to identify possible molecular etiologies of COVID-19 associated coagulopathies. These data sets include sequencing libraries from clinically isolated samples of bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMCs) from SARS-CoV-2 positive patients and healthy controls. We also analyzed a publicly available RNA sequencing dataset derived from in vitro SARS-CoV-2 infected primary normal human bronchial epithelial (NHBE) cells and mock infected samples.\nC_LIO_LIPathway analysis of both NHBE and BALF differential gene expression gene sets. We found that SARS-CoV-2 infection induces the activation of the extrinsic blood coagulation cascade and suppression of the plasminogen activation system in both NHBEs and cells isolated from the BALF. PBMCs did not differentially express genes regulating blood coagulation.\nC_LIO_LIComparison with influenza A virus (IAV)-infected NHBEs revealed that the regulation of the extrinsic blood coagulation cascade is unique to SARS-CoV-2, and not seen with IAV infection.\nC_LI\n\nWhat do these findings mean?O_LIThe hyper-activation of the extrinsic blood coagulation cascade and the suppression of the plasminogen activation system in SARS-CoV-2 infected epithelial cells may drive diverse coagulopathies in the lung and distal organ systems.\nC_LIO_LIThe gene transcription pattern in SARS-CoV-2 infected epithelial cells is distinct from IAV infected epithelial cells with regards to the regulation of blood coagulation.\nC_LI", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ethan S. FitzGerald", + "author_inst": "Brown University" + }, + { + "author_name": "Amanda M. Jamieson", + "author_inst": "Brown University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.07.07.192005", "rel_title": "A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex", @@ -1302266,61 +1305445,6 @@ "type": "contradictory results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.07.07.192203", - "rel_title": "A rapidly adaptable biomaterial vaccine for SARS-CoV-2", - "rel_date": "2020-07-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.07.192203", - "rel_abs": "ABSTRACTThe global COVID-19 pandemic motivates accelerated research to develop safe and efficacious vaccines. To address this need, we leveraged a biomaterial vaccine technology that consists of mesoporous silica rods (MSRs) that provide a sustained release of granulocyte-macrophage colony-stimulating factor (GM-CSF) and adjuvants to concentrate and mature antigen-presenting cells at the vaccine site. Here we explored the humoral responses resulting from the use of monophosphoryl lipid A (MPLA) as the adjuvant and SARS-CoV-2 spike proteins S1, S2, the nucleocapsid (N) protein, and receptor binding domain (RBD) as the target antigens. The dose of antigen and impact of pre-manufacturing of vaccines as versus loading antigen just-in-time was explored in these studies. Single shot MSR vaccines induced rapid and robust antibody titers to the presented antigens, even without the use of a boost, and sera from vaccinated animals demonstrated neutralizing activity against a SARS-CoV-2 pseudovirus. Overall, these results suggest the MSR vaccine system may provide potent protective immunity when utilized to present SARS-CoV-2 antigens.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Fernanda Langellotto", - "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA" - }, - { - "author_name": "Benjamin T. Seiler", - "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA" - }, - { - "author_name": "Jingyou Yu", - "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA" - }, - { - "author_name": "Mark J. Cartwright", - "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA" - }, - { - "author_name": "Des White", - "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA" - }, - { - "author_name": "Chyenne Yeager", - "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA" - }, - { - "author_name": "Michael Super", - "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA" - }, - { - "author_name": "Edward J. Doherty", - "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA" - }, - { - "author_name": "Dan H. Barouch", - "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA. Ragon Institute of MGH, MIT, and " - }, - { - "author_name": "David J. Mooney", - "author_inst": "Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, 02115, USA. Harvard John A. Paulson School of Engineering and A" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.07.07.191973", "rel_title": "Spike protein fusion loop controls SARS-CoV-2 fusogenicity and infectivity", @@ -1303351,6 +1306475,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.07.06.20147751", + "rel_title": "COVID-19 presenting as anosmia and dysgeusia in New York City emergency departments, March - April, 2020", + "rel_date": "2020-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147751", + "rel_abs": "BackgroundIncreasing evidence has been emerging of anosmia and dysgeusia as frequently reported symptoms in COVID-19. Improving our understanding of these presenting symptoms may facilitate the prompt recognition of the disease in emergency departments and prevent further transmission.\n\nMethodsWe examined a cross-sectional cohort using New York City emergency department syndromic surveillance data for March and April 2020. Emergency department visits for anosmia and/or dysgeusia were identified and subsequently matched to the Electronic Clinical Laboratory Reporting System to determine testing results for SARS-CoV-2.\n\nResultsOf the 683 patients with anosmia and/or dysgeusia included, SARS-CoV-2 testing was performed for 232 (34%) and 168 (72%) were found to be positive. Median age of all patients presenting with anosmia and/or dysgeusia symptoms was 38, and 54% were female. Anosmia and/or dysgeusia was the sole complaint of 158 (23%) patients, of whom 35 were tested for SARS-CoV-2 and 23 (66%) were positive. While the remaining patients presented with at least one other symptom, nearly half of all patients (n=334, 49%) and more than a third of those who tested positive (n=62, 37%) did not have any of the CDC-established symptoms used for screening of COVID-19 such as fever, cough, shortness of breath, or sore throat.\n\nConclusions and RelevanceAnosmia and/or dysgeusia have been frequent complaints among patients presenting to emergency departments during the COVID-19 pandemic, and, while only a small proportion of patients ultimately underwent testing for SARS-CoV-19, the majority of patients tested have been positive. Anosmia and dysgeusia likely represent underrecognized symptoms of COVID-19 but may have important future implications in disease diagnosis and surveillance.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tina Z. Wang", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jessica Sell", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Don Weiss", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Ramona Lall", + "author_inst": "New York City Department of Health and Mental Hygiene" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.06.20147702", "rel_title": "COVID-19 screening strategies that permit the safe re-opening of college campuses", @@ -1303460,37 +1306615,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2020.07.07.20147934", - "rel_title": "Chest X-Ray Has Poor Diagnostic Accuracy and Prognostic Significance in COVID-19: A Propensity Matched Database Study", - "rel_date": "2020-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20147934", - "rel_abs": "ObjectivesTo identify the diagnostic accuracy of common imaging modalities, chest X-ray (CXR) and computed tomography (CT) for diagnosis of COVID-19 in the general emergency population in the UK and to find the association between imaging features and outcomes in these patients.\n\nDesignRetrospective analysis of electronic patient records\n\nSettingTertiary academic health science centre and designated centre for high consequence infectious diseases in London, UK.\n\nParticipants1,198 patients who attended the emergency department with paired RT-PCR swabs for SARS-CoV 2 and CXR between 16th March and 16th April 2020\n\nMain outcome measuresSensitivity and specificity of CXR and CT for diagnosis of COVID-19 using the British Society of Thoracic Imaging reporting templates. Reference standard was any reverse transcriptase polymerase chain reaction (RT-PCR) positive naso-oropharyngeal swab within 30 days of attendance. Odds ratios of CXR in association with vital signs, laboratory values and 30-day outcomes were calculated.\n\nResultsSensitivity and specificity of CXR for COVID-19 diagnosis were 0.56 (95% CI 0.51-0.60) and 0.60 (95% CI 0.54-0.65), respectively. For CT scans these were 0.85 (95% CI 0.79-0.90) and 0.50 (95% CI 0.41-0.60), respectively. This gave a statistically significant mean increase in sensitivity with CT compared with CXR, of 29% (95% CI 19%-38%, p<0.0001). Specificity was not significantly different between the two modalities.\n\nChest X-ray findings were not statistically significantly or clinical meaningfully associated with vital signs, laboratory parameters or 30-day outcomes.\n\nConclusionsComputed tomography has substantially improved diagnostic performance over CXR in COVID-19. CT should be strongly considered in the initial assessment for suspected COVID-19. This gives potential for increased sensitivity and considerably faster turnaround time, where capacity allows and balanced against excess radiation exposure risk.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Aditya Borakati", - "author_inst": "Royal Free Hospital, London" - }, - { - "author_name": "Adrian Perera", - "author_inst": "Royal Free Hospital, London, UK" - }, - { - "author_name": "James Johnson", - "author_inst": "Royal Free Hospital, London, UK" - }, - { - "author_name": "Tara Sood", - "author_inst": "Royal Free Hospital, London, UK" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2020.07.06.20140285", "rel_title": "Estimating the establishment of local transmission and the cryptic phase of the COVID-19 pandemic in the USA", @@ -1304773,6 +1307897,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.03.20145797", + "rel_title": "Dengue antibodies can cross-react with SARS-CoV-2 and vice versa-Antibody detection kits can give false-positive results for both viruses in regions where both COVID-19 and Dengue co-exist", + "rel_date": "2020-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145797", + "rel_abs": "Five of thirteen Dengue antibody-positive serum samples, dated 2017 (pre-dating the COVID-19 outbreak) produced false-positive results in SARS-CoV-2 IgG/IgM rapid strip tests. Our results emphasize the importance of NAT and/or virus antigen tests to complement sero-surveillance for definitive diagnosis of COVID-19/Dengue in regions where both viruses are co-endemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Himadri Nath", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "Abinash Mallick", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "Subrata Roy", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "Soumi Sukla", + "author_inst": "NIPER, Kolkata" + }, + { + "author_name": "Keya Basu", + "author_inst": "IPGMER, Kolkata (Department of Pathology)" + }, + { + "author_name": "Abhishek De", + "author_inst": "Calcutta National Medical College, Kolkata (Department of Dermatology)" + }, + { + "author_name": "Subhajit Biswas", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.29.20131367", "rel_title": "Evaluation of Viasure SARS-CoV-2 RT-qPCR kit (CerTest Biotec) using CDC FDA EUA RT-qPCR kit as a gold standard.", @@ -1304854,41 +1308021,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.05.20146324", - "rel_title": "Study of the Dependence of Effective Reproduction Number of COVID-19 on the Temperature and Humidity: A Case Study with the Indian States", - "rel_date": "2020-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.05.20146324", - "rel_abs": "Coronavirus Disease 2019 (COVID-19) started in Wuhan province of China in November 2019 and within a short time, it was declared as a worldwide pandemic by the World Health Organisation due to the very fast worldwide spread of the virus. There were a few studies that look for the correlation with infected individuals and different environmental parameters using early data of COVID-19 but there was no study that deal with the variation of effective reproduction number and environmental factors. Effective reproduction number is the driving parameter of the spread of a pandemic and it is important to study the effect of various environmental factors on effective reproduction numbers to understand the effect of those factors on the spread of the virus. We have used time-dependent models to investigate the variation of different time-dependent driving parameters of COVID-19 like effective reproduction number and contact rate using data from India as a test case. India is a large population country that was highly affected due to the COVID-19 pandemic and has a wide span of different temperature and humidity regions and is ideal for such study. We have studied the impact of temperature and humidity on the spread of the virus of different Indian states using time-dependent epidemiological models SIRD, and SEIRD for a long time scale. We used a linear regression method to look for any dependency between the effective reproduction number with the relative humidity, absolute humidity, and temperature. The effective reproduction number showed a negative correlation with both relative and absolute humidity for most of the Indian states, which are statistically significant. This implies that relative and absolute humidity may have an important role in the variation of effective reproduction numbers. There was no conclusive evidence of a correlation between effective reproduction numbers and average air temperature.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Souvik Manik", - "author_inst": "Midnapore City College" - }, - { - "author_name": "Manoj Mandal", - "author_inst": "Midnapore City College" - }, - { - "author_name": "Sabyasachi Pal", - "author_inst": "Midnapore City College" - }, - { - "author_name": "Subhradeep Patra", - "author_inst": "Midnapore City College" - }, - { - "author_name": "Suman Acharya", - "author_inst": "Midnapore City College" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.01.20143214", "rel_title": "High frequency of cerebrospinal fluid autoantibodies in COVID-19 patients with neurological symptoms", @@ -1305979,6 +1309111,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.02.20143032", + "rel_title": "Characterization of Microbial Co-infections in the Respiratory Tract of hospitalized COVID-19 patients", + "rel_date": "2020-07-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20143032", + "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of Coronavirus disease 2019 (COVID-19). However, microbial composition of the respiratory tract and other infected tissues, as well as their possible pathogenic contributions to varying degrees of disease severity in COVID-19 patients remain unclear.\n\nMethodBetween January 27 and February 26, 2020, serial clinical specimens (sputum, nasal and throat swab, anal swab and feces) were collected from a cohort of hospitalized COVID-19 patients, including 8 mildly and 15 severely ill patients (requiring ICU admission and mechanical ventilation), in the Guangdong province, China. Total RNA was extracted and ultra-deep metatranscriptomic sequencing was performed in combination with laboratory diagnostic assays. Co-infection rates, the prevalence and abundance of microbial communities in these COVID-19 patients were determined.\n\nFindingsNotably, respiratory microbial co-infections were exclusively found in 84.6% of severely ill patients (11/13), among which viral and bacterial co-infections were detected by sequencing in 30.8% (4/13) and 69.2% (9/13) of the patients, respectively. In addition, for 23.1% (3/13) of the patients, bacterial co-infections with Burkholderia cepacia complex (BCC) and Staphylococcus epidermidis were also confirmed by bacterial culture. Further, a time-dependent, secondary infection of B. cenocepacia with expressions of multiple virulence genes in one severely ill patient was demonstrated, which might be the primary cause of his disease deterioration and death one month after ICU admission.\n\nInterpretationOur findings identified distinct patterns of co-infections with SARS-CoV-2 and various respiratory pathogenic microbes in hospitalized COVID-19 patients in relation to disease severity. Detection and tracking of BCC-associated nosocomial infections are recommended to improve the pre-emptive treatment regimen and reduce fatal outcomes of hospitalized patients infected with SARS-CoV-2.\n\nFundingNational Science and Technology Major Project of China, National Major Project for Control and Prevention of Infectious Disease in China, the emergency grants for prevention and control of SARS-CoV-2 of Ministry of Science and Technology and Guangdong province, Guangdong Provincial Key Laboratory of Genome Read and Write, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, and Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Huanzi Zhong", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China. Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denma" + }, + { + "author_name": "Yanqun Wang", + "author_inst": "Guangzhou Institute of Respiratory Health" + }, + { + "author_name": "Zhun Shi", + "author_inst": "BGI-Shenzhen,Shenzhen 518083,China" + }, + { + "author_name": "Lu Zhang", + "author_inst": "Institute of Infectious disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China 510060." + }, + { + "author_name": "Huahui Ren", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Weiqun He", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Zhaoyong Zhang", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Airu Zhu", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Jingxian Zhao", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Fei Xiao", + "author_inst": "Department of Infectious Diseases, Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imag" + }, + { + "author_name": "Fangming Yang", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Tianzhu Liang", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Feng Ye", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Bei Zhong", + "author_inst": "The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong, China" + }, + { + "author_name": "Shicong Ruan", + "author_inst": "Yangjiang People's Hospital, Yangjiang, Guangdong, China" + }, + { + "author_name": "Mian Gan", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Jiahui Zhu", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Fang Li", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Fuqiang Li", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Daxi Wang", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Jiandong Li", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Peidi Ren", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Shida Zhu", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Huanming Yang", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Jian Wang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Karsten Kristiansen", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Hein M Tun", + "author_inst": "HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China." + }, + { + "author_name": "Weijun Chen", + "author_inst": "BGI PathoGenesis Pharmaceutical Technology, Shenzhen, China." + }, + { + "author_name": "Nanshan Zhong", + "author_inst": "State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University" + }, + { + "author_name": "Xun Xu", + "author_inst": "BGI-shenzhen" + }, + { + "author_name": "Yi-min Li", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Junhua LI", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Jincun Zhao", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.02.20145052", "rel_title": "Modeling COVID-19 for lifting non-pharmaceutical interventions", @@ -1306092,33 +1309371,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.07.03.20145953", - "rel_title": "Optimal sample pooling: an efficient tool against SARS-CoV-2", - "rel_date": "2020-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145953", - "rel_abs": "The SARS-CoV-2 pandemic situation has presented multiple imminent challenges to the nations around the globe. While health agencies around the world are exploring various options to contain the spread of this fatal viral infection, multiple strategies and guidelines are being issued to boost the fight against the disease. Identifying and isolating infected individuals at an early phase of the disease has been a very successful approach to stop the chain of transmission. But this approach faces a practical challenge of limited resources. Sample pooling solves this enigma by significantly improving the testing capacity and result turn around time while using no extra resources. However, the general sample pooling method also has the scope of significant improvements. This article describes a process to further optimize the resources with optimal sample pooling. This is a user-friendly technique, scalable on a national or international scale. A mathematical model has been built and validated for its performance using clinical data.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rakesh Sharma", - "author_inst": "Comofi Medtech Private Limited" - }, - { - "author_name": "Saurabh Goyal", - "author_inst": "American Express, Gurugram, India" - }, - { - "author_name": "Priti Bist", - "author_inst": "American Express, Gurugram, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.07.03.20145839", "rel_title": "The Impact of COVID-19 on Adjusted Mortality Risk in Care Homes for Older Adults in Wales, United Kingdom: A retrospective population-based cohort study for mortality in 2016-2020", @@ -1307401,6 +1310653,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.03.20145672", + "rel_title": "A Novel Approach for Estimating the Final Outcome of Global Diseases Like COVID-19", + "rel_date": "2020-07-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145672", + "rel_abs": "The existence of a universal law which maps the bell curve of daily cases to a sigmoid curve for cumulative ones is used for making robust estimations about the final outcome of a disease. Computations of real time effective reproduction rate are presented and its limited usefulness is derived. After using methods ESE & EDE we are able to find the inflection point of the cumulative curve under consideration and study its time evolution. Since mortality processes tend to follow a Gompertz distribution, we apply the properties of it and introduce novel estimations for both the time remaining after inflection time and the capacity of the curve. Special properties of sigmoid curves are used for assessing the quality of estimation and as indices for the cycle completion. Application is presented for COVID-19 evolution for most affected countries and the World.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Demetris T Christopoulos", + "author_inst": "National and Kapodistrian University of Athens" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.03.20146167", "rel_title": "Serial interval, basic reproduction number and prediction of COVID-19 epidemic size in Jodhpur, India", @@ -1307518,57 +1310789,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.03.20145607", - "rel_title": "The mental health impact of the covid-19 pandemic onhealthcare workers, and interventions to help them: a rapid systematic review", - "rel_date": "2020-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145607", - "rel_abs": "BackgroundThe covid-19 pandemic has heavily burdened, and in some cases overwhelmed, healthcare systems throughout the world. Healthcare workers are not only at heightened risk of infection, but also of adverse mental health outcomes. Identification of organizational, collegial and individual risk and resilience factors impacting the mental health of healthcare workers are needed to inform preparedness planning and sustainable response.\n\nMethodsWe performed a rapid systematic review to identify, assess and summarize available research on the mental health impact of the covid-19 pandemic on healthcare workers. On 11 May 2020, we utilized the Norwegian Institute of Public Healths Live map of covid-19 evidence, the visualization of a database of 20,738 screened studies, to identify studies for inclusion. We included studies reporting on any type of mental health outcome in any type of healthcare workers during the pandemic. We described interventions reported by the studies, and narratively summarized mental health-related outcomes, as study heterogeneity precluded meta-analysis. We assessed study quality using design-specific instruments.\n\nResultsWe included 59 studies, reporting on a total of 54,707 healthcare workers. The prevalence of general psychological distress across the studies ranged from 7-97% (median 37%), anxiety 9-90% (median 24%), depression 5-51% (median 21%), and sleeping problems 34-65% (median 37%). Seven studies reported on implementing mental health interventions, and most focused on individual symptom reduction, but none reported on effects of the interventions. In most studies, healthcare workers reported low interest in and use of professional help, and greater reliance on social support and contact with family and friends. Exposure to covid-19 was the most commonly reported correlate of mental health problems, followed by female gender, and worry about infection or about infecting others. Social support correlated with less mental health problems.\n\nDiscussionHealthcare workers in a variety of fields, positions, and exposure risks are reporting anxiety, depression, sleep problems, and distress during the covid-19 pandemic, but most studies do not report comparative data on mental health symptoms. before the pandemic. There seems to be a mismatch between risk factors for adverse mental health outcomes among healthcare workers in the current pandemic and their needs and preferences, and the individual psychopathology focus of current interventions. Efforts to help healthcare workers sustain healthy relationships to colleagues, family and friends over time may be paramount to safeguard what is already an important source of support during the prolonged crisis. Expanding interventions focus to incorporate organizational, collegial and family factors to support healthcare workers responding to the pandemic could improve acceptability and efficacy of interventions.\n\nOtherThe protocol for this review is available online. No funding was received.\n\nO_TEXTBOXSummary boxO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIDuring viral outbreaks such as covid-19, healthcare providers are at increased risk of infection and negative physical and mental health outcomes\nC_LIO_LICovid-19 is a particular challenge to healthcare systems and workers\nC_LI\n\nWhat this study addsO_LIHealthcare workers mental health problems correlate with organizational factors such as workload and exposure to covid-19 patients\nC_LIO_LIHealthcare workers are more interested in occupational protection, rest, and social support than in professional psychological help\nC_LIO_LIInterventions focus more on addressing individual psychopathology, which points towards a mismatch between what workers want and need, and the services available to them\nC_LI\n\nC_TEXTBOX", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Ashley Elizabeth Muller", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Elisabet Vivianne Hafstad", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Jan Peter William Himmels", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Geir Smedslund", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Signe Flottorp", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Synne Stensland", - "author_inst": "Norwegian Centre for Violence and Traumatic Stress Studies, Oslo, Norway, and Research and Communication Unit for Musculoskeletal Health (FORMI), Division of Cl" - }, - { - "author_name": "Stijn Stroobants", - "author_inst": "Humanitarian Services, Belgian Red Cross, Mechelen, Belgium" - }, - { - "author_name": "Stijn Van de Velde", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Gunn Elisabeth Vist", - "author_inst": "Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.07.03.20145664", "rel_title": "Battle with COVID-19 Under Partial to Zero Lockdowns in India", @@ -1308967,6 +1312187,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.01.20129882", + "rel_title": "Retrospective Clinical Evaluation of Four Lateral Flow Assays for the Detection of SARS-CoV-2 Antibodies", + "rel_date": "2020-07-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.01.20129882", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is a potentially life-threatening respiratory infection caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), for which numerous serologic assays are available. In a CLIA laboratory setting, we used a retrospective sample set (n = 457) to evaluate two lateral flow immunoassays (LFIAs; two iterations of Rapid Response COVID-19 Test Cassette, BTNX Inc.) and a subset of to evaluate SARS-COV-2 IgG/IgM Rapid Test, ACON Laboratories (n = 200); and Standard Q COVID-19 IgM/IgG Duo, SD BIOSENSOR (n = 155) for their capacity to detect of SARS-CoV-2 IgG. In a cohort of primarily hospitalized patients with RT-PCR confirmed COVID-19, the BTNX assays demonstrated 95% and 92% agreement with the Abbott SARS-CoV-2 IgG assay and sensitivity was highest at [≥] 14 days from symptom onset [BTNX kit 1, 95%; BTNX kit 2, 91%]. ACON and SD assays demonstrated 99% and 100% agreement with the Abbott assay at [≥] 14 days from symptom onset. Specificity was measured using 74 specimens collected prior to SARS-CoV-2 circulation in the United States and 31 \"cross-reactivity challenge\" specimens, including those from patients with a history of seasonal coronavirus infection and was 98% for BTNX kit 1 and ACON and 100% for BTNX kit 2 and SD. Taken with data from EUA assays, these results suggest that LFIAs may provide adequate results for rapid detection of SARS-CoV-2. Replicating these results in fingerstick blood in outpatient populations, would further support the possibility that LFIAs may be useful to increase access to serologic testing", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kathrine McAulay", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew Bryan", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Alexander L. Greninger", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Francisca Grill", + "author_inst": "Arizona State University" + }, + { + "author_name": "Douglas F. Lake", + "author_inst": "Arizona State University" + }, + { + "author_name": "Erin J. Kaleta", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Thomas E Grys", + "author_inst": "Mayo Clinic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.01.20144667", "rel_title": "Numerical Analysis of Disastrous Effect of Reopening Too Soon in Georgia, USA", @@ -1309088,41 +1312351,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.30.20140715", - "rel_title": "Indication for SARS-CoV-2 serology: first month follow-up", - "rel_date": "2020-07-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20140715", - "rel_abs": "SARS-CoV-2 detection is mainly performed by RT-PCR but recently serological tests were made available. A first one month follow-up of the SARS-CoV-2 serology records was performed in our laboratory to precise the diversity and proportion of the SARS-CoV-2 serology test indications and to identify new valid indications (meningoencephalitis, vasculitis, ...)", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Alix T. Coste", - "author_inst": "Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland" - }, - { - "author_name": "Katia Jaton", - "author_inst": "Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland" - }, - { - "author_name": "Matthaios Papadimitriou-Olivgeris", - "author_inst": "Service of Hospital Preventive Medicine, and Service of Infectious Diseases, Lausanne University Hospital, Switzerland" - }, - { - "author_name": "Antony Croxatto", - "author_inst": "Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland" - }, - { - "author_name": "Gilbert Greub", - "author_inst": "Institute of Microbiology, and Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.02.20145177", "rel_title": "SARS-CoV-2 Detection in Sewage in Santiago, Chile - Preliminary results.", @@ -1310521,6 +1313749,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.30.20143651", + "rel_title": "Identifying main and interaction effects of risk factors to predict intensive care admission in patients hospitalized with COVID-19: a retrospective cohort study in Hong Kong", + "rel_date": "2020-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20143651", + "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) has become a pandemic, placing significant burdens on the healthcare systems. In this study, we tested the hypothesis that a machine learning approach incorporating hidden nonlinear interactions can improve prediction for Intensive care unit (ICU) admission.\n\nMethodsConsecutive patients admitted to public hospitals between 1st January and 24th May 2020 in Hong Kong with COVID-19 diagnosed by RT-PCR were included. The primary endpoint was ICU admission.\n\nResultsThis study included 1043 patients (median age 35 (IQR: 32-37; 54% male). Nineteen patients were admitted to ICU (median hospital length of stay (LOS): 30 days, median ICU LOS: 16 days). ICU patients were more likely to be prescribed angiotensin converting enzyme inhibitors/angiotensin receptor blockers, anti-retroviral drugs lopinavir/ritonavir and remdesivir, ribavirin, steroids, interferon-beta and hydroxychloroquine. Significant predictors of ICU admission were older age, male sex, prior coronary artery disease, respiratory diseases, diabetes, hypertension and chronic kidney disease, and activated partial thromboplastin time, red cell count, white cell count, albumin and serum sodium. A tree-based machine learning model identified most informative characteristics and hidden interactions that can predict ICU admission. These were: low red cells with 1) male, 2) older age, 3) low albumin, 4) low sodium or 5) prolonged APTT. A five-fold cross validation confirms superior performance of this model over baseline models including XGBoost, LightGBM, random forests, and multivariate logistic regression.\n\nConclusionsA machine learning model including baseline risk factors and their hidden interactions can accurately predict ICU admission in COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jiandong Zhou", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Gary Tse", + "author_inst": "Tianjin Medical University" + }, + { + "author_name": "Sharen Lee", + "author_inst": "Laboratory of Cardiovascular Physiology" + }, + { + "author_name": "Tong Liu", + "author_inst": "Tianjin Medical University" + }, + { + "author_name": "William KK Wu", + "author_inst": "LKS Institute of Health Sciences" + }, + { + "author_name": "zhidong cao", + "author_inst": "Institute of Automation, Chinese Academy of Sciences" + }, + { + "author_name": "Dajun Zeng", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Ian CK Wong", + "author_inst": "HKU" + }, + { + "author_name": "Qingpeng Zhang", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Bernard MY Cheung", + "author_inst": "HKU" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.01.20144030", "rel_title": "Broad phenotypic alterations and potential dysfunctions of lymphocytes in COVID-19 recovered individuals", @@ -1310742,33 +1314025,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.01.20144279", - "rel_title": "Using the infection fatality rate to predict the evolution of Covid-19 in Brazil", - "rel_date": "2020-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.01.20144279", - "rel_abs": "In this work we are going to use estimates of Infection Fatality Rate (IFR) for Covid-19 in order to predict the evolution of Covid-19 in Brazil. To this aim, we are going to fit the parameters of the SIR model using the official deceased data available by governmental agencies. Furthermore, we are going to analyse the impact of social distancing policies on the transmission parameters.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Moiseis Santos Cecconello", - "author_inst": "Federal University of Mato Grosso" - }, - { - "author_name": "Geraldo L. Diniz", - "author_inst": "Federal University at Mato Grosso" - }, - { - "author_name": "Eveliny Barroso Silva", - "author_inst": "Federal University of Mato Grosso" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.30.20143560", "rel_title": "Lockdown measures and relative changes in the age-specific incidence of SARS-CoV-2 in Spain", @@ -1312083,6 +1315339,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.23.20132522", + "rel_title": "The advantages of the simplest pandemic models", + "rel_date": "2020-07-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20132522", + "rel_abs": "As a pandemic of coronavirus spreads across the globe, people debate policies to mitigate its severity. Many complex, highly detailed models have been developed to help policy setters make better decisions. However, the basis of these models is unlikely to be understood by non-experts.\n\nWe describe the advantages of simple models for covid-19. We say a model is \"simple\" if its only parameter is the rate of contact between people in the population. This contact rate can vary over time, depending on choices by policy setters. Such models can be understood by a broad audience, and thus can be helpful in explaining the policy decisions to the public. They can be used to evaluate outcomes of different policy strategies. However, simple models have a disadvantage when dealing with inhomogeneous populations.\n\nTo augment the power of a simple model to evaluate complicated situations, we add what we call \"satellite\" equations that do not change the original model. For example, with the help of a satellite equation, one could know what his/her chance is of remaining uninfected through the end of epidemic. Satellite equations can model the effect of the epidemic on high-risk individuals, or death rates, or on nursing homes, and other isolated populations.\n\nTo compare simple models with complex models, we introduce our \"slightly complex\" Model J. We find the conclusions of simple and complex models can be quite similar. But, for each added complexity, a modeler may have to choose additional parameter values describing who will infect whom under what conditions, choices for which there is often little rationale but that can have a big impact on predictions. Our simulations suggest that the added complexity offers little predictive advantage.\n\nAuthor SummaryThere is a large variety of available data about the coronavirus pandemic, but we still lack data about some important factors. Who is likely to infect whom and under what conditions and how long after becoming infected? These factors are the essence of transmission dynamics. Two groups using identical complex models can be expected to make different predictions simply because they make different choices for such transmission parameters in the model. The audience has no way to choose between their predictions. We explain how simple models can be used to answer complex questions by adding what we call satellite equations, addressing questions involving age groups, death rates, and likelihood of transmission to nursing homes and to uninfected, isolated populations. Simple models are ideal for seeing what kinds of interventions are needed to achieve goals of policy setters.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sana Jahedi", + "author_inst": "University of New Brunswick" + }, + { + "author_name": "James Yorke", + "author_inst": "University of Maryland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.24.20138644", "rel_title": "Strong Correlation Between Prevalence of Severe Vitamin D Deficiency and Population Mortality Rate from COVID-19 in Europe", @@ -1312196,53 +1315475,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.26.20140699", - "rel_title": "Superior anticoagulation strategies for renal replacement therapy in critically ill patients with COVID-19: a cohort study", - "rel_date": "2020-07-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.26.20140699", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) patients who are admitted to intensive care units (ICU) have a high risk of requiring renal replacement therapy (RRT) due to acute kidney injury (AKI). Concomitantly, COVID-19 patients exhibit a state of hypercoagulability that can affect circuit lifespan. An optimal anticoagulation strategy is therefore needed in order to maintain circuit patency and therapeutic efficiency of RRT.\n\nMethodsRetrospective single-centre cohort study on 71 critically ill COVID-19 patients at the University of Freiburg Medical Center. Included were all patients aged 18 years and older with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection that were admitted to ICU between February 26 and May 21, 2020. We collected data on the COVID-19 disease course, AKI, RRT, thromboembolic events and anticoagulation. Primary outcome of the study was the effect of different anticoagulation strategies during RRT on extracorporeal circuit lifespans.\n\nResultsAnticoagulation during continuous veno-venous haemodialysis (CVVHD) was performed with unfractionated heparin (UFH) or citrate. Mean treatment time in the UFH group was 21.3h (SEM: {+/-}5.6h). Mean treatment time in the citrate group was 45.6h (SEM: {+/-}2.7h). Citrate anticoagulation prolonged treatment duration significantly by 24.4h (p=0.0014). Anticoagulation during sustained low-efficiency daily dialysis (SLEDD) was performed with UFH, argatroban or low molecular weight heparin (LMWH). Mean dialysis time with UFH was 8.1h (SEM: {+/-}1.3h), argatroban 8.0h (SEM: {+/-}0.9h) and LMWH 11.8h (SEM: {+/-}0.5h). Compared to UFH and argatroban, LMWH significantly prolonged treatment times by 3.7h (p=0.0082) and 3.8h (p=0.0024), respectively.\n\nConclusionsUFH fails to prevent early clotting events in dialysis circuits. For patients, who do not require an effective systemic anticoagulation, regional citrate dialysis is the most effective strategy in our cohort. For patients, who require an effective systemic anticoagulation treatment, the usage of LMWH results in the longest circuit life spans.\n\nFundingBerta-Ottenstein-Programme for Clinician Scientists, Faculty of Medicine, University of Freiburg, Germany. Else Kroner-Fresenius-Stiftung, Bad Homburg, Germany. Deutsche Forschungsgemeinschaft, Bonn, Germany.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Frederic Arnold", - "author_inst": "Department of Medicine IV: Nephrology and Primary Care, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Lukas Westermann", - "author_inst": "Department of Medicine IV: Nephrology and Primary Care, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Siegbert Rieg", - "author_inst": "Department of Medicine II: Division of Infectious Diseases, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germ" - }, - { - "author_name": "Elke Neumann-Haefelin", - "author_inst": "Department of Medicine IV: Nephrology and Primary Care, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Paul Biever", - "author_inst": "Department of Medicine III: Interdisciplinary Medical Intensive Care, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Frei" - }, - { - "author_name": "Gerd Walz", - "author_inst": "Department of Medicine IV: Nephrology and Primary Care, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Johannes Kalbhenn", - "author_inst": "Department of Anesthesiology and Critical Care, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Yakup Tanriver", - "author_inst": "Department of Medicine IV: Nephrology and Primary Care, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2020.06.29.20143131", "rel_title": "Social Distancing Causally Impacts the Spread of SARS-CoV-2: A U.S. Nationwide Event Study", @@ -1313885,6 +1317117,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.30.181297", + "rel_title": "If the link missed\uff1aCould inflammatory skin disorders with barrier dysfunction increase the risk of COVID-19?", + "rel_date": "2020-07-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.30.181297", + "rel_abs": "Since the end of 2019, COVID-19 pandemic caused by the SARS-CoV-2 emerged globally. The angiotensin-converting enzyme 2 (ACE2) on the cell surface is crucial for SARS-COV-2 entering into the cells. We use SARS-COV-2 pseudo virus and humanized ACE2 mice to mimic the possible transmitting of SARS-COV-2 through skin based on the data we found that skin ACE2 level is associated with skin pre-existing cutaneous conditions in human and mouse models and inflammatory skin disorders with barrier dysfunction increased the penetration of topical FITC conjugated spike protein into the skin. Our study indicated the possibility that the pre-existing cutaneous conditions could increase the risk for SARS-COV-2 infection.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC=\"FIGDIR/small/181297v4_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (33K):\norg.highwire.dtl.DTLVardef@14cef60org.highwire.dtl.DTLVardef@1f78c65org.highwire.dtl.DTLVardef@1224834org.highwire.dtl.DTLVardef@1b27475_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Qiannan Xu", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Lihong Chen", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Li Zhang", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Mengyan Hu", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Xiaopan Wang", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Qi Yang", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Yunchen Le", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Feng Xue", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Xia Li", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Jie Zheng", + "author_inst": "Shanghai Ruijin Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.06.24.20134288", "rel_title": "A retrospective study evaluating efficacy and safety of compassionate use of tocilizumab in 13 patients with severe-to-critically ill COVID-19: analysis of well-responding cases and rapidly-worsening cases after tocilizumab administration", @@ -1314102,105 +1317389,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.30.175778", - "rel_title": "Single-cell transcriptional atlas of the Chinese horseshoe bat (Rhinolophus sinicus) provides insight into the cellular mechanisms which enable bats to be viral reservoirs", - "rel_date": "2020-06-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.30.175778", - "rel_abs": "Bats are a major \"viral reservoir\" in nature and there is a great interest in not only the cell biology of their innate and adaptive immune systems, but also in the expression patterns of receptors used for cellular entry by viruses with potential cross-species transmission. To address this and other questions, we created a single-cell transcriptomic atlas of the Chinese horseshoe bat (Rhinolophus sinicus) which comprises 82,924 cells from 19 organs and tissues. This atlas provides a molecular characterization of numerous cell types from a variety of anatomical sites, and we used it to identify clusters of transcription features that define cell types across all of the surveyed organs. Analysis of viral entry receptor genes for known zoonotic viruses showed cell distribution patterns similar to that of humans, with higher expression levels in bat intestine epithelial cells. In terms of the immune system, CD8+ T cells are in high proportion with tissue-resident memory T cells, and long-lived effector memory nature killer (NK) T-like cells (KLRG1, GZMA and ITGA4 genes) are broadly distributed across the organs. Isolated lung primary bat pulmonary fibroblast (BPF) cells were used to evaluate innate immunity, and they showed a weak response to interferon {beta} and tumor necrosis factor- compared to their human counterparts, consistent with our transcriptional analysis. This compendium of transcriptome data provides a molecular foundation for understanding the cell identities, functions and cellular receptor characteristics for viral reservoirs and zoonotic transmission.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Lili Ren", - "author_inst": "National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of M" - }, - { - "author_name": "Chao Wu", - "author_inst": "National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of M" - }, - { - "author_name": "Li Guo", - "author_inst": "National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of M" - }, - { - "author_name": "Jiacheng Yao", - "author_inst": "School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University" - }, - { - "author_name": "Conghui Wang", - "author_inst": "National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of M" - }, - { - "author_name": "Yan Xiao", - "author_inst": "National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of M" - }, - { - "author_name": "Angela Oliveira Pisco", - "author_inst": "Chan Zuckerberg Biohub" - }, - { - "author_name": "Zhiqiang Wu", - "author_inst": "NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College" - }, - { - "author_name": "Xiaobo Lei", - "author_inst": "National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of M" - }, - { - "author_name": "Yiwei Liu", - "author_inst": "National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of M" - }, - { - "author_name": "Leisheng Shi", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation" - }, - { - "author_name": "Lianlian Han", - "author_inst": "National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of M" - }, - { - "author_name": "Hu Zhang", - "author_inst": "National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of M" - }, - { - "author_name": "Xia Xiao", - "author_inst": "National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Meieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Me" - }, - { - "author_name": "Jingchuan Zhong", - "author_inst": "National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of M" - }, - { - "author_name": "Hongping Wu", - "author_inst": "School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Tsinghua University" - }, - { - "author_name": "Mingkun Li", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation" - }, - { - "author_name": "Stephen R. Quake", - "author_inst": "Stanford University" - }, - { - "author_name": "Yanyi Huang", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics (ICG), College of Chemistry, and Peking-Tsinghua Center for Li" - }, - { - "author_name": "Jianbin Wang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "jianwei wang", - "author_inst": "Institute of Pathogen Biology, Chinese Academy of Medical Sciences&Peking Union Medical College" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.06.29.178459", "rel_title": "Mutations from bat ACE2 orthologs markedly enhance ACE2-Fc neutralization of SARS-CoV-2", @@ -1315915,6 +1319103,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.29.20140129", + "rel_title": "Assessment of a Diagnostic Strategy Based on Chest Computed Tomography in Patients Hospitalized for COVID-19 Pneumonia: an observational study", + "rel_date": "2020-06-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20140129", + "rel_abs": "ObjectivesTo assess the relevance of a diagnostic strategy for COVID-19 based on chest computed tomography (CT) in patients with hospitalization criteria.\n\nSettingObservational study with retrospective analysis in a French emergency department (ED).\n\nParticipants and interventionFrom March 3 to April 2, 2020, 385 adult patients presenting to the ED for suspected COVID-19 underwent an evaluation that included history, physical examination, blood tests, real-time reverse transcription-polymerase chain reaction (RT-PCR) and chest CT. When the time-interval between chest CT and RT-PCR assays was longer than 7 days, patients were excluded from the study. Only patients with hospitalization criteria were included. Diagnosis accuracy was assessed using the sensitivity and specificity of RT-PCR.\n\nOutcomesSensitivity and specificity of RT-PCR, chest CT (also accompanied by lymphopenia) were measured and were also analyzed by subgroups of age and sex.\n\nResultsAmong 377 included subjects, RT-PCR was positive in 36%, while chest CT was compatible with a COVID-19 diagnosis in 59%. In the population with positive RT-PCR, there were more men (55% vs 37%, p=0.015), a higher frequency of reticular and, or, interlobular septal thickening (53% vs 31%, p=0.02) as well as a higher frequency of bilateral lesion distribution (98% vs 86%, p=0.01) compared to the population with negative RT-PCR. The proportion of lymphopenia was higher in men vs women (47% vs 39%, p=0.03) and varies between patients >80 versus 50-80 and p<0.001).\n\nUsing CT as reference, RT-PCR obtained a sensitivity of 61%, specificity of 93%. There was a significant difference between CT and RT-PCR diagnosis performance (p<0.001). When CT was accompanied by lymphopenia, sensitivity and specificity of RT-PCR were respectively 71% and 94%. CT abnormalities and lymphopenia provided diagnosis in 29% of patients with negative PCR.\n\nConclusionsChest CT had a superior yield than RT-PCR in COVID-19 hospitalized patients, especially when accompanied by lymphopenia.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Marine Thieux", + "author_inst": "Medipole Hopital Mutualiste Clinical Research Unit" + }, + { + "author_name": "Anne Charlotte Kalenderian", + "author_inst": "Medipole Hopital Mutualiste Imapole" + }, + { + "author_name": "Aurelie Chabrol", + "author_inst": "Medipole Hopital Mutualiste Imapole" + }, + { + "author_name": "Laurent Gendt", + "author_inst": "Medipole Hopital Mutualiste Eurofins CBM 69" + }, + { + "author_name": "Emma Giraudier", + "author_inst": "Lyon 2 University Masters Degree in Medical Translation and Scientific Writing" + }, + { + "author_name": "Herve Lelievre", + "author_inst": "Medipole Hopital Mutualiste Eurofins CBM 69" + }, + { + "author_name": "Samir Lounis", + "author_inst": "Medipole Hopital Mutualiste Imapole" + }, + { + "author_name": "Yves Mataix", + "author_inst": "Medipole Hopital Mutualiste Department of Medicine" + }, + { + "author_name": "Emeline Moderni", + "author_inst": "Lyon 2 University Masters Degree in Medical Translation and Scientific Writing" + }, + { + "author_name": "Laetitia Paradisi", + "author_inst": "Medipole Hopital Mutualiste Clinical Research Unit" + }, + { + "author_name": "Guillaume Ranchon", + "author_inst": "Medipole Hopital Mutualiste Emergency Department" + }, + { + "author_name": "Carlos El Khoury", + "author_inst": "Medipole Hopital Mutualiste Clinical Research Unit" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.28.20141838", "rel_title": "SARS-CoV-2 serological testing using electrochemiluminescence reveals arapid onset of seroconversion in severe COVID-19 patients", @@ -1316132,93 +1319383,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.06.27.175430", - "rel_title": "Citizen Scientists Create an Exascale Computer to Combat COVID-19", - "rel_date": "2020-06-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.27.175430", - "rel_abs": "SARS-CoV-2 has intricate mechanisms for initiating infection, immune evasion/suppression, and replication, which depend on the structure and dynamics of its constituent proteins. Many protein structures have been solved, but far less is known about their relevant conformational changes. To address this challenge, over a million citizen scientists banded together through the Folding@home distributed computing project to create the first exascale computer and simulate an unprecedented 0.1 seconds of the viral proteome. Our simulations capture dramatic opening of the apo Spike complex, far beyond that seen experimentally, which explains and successfully predicts the existence of cryptic epitopes. Different Spike homologues modulate the probabilities of open versus closed structures, balancing receptor binding and immune evasion. We also observe dramatic conformational changes across the proteome, which reveal over 50 cryptic pockets that expand targeting options for the design of antivirals. All data and models are freely available online, providing a quantitative structural atlas.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Maxwell I. Zimmerman", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Justin R. Porter", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Michael D. Ward", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Sukrit Singh", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Neha Vithani", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Artur Meller", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Upasana L. Mallimadugula", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Catherine E. Kuhn", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Jonathan H. Borowsky", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Rafal P. Wiewiora", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Matthew F. D. Hurley", - "author_inst": "Temple University" - }, - { - "author_name": "Aoife M. Harbison", - "author_inst": "Maynooth University" - }, - { - "author_name": "Carl A. Fogarty", - "author_inst": "Maynooth University" - }, - { - "author_name": "Joseph E. Coffland", - "author_inst": "Cauldron Development LLC" - }, - { - "author_name": "Elisa Fadda", - "author_inst": "Maynooth University" - }, - { - "author_name": "Vincent A. Voelz", - "author_inst": "Temple University" - }, - { - "author_name": "John D. Chodera", - "author_inst": "Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Gregory R. Bowman", - "author_inst": "Washington University in St. Louis" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.06.25.172734", "rel_title": "Assessment of the use and quick preparation of saliva for rapid microbiological diagnosis of COVID-19.", @@ -1317893,6 +1321057,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.06.27.20141689", + "rel_title": "Estimating the infection fatality risk of COVID-19 in New York City, March 1-May 16, 2020", + "rel_date": "2020-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.27.20141689", + "rel_abs": "During March 1-May 16, 2020, 191,392 laboratory-confirmed COVID-19 cases were diagnosed and reported and 20,141 confirmed and probable COVID-19 deaths occurred among New York City (NYC) residents. We applied a network model-inference system developed to support the Citys pandemic response to estimate underlying SARS-CoV-2 infection rates. Based on these estimates, we further estimated the infection fatality risk (IFR) for 5 age groups (i.e. <25, 25-44, 45-64, 65-74, and 75+ years) and all ages overall, during March 1-May 16, 2020. We estimated an overall IFR of 1.45% (95% Credible Interval: 1.09-1.87%) in NYC. In particular, weekly IFR was estimated as high as 6.1% for 65-74 year-olds and 17.0% for 75+ year-olds. These results are based on more complete ascertainment of COVID-19-related deaths in NYC and thus likely more accurately reflect the true, higher burden of death due to COVID-19 than previously reported elsewhere. It is thus crucial that officials account for and closely monitor the infection rate and population health outcomes and enact prompt public health responses accordingly as the pandemic unfolds.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Wan Yang", + "author_inst": "Columbia University" + }, + { + "author_name": "Sasikiran Kandula", + "author_inst": "Columbia University" + }, + { + "author_name": "Mary Huynh", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Sharon K Greene", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Gretchen Van Wye", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Wenhui Li", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Hiu Tai Chan", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Emily McGibbon", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Alice Yeung", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Don Olson", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Anne Fine", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Jeffrey Shaman", + "author_inst": "Columbia University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.26.20131144", "rel_title": "The scale and dynamics of COVID-19 epidemics across Europe", @@ -1318010,73 +1321237,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "urology" }, - { - "rel_doi": "10.1101/2020.06.27.20141499", - "rel_title": "Cancer inpatient with COVID-19: a report from the Brazilian National Cancer Institute", - "rel_date": "2020-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.27.20141499", - "rel_abs": "Brazil has been recording a frightening exponential curve of confirmed cases of SARS-CoV-2 infection. Cancer patients with COVID-19 are likely to have a greater risk of complications and death. A retrospective search in the electronic medical records of cancer inpatients admitted to the Brazilian National Cancer Institute from April 30, 2020 to May 26, 2020 granted identification of 181 patients with COVID-19 confirmed by RT-PCR method. The mean age was 55.3 years (SD {+/-}21.1). The most prevalent solid tumors were breast (40 [22.1%]), gastrointestinal (24 [13.3%]), and gynecological (22 [12.2%]). Among hematological malignancies, lymphoma (20 [11%]) and leukemia (10 [5.5%]) predominated. The most common complications were respiratory failure (70 [38.7%]), septic shock (40 [22.1%]) and acute kidney injury (33 [18.2%]). A total of 60 (33.1%) patients died due to COVID-19 complications. By multivariate analysis, cases with admission due to symptoms of COVID-19 (p = 0.027) and with two or more metastatic sites (p <0.001) showed a higher risk of COVID-19-specific death. This is the first study in a cohort of Brazilian cancer patients with COVID-19. The rates of complications and COVID-19-specific death were significantly high. Our data prompts urgent and effective public policies for this group of especially vulnerable patients.\n\nStatement of SignificanceCOVID-19-specific mortality in cancer inpatients is markedly higher than in the general population and the cases with advanced cancer are particularly in a more vulnerable group. Adaptations of cancer management guidelines and more intensive preventive measures should be a priority for this group of patients.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Andreia C de Melo", - "author_inst": "Instituto Nacional do Cancer" - }, - { - "author_name": "Luiz Claudio S Thuler", - "author_inst": "Instituto Nacional do Cancer" - }, - { - "author_name": "Jesse L da Silva", - "author_inst": "Instituto Nacional do Cancer" - }, - { - "author_name": "Lucas Z de Albuquerque", - "author_inst": "Instituto Nacional do Cancer" - }, - { - "author_name": "Ana Carla Pecego", - "author_inst": "Instituto Nacional do Cancer" - }, - { - "author_name": "Luciana O.R. Rodrigues", - "author_inst": "Instituto Nacional do Cancer" - }, - { - "author_name": "Magda S da Conceicao", - "author_inst": "Instituto Nacional do Cancer" - }, - { - "author_name": "Marianne M Garrido", - "author_inst": "Instituto Nacional do Cancer" - }, - { - "author_name": "Gelcio L Mendes", - "author_inst": "Instituto Nacional do Cancer" - }, - { - "author_name": "Ana Cristina M Pereira", - "author_inst": "Instituto Nacional do Cancer" - }, - { - "author_name": "Marcelo A Soares", - "author_inst": "INSTITUTO NACIONAL DE CANCER" - }, - { - "author_name": "Joao P.B. Viola", - "author_inst": "Instituto Nacional do Cancer" - }, - { - "author_name": "- INCA COVID-19 Task Force", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2020.06.27.20141788", "rel_title": "Mapping the Global Research and Clinical Trials in COVID-19", @@ -1319367,6 +1322527,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.29.20142281", + "rel_title": "Early Hemoglobin kinetics in response to ribavirin: Safety lesson learned from Hepatitis C to CoVID-19 therapy", + "rel_date": "2020-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20142281", + "rel_abs": "BackgroundRibavirin (RBV) is been used for SARS-CoV-2 infection. This drug is associated with a wide range of side effects, mainly anemia, so its use in patients with potential respiratory affectation could not be appropriate. The evidences of adverse events associated with RBV-use has mainly been derived in the context of hepatitis C (HCV) treatment, however the possible use of RBV in CoVID-19 patients could be limited to 14 days.\n\nMethodsLongitudinal study including HIV/HCV coinfected patients. We evaluate the hemoglobin dynamics and reductions as well as evaluate the development rate of anemia during the first 2 weeks of therapy in HCV infected patients.\n\nResults189 patients were included in the study. The median hemoglobin levels were 14.6 g/dL (IQR: 13.2-15.6 g/dL) and 13.5 g/dL (IQR: 12.3-14.5 g/dL) at weeks 1 and 2 of therapy, respectively. A cumulative number of 27 (14.2%) patients developed anemia (23 grade 1 [12.1%] and 4 grade 2 [2.1%]). We identify a baseline hemoglobin levels of 14 g/dL as the better cut-off to identify those patients with a high chance to develop anemia. Of the 132 patients with baseline hemoglobin level >14 g/dL, 8 developed anemia (6.1%) compared with 19 of 57 (33.3%) with hemoglobin levels lower than 14 g/dL (p < 0.001).\n\nConclusionsOur study shows valuable information about the early hemoglobin kinetic timing in patients on RBV-therapy, that could be useful to tailor CoVID-19 treatment if RBV use is considered.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Antonio Rivero-Juarez", + "author_inst": "IMIBIC" + }, + { + "author_name": "Mario Frias", + "author_inst": "IMIBIC" + }, + { + "author_name": "Isabel Machuca", + "author_inst": "IMIBIC" + }, + { + "author_name": "Marina Gallo", + "author_inst": "IMIBIC" + }, + { + "author_name": "Pedro Lopez-Lopez", + "author_inst": "IMIBIC" + }, + { + "author_name": "Angela Camacho", + "author_inst": "IMIBIC" + }, + { + "author_name": "Antonio Rivero", + "author_inst": "IMIBIC" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "toxicology" + }, { "rel_doi": "10.1101/2020.06.28.20141960", "rel_title": "Data presented by the UK government as lockdown was eased shows the transmission of COVID-19 had already increased.", @@ -1319436,33 +1322639,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.27.174896", - "rel_title": "Rational Design of the Remdesivir Binding Site in the RNA-dependent RNA Polymerase of SARS-CoV-2: Implications for Potential Resistance", - "rel_date": "2020-06-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.27.174896", - "rel_abs": "ABSTRACTSARS-CoV-2 is rapidly evolving with the continuous emergence of new mutations. There is no specific antiviral therapy for COVID-19, and the use of Remdesivir for treating COVID-19 will likely continue before clinical trials are completed. Due to the lengthening pandemic and evolving nature of the virus, predicting potential residues prone to mutations is crucial for the management of Remdesivir resistance. We used a rational ligand-based interface design complemented with mutational mapping to generate a total of 100,000 mutations and provide insight into the functional outcome of mutations in the Remdesivir-binding site in nsp12. After designing 56 residues in the Remdesivir binding site of nsp12, the designs retained 96-98% sequence identity, which suggests that SARS-CoV-2 attains resistance and develops further infectivity with very few mutations in the nsp12. We also identified affinity-attenuating Remdesivir binding designs of nsp12. Several mutants acquired decreased binding affinity with Remdesivir, which suggested drug resistance. These hotspot residues had a higher probability of undergoing selective mutations in the future to develop Remdesivir and related drug-based resistance. A comparison of 21 nsp12 Remdesivir-bound designs to the 13 EIDD-2801-bound nsp12 designs suggested that EIDD-2801 would be more effective in preventing the emergence of resistant mutations and against Remdesivir-resistance strains due to the restricted mutational landscape. Combined with the availability of more genomic data, our information on mutation repertoires is critical to guide scientists to rational structure-based drug discovery. Knowledge of the potential residues prone to mutation improves our understanding and management of drug resistance and disease pathogenesis.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Aditya Padhi", - "author_inst": "RIKEN" - }, - { - "author_name": "Rohit Shukla", - "author_inst": "North-Eastern Hill University" - }, - { - "author_name": "Timir Tripathi", - "author_inst": "North-Eastern Hill University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.06.26.174557", "rel_title": "Stereotypic Neutralizing VH Clonotypes Against SARS-CoV-2 RBD in COVID-19 Patients and the Healthy Population", @@ -1320757,6 +1323933,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.26.20140616", + "rel_title": "The impact of SARS-CoV-2 transmission fear and COVID-19 pandemic on the mental health of patients with primary immunodeficiency disorders, severe asthma, and other high-risk groups", + "rel_date": "2020-06-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.26.20140616", + "rel_abs": "BackgroundThe adverse effects of COVID-19 pandemic on the mental health of high-risk group patients for morbidity and mortality and its impact on public health in the long term have not been clearly determined.\n\nObjectiveTo determine the level of COVID-19 related transmission fear and anxiety in healthcare workers and patients with primary immunodeficiency disorder (PID), severe asthma, and the ones with other comorbidities.\n\nMethodsThe healthcare workers and patients with PID, severe asthma (all patients receiving biological agent treatment), malignancy, cardiovascular disease, hypertension (90% of patients receiving ACEI or ARB therapy), diabetes mellitus (42 % of patients receiving DPP-4 inhibitor therapy) were included in the study. A total of 560 participants, 80 individuals in each group, were provided. The hospital anxiety and depression scale (HADS) and Fear of illness and virus evaluation (FIVE) scales were applied to the groups with face to face interview methods.\n\nResultsThe mean age was 49.30 {+/-} 13.74 years and 306 (55 %) were female. The FIVE Scale and HADS-A scale scores of health care workers were significantly higher than other groups scores (p = 0.001 and 0.006). The second-highest scores belonged to patients with PID. There was no significant difference between the groups for the HADS-D score (p=0.07). The lowest score in all scales was observed in patients with hypertension.\n\nConclusionsThis study demonstrated that in the pandemic process, patients with primary immunodeficiency, asthma patients, and other comorbid patients, especially healthcare workers, should be referred to the centers for the detection and treatment of mental health conditions.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Fatih Colkesen", + "author_inst": "Department of Clinical Immunology and Allergy, Necmettin Erbakan University Meram Faculty of Medicine," + }, + { + "author_name": "Oguzhan Kilincel", + "author_inst": "Department of Psychiatry, Sakarya Yenikent State Hospital" + }, + { + "author_name": "Mehmet Sozen", + "author_inst": "Department of Endocrinology and Metabolism, Kocaeli University Faculty of Medicine" + }, + { + "author_name": "Eray Yildiz", + "author_inst": "Department of Clinical Immunology and Allergy, Necmettin Erbakan University Meram Faculty of Medicine" + }, + { + "author_name": "Sengul Beyaz", + "author_inst": "Division of Clinical Immunology and Allergy, Department of Internal Medicine, Istanbul Faculty of Medicine, Istanbul University" + }, + { + "author_name": "Fatma Colkesen", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, University of Health Sciences, Konya Training and Research Hospital" + }, + { + "author_name": "Gokhan Aytekin", + "author_inst": "Department of Clinical Immunology and Allergy, University of Health Sciences, Konya Training and Research Hospital" + }, + { + "author_name": "Mehmet Zahit Kocak", + "author_inst": "Department of Medical Oncology, Meram Faculty of Medicine, Necmettin Erbakan University" + }, + { + "author_name": "Yakup Alsancak", + "author_inst": "Department of Cardiology , Meram Faculty of Medicine, Necmettin Erbakan University" + }, + { + "author_name": "Murat Araz", + "author_inst": "Department of Medical Oncology, Meram Faculty of Medicine, Necmettin Erbakan University" + }, + { + "author_name": "Sevket Arslan", + "author_inst": "Department of Clinical Immunology and Allergy, Necmettin Erbakan University Meram Faculty of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.06.25.20139907", "rel_title": "Teach, and teach and teach: does the average citizen use masks correctly during daily activities? Results from an observational study with more than 12,000 participants", @@ -1320898,85 +1324133,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.06.26.20140657", - "rel_title": "The impact of the COVID-19 pandemic on quality of life, physical and psychosocial wellbeing in breast cancer patients and survivors - A prospective, multicenter cohort study", - "rel_date": "2020-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.26.20140657", - "rel_abs": "PurposeThe COVID-19 pandemic and the resulting social distancing and lockdown measures are having a substantial impact on daily life and medical management of people with breast cancer. We evaluated to what extent these changes have affected quality of life and physical, and psychosocial wellbeing of people (being) treated for breast cancer.\n\nMethodsThis study was conducted within the prospective Utrecht cohort for Multiple BREast cancer intervention studies and Long-term evaluation (UMBRELLA). Shortly after the implementation of COVID-19 measures, extra questionnaires were sent to 1595 cohort participants, including standard UMBRELLA quality of life (EORTC) questionnaires. Patient-reported outcomes (PROs) were compared to the most recent PROs collected within UMBRELLA before COVID-19. The impact of COVID-19 on PROs was evaluated using mixed models analysis.\n\nResultsIn total, 1051 patients (66%) completed the questionnaires. One third (n = 327, 31%) reported a higher threshold to contact their general practitioner due to COVID-19. A significant deterioration in emotional functioning was observed (82{middle dot}6 to 77{middle dot}9, p < 0.001) and 505 (48%, 95% CI 45-51) patients reported moderate to severe loneliness. Small significant improvements were observed in QoL, physical-, social- and role functioning scores. In the subgroup of 51 patients under active treatment, there was a strong deterioration in social functioning (69{middle dot}8 to 5{middle dot}0, p = 0{middle dot}03).\n\nConclusionDue to COVID-19, patients (being) treated for breast cancer are less likely to contact physicians, and experience a deterioration in emotional functioning. Patients undergoing active treatment report a strong drop in social functioning. One in two patients reports (severe) loneliness. Online applications facilitating peer contact and e-mental health interventions could support mental health and social interaction times of total lockdown or social distancing.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Claudia A Bargon", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Marilot CT Batenburg", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Lilianne E van Stam", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Dieuwke R Mink van der Molen", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Iris E van Dam", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Femke van der Leij", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Inge O Baas", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Miranda F Ernst", - "author_inst": "Alexander Monro Clinics" - }, - { - "author_name": "Wiesje Maarse", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Nieke Vermulst", - "author_inst": "Rivierenland Hospital" - }, - { - "author_name": "Ernst JP Schoenmaeckers", - "author_inst": "Meander Medisch Centrum" - }, - { - "author_name": "Thijs van Dalen", - "author_inst": "Diakonessenhuis" - }, - { - "author_name": "Rhode M Bijlsma", - "author_inst": "UMC Utrecht" - }, - { - "author_name": "Danny A Young-Afat", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Annemiek Doeksen", - "author_inst": "St. Antonius Hospital" - }, - { - "author_name": "Helena M Verkooijen", - "author_inst": "UMC Utrecht" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2020.06.26.20140780", "rel_title": "Assessing the nationwide impact of COVID-19 mitigation policies on the transmission rate of SARS-CoV-2 in Brazil", @@ -1322367,6 +1325523,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.23.20138222", + "rel_title": "Phylogenomics and phylodynamics of SARS-CoV-2 retrieved genomes from India", + "rel_date": "2020-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20138222", + "rel_abs": "The ongoing SARS-CoV-2 pandemic is one of the biggest outbreaks after the Spanish flu of 1918. Understanding the epidemiology of viral outbreaks is the first step towards vaccine development programs. This is the first phylodynamics study attempted on of SARS-CoV-2 genomes from India to infer its current evolution in the context of an ongoing pandemic. Out of 286 retrieved SARS-CoV-2 whole genomes from India, 138 haplotypes were generated and analyzed. Median-joining network was built to investigate the relatedness of SARS-CoV-2 haplotypes in India. The BDSIR package of BEAST2 was used to calculate the reproduction number (R0) and the infectious rate of the virus. Past and current population trend was investigated using the stamp date method in coalescent Bayesian skyline plot, implemented in BEAST2 and by exponential growth prior in BEAST 1.10.4. Median-joining network reveals two distinct ancestral clusters A and B showing genetic affinities with Wuhan outbreak sample. The network also illustrates the autochthonous development of isolates in a few instances. High basic reproduction number of SARS-nCoV-2 in India points towards the phase of active community transmission. The Bayesian skyline plot revel exponential rise in the effective population size (Ne) of Indian isolates from the first week of January to the first week of April 2020. More genome sequencing and analyses of the virus will be required in coming days to monitor COVID19 after the upliftment of lock down in India.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sameera Farah", + "author_inst": "Department of Zoology, Laboratory of Molecular and Conservation Genetics, Govt. Vidarbha Institute of Science and Humanities, Amravati-444604-India; Department " + }, + { + "author_name": "Ashwin Atkulwar", + "author_inst": "Department of Zoology, Laboratory of Molecular and Conservation Genetics, Govt. Vidarbha Institute of Science and Humanities, VMV Road, Amravati-444604-Indial; " + }, + { + "author_name": "Manas Ranjan Praharaj", + "author_inst": "National Institute of Animal Biotechnology, Gowlidoddy, Hyderabad, Telangana-500032-India." + }, + { + "author_name": "Raja Khan", + "author_inst": "Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P - 243122, India." + }, + { + "author_name": "Ravikumar Gandham", + "author_inst": "National Institute of Animal Biotechnology, Gowlidoddy, Hyderabad, Telangana-500032-India." + }, + { + "author_name": "Mumtaz Baig", + "author_inst": "Department of Zoology, Laboratory of Molecular and Conservation Genetics, Govt. Vidarbha Institute of Science and Humanities, Amravati-444604-India; Department " + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.22.20134130", "rel_title": "Impact of public health interventions on the COVID-19 epidemic: a stochastic model based on data from an African island", @@ -1322484,41 +1325679,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.22.20137653", - "rel_title": "Timeline from receipt to online publication of COVID-19 original research articles", - "rel_date": "2020-06-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20137653", - "rel_abs": "ObjectiveTo examine the timeline from submission of Coronavirus Disease 2019 (COVID)-related original articles compared with non-COVID-related original articles.\n\nBackgroundThere have been growing concerns about the speed and rigor of the review process for COVID-related articles by journals.\n\nMethodsUsing Dimensions, an online searchable platform, we identified PubMed-indexed journals that published >50 COVID-related articles (regardless of article type) between 1/1/2020 and 5/16/2020 and had available data on the date of article receipt. For the control group, we included consecutive full-length original investigations with available receipt date (regardless of topic) published in these journals starting from 3/1/2019 until a 1:2 ratio of COVID to non-COVID-related articles per journal was achieved.\n\nResultsThe final number included 294 COVID-related full-length original investigations with available article receipt dates published in 16 journals with corresponding 588 control articles from the same journals. The median time from article receipt to online publication was 20 (11-32) days for COVID-articles vs. 119 (62-182) days for controls (P<0.001). The median time to final acceptance (available for 97% of the articles) was 13 (5-23) days for COVID vs. 102 (55-161) days for controls (P<0.001). These observations were seen across all the included journals in the analysis.\n\nConclusionsIn this analysis of full-length original investigations published in 16 medical journals, the median time from receipt to final acceptance of COVID-related articles was 8 times faster compared to non-COVID-related articles published in a similar time frame in the previous year. Online publication was 6 times faster for COVID-related articles compared to controls.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Amr F Barakat", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Mohamed Shokr", - "author_inst": "Wayne State University" - }, - { - "author_name": "Joseph Ibrahim", - "author_inst": "University of Pittsburgh Medical Center" - }, - { - "author_name": "John Mandrola", - "author_inst": "Baptist Health Louisville" - }, - { - "author_name": "Islam Y Elgendy", - "author_inst": "Massachusetts General Hospital and Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.24.20139352", "rel_title": "A cross-sectional study of immune seroconversion to SARS-CoV-2 in front-line maternity health professionals", @@ -1323661,6 +1326821,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.24.20139329", + "rel_title": "A Decision Analytic Approach for Social Distancing Policies During the COVID-19 Pandemic", + "rel_date": "2020-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20139329", + "rel_abs": "The COVID-19 pandemic has become a crucial public health issue in many countries including the United States. In the absence of the right vaccine strain and sufficient antiviral stockpiles on hand, non-pharmaceutical interventions have become valuable public health tools at the early stages of the pandemic and they are employed by many countries across the globe. These interventions are designed to increase social distancing between individuals to reduce the transmission of the virus and eventually dampen the burden on the healthcare system. The virus transmissibility is a function of the average number of contacts individuals have in their communities and it is highly dependent on population density and daily mobility patterns, along with other social factors. These show significant variation across the United States. In this article, we study the effectiveness of social distancing measures in communities with different population density. Specifically, first we show how the empirical estimation of reproduction number differs for two completely different states, thus the experience of the COVID-19 outbreak is drastically different, suggesting different outbreak growth rates in practice. Second, we develop an age-structured compartmental model for simulating the disease spread in order to demonstrate the variation in the observed outbreak characteristics. We find that early trigger and late trigger options present a trade-off between the peak magnitude and the overall death toll of the outbreak which may also vary across different populations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Zeynep Ertem", + "author_inst": "University of Southern California" + }, + { + "author_name": "Ozgur Araz", + "author_inst": "University of Nebraska" + }, + { + "author_name": "Maytee Cruz-Aponte", + "author_inst": "University of Puerto Rico" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.25.20140384", "rel_title": "Seroprevalence of Antibodies to SARS-CoV-2 in Six Sites in the United States, March 23-May 3, 2020", @@ -1323814,25 +1327001,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.25.172312", - "rel_title": "Using the nucleocapsid protein to investigate the relationship between SARS-CoV-2 and closely related bat and pangolin coronaviruses", - "rel_date": "2020-06-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.25.172312", - "rel_abs": "An initial outbreak of coronavirus disease 2019 (COVID-19) in China has resulted in a massive global pandemic causing well over 16,500,000 cases and 650,000 deaths worldwide. The virus responsible, SARS-CoV-2, has been found to possess a very close association with Bat-CoV RaTG13 and Pangolin-CoV MP789. The nucleocapsid protein can serve as a decent model for determining phylogenetic, evolutionary, and structural relationships between coronaviruses. Therefore, this study uses the nucleocapsid gene and protein to further investigate the relationship between SARS-CoV-2 and closely related bat and pangolin coronaviruses. Sequence and phylogenetic analyses have revealed the nucleocapsid gene and protein in SARS-CoV-2 are both closely related to those found in Bat-CoV RaTG13 and Pangolin-CoV MP789. Evidence of recombination was detected within the N gene, along with the presence of a double amino acid insertion found in the N-terminal region. Homology modeling for the N-Terminal Domain revealed similar structures but distinct electrostatic surfaces and topological variations in the {beta}-hairpin that likely reflect specific adaptive functions. In respect to SARS-CoV-2, two amino acids (S37 and A267) were found to exist only in its N protein, along with an extended {beta}-hairpin that bends towards the nucleotide binding site. Collectively, this study strengthens the relationship among SARS-CoV-2, Bat-CoV RaTG13, and Pangolin-CoV MP789, providing additional insights into the structure and adaptive nature of the nucleocapsid protein found in these coronaviruses. Furthermore, these data will enhance our understanding of the complete history behind SARS-CoV-2 and help assist in antiviral and vaccine development.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Noah Avery Schuster", - "author_inst": "DePauw University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "confirmatory results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.25.169946", "rel_title": "Neuroinvasive potential of SARS-CoV-2 revealed in a human brain organoid model", @@ -1325351,6 +1328519,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.24.20138982", + "rel_title": "Modeling the Covid-19 Pandemic Response of the US States", + "rel_date": "2020-06-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20138982", + "rel_abs": "BackgroundThe United States of America (USA) has been the country worst affected, in absolute terms, by the Covid-19 pandemic. The country comprises 50 states under a federal system. The impact of the pandemic has resulted in different responses at the state level, which are driven by differing intervention policies, demographics, connectedness and other factors. Understanding the dynamics of the Covid-19 pandemic at the state level is essential in predicting its future evolution.\n\nObjectiveOur objective is to identify and characterize multiple waves of the pandemic by analyzing the reported infected population curve in each of the 50 US states. Based on the intensity of the waves, characterized by declining, stationary, or increasing strengths, each states response can be inferred and quantified.\n\nMethodsWe apply a recently proposed multiple-wave model to fit the infected population data for each state in USA, and use the proposed Pandemic Response Index to quantify their response to the Covid-19 pandemic.\n\nResultsWe have analyzed reported infected cases from each one of the 50 USA states and the District of Columbia, based on the multiple-wave model, and present the relevant parameters. Multiple waves have been identified and this model is found to describe the data better. Each of the states can be classified into one of three distinct classes characterized by declining, increasing, or stationary strength of the waves following the initial one. The effectiveness of intervention measures can be inferred by the peak intensities of the waves, and states with similar population characteristics can be directly compared. We estimate how much lower the number of infections might have been, if early and strict intervention measures had been imposed to stop the disease spread at the first wave, as was the case for certain states. Based on our models results, we compute the value of the Pandemic Response Index, a recently introduced metric for quantifying in an objective manner the response to the pandemic.\n\nConclusionsOur results reveal a series of epidemic waves, characterizing USAs pandemic response at the state level, and also infer to what extent the imposition of early intervention measures could have had on the spread and impact of the disease. As of June 11, 2020, only 19 states and the District of Columbia (40% of the total) clearly exhibit declining trends in the numbers of reported infected cases, while 13 states exhibit stationary and 18 states increasing trends in the numbers of reported cases.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Georgios Neofotistos", + "author_inst": "Institute for Applied Computational Science (IACS), John A. Paulson School of Engineering and Applied Sciences, Harvard University" + }, + { + "author_name": "Efthimios Kaxiras", + "author_inst": "Institute for Applied Computational Science (IACS), John A. Paulson School of Engineering and Applied Sciences, Harvard University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.24.20139196", "rel_title": "How Many Lives Has Lockdown Saved in the UK?", @@ -1325432,29 +1328623,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.24.20138990", - "rel_title": "Liberte, Egalite, Fraternite... Contamine? Estimating the impact of French municipal elections on COVID-19 spread in France", - "rel_date": "2020-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20138990", - "rel_abs": "On March 15, about 20, 000, 000 voters cast their vote for the first round of the 2020 French municipal elections. We investigate the extent to which this event contributed to the COVID-19 epidemics in France. To this end, we first predict each departements own dynamics using information up to the election to calibrate a standard logistic model. We then take advantage of electoral turnout differences between departements to distinguish the impact of the election on prediction errors in hospitalizations from that of simultaneously implemented anti-contagion policies. We report a detrimental effect of the election in locations that were at relatively advanced stages of the epidemics by the time of the election. In contrast, we show that the election did not contribute to the epidemics in departements with lower infection levels by March 15. All in all, our estimates suggest that elections accounted for about 4, 000 excess hospitalizations by the end of March, which represents 15% of all hospitalizations by this time. They also suggest that holding elections in June may not be as detrimental.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Guilhem Cassan", - "author_inst": "University of Namur" - }, - { - "author_name": "Marc Sangnier", - "author_inst": "University of Namur, Aix-Marseille University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.24.20138925", "rel_title": "IMPACT OF COVID-19 PANDEMIC ON MENTAL HEALTH OF MEDICAL STUDENTS:A CROSS-SECTIONAL STUDY USING GAD-7 AND PHQ-9 QUESTIONNAIRES", @@ -1326992,6 +1330160,37 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.06.24.168534", + "rel_title": "Lung expression of genes encoding SARS-CoV-2 cell entry molecules and antiviral restriction factors: interindividual differences are associated with age and germline variants", + "rel_date": "2020-06-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.24.168534", + "rel_abs": "Germline variants in genes involved in SARS-CoV-2 cell entry (i.e. ACE2 and TMPRSS2) may influence the susceptibility to infection, as may polymorphisms in genes involved in the innate host response to viruses (e.g. APOBEC3 family). We searched for polymorphisms acting, in lung tissue, as expression quantitative trait loci (eQTLs) for 15 candidate COVID-19 susceptibility genes, selected for their roles in virus cell entry and host antiviral responses. No significant eQTLs were identified for ACE2 and TMPRSS2 genes, whose expression levels did not associate with either sex or age of the 408 patients whose non-diseased lung tissue was analyzed. Instead, we identified seven cis-eQTLs (FDR<0.05) for APOBEC3D and APOBEC3G (rs139296, rs9611092, rs139331, rs8177832, rs17537581, rs61362448, and rs738469). The genetic control of the expression of APOBEC3 genes, which encode enzymes that interfere with virus replication, may explain interindividual differences in risk or severity of viral infections. Future studies should investigate the role of host genetics in COVID-19 patients using a genome-wide approach, to identify other genes whose expression levels are associated with susceptibility to SARS-CoV-2 infection or COVID-19 severity.\n\nAuthor summaryIdentification of expression quantitative trait loci (eQTLs) has become commonplace in functional studies on the role of individual genetic variants in susceptibility to diseases. In COVID-19, it has been proposed that individual variants in SARS-CoV-2 cell entry and innate host response genes may influence the susceptibility to infection. We searched for polymorphisms acting, in non-diseased lung tissue of 408 patients, as eQTLs for 15 candidate COVID-19 susceptibility genes, selected for their roles in virus cell entry and host antiviral responses. Seven cis-eQTLs were detected for APOBEC3D and APOBEC3G genes, which encode enzymes that interfere with virus replication. No significant eQTLs were identified for ACE2 and TMPRSS2 genes. Therefore, the identified eQTLs may represent candidate loci modulating interindividual differences in risk or severity of SARS-CoV-2 virus infection.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Chiara E. Cotroneo", + "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy" + }, + { + "author_name": "Nunzia Mangano", + "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy" + }, + { + "author_name": "Tommaso A. Dragani", + "author_inst": "Fondazione IRCCS Istituto Nazionale Tumori" + }, + { + "author_name": "Francesca Colombo", + "author_inst": "Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate (MI), Italy" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.06.23.167791", "rel_title": "N-glycosylation network construction and analysis to modify glycans on the spike S glycoprotein of SARS-CoV-2.", @@ -1327101,33 +1330300,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.06.24.169565", - "rel_title": "Development of a fluorescence based, high-throughput SARS-CoV-2 3CLpro reporter assay", - "rel_date": "2020-06-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.24.169565", - "rel_abs": "In late 2019 a human coronavirus, now known as SARS-CoV-2, emerged, likely from a zoonotic reservoir. This virus causes COVID-19 disease, has infected millions of people, and has led to hundreds of thousands of deaths across the globe. While the best interventions to control and ultimately stop the pandemic are prophylactic vaccines, antiviral therapeutics are important to limit morbidity and mortality in those already infected. At this time, only one FDA approved anti-SARS-CoV-2 antiviral drug, remdesivir, is available and unfortunately, its efficacy appears to be limited. Thus, the identification of new and efficacious antivirals is of highest importance. In order to facilitate rapid drug discovery, flexible, sensitive, and high-throughput screening methods are required. With respect to drug targets, most attention is focused on either the viral RNA-dependent RNA polymerase or the main viral protease, 3CLpro. 3CLpro is an attractive target for antiviral therapeutics as it is essential for processing newly translated viral proteins, and the viral lifecycle cannot be completed without protease activity. In this work, we present a new assay to identify inhibitors of the SARS-CoV-2 main protease, 3CLpro. Our reporter is based on a GFP-derived protein that only fluoresces after cleavage by 3CLpro. This experimentally optimized reporter assay allows for antiviral drug screening in human cell culture at biosafety level-2 (BSL2) with high-throughput compatible protocols. Using this screening approach in combination with existing drug libraries may lead to the rapid identification of novel antivirals to suppress SARS-CoV-2 replication and spread.\n\nIMPORTANCEThe COVID-19 pandemic has already led to more than 400,000 deaths and innumerable changes to daily life worldwide. Along with development of a vaccine, identification of effective antivirals to treat infected patients is of the highest importance. However, rapid drug discovery requires efficient methods to identify novel compounds that can inhibit the virus. In this work, we present a method for identifying inhibitors of the SARS-CoV-2 main protease, 3CLpro. This reporter-based assay allows for antiviral drug screening in human cell culture at biosafety level-2 (BSL2) with high-throughput compatible sample processing and analysis. This assay may help identify novel antivirals to control the COVID-19 pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Heather M Froggatt", - "author_inst": "Duke University" - }, - { - "author_name": "Brook E Heaton", - "author_inst": "Duke University" - }, - { - "author_name": "Nicholas S Heaton", - "author_inst": "Duke University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.24.169094", "rel_title": "Modelling donor screening strategies to reduce the risk of SARS-CoV-2 via fecal microbiota transplantation", @@ -1328217,6 +1331389,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.15.20117747", + "rel_title": "SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20117747", + "rel_abs": "Current estimates of COVID-19 prevalence are largely based on symptomatic, clinically diagnosed cases. The existence of a large number of undiagnosed infections hampers population-wide investigation of viral circulation. Here, we use longitudinal wastewater analysis to track SARS-CoV-2 dynamics in wastewater at a major urban wastewater treatment facility in Massachusetts, between early January and May 2020. SARS-CoV-2 was first detected in wastewater on March 3. Viral titers in wastewater increased exponentially from mid-March to mid-April, after which they began to decline. Viral titers in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 4-10 days earlier in wastewater than in clinical data. We inferred viral shedding dynamics by modeling wastewater viral titers as a convolution of back-dated new clinical cases with the viral shedding function of an individual. The inferred viral shedding function showed an early peak, likely before symptom onset and clinical diagnosis, consistent with emerging clinical and experimental evidence. Finally, we found that wastewater viral titers at the neighborhood level correlate better with demographic variables than with population size. This work suggests that longitudinal wastewater analysis can be used to identify trends in disease transmission in advance of clinical case reporting, and may shed light on infection characteristics that are difficult to capture in clinical investigations, such as early viral shedding dynamics.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Fuqing Wu", + "author_inst": "MIT" + }, + { + "author_name": "Amy Xiao", + "author_inst": "MIT" + }, + { + "author_name": "Jianbo Zhang", + "author_inst": "MIT" + }, + { + "author_name": "Katya Moniz", + "author_inst": "MIT" + }, + { + "author_name": "Noriko Endo", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Federica Armas", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "Richard Bonneau", + "author_inst": "New York University" + }, + { + "author_name": "Megan A Brown", + "author_inst": "New York University" + }, + { + "author_name": "Mary Bushman", + "author_inst": "Harvard University" + }, + { + "author_name": "Peter R Chai", + "author_inst": "Harvard University" + }, + { + "author_name": "Claire Duvallet", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Timothy B Erickson", + "author_inst": "Harvard University" + }, + { + "author_name": "Katelyn Foppe", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Newsha Ghaeli", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Xiaoqiong Gu", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "William P Hanage", + "author_inst": "Harvard University" + }, + { + "author_name": "Katherine H Huang", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Wei Lin Lee", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "Mariana Matus", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Kyle A McElroy", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Jonathan Nagler", + "author_inst": "Center for Data Science NYU" + }, + { + "author_name": "Steven F Rhode", + "author_inst": "Massachusetts Water Resources Authority, Boston, MA" + }, + { + "author_name": "Mauricio Santillana", + "author_inst": "Harvard University" + }, + { + "author_name": "Joshua A Tucker", + "author_inst": "Center for Data Science NYU" + }, + { + "author_name": "Stefan Wuertz", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Shijie Zhao", + "author_inst": "MIT" + }, + { + "author_name": "Janelle Thompson", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Eric J Alm", + "author_inst": "Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.22.20132910", "rel_title": "Insufficient social distancing may be related to a future COVID-19 outbreak in Ijui-Brazil: Predictions of further social interventions.", @@ -1328338,29 +1331637,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.06.20.20136283", - "rel_title": "On the secondary waves of the pandemic launched in Iran and other countries", - "rel_date": "2020-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.20.20136283", - "rel_abs": "In the last decade of April 2020, the second epidemic wave began in Iran. If judging by the dynamics of total cases, the birth of this second wave coincides practically with the maximum growth rate of the primary epidemic started in Iran from the very beginning of 2020. Today, the secondary epidemic wave almost doubles the peak of the primary. The new epidemic wave grows rapidly and unpredictably. Also, we admit that the secondary epidemic waves are already getting started in other countries.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Dmitry Kovriguine", - "author_inst": "Nizhny Novgorod State Technical University n.a. R.E. Alexseev" - }, - { - "author_name": "Svetlana Nikitenkova", - "author_inst": "National Research Lobachevsky State University of Nizhny Novgorod" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.06.18.20134593", "rel_title": "Deep convolutional approaches for the analysis of Covid-19 using chest X-Ray images from portable devices", @@ -1329583,6 +1332859,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.21.20136937", + "rel_title": "A Statistical and Dynamical Model for Forecasting COVID-19 Deaths based on a Hybrid Asymmetric Gaussian and SEIR Construct", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.21.20136937", + "rel_abs": "BackgroundThe limitations of forecasting (real-time statistical) and predictive (dynamic epidemiological) models have become apparent as COVID-19 has progressed from a rapid exponential ascent to a slower decent, which is dependent on unknowable parameters such as extent of social distancing and easing. We present a means to optimize a forecasting model by functionalizing our previously reported Asymmetric Gaussian model with SEIR-like parameters. Conversely, SEIR models can be adapted to better incorporate real-time data.\n\nMethodsOur previously reported asymmetric Gaussian model was shown to greatly improve on forecasting accuracy relative to use of symmetric functions, such as Gaussian and error functions for death rates and cumulative deaths, respectively. However, the reported asymmetric Gaussian implementation, which fitted well to the ascent and much of the recovery side of the real death rate data, was not agile enough to respond to changing social behavior that is resulting in persistence of infections and deaths in the later stage of recovery. We have introduced a time-dependent {sigma}(t) parameter to account for transmission rate variability due to the effects of behavioral changes such as social distancing and subsequent social easing. The {sigma}(t) parameter is analogous to the basic reproduction number R0 (infection factor) that is evidently not a constant during the progression of COVID-19 for a particular population. The popularly used SEIR model and its many variants are also incorporating a time dependent R0(t) to better describe the effects of social distancing and social easing to improve predictive capability when extrapolating from real-time data.\n\nResultsComparisons are given for the previously reported Asymmetric Gaussian model and to the revised, what we call, SEIR Gaussian model. We also have developed an analogous model based on R0(t) that we call SEIR Statistical model to show the correspondence that can be attained. It is shown that these two models can replicate each other and therefore provide similar forecasts based on fitting to the same real-time data. We show the results for reported U.S. death rates up to June 12, 2020 at which time the cumulative death count was 113,820. The forecasted cumulative deaths for these two models and compared to the University of Washington (UW) IHME model are 140,440, 139,272, and 149,690 (for 8/4/20) and 147,819, 148, 912, and 201,129 (for 10/1/20), respectively. We also show how the SEIR asymmetric Gaussian model can also account for various scenarios of social distancing, social easing, and even re-bound outbreaks where the death and case rates begin climbing again.\n\nConclusionsForecasting models, based on real-time data, are essential for guiding policy and human behavior to minimize the deadly impact of COVID-19 while balancing the need to socialize and energize the economy. It is becoming clear that changing social behavior from isolation to easing requires models that can adapt to the changing transmission rate in order to more accurately forecast death and case rates. We believe our asymmetric Gaussian approach has advantages over modified SEIR models in offering simpler governing equations that are dependent on fewer variables.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Jack A. Syage", + "author_inst": "ImmunogenX" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.21.20136929", "rel_title": "Derivation and Validation of Clinical Prediction Rule for COVID-19 Mortality in Ontario, Canada", @@ -1329772,29 +1333067,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.22.20137604", - "rel_title": "Universal scaling law for COVID-19 propagation in urban centers", - "rel_date": "2020-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20137604", - "rel_abs": "Due to the COVID-19 pandemic, there is a high demand for Susceptible-Infective-Recovered (SIR) models to adjust and predict the number of cases in urban areas. Forecasting, however, is a difficult task, because the change in peoples behavior reflects in a continuous change in the parameters of the model. An important question is what we can use from one city to another; if what happened in Madrid could have been applied to New York and then, if what we have learned from this city would be useful for Sao Paulo. To answer this question, we present an analysis of the transmission rate of COVID-19 as a function of population density and population size for US counties, cities of Brazil, German, and Portugal. Contrary to the common hypothesis in epidemics modeling, we observe a higher disease transmissibility for higher citys population density/size -with the latter showing more predicting power. We present a contact rate scaling theory that explain the results, predicting that the basic reproductive number R0 of epidemics scales as the logarithm of the city size.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ben-Hur Francisco Cardoso", - "author_inst": "Instituto de Fisica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil" - }, - { - "author_name": "Sebastian Goncalves", - "author_inst": "Universidade Federal do Rio Grande do Sul" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.22.20136960", "rel_title": "Retrospective Methodology to Estimate Daily Infections from Deaths (REMEDID) in COVID-19: the Spain case study", @@ -1331061,6 +1334333,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.23.20137596", + "rel_title": "Platelets can contain SARS-CoV-2 RNA and are hyperactivated in COVID-19", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20137596", + "rel_abs": "RationaleIn addition to the overwhelming lung inflammation that prevails in COVID-19, hypercoagulation and thrombosis contribute to the lethality of subjects infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Platelets are chiefly implicated in thrombosis. Moreover, they can interact with viruses and are an important source of inflammatory mediators. While a lower platelet count is associated with severity and mortality, little is known about platelet function during COVID-19.\n\nObjectiveTo evaluate the contribution of platelets to inflammation and thrombosis in COVID-19 patients.\n\nMethods and ResultsWe document the presence of SARS-CoV-2 RNA in platelets of COVID-19 patients. Exhaustive assessment of cytokines in plasma and in platelets revealed the modulation of platelet-associated cytokine levels in COVID-19, pointing to a direct contribution of platelets to the plasmatic cytokine load. Moreover, we demonstrate that platelets release their alpha- and dense-granule contents and phosphatidylserine-exposing extracellular vesicles. Functionally, platelets were hyperactivated in COVID-19 subjects, with aggregation occurring at suboptimal thrombin concentrations. Furthermore, platelets adhered more efficiently onto collagen-coated surfaces under flow conditions.\n\nConclusionsThese data suggest that platelets could participate in the dissemination of SARS-CoV-2 and in the overwhelming thrombo-inflammation observed in COVID-19. Thus, blockade of platelet activation pathways may improve outcomes in this disease.\n\nKEY POINTSPlatelets are a source of inflammatory cytokines and degranulate in COVID-19 Platelets contain SARS-CoV-2 RNA molecules and are prone to activation in COVID-19\n\nSubject termsInfectious diseases/Emerging infectious diseases, SARS-CoV-2, COVID-19, Hematology, Platelets", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Younes Zaid", + "author_inst": "Cheikh Zaid Hospital; Mohammed V University" + }, + { + "author_name": "Florian Puhm", + "author_inst": "Universite Laval" + }, + { + "author_name": "Isabelle Allaeys", + "author_inst": "Universite Laval" + }, + { + "author_name": "Abdallah Naya", + "author_inst": "Hassan II University" + }, + { + "author_name": "Mounia Oudghiri", + "author_inst": "Hassan II University" + }, + { + "author_name": "Loubna Khalki", + "author_inst": "Mohammed VI University of Health Sciences (UM6SS)" + }, + { + "author_name": "Youness Limami", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Nabil Zaid", + "author_inst": "Mohammed V University" + }, + { + "author_name": "Khalid Sadki", + "author_inst": "Mohammed V University" + }, + { + "author_name": "Rafiqua Ben El Haj", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Wissal Maher", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Lamiae Belayachi", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Bouchra Belefquih", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Amina Benouda", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Amine Cheikh", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Yahia Cherrah", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Louis Flamand", + "author_inst": "Universite Laval" + }, + { + "author_name": "Fadila Guessous", + "author_inst": "Mohammed VI University of Health Sciences (UM6SS); University of Virginia" + }, + { + "author_name": "Eric Boilard", + "author_inst": "Universite Laval" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.23.20137521", "rel_title": "SARS CoV-2 Serosurvey in Addis Ababa, Ethiopia", @@ -1331178,29 +1334541,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.06.15.150482", - "rel_title": "SARS-CoV-2 mutations altering regulatory properties: deciphering host's and virus's perspectives", - "rel_date": "2020-06-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.15.150482", - "rel_abs": "Since the first recorded case of the SARS-CoV-2, it has acquired several mutations in its genome while spreading throughout the globe. However, apart from some changes in protein coding, functional importance of these mutations in disease pathophysiology are still largely unknown. In this study, we investigated the significance of these mutations both from the hosts and viruss perspective by analyzing the host miRNA binding and viruss internal ribosome entry site (IRES), respectively. Strikingly, we observed that due to the acquired mutations, host miRNAs bind differently compared to the reference; where few of the miRNAs lost and few gained the binding affinity for targeting the viral genome. Moreover, functional enrichment analysis suggests that targets of both of these gained and lost miRNAs might be involved in various host immune signaling pathways. Also, we sought to shed some insights on the impacts of mutations on the IRES structure of SARS-CoV-2. Remarkably, we detected that three particular mutations in the IRES can disrupt its secondary structure which can further make the virus less functional. These results could be valuable in exploring the functional importance of the mutations of SARS-CoV-2 and could provide novel insights into the differences observed different parts of the world.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Abul B.M.M.K. Islam", - "author_inst": "Department of Genetic Engineering and Biotechnology, University of Dhaka" - }, - { - "author_name": "Md. Abdullah-Al-Kamran Khan", - "author_inst": "Department of Mathematics and Natural Sciences, BRAC University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.06.23.164335", "rel_title": "Expression of Ace2, Tmprss2, and Furin in mouse ear tissue", @@ -1332639,6 +1335979,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.20.20134387", + "rel_title": "A systematic review and meta-analysis reveals long and dispersive incubation period of COVID-19", + "rel_date": "2020-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.20.20134387", + "rel_abs": "BackgroundThe incubation period of SARS-CoV-2 remains uncertain, which has important implications for estimating transmission potential, forecasting epidemic trends, and decision-making in prevention and control.\n\nPurposeTo estimate the central tendency and dispersion for incubation period of COVID-19 and, in turn, assess the effect of a certain length of quarantine for close contacts in active monitoring.\n\nData SourcesPubMed, Embase, medRxiv, bioRxiv, and arXiv, searched up to April 26, 2020\n\nStudy SelectionCOVID-19 studies that described either individual-level incubation period data or summarized statistics for central tendency and dispersion measures of incubation period were recruited.\n\nData ExtractionFrom each recruited study, either individual-level incubation period data or summarized statistics for central tendency and dispersion measures were extracted, as well as population characteristics including sample size, average age, and male proportion.\n\nData SynthesisFifty-six studies encompassing 4 095 cases were included in this meta-analysis. The estimated median incubation period for general transmissions was 5.8 days [95% confidence interval (95%CI), 5.3 to 6.2 d]. Median and dispersion were higher for SARS-CoV-2 incubation compared to other viral respiratory infections. Furthermore, about 20 in 10 000 contacts in active monitoring would develop symptoms after 14 days, or below 1 in 10 000 for young-age infections or asymptomatic transmissions.\n\nLimitationSmall sample sizes for subgroups; some data were possibly used repeatedly in different studies; limited studies for outside mainland China; non-negligible intra-study heterogeneity.\n\nConclusionThe long, dispersive incubation period of SARS-CoV-2 contributes to the global spread of COVID-19. Yet, a 14-day quarantine period is sufficient to trace and identify symptomatic infections, which while could be justified according to a better understanding of the crucial parameters.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yongyue Wei", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Liangmin Wei", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Yihan Liu", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Lihong Huang", + "author_inst": "Zhongshan Hospital Fudan University" + }, + { + "author_name": "Sipeng Shen", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Ruyang Zhang", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Jiajin Chen", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Yang Zhao", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Hongbing Shen", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Feng Chen", + "author_inst": "Nanjing Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.18.20132571", "rel_title": "Transcriptomic profiling of disease severity in patients with COVID-19 reveals role of blood clotting and vasculature related genes", @@ -1332832,49 +1336227,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.18.20135046", - "rel_title": "Clinical characteristics and outcomes of critically ill patients with COVID-19 in a tertiary community hospital in upstate New York", - "rel_date": "2020-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20135046", - "rel_abs": "BackgroundThere are limited reports describing critically ill COVID-19 patients in New York.\n\nMethodsWe conducted a retrospective analysis of 32 adult critically ill patients admitted to a tertiary community hospital in upstate NY, between March 14th and April 12th, 2020. We collected demographic, laboratory, ventilator, and treatment data, which were analyzed and clinical outcomes tabulated.\n\nResults32 patients admitted to the ICU were included, with mean ({+/-}SD) follow-up duration 21 {+/-} 7 days. Mean ({+/-}SD) age was 62.2 {+/-} 11.2 years, and 62.5% were men. 27 (84.4%) of patients had one or more medical co-morbidities and 50% of the patients were current or former smokers. The mean ({+/-}SD) duration of symptoms was 6.6 ({+/-}4.4) days before presentation, with cough (81.3%), dyspnea (68.7%), and fever (65.6%) being most common. 23 (71.9%) patients received invasive mechanical ventilation. 5 (15.6%) had died, 11 (34.4%) had been discharged home, and 16 (50%) remained hospitalized, 8 (25%) of which were still in ICU. Mean ({+/-}SD) length of ICU stay was 10.2 ({+/-}7.7) days, and mean ({+/-}SD) length of hospital stay was 14.8 ({+/-}7.7) days.\n\nConclusionMajority of patients were of older age and with medical co-morbidities. With adequate resource utilization, mortality of critically ill COVID-19 patients may not be as high as previously suggested.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jyotirmayee Lenka", - "author_inst": "Rochester General Hospital" - }, - { - "author_name": "Mamta S Chhabria", - "author_inst": "Rochester General Hospital" - }, - { - "author_name": "Naman Sharma", - "author_inst": "Rochester General Hospital" - }, - { - "author_name": "Bryan E-Xin Tan", - "author_inst": "Rochester General Hospital" - }, - { - "author_name": "Leela Krishna Teja Boppana", - "author_inst": "Rochester General Hospital" - }, - { - "author_name": "Sharini Venugopal", - "author_inst": "Rochester General Hospital" - }, - { - "author_name": "Damanpaul S Sondhi", - "author_inst": "Rochester General Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.06.18.20134841", "rel_title": "Fuzzy logic assisted COVID 19 safety assessment of dental care", @@ -1333996,6 +1337348,101 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.21.162396", + "rel_title": "Calcitriol, the active form of vitamin D, is a promising candidate for COVID-19 prophylaxis", + "rel_date": "2020-06-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.21.162396", + "rel_abs": "COVID-19, the disease caused by SARS-CoV-2 (1), was declared a pandemic by the World Health Organization (WHO) in March 2020 (2). While awaiting a vaccine, several antivirals are being used to manage the disease with limited success (3, 4). To expand this arsenal, we screened 4 compound libraries: a United States Food and Drug Administration (FDA) approved drug library, an angiotensin converting enzyme-2 (ACE2) targeted compound library, a flavonoid compound library as well as a natural product library. Of the 121 compounds identified with activity against SARS-CoV-2, 7 were shortlisted for validation. We show for the first time that the active form of Vitamin D, calcitriol, exhibits significant potent activity against SARS-CoV-2. This finding paves the way for consideration of host-directed therapies for ring prophylaxis of contacts of SARS-CoV-2 patients.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Chee Keng Mok", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Yan Ling Ng", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Bintou Ahmadou Ahidjo", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Regina Ching Hua Lee", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Marcus Wing Choy Loe", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Jing Liu", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Kai Sen Tan", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Parveen Kaur", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Wee Joo Chng", + "author_inst": "National University of Singapore" + }, + { + "author_name": "John Eu Li Wong", + "author_inst": "National University of Singapore" + }, + { + "author_name": "De Yun Wang", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Er Wei Hao", + "author_inst": "Guangxi University of Chinese Medicine, China" + }, + { + "author_name": "Xiaotao Hao", + "author_inst": "Guangxi University of Chinese Medicine" + }, + { + "author_name": "Yong Wah Tan", + "author_inst": "Agency for Science, Technology and Research, Singapore" + }, + { + "author_name": "Tze Minn Mak", + "author_inst": "National Public Health Laboratory, Singapore" + }, + { + "author_name": "Cui Lin", + "author_inst": "National Public Health Laboratory, Singapore" + }, + { + "author_name": "Raymond V.T.P Lin", + "author_inst": "National Public Health Laboratory, Singapore" + }, + { + "author_name": "Paul A Tambyah", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Jiagang Deng", + "author_inst": "Guangxi University of Chinese Medicine, China" + }, + { + "author_name": "Justin Jang Hann Chu", + "author_inst": "National University of Singapore" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.22.133355", "rel_title": "Companion vaccine Bioinformatic design tool reveals limited functional genomic variability of SARS-Cov-2 Spike Receptor Binding Domain", @@ -1334253,29 +1337700,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.19.20135517", - "rel_title": "The Covid-19 epidemic in the UK", - "rel_date": "2020-06-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.19.20135517", - "rel_abs": "In this note we present some stylised facts about the Covid-19 epidemic in the UK using daily time-series data published by Public Health England and the UK Department of Health and Social Care. We model the data on confirmed new cases using standard count-data models estimated at the country and national levels using a fixed rolling window to capture changes in the model parameters over time. We then use the most recent estimated models to carry out a simple real-time forecasting exercise aimed at predicting the date when the number of confirmed new cases will be approximately zero.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Giulia Faggio", - "author_inst": "City, University of London and Centre for Economic Performance, LSE" - }, - { - "author_name": "Franco Peracchi", - "author_inst": "Georgetown University, EIEF and University of Rome Tor Vergata" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.18.20134858", "rel_title": "Practical considerations for measuring the effective reproductive number, Rt", @@ -1335870,6 +1339294,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.20.162560", + "rel_title": "Multi-Omics and Integrated Network Approach to Unveil Evolutionary Patterns, Mutational Hotspots, Functional Crosstalk and Regulatory Interactions in SARS-CoV-2", + "rel_date": "2020-06-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.20.162560", + "rel_abs": "SARS-CoV-2 pandemic resulted in 92 million cases in a span of one year. The study focuses on understanding population specific variations attributing its high rate of infections in specific geographical regions particularly in USA. Rigorous phylogenomic network analysis of complete SARS-CoV-2 genomes (245) inferred five central clades named a (ancestral), b, c, d and e (subtype e1 & e2). The clade d & e2 were found exclusively comprising of USA. Clades were distinguished by 10 co-mutational combinations in Nsp3, ORF8, Nsp13, S, Nsp12, Nsp2 and Nsp6. Our analysis revealed that only 67.46% of SNP mutations were at amino acid level. T1103P mutation in Nsp3 was predicted to increase protein stability in 238 strains except 6 strains which were marked as ancestral type; whereas co-mutation (P409L & Y446C) in Nsp13 were found in 64 genomes from USA highlighting its 100% co-occurrence. Docking highlighted mutation (D614G) caused reduction in binding of Spike proteins with ACE2, but it also showed better interaction with TMPRSS2 receptor contributing to high transmissibility among USA strains. We also found host proteins, MYO5A, MYO5B, MYO5C had maximum interaction with viral proteins (N, S, M). Thus, blocking the internalization pathway by inhibiting MYO5 proteins which could be an effective target for COVID-19 treatment. The functional annotations of the HPI network were found to be closely associated with hypoxia and thrombotic conditions confirming the vulnerability and severity of infection. We also screened CpG islands in Nsp1 & N conferring ability of SARS-CoV-2 to enter and trigger ZAP activity inside host cell.\n\nImportanceIn the current study we presented a global view of mutational pattern observed in SARS-CoV-2 virus transmission. This provided a who-infect-whom geographical model since the early pandemic. This is hitherto the most comprehensive comparative genomics analysis of full-length genomes for co-mutations at different geographical regions specially in USA strains. Compositional structural biology results suggested that mutations have balance of contrary forces effect on pathogenicity suggesting only few mutations to effective at translation level but not all. Novel HPI analysis and CpG predictions elucidates the proof of concept of hypoxia and thrombotic conditions in several patients. Thus, the current study focuses the understanding of population specific variations attributing high rate of SARS-CoV-2 infections in specific geographical regions which may eventually be vital for the most severely affected countries and regions for sharp development of custom-made vindication strategies.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Vipin Gupta", + "author_inst": "PHIXGEN PVT. LTD" + }, + { + "author_name": "Shazia Haider", + "author_inst": "Jaypee Institute of Information Technology, Noida" + }, + { + "author_name": "Mansi Verma", + "author_inst": "Sri Venkateswara College, University of Delhi" + }, + { + "author_name": "Nirjara Singhvi", + "author_inst": "University of Delhi" + }, + { + "author_name": "Kalaiarasan Ponnusamy", + "author_inst": "Jawaharlal Nehru University" + }, + { + "author_name": "Md. Zubbair Malik", + "author_inst": "Jawaharlal Nehru University, New Delhi, India." + }, + { + "author_name": "Helianthous Verma", + "author_inst": "Ramjas College, University of Delhi" + }, + { + "author_name": "Roshan Kumar", + "author_inst": "Magadh University, Bodh Gaya, Bihar" + }, + { + "author_name": "Utkarsh Sood", + "author_inst": "The Energy and Resources Institute" + }, + { + "author_name": "Princy Hira", + "author_inst": "Maitreyi College, University of Delhi." + }, + { + "author_name": "Shiva Satija", + "author_inst": "Sri Venkateswara College, University of Delhi" + }, + { + "author_name": "Rup Lal", + "author_inst": "The Energy and Resources Institute" + }, + { + "author_name": "Yogendra Singh", + "author_inst": "University of Delhi" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.19.20135996", "rel_title": "The support needs of Australian primary health care nurses during the COVID-19 pandemic", @@ -1335995,57 +1339486,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.06.19.20135905", - "rel_title": "SARS-CoV-2 RT-PCR profile in 298 Indian COVID-19 patients : a retrospective observational study", - "rel_date": "2020-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.19.20135905", - "rel_abs": "BackgroundDespite being in the 5th month of pandemic, knowledge with respect to viral dynamics, infectivity and RT-PCR positivity continues to evolve.\n\nAimTo analyse the SARS CoV-2 nucleic acid RT-PCR profiles in COVID-19 patients.\n\nDesignIt was a retrospective, observational study conducted at COVID facilities under AIIMS, New Delhi.\n\nMethodsPatients admitted with laboratory confirmed COVID-19 were eligible for enrolment. Patients with incomplete details, or only single PCR tests were excluded. Data regarding demographic details, comorbidities, treatment received and results of SARS-CoV-2 RT-PCR performed on nasopharyngeal and oropharyngeal swabs, collected at different time points, was retrieved from the hospital records.\n\nResults298 patients were included, majority were males (75{middle dot}8%) with mean age of 39{middle dot}07 years (0{middle dot}6-88 years). The mean duration from symptom onset to first positive RT-PCR was 4{middle dot}7 days (SD 3{middle dot}67), while that of symptom onset to last positive test was 17{middle dot}83 days (SD 6{middle dot}22). Proportions of positive RT-PCR tests were 100%, 49%, 24%, 8{middle dot}7% and 20{middle dot}6% in the 1st, 2nd, 3rd, 4th & >4 weeks of illness. 12 symptomatic patients had prolonged positive test results even after 3 weeks of symptom onset. Age >= 60 years was associated with prolonged RT-PCR positivity (statistically significant).\n\nConclusionThis study showed that the average period of PCR positivity is more than 2 weeks in COVID-19 patients; elderly patients have prolonged duration of RT-PCR positivity and requires further follow up.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "bisakh bhattacharya", - "author_inst": "AIIMS, New Delhi" - }, - { - "author_name": "Rohit Kumar", - "author_inst": "All India Institute of Medical Sciences" - }, - { - "author_name": "Dr. Ved prakash Meena", - "author_inst": "AIIMS, New Delhi" - }, - { - "author_name": "Manish Soneja", - "author_inst": "AIIMS, New Delhi" - }, - { - "author_name": "Saurabh Vig", - "author_inst": "AIIMS, New Delhi" - }, - { - "author_name": "Vandana Rastogi", - "author_inst": "AIIMS, New Delhi" - }, - { - "author_name": "Sushma Bhatnagar", - "author_inst": "AIIMS, New Delhi" - }, - { - "author_name": "Anant Mohan", - "author_inst": "AIIMS, New Delhi" - }, - { - "author_name": "Naveet Wig", - "author_inst": "AIIMS, New Delhi" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.19.20135418", "rel_title": "Estimating the proportion of coronavirus disease 2019 (COVID-19) cases among households in France : a cross-sectional study on individuals with myocardial infarction history", @@ -1337276,6 +1340716,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.18.20134700", + "rel_title": "Predictable county-level estimates of R0 for COVID-19 needed for public health planning in the USA", + "rel_date": "2020-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20134700", + "rel_abs": "The basic reproduction number, R0, determines the rate of spread of a communicable disease and therefore gives fundamental information needed to plan public health interventions. Estimated R0 values are only useful, however, if they accurately predict the future potential rate of spread. Using mortality records, we estimated the rate of spread of COVID-19 among 160 counties and county-aggregates in the USA. Most of the high among-county variance in the rate of spread was explained by four factors: the timing of the county-level outbreak (partial R2 = 0.093), population size (partial R2 = 0.34), population density (partial R2 = 0.13), and spatial location (partial R2 = 0.42). Of these, the effect of timing is explained by early steps that people and governments took to reduce transmission, and population size is explained by the sample size of deaths that affects the statistical ability to estimate R0. For predictions of future spread, population density is important, likely because it scales the average contact rate among people. To generate support for a possible explanation for the importance of spatial location, we show that SARS-CoV-2 strains containing the G614 mutation to the spike gene are associated with higher rates of spread (P = 0.016). The high predictability of R0 based on population density and spatial location allowed us to extend estimates to all 3109 counties in the lower 48 States. The high variation of R0 among counties argues for public health policies that are enacted at the county level for controlling COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Anthony R Ives", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Claudio Bozzuto", + "author_inst": "Wildlife Analysis GmbH, Zurich, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.18.20134346", "rel_title": "The Relationship between the Global Burden of Influenza from 2017-2019 and COVID-19", @@ -1337457,69 +1340920,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.18.20134734", - "rel_title": "Epidemiological characterization of asymptomatic carriers of COVID-19 in Colombia", - "rel_date": "2020-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20134734", - "rel_abs": "ObjectiveAsymptomatic carriers (AC) of the new Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) represent an important source of spread for Coronavirus Disease 2019 (COVID-19). Early diagnosis of these cases is a powerful tool to control the pandemic. Our objective was to characterize patients with AC status and identify associated sociodemographic factors.\n\nMethodsUsing a cross-sectional design and the national database of daily occurrence of COVID-19, we characterized both socially and demographically all ACs. Additional Correspondence Analysis and Logistic Regression Model were performed to identify characteristics associated with AC state (OR, 95% CI).\n\nResults2338 ACs (11.8%; 95% CI, 11.3-12.2%) were identified, mainly in epidemiological week 18 [EW] (3.98; 3.24-4.90). Age [≤] 39 years (1.56; 1.42-1.72). Male sex (1.39; 1.26-1.53), cases imported from Argentina, Spain, Peru, Brazil, Costa Rica or Mexico (3.37; 1.47-7.71) and autochthonous cases (4.35; 2.12-8.93) increased the risk of identifying AC. We also identified groups of departments with moderate (3.68; 3.13-4.33) and strong (8.31; 6.10-7.46) association with AC.\n\nDiscussionSociodemographic characteristics strongly associated with AC were identified, which may explain its epidemiological relevance and usefulness to optimize mass screening strategies and prevent person-to-person transmission.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Anibal A Teheran", - "author_inst": "Cruz Roja de Colombia" - }, - { - "author_name": "Gabriel Camero", - "author_inst": "Cruz Roja Colombia" - }, - { - "author_name": "Ronald Prado de la Guardia", - "author_inst": "Cruz Roja Colombia" - }, - { - "author_name": "Carolina Hernandez", - "author_inst": "Universidad del Rosario" - }, - { - "author_name": "Giovanny Herrera", - "author_inst": "Universidad del Rosario" - }, - { - "author_name": "Luis M Pombo", - "author_inst": "Fundacion Universitaria Juan N Corpas" - }, - { - "author_name": "Albert Avila", - "author_inst": "Universidad de la Sabana" - }, - { - "author_name": "Carolina Florez", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Esther C Barros", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Luis Perez Garcia", - "author_inst": "Incubadora Venezolana de Ciencia" - }, - { - "author_name": "Alberto Paniz Mondolfi", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Juan David Ramirez", - "author_inst": "Universidad del Rosario" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.19.20134437", "rel_title": "LOCKDOWN AS A PANDEMIC MITIGATING POLICY INTERVENTION IN INDIA", @@ -1339602,6 +1343002,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.19.161687", + "rel_title": "Cytosine deamination in SARS-CoV-2 leads to progressive CpG depletion.", + "rel_date": "2020-06-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.19.161687", + "rel_abs": "RNA viruses use CpG reduction to evade the host cell defense, but the driving mechanisms are still largely unknown. In an attempt to address this we used a rapidly growing genomic dataset of SARS-CoV-2 with relevant metadata information. Remarkably, by simply ordering SARS-CoV-2 genomes by their date of collection, we find a progressive increase of C-to-U substitutions resulting in 5'-UCG-3' motif reduction that in turn have reduced the CpG frequency over just a few months of observation. This is consistent with APOBEC-mediated RNA editing resulting in CpG reduction, thus allowing the virus to escape ZAP-mediated RNA degradation. Our results thus link the dynamics of target sequences in the viral genome for two known host molecular defense mechanisms, mediated by the APOBEC and ZAP proteins.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Mukhtar Sadykov", + "author_inst": "King Abdullah University of Science and Technology" + }, + { + "author_name": "Tobias Mourier", + "author_inst": "King Abdullah University of Science and Technology" + }, + { + "author_name": "Qingtian Guan", + "author_inst": "King Abdullah University of Science and Technology" + }, + { + "author_name": "Arnab Pain", + "author_inst": "King Abdullah University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.19.158717", "rel_title": "No evidence of coronaviruses or other potentially zoonotic viruses in Sunda pangolins (Manis javanica) entering the wildlife trade via Malaysia.", @@ -1339739,121 +1343170,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.06.19.161141", - "rel_title": "High-density amplicon sequencing identifies community spread and ongoing evolution of SARS-CoV-2 in the Southern United States", - "rel_date": "2020-06-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.19.161141", - "rel_abs": "SARS-CoV-2 is constantly evolving. Prior studies have focused on high case-density locations, such as the Northern and Western metropolitan areas in the U.S. This study demonstrates continued SARS-CoV-2 evolution in a suburban Southern U.S. region by high-density amplicon sequencing of symptomatic cases. 57% of strains carried the spike D614G variant. The presence of D614G was associated with a higher genome copy number and its prevalence expanded with time. Four strains carried a deletion in a predicted stem loop of the 3 untranslated region. The data are consistent with community spread within the local population and the larger continental U.S. No strain had mutations in the target sites used in common diagnostic assays. The data instill confidence in the sensitivity of current tests and validate \"testing by sequencing\" as a new option to uncover cases, particularly those not conforming to the standard clinical presentation of COVID-19. This study contributes to the understanding of COVID-19 by providing an extensive set of genomes from a non-urban setting and further informs vaccine design by defining D614G as a dominant and emergent SARS-CoV-2 isolate in the U.S.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Ryan P McNamara", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Carolina Caro-Vegas", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Justin T Landis", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Razia Moorad", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Linda J Pluta", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Anthony B Eason", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Cecilia Thompson", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Aubrey Bailey", - "author_inst": "Kuopio Center for Gene and Cell Therapy" - }, - { - "author_name": "Femi Cleola S Villamor", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Philip T Lange", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Jason P Wong", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Tischan Seltzer", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Jedediah Seltzer", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Yijun Zhou", - "author_inst": "The University of North Carolina at Chapel Hill School of Medicine" - }, - { - "author_name": "Wolfgang Vahrson", - "author_inst": "Basel" - }, - { - "author_name": "Angelica Juarez", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "James O Meyo", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Tiphaine Calabre", - "author_inst": "Ecole superieure de Chimie Physique Electronique (CPE) Lyon" - }, - { - "author_name": "Grant Broussard", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Ricardo Rivera-Soto", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Danielle L Chappell", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Ralph S Baric", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Blossom Damania", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Melissa B Miller", - "author_inst": "The University of North Carolina at Chapel Hill" - }, - { - "author_name": "Dirk Dittmer", - "author_inst": "University of North Carolina at Chapel Hill" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.19.161612", "rel_title": "Disruption of Adaptive Immunity Enhances Disease in SARS-CoV-2 Infected Syrian Hamsters", @@ -1341100,6 +1344416,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.16.20132423", + "rel_title": "Seroprevalence and epidemiological characteristics of immunoglobulin M and G antibodies against SARS-CoV-2 in asymptomatic people in Wuhan, China", + "rel_date": "2020-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20132423", + "rel_abs": "ObjectivesPopulation screening for IgG and IgM against SARS-CoV-2 was initiated on March 25 and was open to all residents of Wuhan who were symptom-free. All ages with no fever, headache or other symptoms of COVID-19 among residents in Wuhan were included.\n\nMethodsThis study adopted a cross-sectional study. Pearson Chi-square test, T-test, and Mann-Whitney test were used in comparison between different groups. To correct the effects of gender and age, the seroprevalence of IgM positivity, IgG positivity, and IgM and/or IgG positivity were standardized according to the gender and age-specific population of Wuhan in 2017.\n\nResultsThe seroprevalence of IgG and IgM standardized for age and gender in Wuhan showed a downward trend. No significant correlation was observed between the seroprevalence of IgG and the different age groups. The seroprevalence was significantly higher for females than males (x2 =35.702, p < 0.001), with an odds ratio of 1.36 (95% CI: 1.24-1.48). A significant difference was seen in the seroprevalence of IgG among people from different geographic areas and different types of workplaces (respectively, x2 = 42.871, p < 0.001 and x2 = 202.43, p < 0.001). The IgG antibody-positive cases had a greater number of abnormalities in CT imaging than IgG-negative cases (30.7% vs 19.7%).\n\nConclusionsOur work found the reported number of confirmed patients in Wuhan only represents a small proportion of the total number of infections. There was a significant aggregation of asymptomatic infections in individuals from some occupations, and based on CT and laboratory findings, some damage may have occurred in asymptomatic individuals positive for IgG antibody.\n\nO_LSTStrengths and limitations of this studyC_LSTO_LIThis study has the important feature of having been designed as repeated five-day serosurveys, which allowed for the monitoring of seroprevalence progression.\nC_LIO_LIThis study applied scientific statistical methods accounting for the demographic structure of the general population and imperfect diagnostic tests to estimate seroprevalence in the overall population.\nC_LIO_LIThis study had selection bias since the analyzed medical records were based on examinees directed by their work units.\nC_LIO_LIPeople under the age of 19 and over age 65 were too few to be fully covered in analyses.\nC_LI", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Ruijie Ling", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Yihan Yu", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Jiayu He", + "author_inst": "National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Jixian Zhang", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Sha Xu", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Renrong Sun", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Wangcai Zhu", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Mingfeng Chen", + "author_inst": "National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Tao Li", + "author_inst": "National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Honglong Ji", + "author_inst": "Department of Cellular and Molecular Biology, University of Texas Health Science Centre at Tyler, Tyler, Texas, USA" + }, + { + "author_name": "Huanqiang Wang", + "author_inst": "National Institute of Occupational Health and Poisons Control,Chinese CDC" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.16.20133207", "rel_title": "Downsides of face masks and possible mitigation strategies: a systematic review and meta-analysis", @@ -1341281,101 +1344656,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.17.20133637", - "rel_title": "Two distinct immunopathological profiles in lungs of lethal COVID-19", - "rel_date": "2020-06-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20133637", - "rel_abs": "Coronavirus Disease 19 (COVID-19) is a respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has grown to a worldwide pandemic with substantial mortality. Immune mediated damage has been proposed as a pathogenic factor, but immune responses in lungs of COVID-19 patients remain poorly characterized. Therefore we conducted transcriptomic, histologic and cellular profiling of post mortem COVID-19 (n=34 tissues from 16 patients) and normal lung tissues (n=9 tissues from 6 patients). Two distinct immunopathological reaction patterns of lethal COVID-19 were identified. One pattern showed high local expression of interferon stimulated genes (ISGhigh) and cytokines, high viral loads and limited pulmonary damage, the other pattern showed severely damaged lungs, low ISGs (ISGlow), low viral loads and abundant infiltrating activated CD8+ T cells and macrophages. ISGhigh patients died significantly earlier after hospitalization than ISGlow patients. Our study may point to distinct stages of progression of COVID-19 lung disease and highlights the need for peripheral blood biomarkers that inform about patient lung status and guide treatment.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Ronny Nienhold", - "author_inst": "Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland" - }, - { - "author_name": "Yari Ciani", - "author_inst": "Laboratory of Computational and Functional Oncology, Department for Cellular, Computational and Integrative Biology CIBIO, University of Trento, Trento, Italy" - }, - { - "author_name": "Viktor H Koelzer", - "author_inst": "Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland" - }, - { - "author_name": "Alexandar Tzankov", - "author_inst": "Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland" - }, - { - "author_name": "Jasmin D Haslbauer", - "author_inst": "Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland" - }, - { - "author_name": "Thomas Menter", - "author_inst": "Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland" - }, - { - "author_name": "Nathalie Schwab", - "author_inst": "Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland" - }, - { - "author_name": "Maurice Henkel", - "author_inst": "Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland" - }, - { - "author_name": "Angela Frank", - "author_inst": "Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland" - }, - { - "author_name": "Veronika Zsikla", - "author_inst": "Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland" - }, - { - "author_name": "Niels Willi", - "author_inst": "Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland" - }, - { - "author_name": "Werner Kempf", - "author_inst": "Kempf und Pfaltz Histologische Diagnostik, Zurich, Switzerland" - }, - { - "author_name": "Thomas Hoyler", - "author_inst": "Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland" - }, - { - "author_name": "Mattia Barbareschi", - "author_inst": "Anatomia ed Istologia Patologica, Ospedale S. Chiara di Trento, Trento, Italy" - }, - { - "author_name": "Holger Moch", - "author_inst": "Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland" - }, - { - "author_name": "Markus Tolnay", - "author_inst": "Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland" - }, - { - "author_name": "Gieri Cathomas", - "author_inst": "Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland" - }, - { - "author_name": "Francesca Demichelis", - "author_inst": "Laboratory of Computational and Functional Oncology, Department for Cellular, Computational and Integrative Biology CIBIO, University of Trento, Trento, Italy" - }, - { - "author_name": "Tobias Junt", - "author_inst": "Novartis Institutes for BioMedical Research (NIBR), Basel, Switzerland" - }, - { - "author_name": "Kirsten D Mertz", - "author_inst": "Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.06.17.20134098", "rel_title": "SEROPREVALENCE AND CLINICAL SPECTRUM OF SARS-CoV-2 INFECTION IN THE FIRST VERSUS THIRD TRIMESTER OF PREGNANCY", @@ -1342610,6 +1345890,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.06.17.20133611", + "rel_title": "Knowledge, Attitudes, and Fear of COVID-19 during the Rapid Rise Period in Bangladesh", + "rel_date": "2020-06-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20133611", + "rel_abs": "ObjectivesTo determine the level of Knowledge, Attitude, and Practice (KAP) related to COVID-19 preventive health habits and perception of Fear towards COVID-19 in subjects living in Bangladesh.\n\nDesignProspective, cross-sectional survey of (n= 2157) male and female subjects, 13-90 years of age, living in Bangladesh.\n\nMethodsEthical Approval and Trial registration were obtained prior to the commencement of the study. Subjects who volunteered to participate and signed the informed consent were enrolled in the study and completed the \"Fear of COVID-19 Scale\" (FCS).\n\nResultsTwenty-eight percent (28.69%) of subjects reported one or more COVID-19 symptoms and 21.4% of subjects reported one or more comorbidities. Knowledge scores were slightly higher in males (8.75{+/-} 1.58) than females (8.66{+/-} 1.70). Knowledge was significantly correlated with age (p<.005), an education level (p<.001), Attitude (p<.001), and urban location (p=<.001). Knowledge scores showed an inverse correlation with Fear scores (p=<.001). Eighty-three percent (83.7%) of subjects with COVID-19 symptoms reported wearing a mask in public and 75.4% of subjects reported staying away from crowded places. Subjects with one or more symptoms reported higher Fear compared to subjects without (18.73{+/-} 4.6; 18.45{+/-} 5.1).\n\nConclusionsOverall, Bangladeshis reported a high prevalence of self-isolation, positive preventive health behaviors related to COVID-19, and moderate to high fear levels. Higher Knowledge and Practice were found in males, higher education levels, older age, and urban location. \"Fear\" of COVID-19 was more prevalent in female and elderly subjects. Positive \"Attitude\" was reported for the majority of subjects, reflecting the belief that COVID-19 was controllable and containable.\n\nEthical approvalEthical permission obtained from the Institutional review board (BPA-IPRR/IRB/29/03/2020/021) of Institute of Physiotherapy, Rehabilitation, and Research (IPRR), the academic organization of the Bangladesh Physiotherapy Association.\n\nWHO Trial registryThe trial registration obtained prospectively from a primary trial registry of WHO (CTRI/2020/04/024413).\n\nData AvailabilityThe data are available regarding this study and can be viewed upon request", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Mohammad Anwar Hossain", + "author_inst": "Centre for the Rehabilitation of the Paralysed" + }, + { + "author_name": "K M Amran Hossain", + "author_inst": "Bangladesh Health Professions Institute" + }, + { + "author_name": "Lori Maria Walton", + "author_inst": "University of Scranton" + }, + { + "author_name": "Zakir Uddin", + "author_inst": "McGill University" + }, + { + "author_name": "Md. Obaidul Haque", + "author_inst": "Bangladesh Health Professions Institute" + }, + { + "author_name": "Md. Feroz Kabir", + "author_inst": "Jashore University of Science and Technology" + }, + { + "author_name": "S. M. Yasir Arafat", + "author_inst": "Enam Medical College & Hospital" + }, + { + "author_name": "Mohamed Sakel", + "author_inst": "East Kent University NHS Hospital" + }, + { + "author_name": "Rafey Faruqui", + "author_inst": "Kent & Medway NHS and Social care Partnership Trust" + }, + { + "author_name": "Ikbal Kabir Jahid", + "author_inst": "Jashore University of Science and Technology" + }, + { + "author_name": "Zahid Hossain", + "author_inst": "Bangladesh Health Professions Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.16.20133215", "rel_title": "The first proof of the capability of wastewater surveillance for COVID-19 in India through the detection of the genetic material of SARS-CoV-2", @@ -1342803,57 +1346142,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.16.20132787", - "rel_title": "State-wise estimates of current hospital beds, intensive care unit (ICU) beds and ventilators in India: Are we prepared for a surge in COVID-19 hospitalizations?", - "rel_date": "2020-06-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20132787", - "rel_abs": "BackgroundThe rapid spread of COVID-19 globally has prompted policymakers to evaluate the capacity of health care infrastructure in their communities. Many hard-hit localities have witnessed a large influx of severe cases that strained existing hospitals. As COVID-19 spreads in India, it is essential to evaluate the countrys capacity to treat severe cases.\n\nMethodsWe combined data on public and private sector hospitals in India to produce state level estimates of hospital beds, ICU beds, and mechanical ventilators. Based on the number of public sector hospitals from the 2019 National Health Profile (NHP) of India and the relative proportions of public and private health care facilities from the National Sample Survey (NSS) 75th round (2017-2018), we estimated capacity in each Indian state and union territory (UT). We assumed that 5% of all hospital beds were ICU beds and that 50% of ICU beds were equipped with ventilators.\n\nResultsWe estimated that India has approximately 1.9 million hospital beds, 95,000 ICU beds and 48,000 ventilators. Nationally, resources are concentrated in the private sector (hospital beds: 1,185,242 private vs 713,986 public; ICU beds: 59,262 private vs 35,699 public; ventilators: 29,631 private vs. 17,850 public). Our findings suggest substantial variation in available resources across states and UTs.\n\nConclusionSome projections shave suggested a potential need for approximately 270,000 ICU beds in an optimistic scenario, over 2.8 times the estimated number of total available ICU beds in India. Additional resources will likely be required to accommodate patients with severe COVID-19 infections in India.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Geetanjali Kapoor", - "author_inst": "Center for Disease Dynamics, Economics & Policy" - }, - { - "author_name": "Stephanie Hauck", - "author_inst": "Center for Disease Dynamics, Economics & Policy" - }, - { - "author_name": "Aditi Sriram", - "author_inst": "Center for Disease Dynamics, Economics & Policy" - }, - { - "author_name": "Jyoti Joshi", - "author_inst": "Center for Disease Dynamics, Economics & Policy" - }, - { - "author_name": "Emily Schueller", - "author_inst": "Center for Disease Dynamics, Economics & Policy" - }, - { - "author_name": "Isabel Frost", - "author_inst": "Center for Disease Dynamics, Economics & Policy" - }, - { - "author_name": "Ruchita Balasubramanian", - "author_inst": "Center for Disease Dynamics, Economics & Policy" - }, - { - "author_name": "Ramanan Laxminarayan", - "author_inst": "Center for Disease Dynamics, Economics & Policy" - }, - { - "author_name": "Arindam Nandi", - "author_inst": "The Center for Disease Dynamics, Economics & Policy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.06.16.20132878", "rel_title": "The Cardiac Toxicity of Chloroquine or Hydroxychloroquine in COVID-19 Patients: A Systematic Review and Meta-regression Analysis", @@ -1344484,6 +1347772,25 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.06.16.154559", + "rel_title": "in-silica Analysis of SARS-CoV-2 viral strain using Reverse Vaccinology Approach: A Case Study for USA", + "rel_date": "2020-06-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.154559", + "rel_abs": "The recent pandemic of COVID19 that has struck the world is yet to be battled by a potential cure. Countless lives have been claimed due to the existing pandemic and the societal normalcy has been damaged permanently. As a result, it becomes crucial for academic researchers in the field of bioinformatics to combat the existing pandemic. The study involved collecting the virulent strain sequence of SARS-nCoV19 for the country USA against human host through publically available bioinformatics databases. Using in-silica analysis and reverse vaccinology, two leader proteins were identified to be potential vaccine candidates for development of a multi-epitope drug. The results of this study can provide further researchers better aspects and direction on developing vaccine and immune responses against COVID19. This work also aims at promoting the use of existing bioinformatics tools to faster streamline the pipeline of vaccine development.\n\nThe Situation of COVID19A new infection respiratory disease was first observed in the month of December 2019, in Wuhan, situated in the Hubei province, China. Studies have indicated that the reason of this disease was the emergence of a genetically-novel coronavirus closely related to SARS-CoV. This coronavirus, now named as nCoV-19, is the reason behind the spread of this fatal respiratory disease, now named as COVID-19. The initial group of infections is supposedly linked with the Huanan seafood market, most likely due to animal contact. Eventually, human-to-human interaction occurred and resulted in the transmission of the virus to humans. [13].\n\nSince then, nCoV-19 has been rapidly spreading within China and other parts of World. At the time of writing this article (mid-March 2020), COVID-19 has spread across 146 countries. A count of 164,837 cases have been confirmed of being diagnosed with COVID-19, and a total of 6470 deaths have occurred. The cumulative cases have been depicting a rising trend and the numbers are just increasing. WHO has declared COVID-19 to be a \"global health emergency\". [14].\n\nCurrent Scenario and ObjectivesCurrently, research is being conducted on a massive level to understand the immunology and genetic characteristics of the disease. However, no cure or vaccine of nCoV-19 has been developed at the time of writing this article.\n\nThough, nCoV-19 and SARS-CoV are almost genetically similar, the respiratory syndrome caused by both of them, COVID-19 and SARS respectively, are completely different. Studies have indicated that -\n\n\"SARS was more deadly but much less infectious than COVID-19\".\n\n-World Health Organization", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ajay Agarwal", + "author_inst": "DIT University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.06.15.20130328", "rel_title": "Can we trust the prediction model? Demonstrating the importance of external validation by investigating the COVID-19 Vulnerability (C-19) Index across an international network of observational healthcare datasets", @@ -1344705,85 +1348012,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.15.20131540", - "rel_title": "Causes of Death and Comorbidities in Patients with COVID-19", - "rel_date": "2020-06-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20131540", - "rel_abs": "Infection by the new corona virus strain SARS-CoV-2 and its related syndrome COVID-19 has caused several hundreds of thousands of deaths worldwide. Patients of higher age and with preexisting chronic health conditions are at an increased risk of fatal disease outcome. However, detailed information on causes of death and the contribution of comorbidities to death yet is missing. Here, we report autopsy findings on causes of death and comorbidities of 26 decedents that had clinically presented with severe COVID-19. We found that septic shock and multi organ failure was the most common immediate cause of death, often due to suppurative pulmonary infection. Respiratory failure due to diffuse alveolar damage presented as the most immediate cause of death in fewer cases. Several comorbidities, such as hypertension, ischemic heart disease, and obesity were present in the vast majority of patients. Our findings reveal that causes of death were directly related to COVID-19 in the majority of decedents, while they appear not to be an immediate result of preexisting health conditions and comorbidities. We therefore suggest that the majority of patients had died of COVID-19 with only contributory implications of preexisting health conditions to the mechanism of death.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Sefer Elezkurtaj", - "author_inst": "Charite - Universitaetsmedizin Berlin, Germany" - }, - { - "author_name": "Selina Greuel", - "author_inst": "Charite - Universitaetsmedizin Berlin, Germany" - }, - { - "author_name": "Jana Ihlow", - "author_inst": "Charite - Universitaetsmedizin Berlin, Germany" - }, - { - "author_name": "Edward Michaelis", - "author_inst": "Charite - Universitaetsmedizin Berlin, Germany" - }, - { - "author_name": "Philip Bischoff", - "author_inst": "Charite - Universitaetsmedizin Berlin, Germany" - }, - { - "author_name": "Catarina Alisa Kunze", - "author_inst": "Charite - Universitaetsmedizin Berlin, Germany" - }, - { - "author_name": "Bruno Valentin Sinn", - "author_inst": "Charite - Universitaetsmedizin Berlin, Germany" - }, - { - "author_name": "Manuela Gerhold", - "author_inst": "Charite - Universitaetsmedizin Berlin, Germany" - }, - { - "author_name": "Kathrin Hauptmann", - "author_inst": "Charite - Universitaetsmedizin Berlin, Germany" - }, - { - "author_name": "Barbara Ingold-Heppner", - "author_inst": "DRK Kliniken Berlin, Germany" - }, - { - "author_name": "Florian Miller", - "author_inst": "Vivantes GmbH, Berlin, Germany" - }, - { - "author_name": "Hermann Herbst", - "author_inst": "Vivantes GmbH, Berlin, Germany" - }, - { - "author_name": "Victor Max Corman", - "author_inst": "Charite - Universitaetsmedizin Berlin, Germany" - }, - { - "author_name": "Hubert Martin", - "author_inst": "Charite - Universitaetsmedizin Berlin, Germany" - }, - { - "author_name": "Frank L Heppner", - "author_inst": "Charite - Universitaetsmedizin Berlin, Germany" - }, - { - "author_name": "David Horst", - "author_inst": "Charite - Universitaetsmedizin Berlin, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.06.15.20131532", "rel_title": "Risk of Depression in Family Caregivers: Unintended Consequence of COVID-19", @@ -1346146,6 +1349374,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.06.16.151555", + "rel_title": "Decoding of persistent multiscale structures in complex biological networks", + "rel_date": "2020-06-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.151555", + "rel_abs": "In any omics study, the scale of analysis can dramatically affect the outcome. For instance, when clustering single-cell transcriptomes, is the analysis tuned to discover broad or specific cell types? Likewise, protein communities revealed from protein networks can vary widely in sizes depending on the method. Here we use the concept of \"persistent homology\", drawn from mathematical topology, to identify robust structures in data at all scales simultaneously. Application to mouse single-cell transcriptomes significantly expands the catalog of identified cell types, while analysis of SARS-COV-2 protein interactions suggests hijacking of WNT. The method, HiDeF, is available via Python and Cytoscape.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Fan Zheng", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "She Zhang", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Christopher Churas", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Dexter Pratt", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Ivet Bahar", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Trey Ideker", + "author_inst": "University of California, San Diego" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2020.06.17.157982", "rel_title": "Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding", @@ -1346387,129 +1349654,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.06.16.155101", - "rel_title": "Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection", - "rel_date": "2020-06-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.155101", - "rel_abs": "Identification of host genes essential for SARS-CoV-2 infection may reveal novel therapeutic targets and inform our understanding of COVID-19 pathogenesis. Here we performed a genome-wide CRISPR screen with SARS-CoV-2 and identified known SARS-CoV-2 host factors including the receptor ACE2 and protease Cathepsin L. We additionally discovered novel pro-viral genes and pathways including the SWI/SNF chromatin remodeling complex and key components of the TGF-{beta} signaling pathway. Small molecule inhibitors of these pathways prevented SARS-CoV-2-induced cell death. We also revealed that the alarmin HMGB1 is critical for SARS-CoV-2 replication. In contrast, loss of the histone H3.3 chaperone complex sensitized cells to virus-induced death. Together this study reveals potential therapeutic targets for SARS-CoV-2 and highlights host genes that may regulate COVID-19 pathogenesis.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Jin Wei", - "author_inst": "Yale University" - }, - { - "author_name": "Mia Alfajaro", - "author_inst": "Yale University" - }, - { - "author_name": "Ruth Hanna", - "author_inst": "Broad Institute" - }, - { - "author_name": "Peter DeWeirdt", - "author_inst": "Broad Institute" - }, - { - "author_name": "Madison Strine", - "author_inst": "Yale University" - }, - { - "author_name": "William Lu-Culligan", - "author_inst": "Yale University" - }, - { - "author_name": "Shang-Min Zhang", - "author_inst": "Yale University" - }, - { - "author_name": "Vincent Graziano", - "author_inst": "Yale University" - }, - { - "author_name": "Cameron Schmitz", - "author_inst": "Yale University" - }, - { - "author_name": "Jennifer Chen", - "author_inst": "Yale University" - }, - { - "author_name": "Madeleine Mankowski", - "author_inst": "Yale University" - }, - { - "author_name": "Renata Filler", - "author_inst": "Yale University" - }, - { - "author_name": "Victor Gasque", - "author_inst": "Yale University" - }, - { - "author_name": "Fernando de Miguel", - "author_inst": "Yale University" - }, - { - "author_name": "Huacui Chen", - "author_inst": "Yale University" - }, - { - "author_name": "Kasopefoluwa Y Oguntuyo", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Laura Abriola", - "author_inst": "Yale University" - }, - { - "author_name": "Yulia Surovtseva", - "author_inst": "Yale University" - }, - { - "author_name": "Robert Orchard", - "author_inst": "University of Texas Southwestern Medical School" - }, - { - "author_name": "Benhur Lee", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Brett Lindenbach", - "author_inst": "Yale University" - }, - { - "author_name": "Katerina Politi", - "author_inst": "Yale University" - }, - { - "author_name": "David van Dijk", - "author_inst": "Yale University" - }, - { - "author_name": "Matthew Simon", - "author_inst": "Yale University" - }, - { - "author_name": "Qin Yan", - "author_inst": "Yale University" - }, - { - "author_name": "John G Doench", - "author_inst": "Broad Institute" - }, - { - "author_name": "Craig B Wilen", - "author_inst": "Yale University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.06.16.155812", "rel_title": "Crystal structure of SARS-CoV-2 main protease in complex with a Chinese herb inhibitor shikonin", @@ -1347960,6 +1351104,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.13.20130062", + "rel_title": "Guillain Barr e syndrome in COVID-19:A scoping review", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130062", + "rel_abs": "IntroductionThe novel corona virus (COVID19) can result in several neurological complications. Guillain-Barre Syndrome (GBS) is one of them and has been reported from different parts of the world in this pandemic. It is an acute post infectious polyneuropathy. The review aims to summarize the demographic features, clinical presentation, diagnostics workup, and management strategies of COVID-19 associated GBS reported in literature.\n\nMaterial and methodWe searched Medline, PubMed Central, SCOPUS and Google Scholar using pre-defined keywords, with no time limits and in English language only. We aimed to include all kind of manuscripts. Last search was done on 18th May 2020.\n\nDemographics, clinical features, diagnostic workup, management, and outcomes were documented in the data sheet.\n\nResultsWe identified 24 cases of COVID-19 associated GBS. Most of the cases were reported from Italy followed by USA. Majority were males (18 /24) The age ranged from 23 -84 years. The clinical presentation was typical sensory-motor GBS in most. Nine patients had facial palsy of which five had bilateral involvement. Two patients had bilateral abducent nerve palsy while two presented as paraparetic GBS variant with autonomic dysfunction. Electrodiagnostics was performed in 17 patients only and 12 had typical features of acute inflammatory demyelinating polyneuropathy.. Intravenous immunoglobulins were the preferred mode of treatment in most of the patient. There was one death, and most were discharged to rehabilitation or home.\n\nConclusionGBS is a frequent neurological complication associated with COVID-19. There is no clear causative relationship between GBS, and COVID-19 at present and more data are needed to establish the casualty. However, most cases have a post-infectious onset with male preponderance. Most of the cases have a typical presentation but some may present in an atypical way. Prognosis is generally good.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Imran Ahmad", + "author_inst": "Bahria University Medical and Dental College" + }, + { + "author_name": "Farooq Azam Rathore", + "author_inst": "Bahria University Medical and Dental College" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.06.13.20130310", "rel_title": "COVID-19: a crash test for biomedical publishing?", @@ -1348057,37 +1351224,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.13.20130245", - "rel_title": "A systematic review protocol of the antiviral activity of chloroquine and hydroxychloroquine against COVID-19.", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130245", - "rel_abs": "IntroductionThe recent outbreak of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), or COVID-19 with no approved medicines has led to global health threat. Currently, repositioning of old medicines seems the most responsible strategy for potential cure and prevention COVID-19. Hydroxychloroquine and chloroquine have shown promising efficacy against COVID-19 related pneumonia in clinical studies. However, the mode of drug action of chloroquine and hydroxychloroquine against SARS-CoV-2 infection is not clear. This review aims to gather evidence on antiviral activity and possible mechanism of drug action of chloroquine and hydroxychloroquine on SARS-CoV-2, including in-vitro, animal studies, and studies in humans.\n\nMethodA structured search of five bibliographic databases namely; Medline, Web of Science, PubMed, Cochrane CENTRAL, and Google Scholar will be undertaken to retrieve studies that describe the antiviral activity and possible mechanism of drug action of chloroquine and hydroxychloroquine on SARS-CoV-2. No restrictions will be placed on publication date, but studies will be limited to only publications in English. Duplication of studies will be removed using EndNote reference manager. Three authors will screen the citations independently based on inclusion criteria. Data extraction and assessment of risk of bias will be done independently. Meta-analysis of selected studies will be done wherever suitable.\n\nEthics and disseminationPrimary data collection will not be involved in this study, hence no need for formal ethical clearance. Findings from the study will be disseminated through a peer-reviewed publication and conference meeting.\n\nTrial registration numberhttps://doi.org/10.17605/OSF.IO/7DJMU\n\nStrengths and limitations of this studyO_LIThis study is the first systematic review to gather current evidence on the antiviral effect and mode of action of chloroquine and hydroxychloroquine on SARS-CoV-2 infection. We expect that data that will be synthesis will provide enough information to inform COVID-19 care pathways and help clinicians caring for COVID-19 patients.\nC_LIO_LIFurthermore, this systematic review will expand our knowledge on the benefits and risks of chloroquine and hydroxychloroquine in management of COVID-19 patients and identify areas of controversies, and quality assessment.\nC_LIO_LIWe anticipate that there will be few studies reporting on the mechanism of drug action and antiviral effects of chloroquine and hydroxychloroquine on SARS-CoV-2 infection.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Kofi Boamah Mensah", - "author_inst": "Kwame Nkrumah University of Science and Technology" - }, - { - "author_name": "Adwoa Bemah Boamah Mensah", - "author_inst": "Kwame NkrumahUniversity of Science and Technology" - }, - { - "author_name": "Varsha Bangalee", - "author_inst": "University of KwaZulu-Natal" - }, - { - "author_name": "Frasia Oosthuizen", - "author_inst": "University of Kwazulu-Natal" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.13.20130237", "rel_title": "Quantification of SARS-CoV-2 viral copy number in saliva mouthwash samples using digital droplet PCR", @@ -1349066,6 +1352202,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.13.20130617", + "rel_title": "Is tracking and modeling Covid-19 infection dynamics for Bangladesh using daily data feasible?", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130617", + "rel_abs": "Given the low Covid-19 testing coverage in the country, this study tested whether the daily change in the number of new Covid-19 cases is due to increase (or decrease) in the number of tests done daily. We performed Granger causality test based on vector autoregressive models on Bangladeshs case and test numbers between 8 March and 5 June 2020, using publicly available data. The test results show that the daily number of tests Granger-cause the number of new cases (p <0.001), meaning the daily number of new cases is perhaps due to an increase in test capacity rather than a change in the infection rates. From the results of this test we can infer that if the number of daily tests does not increase substantially, data on new infections will not give much information for understanding covid-19 infection dynamics in Bangladesh.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Karar Zunaid Ahsan", + "author_inst": "Gillings School of Global Public Health, the University of North Carolina at Chapel Hill, NC, USA" + }, + { + "author_name": "Rashida Ijdi", + "author_inst": "Carolina Population Center, University of North Carolina at Chapel Hill, NC, USA" + }, + { + "author_name": "Peter Kim Streatfield", + "author_inst": "Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.13.20130088", "rel_title": "Compassionate Use of Tocilizumab in Severe SARS-CoV2 Pneumonia. When late administration is too late.", @@ -1349255,153 +1352418,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.06.12.20129056", - "rel_title": "Symptom clusters in Covid19: A potential clinical prediction tool from the COVID Symptom study app", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20129056", - "rel_abs": "As no one symptom can predict disease severity or the need for dedicated medical support in COVID-19, we asked if documenting symptom time series over the first few days informs outcome. Unsupervised time series clustering over symptom presentation was performed on data collected from a training dataset of completed cases enlisted early from the COVID Symptom Study Smartphone application, yielding six distinct symptom presentations. Clustering was validated on an independent replication dataset between May 1-May 28th, 2020. Using the first 5 days of symptom logging, the ROC-AUC of need for respiratory support was 78.8%, substantially outperforming personal characteristics alone (ROC-AUC 69.5%). Such an approach could be used to monitor at-risk patients and predict medical resource requirements days before they are required.\n\nOne sentence summaryLongitudinal clustering of symptoms can predict the need for respiratory support in severe COVID-19.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Carole H Sudre", - "author_inst": "King's College London" - }, - { - "author_name": "Karla Lee", - "author_inst": "Department of Twin Research and Genetic Epidemiology" - }, - { - "author_name": "Mary Ni Lochlainn", - "author_inst": "King's College London" - }, - { - "author_name": "Thomas Varsavsky", - "author_inst": "King's College London" - }, - { - "author_name": "Benjamin Murray", - "author_inst": "King's College London" - }, - { - "author_name": "Mark S. Graham", - "author_inst": "King's College London" - }, - { - "author_name": "Cristina Menni", - "author_inst": "King's College London" - }, - { - "author_name": "Marc Modat", - "author_inst": "King's College London" - }, - { - "author_name": "Ruth C.E. Bowyer", - "author_inst": "King's College London" - }, - { - "author_name": "Long H Nguyen", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "David Alden Drew", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Amit D Joshi", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Wenjie Ma", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Chuan Guo Guo", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Chun Han Lo", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Sajaysurya Ganesh", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Abubakar Buwe", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Joan Capdevila Pujol", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Julien Lavigne du Cadet", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Alessia Visconti", - "author_inst": "King's College London" - }, - { - "author_name": "Maxim Freydin", - "author_inst": "King's College London" - }, - { - "author_name": "Julia S. El Sayed Moustafa", - "author_inst": "King's College London" - }, - { - "author_name": "Mario Falchi", - "author_inst": "King's College London" - }, - { - "author_name": "Richard Davies", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Maria F. Gomez", - "author_inst": "Lund University" - }, - { - "author_name": "Tove Fall", - "author_inst": "Lund University" - }, - { - "author_name": "M. Jorge Cardoso", - "author_inst": "King's College London" - }, - { - "author_name": "Jonathan Wolf", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Paul W Franks", - "author_inst": "Lund University" - }, - { - "author_name": "Andrew T Chan", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Timothy D Spector", - "author_inst": "King's College London" - }, - { - "author_name": "Claire J Steves", - "author_inst": "King's College London" - }, - { - "author_name": "Sebastien Ourselin", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.06.15.20131227", "rel_title": "Remdesivir Efficacy in Coronavirus Disease 2019 (COVID-19): A Systematic Review", @@ -1350864,6 +1353880,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.15.153692", + "rel_title": "Bio-JOIE: Joint Representation Learning of Biological Knowledge Bases", + "rel_date": "2020-06-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.15.153692", + "rel_abs": "The widespread of Coronavirus has led to a worldwide pandemic with a high mortality rate. Currently, the knowledge accumulated from different studies about this virus is very limited. Leveraging a wide-range of biological knowledge, such as gene on-tology and protein-protein interaction (PPI) networks from other closely related species presents a vital approach to infer the molecular impact of a new species. In this paper, we propose the transferred multi-relational embedding model Bio-JOIE to capture the knowledge of gene ontology and PPI networks, which demonstrates superb capability in modeling the SARS-CoV-2-human protein interactions. Bio-JOIE jointly trains two model components. The knowledge model encodes the relational facts from the protein and GO domains into separated embedding spaces, using a hierarchy-aware encoding technique employed for the GO terms. On top of that, the transfer model learns a non-linear transformation to transfer the knowledge of PPIs and gene ontology annotations across their embedding spaces. By leveraging only structured knowledge, Bio-JOIE significantly outperforms existing state-of-the-art methods in PPI type prediction on multiple species. Furthermore, we also demonstrate the potential of leveraging the learned representations on clustering proteins with enzymatic function into enzyme commission families. Finally, we show that Bio-JOIE can accurately identify PPIs between the SARS-CoV-2 proteins and human proteins, providing valuable insights for advancing research on this new disease.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Junheng Hao", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Chelsea Jui-Ting Ju", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Muhao Chen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Yizhou Sun", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Carlo Zaniolo", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Wei Wang", + "author_inst": "University of California, Los Angeles" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.06.16.153403", "rel_title": "Oral drug repositioning candidates and synergistic remdesivir combinations for the prophylaxis and treatment of COVID-19", @@ -1351077,89 +1354132,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2020.06.16.154211", - "rel_title": "TMPRSS2, a SARS-CoV-2 internalization protease is downregulated in head and neck cancer patients.", - "rel_date": "2020-06-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.154211", - "rel_abs": "ObjectivesTwo of the main target tissues of SARS-coronavirus 2 are the oral cavity pharynx-larynx epithelium, the main virus entry site, and the lung epithelium. The virus enters host cells through binding of the Spike protein to ACE2 receptor and subsequent S priming by the TMPRSS2 protease. Herein we aim to assess differences in both ACE2 and TMPRSS2 expression in normal tissues from oral cavity-pharynx-larynx and lung tissues as well as neoplastic tissues from the same histological areas. The information provided in this study may contribute to better understanding of SARS-coronavirus 2 ability to interact with different biological systems and contributes to cumulative knowledge on potential mechanisms to inhibit its diffusion.\n\nMaterials and MethodsThe study has been conducted using The Cancer Genome Atlas (TCGA) and the Regina Elena Institute (IRE) databases and validated by experimental model in HNSCC and Lung cancer cells. Data from one COVID19 positive patient who was operated on for HNSCC was also included. We have analyzed 478 tumor samples and 44 normal samples from TCGA HNSCC cohort for whom both miRNA and mRNA sequencing was available. The dataset included 391 HPV- and 85 HPV+ cases, with 331 P53 mutated and 147 P53 wild type cases respectively. 352 out of 478 samples were male and 126 female. In IRE cohort we analyzed 66 tumor samples with matched normal sample for miRNA profiling and 23 tumor\\normal matched samples for mRNA profiling. 45 out of 66 tumors from IRE cohort were male and 21 female, 38 were P53 mutated and 27 wild type. Most patients (63 of 66) in IRE cohort were HPV negative. Normalized TCGA HNSCC gene expression and miRNA expression data were obtained from Broad Institute TCGA Genome Data Analysis Center (http://gdac.broadinstitute.org/). mRNA expression data from IRE cohort used in this study has been deposited to NCBIs Gene Expression Omnibus and is accessible through GEO series accession number GSE107591. In order to inference about potential molecular modulation of TMPRSS2, we also included miRNAs expression for the 66 IRE cohort matched tumor and normal samples from Agilent platform. DNA methylation data for TCGA tumors were obtained from Wanderer (http://maplab.imppc.org/wanderer/). We used miRWalk and miRNet web tools for miRNA-target interaction prediction and pathway enrichment analysis. The correlation and regression analyses as well as the miRNA and gene modulation and the survival analysis were conducted using Matlab R2019.\n\nResultsTMPRSS2 expression in HNSCC was significantly reduced compared to the normal tissues and had a prognostic value in HNSCC patients. Reduction of TMPRSS2 expression was more evident in women than in men, in TP53 mutated versus wild TP53 tumors as well as in HPV negative patients compared to HPV positive counterparts. Functionally, we assessed the multivariate effect on TMPRSS2 in a single regression model. We observed that all variables had an independent effect on TMPRSS2 in HNSCC patients with HPV negative, TP53 mutated status and with elevated TP53-dependent Myc-target genes associated with low TMPRSS2 expression. Investigation of the molecular modulation of TMPRSS2 in both HNSCC and lung cancers revealed that expression of microRNAs targeting TMPRSS2 anti-correlated in both TCGA and IRE HNSCC datasets, while there was not evidence of TMPRSS2 promoter methylation in both tumor cohorts. Interestingly, the anti-correlation between microRNAs and TMPRSS2 expression was corroborated by testing this association in a SARS-CoV-2 positive HNSCC patient.\n\nConclusionsCollectively, these findings suggest that tumoral tissues, herein exemplified by HNSCC and lung cancers might be more resistant to SARS-CoV-2 infection due to reduced expression of TMPRSS2. The protective mechanism might occur, at least partially, through the aberrant activation of TMPRSS2 targeting microRNAs; thereby providing strong evidence on the role of non-coding RNA molecule in host viral infection. These observations may help to better assess the frailty of SARS-CoV-2 positive cancer patients.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Andrea Sacconi", - "author_inst": "IRCCS Regina Elena National Cancer Institute" - }, - { - "author_name": "Sara Donzelli", - "author_inst": "IRCCS Regina Elena National Cancer Institute" - }, - { - "author_name": "Claudio Pulito", - "author_inst": "IRCCS Regina Elena National Cancer Institute" - }, - { - "author_name": "Stefano Ferrero", - "author_inst": "University of Milan La Statale" - }, - { - "author_name": "Aldo Morrone", - "author_inst": "San Gallicano Dermatological Institute IRCCS" - }, - { - "author_name": "Marta Rigoni", - "author_inst": "University of Trento" - }, - { - "author_name": "Fulvia Pimipinelli", - "author_inst": "San Gallicano Dermatologic Institute IRCCS" - }, - { - "author_name": "Fabrizio Ensoli", - "author_inst": "San Gallicano Dermatologic Institute IRCCS" - }, - { - "author_name": "Giuseppe Sanguineti", - "author_inst": "IRCCS Regina Elena National Cancer Institute" - }, - { - "author_name": "Raul Pellini", - "author_inst": "IRCCS Regina Elena National Cancer Institute" - }, - { - "author_name": "Nishant Agrawal", - "author_inst": "University of Chicago Medicine and Biological Sciences" - }, - { - "author_name": "Evgeny Izumchenko", - "author_inst": "University of Chicago Medicine and Biological Sciences" - }, - { - "author_name": "Gennaro Ciliberto", - "author_inst": "IRCCS Regina Elena National Cancer Institute" - }, - { - "author_name": "Aldo Gianni", - "author_inst": "University of Milan La Statale" - }, - { - "author_name": "Paola Muti", - "author_inst": "University of Milan La Statale" - }, - { - "author_name": "Sabrina Strano", - "author_inst": "IRCCS Regina Elena National Cancer Institute" - }, - { - "author_name": "Giovanni Blandino", - "author_inst": "IRCCS Regina Elena National Cancer Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cancer biology" - }, { "rel_doi": "10.1101/2020.06.16.154658", "rel_title": "Lack of susceptibility of poultry to SARS-CoV-2 and MERS-CoV", @@ -1352706,6 +1355678,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.11.20128330", + "rel_title": "Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador.", + "rel_date": "2020-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128330", + "rel_abs": "SARS-CoV-2, the etiological agent of COVID-19 was first described in Wuhan in December 2019 and has now spread globally. Ecuador was the second country in South America to report confirmed cases. The first case reported in Quito, the capital city of Ecuador, was a tourist who came from the Netherlands and presented symptoms on March 10th, 2020 (index case). In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the metagenome of the bronchoalveolar lavage (BAL) from this case reported, and subsequently we sequenced the whole genome of the index case and other three patients using the ARTIC network protocols. Our data from the metagenomic approach confirmed the presence of SARS-CoV-2 coexisting with pathogenic bacteria suggesting coinfection. Relevant bacteria found in the BAL metagenome were Streptococcus pneumoniae, Mycobacterium tuberculosis, Staphylococcus aureus and Chlamydia spp. Lineage assignment of the four whole genomes revealed three different origins. The variant HEE-01 was imported from the Netherlands and was assigned to B lineage, HGSQ-USFQ-018, belongs to the B.1 lineage showing nine nucleotide differences with the reference strain and grouped with sequences from the United Kingdom, and HGSQ-USFQ-007 and HGSQ-USFQ-010 belong to the B lineage and grouped with sequences from Scotland. All genomes show mutations in their genomes compared to the reference strain, which could be important to understand the virulence, severity and transmissibility of the virus. Our findings also suggest that there were at least three independent introductions of SARS-CoV-2 to Ecuador.\n\nIMPORTANCECOVID-19, an infectious disease caused by SARS-CoV-2, has spread globally including Latin American countries including Ecuador. The first strain of SARS-CoV-2 sequenced was from Wuhan, which is considered as the reference strain. There were no data about the SARS-CoV-2 lineages in Ecuador, and the purpose of this study was to find out the origin of the different lineages circulating in the population. We also were interested in the mutations present in these genomes as they can influence virulence, transmission and infectivity.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Sully Marquez", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + }, + { + "author_name": "Belen Prado-Vivar", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + }, + { + "author_name": "Juan Jose Guadalupe", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Laboratorio de Biotecnologia Vegetal" + }, + { + "author_name": "Bernardo Gutierrez Granja", + "author_inst": "Department of Zoology, University of Oxford" + }, + { + "author_name": "Manuel Jibaja", + "author_inst": "Hospital Eugenio Espejo, Quito" + }, + { + "author_name": "Milton Tobar", + "author_inst": "Hospital Eugenio Espejo, Quito" + }, + { + "author_name": "Francisco Mora", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Juan Gaviria", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Maria Garcia", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Edison Ligna", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Franklin Espinosa", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Jorge Reyes", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Veronica Barragan", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + }, + { + "author_name": "Patricio Rojas-Silva", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + }, + { + "author_name": "Gabriel Trueba", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + }, + { + "author_name": "Michelle Grunauer", + "author_inst": "Universidad San Francisco de Quito, Escuela de Medicina, COCSA" + }, + { + "author_name": "Paul Cardenas", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.12.20129098", "rel_title": "Laboratory Testing Implications of Risk-Stratification and Management for Improving Clinical Outcomes of COVID-19 Patients", @@ -1352859,29 +1355914,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, - { - "rel_doi": "10.1101/2020.06.11.20128850", - "rel_title": "When is SARS-CoV-2 in your shopping list?", - "rel_date": "2020-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128850", - "rel_abs": "The pandemic of coronavirus disease 2019 (COVID-19) has caused, by May 24th 2020, more than 5.3 million confirmed cases worldwide. The necessity of keeping open and accessible public commercial establishments such as supermarkets or pharmacies increases during the pandemic provided that distancing rules and crowd control are satisfied.\n\nHerein, using agent-based models, we explore the potential spread of the novel SARS-CoV-2 considering the case of a small size supermarket. For diverse distancing rules and number of simultaneous users (customers), we question flexible and limited movement policies, guiding the flow and interactions of users in place. Results indicate that a guided, limited in movement and well-organized policy combined with a distance rule of at least 1 m between users and a small number of them (15) may aid in the mitigation of potential new contagions in more than 90% compared to the usual policy of flexible movement with more users (30) which may reach up to 64% of mitigation of potential new infections under the same distancing conditions. This study may guide novel strategies for the mitigation of the current COVID-19 pandemic, at any stage, and prevention of future outbreaks of SARS-CoV-2 or related viruses.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Gustavo Hernandez Mejia", - "author_inst": "Frankfurt Institute for Advanced Studies" - }, - { - "author_name": "Esteban A. Hernandez-Vargas", - "author_inst": "Frankfurt Institute for Advanced Studies" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.11.20129072", "rel_title": "Asymptomatic and presymptomatic transmission of SARS-CoV-2: A systematic review", @@ -1354216,6 +1357248,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.11.20127241", + "rel_title": "Critical Questions when Interpreting Coronavirus PCR Diagnostics", + "rel_date": "2020-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20127241", + "rel_abs": "The results of PCR measurements are regarded as unquestionable. This statement must be put into perspective. This relativization is particularly important in connection with the interpretation of SARS-CoV-2 results. Members of the critical infrastructure, such as nurses, may be quarantined although this is not necessary and are therefore missing from patient care. With our small but impressive comparison of methods and transport media for SARS-CoV-2, we not only show the different sensitivity of common routine systems and media in laboratory medicine. Further, we would like to inform clinically working physicians, who are not familiar with the technical weaknesses of the PCR investigation, about gaps and present solutions for their daily work.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Juergen Durner", + "author_inst": "Department of Operative/Restorative Dentistry, Periodontology and Pedodontics, Ludwig- Maximilians-" + }, + { + "author_name": "Siegfried Burggraf", + "author_inst": "Laboratory Becker & Colleagues" + }, + { + "author_name": "Ludwig Czibere", + "author_inst": "Laboratory Becker & Colleagues" + }, + { + "author_name": "Tobias Fleige", + "author_inst": "Laboratory Becker & Colleagues" + }, + { + "author_name": "Michael Spannagl", + "author_inst": "Haemophilia Treatment Centre, Ludwig-Maximilians-University of Munich" + }, + { + "author_name": "David Watts", + "author_inst": "School of Medical Sciences and Photon Science Institute, University of Manchester, UK" + }, + { + "author_name": "Marc Becker", + "author_inst": "Laboratory Becker & Colleagues" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.11.20128991", "rel_title": "Transformed time series analysis of first-wave COVID-19: universal similarities found in the Group of Twenty (G20) Countries", @@ -1354293,41 +1357368,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.12.147819", - "rel_title": "Overhauling a faulty control in the CDC-recommended SARS-CoV-2 RT-PCR test", - "rel_date": "2020-06-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.12.147819", - "rel_abs": "To battle the COVID-19 pandemic, widespread testing for the presence of the SARS-CoV-2 virus is worldwide being employed by specific real-time RT-PCR (rRT-PCR) of viral RNA. The CDC has issued a recommended panel of PCR-based test sets that entail several primer/probe sets that target the SARS-CoV-2 N-gene, but also one that targets the human RNase P gene (h-RP) as a positive control for RNA extraction and/or reverse-transcription (RT) efficacy.\n\nWe discovered that the CDC-recommended h-RP primer/probe set has a faulty design, because both PCR primers are located in the same exon, which allows for unwanted PCR-amplification of background genomic DNA (gDNA). By removing RNA from nose-swab samples by an RNase treatment, we showed that the presence of gDNA in samples resulted in false-positive signals for the h-RP test control. This is rather serious, because it could lead to false-negative test outcomes, since the CDC interpretation of an absent SARS-CoV-2 rRT-PCR signal plus a positive h-RP rRT-PCR signal is interpreted as \"2019-nCoV not detected\", whereas a false-positive h-RP rRT-PCR signal resulting from amplification of gDNA should be interpreted as \"Invalid Result\" and the procedure should be repeated.\n\nIn order to overhaul the faulty h-RP rRT-PCR primer/probe set with minimal modification, we designed and tested several new h-RP reverse primers. Replacement of the CDC-recommended PCR reverse primer with our selected exon-exon junction reverse primer corrected the problem of false-positive results with this important SARS-CoV-2 RT-PCR test control and thus eliminated the problem of potential false-negative COVID-19 diagnoses.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Rob J. Dekker", - "author_inst": "Universiteit van Amsterdam Swammerdam Institute for Life Sciences" - }, - { - "author_name": "Wim A. Ensink", - "author_inst": "Universiteit van Amsterdam Swammerdam Institute for Life Sciences" - }, - { - "author_name": "Selina van Leeuwen", - "author_inst": "Universiteit van Amsterdam Swammerdam Institute for Life Sciences" - }, - { - "author_name": "Han Rauwerda", - "author_inst": "Universiteit van Amsterdam Swammerdam Institute for Life Sciences" - }, - { - "author_name": "Timo M. Breit", - "author_inst": "Universiteit van Amsterdam Swammerdam Institute for Life Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.13.149930", "rel_title": "Receptor utilization of angiotensin converting enzyme 2 (ACE2) indicates a narrower host range of SARS-CoV-2 than that of SARS-CoV", @@ -1355562,6 +1358602,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.11.20107086", + "rel_title": "COVID-19: Comparison between 8-days and extended 4-weeks outbreak periods through socioeconomic and natural factors", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20107086", + "rel_abs": "Since mid-March 2020, global COVID-19 pandemic has experienced an exponential growth in process from sporadic to sudden outbreaks. This paper selects the 8-day surge data of daily cases, death and recovery rates (March 19-26, 2020) from 18 countries with severe pandemic situation to discuss the impact of 9 factors of both socioeconomic and natural on the pathogen outbreak. Moreover, the paper also elaborates analysis and comparison of relatively slow 4-week (February 1-29, 2020) data of Chinas surge cases to determine the relationship between social and natural factors and on the spread of pandemic, which provides an effective reference for delaying and controlling the pandemic development.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Sana Ullah", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Jianghua ZHENG", + "author_inst": "College of Resources and Environment Science, Xinjiang University, Urumqi, 830046, China" + }, + { + "author_name": "Zhengkang ZUO", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Feizhou ZHANG", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Ke SHANG", + "author_inst": "School of Geophysics and Information Technology, China University of Geosciences, Beijing, 100083, China." + }, + { + "author_name": "Wenjie YU", + "author_inst": "College of Resources and Environment Science, Xinjiang University, Urumqi, 830046, China." + }, + { + "author_name": "Yu FU", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Chuqiao HAN", + "author_inst": "College of Resources and Environment Science, Xinjiang University, Urumqi, 830046, China." + }, + { + "author_name": "Yi LIN", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Kaiwen JIANG", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Shanlin SUN", + "author_inst": "College of Electronic Information and Automation, Guilin University of Aerospace Technology, Guilin 541004, Guangxi Province China." + }, + { + "author_name": "Yiyuan SUN", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Shoujiang ZHAO", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Lei YAN", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.09.20120139", "rel_title": "Prevalence and Predictors of General Psychiatric Disorders and Loneliness during COVID-19 in the United Kingdom: Results from the Understanding Society UKHLS", @@ -1355687,45 +1358798,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.06.04.20119206", - "rel_title": "A Comparative Study of Target Reconstruction of Ultra-High-Resolution CT for Patients with Corona-Virus Disease 2019 (COVID-19)", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20119206", - "rel_abs": "BackgroundThe corona-virus disease 2019 (COVID-19) pandemic has caused a serious public health risk. Compared with conventional high-resolution CT (C-HRCT, matrix 512), ultra-high resolution CT (U-HRCT, matrix 1024) can increase the effective pixel per unit volume by about 4 times. Our study is to evaluate the value of target reconstruction of U-HRCT in the accurate diagnosis of COVID-19.\n\nMethodsA total of 13 COVID-19 cases, 44 cases of other pneumonias, and 6 cases of ground-glass nodules were retrospectively analyzed. The data were categorized into groups A (C-HRCT) and B (U-HRCT), following which iDose4-3 and iDose4-5 were used for target reconstruction, respectively. CT value, noise, and signal-to-noise ratio (SNR) in different reconstructed images were measured. Two senior imaging doctors scored the image quality and the structure of the lesions on a 5-point scale. Chi-square test, variance analysis, and binarylogistic regression analysis were used for statistical analysis.\n\nResultsU-HRCT image can reduce noise and improve SNR with an increase of the iterative reconstruction level. The SNR of U-HRCT image was lower than that of the C-HRCT image of the same iDose4level, and the noise of U-HRCT was higher than that of C-HRCT image; the difference was statistically significant (P< 0.05). Logistic regression analysis showed thatperipleural distribution, thickening of blood vessels and interlobular septum, and crazy-paving pattern were independent indictors of the COVID-19 on U-HRCT. U-HRCT was superior to C-HRCT in showing the blood vessels, bronchial wall, and interlobular septum in the ground-glass opacities; the difference was statistically significant (P < 0.05).\n\nConclusionsPeripleural distribution, thickening of blood vessels and interlobular septum, and crazy-paving pattern on U-HRCT are favorable signs for COVID-19. U-HRCT is superior to C-HRCT in displaying the blood vessels, bronchial walls, and interlobular septum for evaluating COVID-19.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Shaomao Lv", - "author_inst": "Zhongshan Hospital, Xiamen University" - }, - { - "author_name": "Yu Lin", - "author_inst": "Department of Radiology, Zhongshan Hospital, Xiamen University" - }, - { - "author_name": "Jianghe Kang", - "author_inst": "Department of Radiology, Zhongshan Hospital, Xiamen University" - }, - { - "author_name": "Shaoyin Duan", - "author_inst": "Department of Radiology, Zhongshan Hospital, Xiamen University" - }, - { - "author_name": "Weiguo Zhang", - "author_inst": "Department of Radiology, Daping Hospital, Army Medical University" - }, - { - "author_name": "Jin-an Wang", - "author_inst": "Department of Radiology, Zhongshan Hospital, Xiamen University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.06.05.20122705", "rel_title": "Hydroxychloroquine plus standard care compared with the standard care alone in COVID-19: a meta-analysis of randomized controlled trials", @@ -1356912,6 +1359984,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.09.20126086", + "rel_title": "Private Health Sector in India: Ready and willing, yet underutilized in the Covid-19 pandemic.", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20126086", + "rel_abs": "BackgroundThe private medical sector is a resource that must be estimated for efficient inclusion into public healthcare during pandemics.\n\nMethodsA survey was conducted among private healthcare workers to ascertain their views on the potential resources that can be accessed from the private sector and methods to do the same.\n\nResultsThere were 213 respondents, 80% of them being doctors. Nearly half (47.4%) felt that the contribution from the private medical sector has been suboptimal. Areas suggested for improved contributions by the private sector related to patient care (71.8%) and provision of equipment (62.4%), with fewer expectations (39.9%) on the research front. Another area of deemed support was maintaining continuity of care for non-COVID patients using virtual consultation services (77.4%), tele-consultation being the preferred option (60%). 58.2% felt that the Government had not involved the private sector adequately; and 45.1% felt they should be part of policy-making.\n\nConclusionA streamlined pathway to facilitate the private sector to join hands with the public sector for a national cause is the need of the hour. Through our study, we have identified gaps in the current contribution by the private sector and identified areas in which they could contribute, by their own admission.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Samira Davalbhakta", + "author_inst": "Byramjee Jeejeebhoy Government Medical College and Sassoon General Hospitals" + }, + { + "author_name": "Supriya Sharma", + "author_inst": "Department of Surgical Gastroenterology Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India" + }, + { + "author_name": "Shefali Gupta", + "author_inst": "Department of Microbiology Maharishi Markandeshwar Institute of Medical Sciences and Research (MMIMSR) Haryana, India" + }, + { + "author_name": "Vishwesh Agarwal", + "author_inst": "Mahatma Gandhi Missions Medical College" + }, + { + "author_name": "Gaurav Pandey", + "author_inst": "Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India" + }, + { + "author_name": "Durga Prasanna Misra", + "author_inst": "Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India" + }, + { + "author_name": "Bijaya Nanda Naik", + "author_inst": "Dept of Community Medicine NAMO Medical Education and Research Institute, Silvassa, DNH" + }, + { + "author_name": "Ashish Goel", + "author_inst": "University College Of Medical Sciences, New Delhi" + }, + { + "author_name": "Latika Gupta", + "author_inst": "Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India" + }, + { + "author_name": "Vikas Agarwal", + "author_inst": "Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.10.20127266", "rel_title": "Resource requirements for reintroducing elective surgery in England during the COVID-19 pandemic: a modelling study", @@ -1357025,61 +1360152,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.06.10.20126847", - "rel_title": "Laboratory based surveillance of SARS-CoV-2 in Pakistan", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20126847", - "rel_abs": "COVID-19 cases are alarmingly increasing in Pakistan since May 2020. Laboratory based surveillance system has been in place since the start of the pandemic. The genomic surveillance of SARS-CoV-2 strains isolated locally has been conducted based on partial ORF1b. The sequences were classified to show the phylogenetic correlation and showed 100% homology with those detected in neighboring countries India and China. The rapid increase in cases has led to development of robust strategies to enhance the laboratory testing capacity. We are currently meeting the country requirement to diagnose the virus in the community. Nonetheless, factors like recent ease in lockdown measures has led to massive rise in number of cases in few weeks time.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Nazish Badar", - "author_inst": "NIH" - }, - { - "author_name": "Aamer Ikram", - "author_inst": "NIH" - }, - { - "author_name": "Hamza Ahmad Mirza", - "author_inst": "NIH" - }, - { - "author_name": "Abdul Ahad", - "author_inst": "NIH" - }, - { - "author_name": "Muhammad Masroor Alam", - "author_inst": "NIH" - }, - { - "author_name": "Yasir Arshad", - "author_inst": "NIH" - }, - { - "author_name": "Massab Umair", - "author_inst": "NIH" - }, - { - "author_name": "Salman Sharif", - "author_inst": "NIH" - }, - { - "author_name": "Afreenish Amir", - "author_inst": "NIH" - }, - { - "author_name": "Muhammad Salman", - "author_inst": "NIH" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.09.20127043", "rel_title": "Serial Interval Distribution of SARS-CoV-2 Infection in Brazil", @@ -1358438,6 +1361510,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.11.20127894", + "rel_title": "A scenario modeling pipeline for COVID-19 emergency planning", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20127894", + "rel_abs": "Coronavirus disease 2019 (COVID-19) has caused strain on health systems worldwide due to its high mortality rate and the large portion of cases requiring critical care and mechanical ventilation. During these uncertain times, public health decision makers, from city health departments to federal agencies, sought the use of epidemiological models for decision support in allocating resources, developing non-pharmaceutical interventions, and characterizing the dynamics of COVID-19 in their jurisdictions. In response, we developed a flexible scenario modeling pipeline that could quickly tailor models for decision makers seeking to compare projections of epidemic trajectories and healthcare impacts from multiple intervention scenarios in different locations. Here, we present the components and configurable features of the COVID Scenario Pipeline, with a vignette detailing its current use. We also present model limitations and active areas of development to meet ever-changing decision maker needs.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Joseph Chadi Lemaitre", + "author_inst": "EPFL" + }, + { + "author_name": "Kyra H Grantz", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Joshua Kaminsky", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Hannah R Meredith", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Shaun A Truelove", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Stephen A Lauer", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Lindsay T Keegan", + "author_inst": "University of Utah" + }, + { + "author_name": "Sam Shah", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Josh Wills", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Kathryn Kaminsky", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Javier Perez-Saez", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Justin Lessler", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Elizabeth C Lee", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.10.20127589", "rel_title": "Effect of social distancing on COVID-19 incidence and mortality in the US", @@ -1358575,53 +1361714,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.10.20126771", - "rel_title": "Meso-scale modeling of COVID-19 spatio-temporal outbreak dynamics in Germany", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20126771", - "rel_abs": "The COVID-19 pandemic has kept the world in suspense for the past months. In most federal countries such as Germany, locally varying conditions demand for state- or county-level decisions. However, this requires a deep understanding of the meso-scale outbreak dynamics between micro-scale agent models and macro-scale global models. Here, we introduce a reparameterized SIQRD network model that accounts for local political decisions to predict the spatio-temporal evolution of the pandemic in Germany at county and city resolution. Our optimized model reproduces state-wise cumulative infections and deaths as reported by the Robert-Koch Institute, and predicts development for individual counties at convincing accuracy. We demonstrate the dominating effect of local infection seeds, and identify effective measures to attenuate the rapid spread. Our model has great potential to support decision makers on a state and community politics level to individually strategize their best way forward.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Andreas Kergassner", - "author_inst": "Friedrich-Alexander-University Erlangen-Nuernberg" - }, - { - "author_name": "Christian Burkhardt", - "author_inst": "Friedrich-Alexander-University Erlangen-Nuernberg" - }, - { - "author_name": "Dorothee Lippold", - "author_inst": "Friedrich-Alexander-University Erlangen-Nuernberg" - }, - { - "author_name": "Sarah Nistler", - "author_inst": "Friedrich-Alexander-University Erlangen-Nuernberg" - }, - { - "author_name": "Matthias Kergassner", - "author_inst": "Friedrich-Alexander-University Erlangen-Nuernberg" - }, - { - "author_name": "Paul Steinmann", - "author_inst": "Friedrich-Alexander-University Erlangen-Nuernberg" - }, - { - "author_name": "Dominik Budday", - "author_inst": "Friedrich-Alexander-University Erlangen-Nuernberg" - }, - { - "author_name": "Silvia Budday", - "author_inst": "Friedrich-Alexander-University Erlangen-Nuernberg" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.08.20125575", "rel_title": "Effects of physical activity and exercise on well-being in the context of the Covid-19 pandemic", @@ -1359812,6 +1362904,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.11.20128389", + "rel_title": "Profiling the positive detection rate of SARS-CoV-2 using polymerase chain reaction in different types of clinical specimens: a systematic review and meta-analysis", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128389", + "rel_abs": "BackgroundTesting is one of the commendable preventive measures against coronavirus disease (COVID-19), and needs to be done using both most appropriate specimen and an accurate diagnostic test like real time reverse transcription polymerase chain reaction (qRT-PCR). However, the detection rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA from different clinical specimens after onset of symptoms is not yet well established. For guiding the selection of specimens for clinical diagnosis of COVID-19, a systematic review aiming at profiling the positive detection rate from different clinical specimens using PCR was conducted.\n\nMethodsThe systematic search was done using PubMed/MEDLINE, Science direct, Google Scholar, among others. The search included studies on laboratory diagnosis of SARS-CoV-2 from different clinical specimens using PCR. Data extraction was done using Microsoft Excel spread sheet 2010 and reported according to PRISMA-P guidelines. Using Open Meta Analyst software, DerSimonian-Laird random effects analysis was performed to determine a summary estimate (positive rate [PR]/proportions) and their 95% confidence interval (95%CI).\n\nResultsA total of 8136 different clinical specimens were analyzed to detect SARS-CoV-2, with majority being nasopharyngeal swabs (69.6%). Lower respiratory tract (LRT) specimens had a PR of 71.3% (95%CI:60.3%-82.3%) while no virus was detected from the urinogenital specimens. Bronchoalveolar lavage fluid (BLF) specimen had the PR of 91.8% (95%CI:79.9-103.7%), followed by rectal swabs, 87.8 % (95%CI:78.6%-96.9%) then sputum, 68.1% (95%CI:56.9%-79.4%). Low PR was observed in oropharyngeal swabs, 7.6% (95%CI:5.7%-9.6%) and blood samples, 1.0% (95%CI: -0.1%-2.1%), whilst no SARS-CoV-2 was detected in urine samples. Nasopharyngeal swab, a widely used specimen had a PR of 45.5% (95%CI:31.2%-59.7%).\n\nConclusionIn this study, SARS-CoV-2 was highly detected in lower respiratory tract specimens while there was no detected virus in urinogenital specimens. Regarding the type of clinical specimens, bronchoalveolar lavage fluid had the highest positive rate followed by rectal swab then sputum. Nasopharyngeal swab which is widely used had a moderate detection rate. Low positive rate was recorded in oropharyngeal swab and blood sample while no virus was found in urine samples. More importantly, the virus was detected in feces, suggesting SARS-CoV-2 transmission by the fecal route.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "George M. Bwire", + "author_inst": "School of Pharmacy, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania." + }, + { + "author_name": "Mtebe V. Majigo", + "author_inst": "School of Medicine, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania" + }, + { + "author_name": "Belinda J. Njiro", + "author_inst": "School of Medicine, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania" + }, + { + "author_name": "Akili Mawazo", + "author_inst": "Institute of Allied Health Sciences, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.11.20128165", "rel_title": "Easing social distancing index after COVID-19 pandemic", @@ -1359965,37 +1363088,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.11.20128884", - "rel_title": "Stability of SARS-CoV-2 on Critical Personal Protective Equipment", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128884", - "rel_abs": "The spread of COVID-19 in healthcare settings is concerning, with healthcare workers representing a disproportionately high percentage of confirmed cases. Although SARS-CoV-2 virus has been found to persist on surfaces for a number of days, the extent and duration of fomites as a mode of transmission, particularly in healthcare settings, has not been fully characterized. To shed light on this critical matter, the present study provides the first comprehensive assessment of SARS-CoV-2 stability on experimentally contaminated personal protective equipment (PPE) widely used by healthcare workers and the general public. Persistence of viable virus was monitored over 21 days on eight different materials, including nitrile medical examination gloves, reinforced chemical resistant gloves, N-95 and N-100 particulate respirator masks, Tyvek(R), plastic, cotton, and stainless steel. Unlike previous reports, viable SARS-CoV-2 in the presence of a soil load persisted for up to 21 days on experimentally inoculated PPE, including materials from filtering facepiece respirators (N-95 and N-100 masks) and a plastic visor. Conversely, when applied to 100% cotton fabric, the virus underwent rapid degradation and became undetectable in less than 24 hours. These findings underline the importance of appropriate handling of contaminated PPE during and following use in high-risk settings and provide interesting insight into the potential utility of cotton, including cotton masks, in limiting COVID-19 transmission.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Samantha B Kasloff", - "author_inst": "National Microbiology Laboratory, Public Health Agency of Canada" - }, - { - "author_name": "James E Strong", - "author_inst": "National Microbiology Laboratory, Public Health Agency of Canada" - }, - { - "author_name": "Duane Funk", - "author_inst": "Department of Anaesthesia and Medicine, College of Medicine, Faculty of Health Sciences, University of Manitoba" - }, - { - "author_name": "Todd A Cutts", - "author_inst": "National Microbiology Laboratory, Public Health Agency of Canada" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.11.20128074", "rel_title": "Estimating the impact of physical distancing measures in containing COVID-19: an empirical analysis", @@ -1361698,6 +1364790,137 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.10.20127175", + "rel_title": "Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.", + "rel_date": "2020-06-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127175", + "rel_abs": "BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both \"direct\", through infection, and \"indirect\", through changes in healthcare.\n\nMethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(\"direct\" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For \"indirect\" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020.\n\nFindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths.\n\nInterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic.\n\nFundingNIHR, HDR UK, Astra Zeneca", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Amitava Banerjee", + "author_inst": "University College London" + }, + { + "author_name": "Suliang Chen", + "author_inst": "University College London" + }, + { + "author_name": "Laura Pasea", + "author_inst": "University College London" + }, + { + "author_name": "Alvina Lai", + "author_inst": "University College London" + }, + { + "author_name": "Michail Katsoulis", + "author_inst": "UCL" + }, + { + "author_name": "Spiros Denaxas", + "author_inst": "University College London" + }, + { + "author_name": "Vahe Nafilyan", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Bryan Williams", + "author_inst": "UCL" + }, + { + "author_name": "Wai Keong Wong", + "author_inst": "University College London Hospitals NHS Trust" + }, + { + "author_name": "Ameet Bakhai", + "author_inst": "Royal Free Hospitals NHS Trust" + }, + { + "author_name": "Kamlesh Khunti", + "author_inst": "University of Leicester" + }, + { + "author_name": "Deenan Pillay", + "author_inst": "UCL" + }, + { + "author_name": "Mahdad Noursadeghi", + "author_inst": "UCL" + }, + { + "author_name": "Honghan Wu", + "author_inst": "UCL" + }, + { + "author_name": "Nilesh Pareek", + "author_inst": "King's College Hospital" + }, + { + "author_name": "Daniel Bromage", + "author_inst": "Kings College London" + }, + { + "author_name": "Theresa Mcdonagh", + "author_inst": "Kings College London" + }, + { + "author_name": "Jonathan Byrne", + "author_inst": "Kings London NHS Trust" + }, + { + "author_name": "James T Teo", + "author_inst": "Kings College Hospital NHS Foundation Trust" + }, + { + "author_name": "Ajay Shah", + "author_inst": "King's College London" + }, + { + "author_name": "Ben Humberstone", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Liang V Tang", + "author_inst": "Huazhong University of Science and Technology, Wuhan, China" + }, + { + "author_name": "Anoop SV Shah", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Andrea Rubboli", + "author_inst": "Ospedale S. Maria delle Croci, Ravenna, Italy" + }, + { + "author_name": "Yutao Guo", + "author_inst": "PLA General Hospital, Beijing, China." + }, + { + "author_name": "Yu Hu", + "author_inst": "Huazhong University of Science and Technology, Wuhan, China." + }, + { + "author_name": "Cathie LM Sudlow", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Gregory YH Lip", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Harry Hemingway", + "author_inst": "UCL" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.06.10.20127258", "rel_title": "Knowledge, attitudes, and practices among the general population during COVID-19 outbreak in Iran: A national cross-sectional survey", @@ -1361871,41 +1365094,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.06.09.20126326", - "rel_title": "Mathematical estimation of COVID-19 prevalence in Latin America", - "rel_date": "2020-06-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20126326", - "rel_abs": "After the rapid spread with severe consequences in Europe and China, the SARS-CoV-2 virus is now manifesting itself in more vulnerable countries, including those in Latin America. In order to guide political decision-making via epidemiological criteria, it is crucial to assess the real impact of the epidemic. However, the use of large-scale population testing is unrealistic or not feasible in some countries. Based on a newly developed mathematical model, we estimated the seroprevalence of SARS-CoV-2 in Latin American countries. The results show that the virus spreads unevenly across countries. For example, Ecuador and Brazil are the most affected countries, with approximately 3% of the infected population. Currently, the number of new infections is increasing in all countries examined, with the exception of some Caribbean countries as Cuba. Moreover, in these countries, the peak of newly infected patients has not yet been reached.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Marcos Matabuena", - "author_inst": "CiTIUS (Centro Singular de Investigacion en Tecnoloxias Intelixentes)" - }, - { - "author_name": "Pablo Rodriguez Mier", - "author_inst": "Toxalim (Research Centre in Food Toxicology), Universite de Toulouse, INRAE, ENVT,INP-Purpan, UPS, Toulouse, France" - }, - { - "author_name": "Carlos Meijide-Garcia", - "author_inst": "Universidad de Santiago de Compostela" - }, - { - "author_name": "Victor Leboran", - "author_inst": "CiTIUS (Centro Singular de Investigacion en Tecnoloxias Intelixentes)" - }, - { - "author_name": "Francisco Gude", - "author_inst": "Clinical Epidemiology Unit, Hospital Clinico Universitario de Santiago de Compostela, Santiago de Compostela, Spain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.06.09.20126516", "rel_title": "COVID-19 infections and outcomes in patients with multiple myeloma in New York City: a cohort study from five academic centers", @@ -1363256,6 +1366444,73 @@ "type": "confirmatory results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.06.10.144816", + "rel_title": "Remdesivir but not famotidine inhibits SARS-CoV-2 replication in human pluripotent stem cell-derived intestinal organoids", + "rel_date": "2020-06-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.10.144816", + "rel_abs": "Gastrointestinal symptoms in COVID-19 are associated with prolonged symptoms and increased severity. We employed human intestinal organoids derived from pluripotent stem cells (PSC-HIOs) to analyze SARS-CoV-2 pathogenesis and to validate efficacy of specific drugs in the gut. Certain, but not all cell types in PSC-HIOs express SARS-CoV-2 entry factors ACE2 and TMPRSS2, rendering them susceptible to SARS-CoV-2 infection. Remdesivir, a promising drug to treat COVID-19, effectively suppressed SARS-CoV-2 infection of PSC-HIOs. In contrast, the histamine-2-blocker famotidine showed no effect. Thus, PSC-HIOs provide an interesting platform to study SARS-CoV-2 infection and to identify or validate drugs.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jan Krueger", + "author_inst": "Ulm University" + }, + { + "author_name": "Ruediger Gross", + "author_inst": "Ulm University" + }, + { + "author_name": "Carina Conzelmann", + "author_inst": "Ulm University" + }, + { + "author_name": "Janis A Mueller", + "author_inst": "Ulm University" + }, + { + "author_name": "Lennart Koepke", + "author_inst": "Ulm University" + }, + { + "author_name": "Konstantin Sparrer", + "author_inst": "Ulm University" + }, + { + "author_name": "Desiree Schuetz", + "author_inst": "Ulm University" + }, + { + "author_name": "Thomas Seufferlein", + "author_inst": "Ulm University" + }, + { + "author_name": "Thomas F.E. Barth", + "author_inst": "Ulm University" + }, + { + "author_name": "Steffen Stenger", + "author_inst": "Ulm University" + }, + { + "author_name": "Sandra Heller", + "author_inst": "Ulm University" + }, + { + "author_name": "Alexander Kleger", + "author_inst": "Ulm University" + }, + { + "author_name": "Jan Muench", + "author_inst": "Ulm University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.11.140285", "rel_title": "ROBOCOV: An affordable open-source robotic platform for COVID-19 testing by RT-qPCR", @@ -1363397,73 +1366652,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.06.10.144964", - "rel_title": "Hijacking SARS-Cov-2/ACE2 receptor interaction by natural and semi-synthetic steroidal agents acting on functional pockets on receptor binding region", - "rel_date": "2020-06-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.10.144964", - "rel_abs": "The coronavirus disease 2019 (COVID-19) is a respiratory tract infection caused by the severe acute respiratory syndrome coronavirus (SARS)-CoV-2. In the light of the urgent need to identify novel approaches to be used in the emergency phase, a largely explored strategy has been the repurpose of clinically available drugs as new antivirals, by targeting different viral proteins. In this paper, we describe a drug repurposing strategy based on a virtual screening of druggable pockets located in the central \u03b2-sheet core of the SARS-CoV-2 Spike protein RBD supported by in vitro tests identifying several steroidal derivatives as SARS-CoV-2 entry inhibitors. Our results demonstrate that several potential binding sites exist in the SARS CoV-2 S protein, and that the occupancy of these pockets reduces the ability of the S protein RBD to bind to the ACE2 consensus in vitro. In particular, natural occurring and clinically available steroids as glycyrrhetinic and oleanolic acids, as well as the bile acids derivatives glyco-UDCA and obeticholic acid have been shown to be effective in preventing virus entry in the case of low viral load. All together, these results might help to define novel approaches to reduce the viral load by using SARS-CoV-2 entry inhibitors.Competing Interest StatementThis paper was supported by a research grant by BAR Pharmaceuticals S.r.L. to the Department of Pharmacy of the University of Napoli Federico II and to the Department of Surgical and Biomedical Sciences, University of Perugia.\nThe authors declare the following competing financial interest(s): S.F., A.Z. and B.C. have filed an Italian patent application no.102020000011092 in the name of BAR Pharmaceuticals S.r.L. on the compounds described in this paper.\nView Full Text", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Adriana Carino", - "author_inst": "University of Perugia, Department of Surgical and Biomedical Sciences, Perugia, Italy" - }, - { - "author_name": "Federica Moraca", - "author_inst": "University of Naples Federico II, Department of Pharmacy, Naples, Italy" - }, - { - "author_name": "Bianca Fiorillo", - "author_inst": "University of Naples Federico II, Department of Pharmacy, Naples, Italy" - }, - { - "author_name": "Silvia Marcan\u00f3", - "author_inst": "University of Perugia, Department of Surgical and Biomedical Sciences, Perugia, Italy" - }, - { - "author_name": "Valentina Sepe", - "author_inst": "University of Naples Federico II, Department of Pharmacy, Naples, Italy" - }, - { - "author_name": "Michele Biagioli", - "author_inst": "University of Perugia, Department of Surgical and Biomedical Sciences, Perugia, Italy" - }, - { - "author_name": "Claudia Finamore", - "author_inst": "University of Naples Federico II, Department of Pharmacy, Naples, Italy" - }, - { - "author_name": "Silvia Bozza", - "author_inst": "University of Perugia, Department of Medicine, Microbiology Section, Perugia, Italy" - }, - { - "author_name": "Daniela Francisci", - "author_inst": "University of Perugia, Department of Medicine, Microbiology Section, Perugia, Italy" - }, - { - "author_name": "Eleonora Distrutti", - "author_inst": "SC di Gastroenterologia ed Epatologia, Azienda Ospedaliera di Perugia, Perugia, Italy" - }, - { - "author_name": "Bruno Catalanotti", - "author_inst": "University of Napoli Federico II" - }, - { - "author_name": "Angela Zampella", - "author_inst": "University of Naples Federico II, Department of Pharmacy, Naples, Italy" - }, - { - "author_name": "Stefano Fiorucci", - "author_inst": "University of Perugia, Department of Surgical and Biomedical Sciences, Perugia, Italy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.06.10.145086", "rel_title": "Investigation of the effect of temperature on the structure of SARS-Cov-2 Spike Protein by Molecular Dynamics Simulations", @@ -1365098,6 +1368286,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.08.20125658", + "rel_title": "Temporal evolution of COVID-19 in the states of India using SIQR Model", + "rel_date": "2020-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125658", + "rel_abs": "COVID 19 entered during the last week of April 2020 in India has caused 3,546 deaths with 1,13,321 number of reported cases. Indian government has taken many proactive steps, including strict lockdown of the entire nation for more than 50 days, identification of hotspots, app-based tracking of citizens to track infected. This paper investigated the evolution of COVID 19 in five states of India (Maharashtra, UP, Gujrat, Tamil Nadu, and Delhi) from 1st April 2020 to 20th May 2020. Variation of doubling rate and reproduction number (from SIQR) with time is used to analyse the performance of the majorly affected Indian states. It has been determined that Uttar Pradesh is one of the best performers among five states with the doubling rate crossing 18 days as of 20th May. Tamil Nadu has witnessed the second wave of infections during the second week of May. Maharashtra is continuously improving at a steady rate with its doubling rate reaching to 12.67 days. Also these two states are performing below the national average in terms of infection doubling rate. Gujrat and Delhi have reported the doubling rate of 16.42 days and 15.49 days respectively. Comparison of these states has also been performed based on time-dependent reproduction number. Recovery rate of India has reached to 40 % as the day paper is written.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "ALOK TIWARI", + "author_inst": "IIT BOMBAY" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.08.20125062", "rel_title": "Principles and Practice of SARS-CoV-2 Decontamination of N95 Masks with UV-C", @@ -1365219,69 +1368426,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.08.20125179", - "rel_title": "Seroprevalence of IgG antibodies against SARS coronavirus 2 in Belgium: a prospective cross-sectional study of residual samples", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125179", - "rel_abs": "To assess the evolving SARS-CoV-2 seroprevalence and seroincidence related to the national lock-down in Belgium, a nationwide seroprevalence study, stratified by age, sex and region using 3000-4000 residual samples was performed during 7 periods between 30 March and 17 October 2020. Residual sera from ambulatory patients were analyzed for IgG antibodies against S1 proteins of SARS-CoV-2 with a semi-quantitative commercial ELISA. Weighted seroprevalence (overall, by age category and sex) and seroincidence during 7 consecutive periods were estimated for the Belgian population while accommodating test-specific sensitivity and specificity.\n\nThe weighted overall seroprevalence initially increased from 1.8% (95% CrI 1.0-2.6) to 5.3% (95% CrI 4.2-6.4), implying a seroincidence of 3.4% (95% CrI 2.4-4.6) between the 1st and 2nd collection period over a period of 3 weeks during the lockdown period (start lockdown mid March 2020). Thereafter, seroprevalence stabilized, however, significant decreases are observed when comparing the 3rd with the 5th and also with the 6th period resulting in negative seroincidence estimates after lockdown was lifted. We estimated for the last collection period mid October 2020 a weighted overall seroprevalence of 4.2% (95% CrI 3.1-5.2).\n\nDuring lockdown, an initial small but increasing fraction of the Belgian population showed serologically detectable signs of exposure to SARS-CoV-2, which did not further increase when confinement measures eased and full lockdown was lifted.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Sereina A Herzog", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Jessie De Bie", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Steven Abrams", - "author_inst": "University of Antwerp, University of Hasselt" - }, - { - "author_name": "Ine Wouters", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Esra Ekinci", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Lisbeth Patteet", - "author_inst": "Algemeen Medisch Laboratorium (AML)" - }, - { - "author_name": "Astrid Coppens", - "author_inst": "Algemeen Medisch Laboratorium (AML)" - }, - { - "author_name": "Sandy De Spiegeleer", - "author_inst": "Laboratoire Luc OLIVIER" - }, - { - "author_name": "Philippe Beutels", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Pierre Van Damme", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Niel Hens", - "author_inst": "University of Antwerp, University of Hasselt" - }, - { - "author_name": "Heidi Theeten", - "author_inst": "University of Antwerp" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.08.20125765", "rel_title": "Quantifying hospital flows and occupancy due to COVID-19 outbreak in France. Was French lockdown effective?", @@ -1367051,6 +1370195,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.08.139477", + "rel_title": "An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance", + "rel_date": "2020-06-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.08.139477", + "rel_abs": "With a view to extending testing capabilities for the ongoing SARS-CoV-2 pandemic we have developed a test that lowers cost and does not require real time quantitative reverse transcription polymerase chain reaction (RT-qPCR). We developed a reverse transcription nested PCR endpoint assay (RT-nPCR) and showed that RT-nPCR has comparable performance to the standard RT-qPCR test. In the course of comparing the results of both tests, we found that the standard RT-qPCR test can have low detection efficiency (less than 50%) in a real testing scenario which may be only partly explained by low viral representation in many samples. This finding points to the importance of directly monitoring detection efficiency in test environments. We also suggest measures that would improve detection efficiency.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jayeshkumar Narsibhai Davda", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Keith Frank", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Sivakumar Prakash", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Gunjan Purohit", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Devi Prasad Vijayashankar", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Dhiviya Vedagiri", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Karthik Bharadwaj Tallapaka", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Krishnan Harinivas Harshan", + "author_inst": "CSIR-Centre for Cellular and Molecular Biollgy" + }, + { + "author_name": "Archana Bharadwaj Siva", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Rakesh Kumar Mishra", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Jyotsna Dhawan", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Imran Siddiqi", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.06.07.20121939", "rel_title": "Mortality Analysis of COVID-19 Confirmed cases in Pakistan", @@ -1367240,177 +1370447,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.07.20124636", - "rel_title": "Dynamics of IgG seroconversion and pathophysiology of COVID-19 infections", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.07.20124636", - "rel_abs": "We report dynamics of seroconversion to SARS-CoV-2 infections detected by IgG ELISA in 177 individuals diagnosed by RT-PCR. Longitudinal analysis identifies 2-8.5% of individuals who do not seroconvert even weeks after infection. They are younger than seroconverters who have increased co-morbidity and higher inflammatory markers such as C-Reactive Protein. Higher antibody responses are associated with non-white ethnicity. Antibody responses do not decline during follow up almost to 2 months. Serological assays increase understanding of disease severity. Their application in regular surveillance will clarify the duration and protective nature of humoral responses to SARS-CoV-2.", - "rel_num_authors": 39, - "rel_authors": [ - { - "author_name": "Henry M Staines", - "author_inst": "Centre for Diagnostics and Antimicrobial Resistance,Institute for Infection & Immunity,St George's University of London,UK" - }, - { - "author_name": "Daniela E Kirwan", - "author_inst": "Centre for Diagnostics and Antimicrobial Resistance,Institute for Infection & Immunity,St George's University of London,UK" - }, - { - "author_name": "David J Clark", - "author_inst": "Centre for Diagnostics and Antimicrobial Resistance,Institute for Infection & Immunity,St George's University of London,UK" - }, - { - "author_name": "Emily R Adams", - "author_inst": "Tropical Disease Biology,Centre for Drugs and Diagnostics,Liverpool School of Tropical Medicine,Liverpool,UK" - }, - { - "author_name": "Yolanda Augustin", - "author_inst": "St George's University of London" - }, - { - "author_name": "Rachel L Byrne", - "author_inst": "Tropical Disease Biology, Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK" - }, - { - "author_name": "Michael Cocozza", - "author_inst": "Mologic COVID-19 Diagnostics Development Team" - }, - { - "author_name": "Ana I Cubas-Atienza", - "author_inst": "Tropical Disease Biology, Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK" - }, - { - "author_name": "Luis E Cuevas", - "author_inst": "Tropical Disease Biology, Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK" - }, - { - "author_name": "Martina Cusinato", - "author_inst": "Centre for Diagnostics and Antimicrobial Resistance,Institute for Infection & Immunity,St George's University of London,UK" - }, - { - "author_name": "Benedict M O Davies", - "author_inst": "Centre for Diagnostics and Antimicrobial Resistance,Institute for Infection & Immunity,St George's University of London,UK" - }, - { - "author_name": "Mark Davis", - "author_inst": "Mologic COVID-19 Diagnostics Development Team" - }, - { - "author_name": "Paul Davis", - "author_inst": "Mologic COVID-19 Diagnostics Development Team" - }, - { - "author_name": "Annelyse Duvoix", - "author_inst": "Mologic COVID-19 Diagnostics Development Team" - }, - { - "author_name": "Nicholas M Eckersley", - "author_inst": "Centre for Diagnostics and Antimicrobial Resistance,Institute for Infection & Immunity,St Georges University of London,UK" - }, - { - "author_name": "Daniel Forton", - "author_inst": "Centre for Diagnostics and Antimicrobial Resistance,Institute for Infection & Immunity,St George's University of London,UK" - }, - { - "author_name": "Alice Fraser", - "author_inst": "Tropical Disease Biology, Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK" - }, - { - "author_name": "Gala Garrod", - "author_inst": "Tropical Disease Biology, Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK" - }, - { - "author_name": "Linda Hadcocks", - "author_inst": "Centre for Diagnostics and Antimicrobial Resistance,Institute for Infection & Immunity,St George's University of London,UK" - }, - { - "author_name": "Qinxue Hu", - "author_inst": "Centre for Diagnostics and Antimicrobial Resistance,Institute for Infection & Immunity,St George's University of London,UK" - }, - { - "author_name": "Michael Johnson", - "author_inst": "Mologic COVID-19 Diagnostics Development Team" - }, - { - "author_name": "Grant A Kay", - "author_inst": "Tropical Disease Biology, Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK" - }, - { - "author_name": "Kesja Klekotko", - "author_inst": "Mologic COVID-19 Diagnostics Development Team" - }, - { - "author_name": "Zawditu Lewis", - "author_inst": "Mologic COVID-19 Diagnostics Development Team" - }, - { - "author_name": "Josephine Mensah-Kane", - "author_inst": "Mologic COVID-19 Diagnostics Development Team" - }, - { - "author_name": "Stefanie Menzies", - "author_inst": "Tropical Disease Biology, Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK" - }, - { - "author_name": "Irene Monahan", - "author_inst": "Centre for Diagnostics and Antimicrobial Resistance,Institute for Infection & Immunity,St George's University of London,UK" - }, - { - "author_name": "Catherine Moore", - "author_inst": "Centre for Diagnostics and Antimicrobial Resistance,Institute for Infection & Immunity,St George's University of London,UK" - }, - { - "author_name": "Gerhard Nebe-von-Caron", - "author_inst": "Mologic COVID-19 Diagnostics Development Team" - }, - { - "author_name": "Sophie I Owen", - "author_inst": "Centre for Diagnostics and Antimicrobial Resistance,Institute for Infection & Immunity,St George's University of London,UK" - }, - { - "author_name": "Chris Sainter", - "author_inst": "Mologic COVID-19 Diagnostics Development Team" - }, - { - "author_name": "Amadou A Sall", - "author_inst": "Institut Pasteur de Dakar, Dakar, Senegal" - }, - { - "author_name": "James Schouten", - "author_inst": "Mologic COVID-19 Diagnostics Development Team" - }, - { - "author_name": "Chris Williams", - "author_inst": "Tropical Disease Biology, Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK" - }, - { - "author_name": "John Wilkins", - "author_inst": "Mologic COVID-19 Diagnostics Development Team" - }, - { - "author_name": "Kevin Woolston", - "author_inst": "Mologic COVID-19 Diagnostics Development Team" - }, - { - "author_name": "Joseph R A Fitchett", - "author_inst": "Mologic COVID-19 Diagnostics Development Team" - }, - { - "author_name": "Sanjeev Krishna", - "author_inst": "Centre for Diagnostics and Antimicrobial Resistance,Institute for Infection & Immunity,St George's University of London,UK" - }, - { - "author_name": "Tim Planche", - "author_inst": "Centre for Diagnostics and Antimicrobial Resistance,Institute for Infection & Immunity,St George's University of London,UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.05.20122721", "rel_title": "Validation of a Self-administrable, Saliva-based RT-qPCR Test Detecting SARS-CoV-2", @@ -1368901,6 +1371937,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.08.20125377", + "rel_title": "Weather variables impact on COVID-19 incidence", + "rel_date": "2020-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125377", + "rel_abs": "We test the hypothesis of COVID-19 contagion being influenced by meteorological parameters such as temperature or humidity. We analysed data at high spatial resolution (regions in Italy and counties in the USA) and found that while at low resolution this might seem the case, at higher resolution no correlation is found. Our results are consistent with a poor outdoors transmission of the disease. However, a possible indirect correlation between good weather and a decrease in disease spread may occur, as people spend longer time outdoors.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Javier G. Corripio", + "author_inst": "meteoexploration.com" + }, + { + "author_name": "Lorna Raso", + "author_inst": "meteoexploration.com" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.08.20124305", "rel_title": "Time-series plasma cell-free DNA analysis reveals disease severity of COVID-19 patients", @@ -1369094,53 +1372153,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.07.20115188", - "rel_title": "Functional and cognitive outcomes after COVID-19 delirium", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.07.20115188", - "rel_abs": "PurposeTo ascertain delirium prevalence and outcomes in COVID-19.\n\nMethodsWe conducted a point-prevalence study in a cohort of COVID-19 inpatients at University College Hospital. Delirium was defined by DSM-IV criteria. The primary outcome was all-cause mortality at 4 weeks; secondary outcomes were physical and cognitive function.\n\nResultsIn 71 patients, 31 (42%) had delirium, of which only 19 had been recognised by the clinical team. At 4 weeks, 20 (28%) had died, 26 (36%) were interviewed by telephone and 21 (30%) remained as inpatients. Physical function was substantially worse in people after delirium (-39 points on functional scale/166, 95% CI -92 to -21, p=0.01) (Table 2). Mean cognitive scores at follow-up were similar and delirium was not associated with mortality in this sample.\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@1062c36org.highwire.dtl.DTLVardef@40a765org.highwire.dtl.DTLVardef@ae062dorg.highwire.dtl.DTLVardef@1179aa8org.highwire.dtl.DTLVardef@aac078_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 2.C_FLOATNO O_TABLECAPTIONUnivariable and multivariable models estimating the associations with physical function at 4 weeks on a combined Barthel (100 points) and Nottingham Extended Activities of Daily Living score (66 points).\n\nC_TABLECAPTION C_TBL ConclusionsOur findings indicate that delirium is common, yet under-recognised. Delirium is associated with functional impairments in the medium-term.\n\nKey summary points\n\nAimTo investigate functional and cognitive outcomes among patients with delirium in COVID-19.\n\nFindingsDelirium in COVID-19 was prevalent (42%) but only a minority had been recognised by the clinical team. At 4-week follow-up, delirium was significantly associated with worse functional outcomes, independent of pre-morbid frailty. Cognitive outcomes were not appreciably worse.\n\nMessageThe presence of delirium is a significant factor in predicting worse functional outcomes in patients with COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Benjamin C Mcloughlin", - "author_inst": "University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Amy Miles", - "author_inst": "University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Thomas E Webb", - "author_inst": "University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Paul Knopp", - "author_inst": "University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Clodagh Eyres", - "author_inst": "University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Ambra Fabbri", - "author_inst": "University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Fiona Humphries", - "author_inst": "University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Daniel Davis", - "author_inst": "UCL" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "geriatric medicine" - }, { "rel_doi": "10.1101/2020.06.07.20120527", "rel_title": "Presenting features of COVID-19 in older people: relationships with frailty, inflammation and mortality", @@ -1370283,6 +1373295,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.06.20124149", + "rel_title": "Hawkes process modeling of COVID-19 with mobility leading indicators and spatial covariates", + "rel_date": "2020-06-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.06.20124149", + "rel_abs": "Hawkes processes are used in machine learning for event clustering and causal inference, while they also can be viewed as stochastic versions of popular compartmental models used in epidemiology. Here we show how to develop accurate models of COVID-19 transmission using Hawkes processes with spatial-temporal covariates. We model the conditional intensity of new COVID-19 cases and deaths in the U.S. at the county level, estimating the dynamic reproduction number of the virus within an EM algorithm through a regression on Google mobility indices and demographic covariates in the maximization step. We validate the approach on short-term forecasting tasks, showing that the Hawkes process outperforms several benchmark models currently used to track the pandemic, including an ensemble approach and a SEIR-variant. We also investigate which covariates and mobility indices are most important for building forecasts of COVID-19 in the U.S.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Wen-Hao Chiang", + "author_inst": "Indiana University-Purdue University Indianapolis" + }, + { + "author_name": "Xueying Liu", + "author_inst": "Indiana University-Purdue University Indianapolis" + }, + { + "author_name": "George Mohler", + "author_inst": "Indiana University-Purdue University Indianapolis" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.04.20122325", "rel_title": "Sub-weekly cycle uncovers the hidden link of 1atmospheric pollution to Kawasaki Disease", @@ -1370376,69 +1373415,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.06.20124495", - "rel_title": "Less Wrong COVID-19 Projections With Interactive Assumptions", - "rel_date": "2020-06-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.06.20124495", - "rel_abs": "COVID-19 pandemic is an enigma with uncertainty caused by biological and health systems factors. Although many models have been developed all around the world, transparent models that allow interacting with the assumptions will become more important as we test various strategies for lockdown, testing and social interventions and enable effective policy decisions. In this paper we developed a suite of models to guide development of policies under different scenarios when the lockdown opens. These had been deployed to create an interactive dashboard called COVision which includes the Agent based Models (ABM) and classical compartmental models i.e. Susceptible-Infected-Recovered (SIR) and Susceptible-Exposed-Infected-Recovered (SEIR) approaches. Our tool allows simulation of scenarios by changing strength of lockdown, basic reproduction number(R0), asymptomatic spread, testing rate, contact rate (Beta), recovery rate (Gamma), incubation period and starting number of cases. We optimized ABMs and classical compartmental models to fit the actual data, both of which performed well in terms of R-squared, root mean squared error (RMSE) and mean absolute percentage error (MAPE). Out of the three models in our suite, ABM was able to capture the data better than SIR and SEIR and achieved an RSQ of 92.3% for India and 89% for Maharashtra for the next 30 days. We also computed R0 using SIR and SEIR models which were found to be decreasing over the different periods of lockdown indicating the effectiveness of policies and interventions. Finally, we formulated ICU bed requirements using our best models. Our evaluation suggests that ABM models were able to capture the dynamic nature of the epidemic for a longer duration of time while classical SIR and SEIR models performed inefficiently for longer terms. The visual interactivity and ability to simulate outcomes under different parameters will allow the policymakers to make informed decisions for estimating the strength of lockdown to be implemented and testing rates. Further, our models were able to highlight the differences at state level for the parameters such as R0 and contact rates and hence can be applied for state specific decision making. An interactive dashboard http://covision.tavlab.iiitd.edu.in have been hosted as a web-server for the war level monitoring of the covid19 pandemic in India in public domain", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Aditya Nagori", - "author_inst": "CSIR-Institute of genomics and integrative biology, New Delhi" - }, - { - "author_name": "Raghav Awasthi", - "author_inst": "IIIT-Delhi" - }, - { - "author_name": "Vineet Joshi", - "author_inst": "IIIT-Delhi" - }, - { - "author_name": "Suryatej Reddy Vyalla", - "author_inst": "IIIT-Delhi" - }, - { - "author_name": "Akhil Jarodia", - "author_inst": "IIIT-Delhi" - }, - { - "author_name": "Chandan Gupta", - "author_inst": "IIIT-Delhi" - }, - { - "author_name": "Amogh Gulati", - "author_inst": "IIIT-Delhi" - }, - { - "author_name": "Harsh Bandhey", - "author_inst": "IIIT-Delhi" - }, - { - "author_name": "Keerat Kaur Guliani", - "author_inst": "Indian Institute of Technology Roorkee" - }, - { - "author_name": "Mehrab Singh Gill", - "author_inst": "IIIT-Delhi" - }, - { - "author_name": "Ponnurangam Kumaraguru", - "author_inst": "IIIT-Delhi" - }, - { - "author_name": "Tavpritesh Sethi", - "author_inst": "IIIT-Delhi" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.06.20123505", "rel_title": "Knowledge and Awareness-based Survey of COVID-19 within the Eye Care Profession in Nepal: Misinformation is Hiding the Truth.", @@ -1372105,6 +1375081,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2020.06.05.20123117", + "rel_title": "Serology confirms SARS-CoV-2 infection in PCR-negative children presenting with Paediatric Inflammatory Multi-System Syndrome", + "rel_date": "2020-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20123117", + "rel_abs": "BackgroundDuring the COVID-19 outbreak, reports have surfaced of children who present with features of a multisystem inflammatory syndrome with overlapping features of Kawasaki disease and toxic shock syndrome - Paediatric Inflammatory Multisystem Syndrome-temporally associated with SARS-CoV-2 pandemic (PIMS-TS). Initial reports find that many of the children are PCR-negative for SARS-CoV-2, so it is difficult to confirm whether this syndrome is a late complication of viral infection in an age group largely spared the worst consequences of this infection, or if this syndrome reflects enhanced surveillance.\n\nMethodsChildren hospitalised for symptoms consistent with PIMS-TS between 28 April and 8 May 2020, and who were PCR-negative for SARS-CoV-2, were tested for antibodies to viral spike glycoprotein using an ELISA test.\n\nResultsEight patients (age range 7-14 years, 63% male) fulfilled case-definition for PIMS-TS during the study period. Six of the eight patients required admission to intensive care. All patients exhibited significant IgG and IgA responses to viral spike glycoprotein. Further assessment showed that the IgG isotypes detected in children with PIMS-TS were of the IgGl and lgG3 subclasses, a distribution similar to that observed in samples from hospitalised adult COVID-19 patients. In contrast, lgG2 and lgG4 were not detected in children or adults. IgM was not detected in children, which contrasts with adult hospitalised adult COVID-19 patients of whom all had positive IgM responses.\n\nConclusionsStrong IgG antibody responses can be detected in PCR-negative children with PIMS-TS. The low detection rate of IgM in these patients is consistent with infection having occurred weeks previously and that the syndrome onset occurs well after the control of SARS-CoV-2 viral load. This implies that the disease is largely immune-mediated. Lastly, this indicates that serology can be an appropriate diagnostic tool in select patient groups.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Marisol Perez-Toledo", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Sian E. Faustini", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Sian E. Jossi", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Adrian Shields", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Hari Krishnan Kanthimathinathan", + "author_inst": "Birmingham Women and Children's NHS Foundation Trust" + }, + { + "author_name": "Joel D. Allen", + "author_inst": "University of Southampton" + }, + { + "author_name": "Yasunori Watanabe", + "author_inst": "University of Southampton" + }, + { + "author_name": "Margaret Goodall", + "author_inst": "University of Birmingham" + }, + { + "author_name": "David C. Wraith", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Tonny V. Veenith", + "author_inst": "University Hospitals Birmingham NHS Trust" + }, + { + "author_name": "Mark T. Drayson", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Deepthi Jyothish", + "author_inst": "Birmingham Women's and Children's NHS Foundation Trust" + }, + { + "author_name": "Eslam Al-Abadi", + "author_inst": "Birmingham Women's and Children's NHS Foundation Trust" + }, + { + "author_name": "Ashish Chikermane", + "author_inst": "Birmingham Women's and Children's NHS Foundation Trust" + }, + { + "author_name": "Steven Welch", + "author_inst": "University Hospitals Birmingham" + }, + { + "author_name": "Kavitha Masilamani", + "author_inst": "Birmingham Women's and Children's NHS Foundation Trust" + }, + { + "author_name": "Scott Hackett", + "author_inst": "University Hospitals Birmingham" + }, + { + "author_name": "Max Crispin", + "author_inst": "University of Southampton" + }, + { + "author_name": "Barnaby Scholefield", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Adam F. Cunningham", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Alex G. Richter", + "author_inst": "University of Birmingham" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.05.20123745", "rel_title": "Combined oropharyngeal/nasal swab is equivalent to nasopharyngeal sampling for SARS-CoV-2 diagnostic PCR", @@ -1372230,85 +1375305,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.05.20123463", - "rel_title": "UV-C irradiation is highly effective in inactivating and inhibiting SARS-CoV-2 replication", - "rel_date": "2020-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20123463", - "rel_abs": "The potential virucidal effects of UV-C irradiation on SARS-CoV-2 were experimentally evaluated for different illumination doses and virus concentrations (1000, 5, 0.05 MOI). At a virus density comparable to that observed in SARS-CoV-2 infection, an UV-C dose of just 3.7 mJ/cm2 was sufficient to achieve a more than 3-log inactivation without any sign of viral replication. Moreover, a complete inactivation at all viral concentrations was observed with 16.9 mJ/cm2. These results could explain the epidemiological trends of COVID-19 and are important for the development of novel sterilizing methods to contain SARS-CoV-2 infection.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Andrea Bianco", - "author_inst": "Italian National Institute for Astrophysics (INAF) Milano/Merate, Italy." - }, - { - "author_name": "Mara Biasin", - "author_inst": "Department of Biomedical and Clinical Sciences L. Sacco, University of Milano, Milano, Italy" - }, - { - "author_name": "Giovanni Pareschi", - "author_inst": "Italian National Institute for Astrophysics (INAF) Milano/Merate, Italy." - }, - { - "author_name": "Adalberto Cavalleri", - "author_inst": "Department of Imaging Diagnostic and Radioterapy, IRCCS Foundation, Istituto Nazionale dei Tumori, Milan, Italy" - }, - { - "author_name": "Claudia Cavatorta", - "author_inst": "Department of Imaging Diagnostic and Radioterapy, IRCCS Foundation, Istituto Nazionale dei Tumori, Milan, Italy." - }, - { - "author_name": "Claudio Fenizia", - "author_inst": "Department of Biomedical and Clinical Sciences L. Sacco, University of Milano, Milano, Italy" - }, - { - "author_name": "Paola Galli", - "author_inst": "1 Italian National Institute for Astrophysics (INAF) Milano/Merate, Italy." - }, - { - "author_name": "Luigi Lessio", - "author_inst": "4 Italian National Institute for Astrophysics (INAF) Padova, Italy." - }, - { - "author_name": "Manuela Lualdi", - "author_inst": "Department of Imaging Diagnostic and Radioterapy, IRCCS Foundation, Istituto Nazionale dei Tumori, Milan, Italy" - }, - { - "author_name": "Enrico Trombetti", - "author_inst": "Department of Biomedical and Clinical Sciences L. Sacco, University of Milano, Milano, Italy" - }, - { - "author_name": "Alessandro Ambrosi", - "author_inst": "University Life and health San Raffaele, Milan, Italy" - }, - { - "author_name": "Edoardo Redaelli", - "author_inst": "1 Italian National Institute for Astrophysics (INAF) Milano/Merate, Italy." - }, - { - "author_name": "Irma Saulle", - "author_inst": "Department of Biomedical and Clinical Sciences L. Sacco, University of Milano, Milano, Italy." - }, - { - "author_name": "Daria Trabattoni", - "author_inst": "Department of Biomedical and Clinical Sciences L. Sacco, University of Milano, Milano, Italy." - }, - { - "author_name": "Alessio Zanutta", - "author_inst": "Italian National Institute for Astrophysics (INAF) Milano/Merate, Italy." - }, - { - "author_name": "Mario Clerici", - "author_inst": "Department of Pathophysiology and Transplantation, University of Milano and Don Gnocchi Foundation (Milano)" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.06.20123901", "rel_title": "CLINICAL PROPERTIES AND DIAGNOSTIC METHODS OF COVID-19 INFECTION IN PREGNANCIES: META-ANALYSIS", @@ -1373283,6 +1376279,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.04.20122317", + "rel_title": "Heart Disease Deaths during the Covid-19 Pandemic", + "rel_date": "2020-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122317", + "rel_abs": "The SARS-CoV-2 pandemic is associated with a reduction in hospitalization for an acute cardiovascular conditions. In a major health system in Massachusetts, there was a 43% reduction in these types of hospitalizations in March 2020 compared with March 2019.4 Whether mortality rates from heart disease have changed over this period is unknown.\n\nWe assembled information from the National Center for Health Statistics (Centers for Disease Control and Prevention) for 118,356,533 person-weeks from Week 1 (ending January 4) through Week 17 (ending April 25) of 2020 for the state of Massachusetts. We found that heart disease deaths are unchanged during the Covid-19 pandemic period as compared to the corresponding period of 2019. This is despite reports that admissions for acute myocardial infarction have fallen during this time.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jeremy Faust", + "author_inst": "Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "Zhenqiu Lin", + "author_inst": "Yale-New Haven Hospital, Center for Outcomes Research and Evaluation" + }, + { + "author_name": "Harlan Krumholz", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.07.137802", "rel_title": "Neuropilin-1 facilitates SARS-CoV-2 cell entry and provides a possible pathway into the central nervous system", @@ -1373524,45 +1376547,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.06.07.138800", - "rel_title": "Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism", - "rel_date": "2020-06-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.07.138800", - "rel_abs": "As the coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), rages across the world, killing hundreds of thousands and infecting millions, researchers are racing against time to elucidate the viral genome. Some Bangladeshi institutes are also in this race, sequenced a few isolates of the virus collected from Bangladesh. Here, we present a genomic analysis of 14 isolates. The analysis revealed that SARS-CoV-2 isolates sequenced from Dhaka and Chittagong were the lineage of Europe and the Middle East, respectively. Our analysis identified a total of 42 mutations, including three large deletions, half of which were synonymous. Most of the missense mutations in Bangladeshi isolates found to have weak effects on the pathogenesis. Some mutations may lead the virus to be less pathogenic than the other countries. Molecular docking analysis to evaluate the effect of the mutations on the interaction between the viral spike proteins and the human ACE2 receptor, though no significant interaction was observed. This study provides some preliminary insights into the origin of Bangladeshi SARS-CoV-2 isolates, mutation spectrum and its possible pathomechanism, which may give an essential clue for designing therapeutics and management of COVID-19 in Bangladesh.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Md Sorwer Alam Parvez", - "author_inst": "Shahjalal University of Science & Technology" - }, - { - "author_name": "Mohammad Mahfujur Rahman", - "author_inst": "Shahjalal University of Science & Technology" - }, - { - "author_name": "Md Niaz Morshed", - "author_inst": "Shahjalal University of Science & Technology" - }, - { - "author_name": "Dolilur Rahman", - "author_inst": "Shahjalal University of Science & Technology" - }, - { - "author_name": "Saeed Anwar", - "author_inst": "Faculty of Medicine and Dentistry, University of Alberta" - }, - { - "author_name": "Mohammad Jakir Hosen", - "author_inst": "Shahjalal University of Science and Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.06.06.137604", "rel_title": "Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype", @@ -1375305,6 +1378289,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.02.20117499", + "rel_title": "Emergency calls are early indicators of ICU bed requirement during the COVID-19 epidemic", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20117499", + "rel_abs": "BackgroundAlthough the number of intensive care unit (ICU) beds is crucial during the COVID-19 epidemic caring for the most critically ill infected patients, there is no recognized early indicator to anticipate ICU bed requirements.\n\nMethodsIn the Ile-de-France region, from February 20 to May 5, 2020, emergency medical service (EMS) calls and the response provided (ambulances) together the percentage of positive reverse transcriptase polymerase chain reaction (RT-PCR) tests, general practitioner (GP) and emergency department (ED) visits, and hospital admissions of COVID-19 patients were recorded daily and compared to the number of COVID-19 ICU patients. Correlation curve analysis was performed to determine the best correlation coefficient (R), depending on the number of days the indicator has been shifted. A delay [≥]7 days was considered as an early alert, and a delay [≥]14 days a very early alert.\n\nFindingsEMS calls, percentage of positive RT-PCR tests, ambulances used, ED and GP visits of COVID-19 patients were strongly associated with COVID-19 ICU patients with an anticipation delay of 23, 15, 14, 13, and 12 days respectively. Hospitalization did not anticipate ICU bed requirement.\n\nInterpretationThe daily number of COVID19-related telephone calls received by the EMS and corresponding dispatch ambulances, and the proportion of positive RT-PCR tests were the earliest indicators of the number of COVID19 patients requiring ICU care during the epidemic crisis in the Ile-de-France region, rapidly followed by ED and GP visits. This information may help health authorities to anticipate a future epidemic, including a second wave of COVID19 or decide additional social measures.\n\nFundingOnly institutional funding was provided.\n\nResearch in contextO_ST_ABSEvidence before the studyC_ST_ABSWe searched PubMed and preprint archives for articles published up to May 17, 2020, that contained information about the anticipation of intensive care unit (ICU) bed requirement during the COVID-19 outbreak using the terms \"coronavirus\", \"2009-nCOV\", \"COVID-19\", SARS-CoV2\", \"prediction\" \"resource\" and \"intensive care\". We also reviewed relevant references in retrieved articles and the publicly available publication list of the COVID-19 living systematic review.22 This list contains studies on covid-19 published on PubMed and Embase through Ovid, bioRxiv, and medRxiv, and is continuously updated. Although many studies estimated the number of patients who would have severe COVID-19 requiring ICU, very few contained assessment for early signals (from internet or social media), and we retrieved no study whose data came from suspected or infected patients.\n\nAdded values of this studyDuring the COVID-19 epidemic, emergency medical system (EMS) calls, percentage of positive reverse transcriptase polymerase chain reaction (RT-PCR) tests, ambulance dispatch, emergency department (ED) and general practitioner (GP) visits of COVID-19 patients were strongly associated with COVID-19 ICU patients with an anticipation delay of 23, 15, 14, 13, and 12 days respectively. Hospitalization did not anticipated COVID-19 ICU bed requirement.\n\nImplication of all available evidenceEMS calls and ambulance dispatch, percent of positive RT-PCR, and ED and GP visits could be valuable tools as daily alert signals to set up plan to face the burden of ICU bed requirement during the initial wave of the COVID-19 epidemic, and may possibly also help anticipating a second wave. These results are important since mortality has been reported being correlated to health care resources.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "- The COVID-19 APHP-Universities-INRIA-INSERM Group", + "author_inst": "" + }, + { + "author_name": "Bruno Riou", + "author_inst": "Sorbonne Universite and Assistance Publique-Hopitaux de Paris, Paris, France" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.06.01.20119560", "rel_title": "Covid-19 Epidemiological Factor Analysis: Identifying Principal Factors with Machine Learning", @@ -1375410,61 +1378417,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.04.20112011", - "rel_title": "Reparations for Black American Descendants of Persons Enslaved in the U.S. and Their Estimated Impact on SARS-CoV-2 Transmission", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20112011", - "rel_abs": "BackgroundIn the United States, Black Americans are suffering from significantly disproportionate incidence and mortality rates of COVID-19. The potential for racial-justice interventions, including reparations payments, to ameliorate these disparities has not been adequately explored.\n\nMethodsWe compared the COVID-19 time-varying Rt curves of relatively disparate polities in terms of social equity (South Korea vs. Louisiana). Next, we considered a range of reproductive ratios to back-calculate the transmission rates {beta}i[->]j for 4 cells of the simplified next-generation matrix (from which R0 is calculated for structured models) for the outbreak in Louisiana. Lastly, we modeled the effect that monetary payments as reparations for Black American descendants of persons enslaved in the U.S. would have had on pre-intervention {beta}i[->]j.\n\nResultsOnce their respective epidemics begin to propagate, Louisiana displays Rt values with an absolute difference of 1.3 to 2.5 compared to South Korea. It also takes Louisiana more than twice as long to bring Rt below 1. We estimate that increased equity in transmission consistent with the benefits of a successful reparations program (reflected in the ratio {beta}b[->]b / {beta}w[->]w) could reduce R0 by 31 to 68%.\n\nDiscussionWhile there are compelling moral and historical arguments for racial injustice interventions such as reparations, our study describes potential health benefits in the form of reduced SARS-CoV-2 transmission risk. As we demonstrate, a restitutive program targeted towards Black individuals would not only decrease COVID-19 risk for recipients of the wealth redistribution; the mitigating effects would be distributed across racial groups, benefitting the population at large.\n\nFundingETR and LW are supported by NIGMS MIDAS grant R01 GM130900. ETR is also supported by NIAID K08 AI139361. WAD is supported by NIMHD R01 MD011606, NSF SES 1851845, and IES R305A190484. MMM is supported by the Ethics and Governance of Artificial Intelligence Fund.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Eugene T Richardson", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Momin M Malik", - "author_inst": "Harvard University" - }, - { - "author_name": "William A Darity Jr.", - "author_inst": "Duke University" - }, - { - "author_name": "A Kirsten Mullen", - "author_inst": "Artefactual" - }, - { - "author_name": "Maya Malik", - "author_inst": "McGill University" - }, - { - "author_name": "Adia Benton", - "author_inst": "Northwestern University" - }, - { - "author_name": "Mary T Bassett", - "author_inst": "Harvard School of Public Health" - }, - { - "author_name": "Paul E. Farmer", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Lee Worden", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "James Holland Jones", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.03.20116327", "rel_title": "Performance characteristics of the ID NOW COVID-19 assay: A regional health care system experience", @@ -1376647,6 +1379599,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.06.03.20121590", + "rel_title": "Deep Learning and Holt-Trend Algorithms for predicting COVID-19 pandemic", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20121590", + "rel_abs": "According to WHO, more than one million individuals are infected with COVID-19, and around 20000 people have died because of this infectious disease around the world. In addition, COVID-19 epidemic poses serious public health threat to the world where people with little or no pre-existing human immunity can be more vulnerable to the effects of the effects of the coronavirus. Thus, developing surveillance systems for predicting COVID-19 pandemic in an early stage saves millions of lives. In this study, the deep learning algorithm and Holt-trend model is proposed to predict coronavirus. The Long-Short Term Memory (LSTM) algorithm and Holt-trend were applied to predict confirmed numbers and death cases. The real time data have been collected from the World Health Organization (WHO). In the proposed research, we have considered three countries to test the proposed model namely Saudi Arabia, Spain and Italy. The results suggest that the LSTM models showed better performance in predicting the cases of coronavirus patients. Standard measure performance MSE, RMSE, Mean error and correlation are employed to estimate the results of the proposed models. The empirical results of the LSTM by using correlation metric are 99.94%, 99.94% and 99.91 to predict number of confirmed cases on COVID-19 in three countries. Regarding the prediction results of LSTM model to predict the number of death on COVID-19 are 99.86%, 98.876% and 99.16 with respect to the Saudi Arabia, Italy and Spain respectively. Similarly the experimented results of Holt-Trend to predict the number of confirmed cases on COVID-19 by using correlation metrics are 99.06%, 99.96% and 99.94, whereas the results of Holt-Trend to predict the number of death cases are 99.80%, 99.96 and 99.94 with respect to the Saudi Arabia, Italy and Spain respectively. The empirical results indicate the efficient performance of the presented model in predicting the number of confirmed and death cases of COVID-19 in these countries. Such findings provide better insights about the future of COVID-19 in general. The results were obtained by applying the time series models which needs to be considered for the sake of saving the lives of many people.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Theyazn H.H Aldhyani", + "author_inst": "Department of Computer Science and Information at king faisal University, Kingdom of Saudi Arabia" + }, + { + "author_name": "Melfi Alrasheed Sr.", + "author_inst": "Department of Quantitative Methods, School of Business, King Faisal University. Saudi" + }, + { + "author_name": "Ahmed i Abdullah Alqarn Sr.", + "author_inst": "Department of Computer Sciences and Information Technology, Albaha University," + }, + { + "author_name": "Mohammed Y. Alzahrani", + "author_inst": "Department of Computer Sciences and Information Technology, Albaha University" + }, + { + "author_name": "Ahmed H., Alahmadi", + "author_inst": "Department of Computer Science and Information at Taibah University," + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.06.04.20121848", "rel_title": "An Agent Based Model methodology for assessing spread and health systems burden for Covid-19 using a synthetic population from India", @@ -1376804,33 +1379791,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.03.20121467", - "rel_title": "Comparison of epidemiological characteristics of COVID-19 patients in Vietnam", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20121467", - "rel_abs": "BackgroundThere are limited data on COVID-19 patients in Vietnam. The paper examined and compared epidemiological characteristics of COVID-19 patients in Vietnam\n\nMethodThe data was obtained using publicly available information from the official website of Vietnam Ministry of Health covering a period of 01/23/2020 to 05/27/2020. T-test, Chi-square test and Fishers Exact test were utilized to compare characteristics of COVID-19 patients between under-treatment and discharge groups and between overseas and non-overseas travel groups.\n\nResultsVietnam had a total of 327 cases of COVID-19 as of May 27, 2020. The median age of patients was 30 years (ranging from 3 months to 88 years). About 68% of patients (n=223) had acquired the disease from overseas while 32% were infected from local transmission. Among those infected from local transmission, 66% were women. Men were more likely than women to be infected with COVID-19 from overseas (p<0.001). Younger patients were significantly associated with international travel (p=.001). While patients in the South reported highest levels of overseas travel history (77.9%), those (100%) in the Central reported the highest level of being discharged (p<0.001). Women (54.7%) had a higher rate of discharge compared to men (45.3%) [p <0.001]. Nearly 86% have recovered and discharged from hospitals. There has been no reported fatality.\n\nConclusionsA majority of COVID-19 cases in Vietnam were acquired overseas. A significantly higher number of women than men were infected inside the country calling for further research about gender disparities in the fight against COVID-19 in Vietnam.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Toan H Ha", - "author_inst": "University of Connecticut School of Medicine" - }, - { - "author_name": "Gualberto Ruano", - "author_inst": "University of Connecticut Health, Connecticut Convergence Institute for Translation in Regenerative Engineering" - }, - { - "author_name": "Judy Lewis", - "author_inst": "University of Connecticut School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.03.20121517", "rel_title": "A modified SEIR meta-population transmission based Modeling and Forecasting of the COVID-19 pandemic in Pakistan", @@ -1378804,6 +1381764,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.06.04.20122846", + "rel_title": "A tertiary center experience of multiple myeloma patients with COVID-19: lessons learned and the path forward", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122846", + "rel_abs": "BackgroundThe COVID-19 pandemic, caused by SARS-CoV-2 virus, has resulted in over 100,000 deaths in the United States. Our institution has treated over 2,000 COVID-19 patients during the pandemic in New York City. The pandemic directly impacted cancer patients and the organization of cancer care. Mount Sinai Hospital has a large and diverse multiple myeloma (MM) population. Herein, we report the characteristics of COVID-19 infection and serological response in MM patients in a large tertiary care institution in New York.\n\nMethodsWe performed a retrospective study on a cohort of 58 patients with a plasma-cell disorder (54 MM, 4 smoldering MM) who developed COVID-19 between March 1, 2020 and April 30, 2020. We report epidemiological, clinical and laboratory characteristics including persistence of viral detection by polymerase chain reaction (PCR) and anti-SARS-CoV-2 antibody testing, treatments initiated, and outcomes.\n\nResultsOf the 58 patients diagnosed with COVID-19, 36 were hospitalized and 22 were managed at home. The median age was 67 years; 52% of patients were male and 63% were non-white. Hypertension (64%), hyperlipidemia (62%), obesity (37%), diabetes mellitus (28%), chronic kidney disease (24%) and lung disease (21%) were the most common comorbidities. In the total cohort, 14 patients (24%) died. Older age (>70 years), male sex, cardiovascular risk, and patients not in complete remission (CR) or stringent CR were significantly (p<0.05) associated with hospitalization. Among hospitalized patients, laboratory findings demonstrated elevation of traditional inflammatory markers (CRP, ferritin, D-dimer) and a significant (p<0.05) association between elevated inflammatory markers, severe hypogammaglobulinemia, non-white race, and mortality. Ninety-six percent (22/23) of patients developed antibodies to SARS-CoV-2 at a median of 32 days after initial diagnosis. Median time to PCR negativity was 43 (range 19-68) days from initial positive PCR.\n\nConclusionsDrug exposure and MM disease status at the time of contracting COVID-19 had no bearing on mortality. Mounting a severe inflammatory response to SARS-CoV-2 and severe hypogammaglobulinemia were associated with higher mortality. The majority of patients mounted an antibody response to SARS-CoV-2. These findings pave a path to identification of vulnerable MM patients who need early intervention to improve outcome in future outbreaks of COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Bo Wang", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Oliver Van Oekelen", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Tarek Mouhieddine", + "author_inst": "Mount Sinai Hospital" + }, + { + "author_name": "Diane Marie Del Valle", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Joshua Richter", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Hearn Jay Cho", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Shambavi Richard", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Ajai Chari", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Sacha Gnjatic", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Miriam Merad", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sundar Jagannath", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Samir Parekh", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Deepu Madduri", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2020.06.04.20122564", "rel_title": "Adverse effects of COVID-19 related lockdown on pain, physical activity and psychological wellbeing in people with chronic pain", @@ -1378893,45 +1381920,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.06.04.20122879", - "rel_title": "CoVID-19 in Singapore: Impact of Contact Tracing and Self-awareness on Healthcare Demand", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122879", - "rel_abs": "BackgroundA great concern around the globe now is to mitigate the COVID-19 pandemic via contact tracing. Analyzing the control strategies during the first five months of 2020 in Singapore is important to estimate the effectiveness of contacting tracing measures.\n\nMethodsWe developed a mathematical model to simulate the COVID-19 epidemic in Singapore, with local cases stratified into 5 categories according to the conditions of contact tracing and self-awareness. Key parameters of each category were estimated from local surveillance data. We also simulated a set of possible scenarios to predict the effects of contact tracing and self-awareness for the following month.\n\nFindingsDuring January 23 - March 16, 2020, the success probabilities of contact tracing and self-awareness were estimated to be 31% (95% CI 28%-33%) and 54% (95% CI 51%-57%), respectively. During March 17 - April 7, 2020, several social distancing measures (e.g., limiting mass gathering) were introduced in Singapore, which, however, were estimated with minor contribution to reduce the non-tracing reproduction number per local case (R{iota},2). If contact tracing and self-awareness cannot be further improved, we predict that the COVID-19 epidemic will continue to spread in Singapore if R{iota},2 [≥] 1.5.\n\nConclusionContact tracing and self-awareness can mitigate the COVID-19 transmission, and can be one of the key strategies to ensure a sustainable reopening after lifting the lockdown.\n\nSummaryWe evaluate the efficiency of contact tracing and self-awareness in Singapores early-stage control of COVID-19. Then use a branching model to simulate and evaluate the possible prospective outcomes of Singapores COVID-19 control in different scenarios.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Qiuyang Huang", - "author_inst": "College of Computer Science and Technology, Jilin University, Changchun, 130012, China" - }, - { - "author_name": "Lin Wang", - "author_inst": "Department of Genetics, University of Cambridge, Cambridge, UK" - }, - { - "author_name": "Yongjian Yang", - "author_inst": "College of Computer Science and Technology, Jilin University, Changchun, 130012, China" - }, - { - "author_name": "Liping Huang", - "author_inst": "School of Electrical and Electronic Engineering, Nanyang Technology University, Singapore" - }, - { - "author_name": "Zhanwei Du", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Gaoxi Xiao", - "author_inst": "School of Electrical and Electronic Engineering, Nanyang Technology University, Singapore" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.06.03.20112540", "rel_title": "ACUTE VISION LOSS IN A PATIENT WITH COVID-19", @@ -1380114,6 +1383102,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.03.132639", + "rel_title": "Human iPSC-derived alveolar and airway epithelial cells can be cultured at air-liquid interface and express SARS-CoV-2 host factors", + "rel_date": "2020-06-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.03.132639", + "rel_abs": "Development of an anti-SARS-CoV-2 therapeutic is hindered by the lack of physiologically relevant model systems that can recapitulate host-viral interactions in human cell types, specifically the epithelium of the lung. Here, we compare induced pluripotent stem cell (iPSC)-derived alveolar and airway epithelial cells to primary lung epithelial cell controls, focusing on expression levels of genes relevant for COVID-19 disease modeling. iPSC-derived alveolar epithelial type II-like cells (iAT2s) and iPSC-derived airway epithelial lineages express key transcripts associated with lung identity in the majority of cells produced in culture. They express ACE2 and TMPRSS2, transcripts encoding essential host factors required for SARS-CoV-2 infection, in a minor subset of each cell sub-lineage, similar to frequencies observed in primary cells. In order to prepare human culture systems that are amenable to modeling viral infection of both the proximal and distal lung epithelium, we adapt iPSC-derived alveolar and airway epithelial cells to two-dimensional air-liquid interface cultures. These engineered human lung cell systems represent sharable, physiologically relevant platforms for SARS-CoV-2 infection modeling and may therefore expedite the development of an effective pharmacologic intervention for COVID-19.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Kristine M Abo", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Liang Ma", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Taylor Matte", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Jessie Huang", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Konstantinos D Alysandratos", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Rhiannon B Werder", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Aditya Mithal", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Mary Lou Beermann", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Jonathan Lindstrom-Vautrin", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Gustavo Mostoslavsky", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Laertis Ikonomou", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Darrell N Kotton", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Finn Hawkins", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Andrew Wilson", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Carlos Villacorta-Martin", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.06.04.135012", "rel_title": "Olfactory transmucosal SARS-CoV-2 invasion as port of Central Nervous System entry in COVID-19 patients", @@ -1380439,49 +1383502,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.03.20121020", - "rel_title": "Regional Difference in Seroprevalence of SARS-CoV-2 in Tokyo: Results from the community point-of-care antibody testing", - "rel_date": "2020-06-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20121020", - "rel_abs": "The serosurvey is an alternative way to know the magnitude of the population infected by coronavirus disease 2019 (COVID-19) since the expansion of capacity of the polymerase chain reaction (PCR) to detect the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was delayed. We herein report seroprevalence of COVID-19 accessed in the two community clinics in Tokyo. The point-of-care immunodiagnostic test was implemented to detect the SARS-CoV-2 specific IgG antibody in the peripheral capillary blood. The overall positive percentage of SARS-CoV-2 IgG antibody is 3.83% (95% confidence interval: 2.76-5.16) for the entire cohort (n =1,071). The central Tokyo of 23 special wards exhibited a significantly higher prevalence compared to the other area of Tokyo (p =0.02, 4.68% [95%CI: 3.08-6.79] versus 1.83 [0.68-3.95] in central and suburban Tokyo, respectively). The seroprevalence of the cohort surveyed in this study is low for herd immunity, which suggests the need for robust disease control and prevention. A community-based approach, rather than state or prefectural levels, is of importance to figure out profiles of the SARS-COV-2 outbreak.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Morihito Takita", - "author_inst": "Navitas Clinic Tachikawa" - }, - { - "author_name": "Tomoko Matsumura", - "author_inst": "Navitas Clinic Tachikawa" - }, - { - "author_name": "Kana Yamamoto", - "author_inst": "Navitas Clinic Shinjuku" - }, - { - "author_name": "Erika Yamashita", - "author_inst": "Navitas Clinic Shinjuku" - }, - { - "author_name": "Kazutaka Hosoda", - "author_inst": "Navitas Clinic Tachikawa" - }, - { - "author_name": "Tamae Hamaki", - "author_inst": "Navitas Clinic Shinjuku" - }, - { - "author_name": "Eiji Kusumi", - "author_inst": "Navitas Clinic Tachikawa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.03.20120998", "rel_title": "Genetic polymorphisms mediating behavioural and immune response to pathogens may moderate the impact of the COVID-19 pandemic: a pilot study", @@ -1381736,6 +1384756,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.06.01.20119347", + "rel_title": "COVID-19 Public Sentiment Insights and MachineLearning for Tweets Classification", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119347", + "rel_abs": "Along with the Coronavirus pandemic, another crisis has manifested itself in the form of mass fear and panic phenomena, fueled by incomplete and often inaccurate information. There is therefore a tremendous need to address and better understand COVID-19s informational crisis and gauge public sentiment, so that appropriate messaging and policy decisions can be implemented. In this research article, we identify public sentiment associated with the pandemic using Coronavirus specific Tweets and R statistical software, along with its sentiment analysis packages. We demonstrate insights into the progress of fear-sentiment over time as COVID-19 approached peak levels in the United States, using descriptive textual analytics supported by necessary textual data visualizations. Furthermore, we provide a methodological overview of two essential machine learning (ML) classification methods, in the context of textual analytics, and compare their effectiveness in classifying Coronavirus Tweets of varying lengths. We observe a strong classification accuracy of 91% for short Tweets, with the Naive Bayes method. We also observe that the logistic regression classification method provides a reasonable accuracy of 74% with shorter Tweets, and both methods showed relatively weaker performance for longer Tweets. This research provides insights into Coronavirus fear sentiment progression, and outlines associated methods, implications, limitations and opportunities.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jim Samuel", + "author_inst": "University of Charleston, Charleston, WV" + }, + { + "author_name": "Ali G. G. Md. Nawaz", + "author_inst": "University of Charleston, Charleston, WV" + }, + { + "author_name": "Md Mokhlesur Rahman", + "author_inst": "University of North Carolina at Charlotte, Charlotte, NC; Khulna University of Engineering & Technology (KUET), Khulna, Bangladesh" + }, + { + "author_name": "Ek Esawi", + "author_inst": "University of Charleston, Charleston, WV" + }, + { + "author_name": "Yana Samuel", + "author_inst": "Northeastern University, Boston, MA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.29.20117143", "rel_title": "Detection of lung hypoperfusion in Covid-19 patients during recovery by digital imaging quantification", @@ -1381841,41 +1384896,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2020.05.30.20117788", - "rel_title": "The Role of Host Genetic Factors in Coronavirus Susceptibility: Review of Animal and Systematic Review of Human Literature", - "rel_date": "2020-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117788", - "rel_abs": "BackgroundThe recent SARS-CoV-2 pandemic raises many scientific and clinical questions. One set of questions involves host genetic factors that may affect disease susceptibility and pathogenesis. New work is emerging related to SARS-CoV-2; previous work on other coronaviruses in humans or other host species may be relevant.\n\nObjectivesTo review existing literature on host genetic factors and their association with infection and disease with coronaviruses in humans and in other host species.\n\nMethodsWe conducted a systematic review of literature on host genetic factors in humans associated with coronavirus outcomes. We also reviewed studies of host genetic factors associated with coronavirus outcomes in non-human species. We categorized articles, summarized themes related to animal studies, and extracted data from human studies for analyses.\n\nResultsWe identified 1,187 articles of potential relevance. Forty-five studies examined human host genetic factors related to coronavirus, of which 35 involved analysis of specific genes or loci; aside from one meta-analysis on respiratory infections, all were candidate-driven studies, typically investigating small numbers of research subjects and loci. Multiple significant loci were identified, including 16 related to susceptibility to coronavirus (of which 7 identified protective alleles), and 16 related to outcomes or clinical variables (of which 3 identified protective alleles). The types of cases and controls used varied considerably; four studies used traditional replication/validation cohorts. Of the other studies, 28 involved both human and non-human host genetic factors related to coronavirus, and 174 involved study of non-human (animal) host genetic factors related to coronavirus.\n\nKey findingsWe have outlined key genes and loci from animal and human host genetic studies that may bear investigation in the nascent host genetic factor studies of COVID-19. Previous human studies have been limited by relatively low numbers of eligible participants and limited availability of advanced genomic methods. These limitations may be less important to studies of SARS-CoV-2.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Marissa LoPresti", - "author_inst": "University of Florida" - }, - { - "author_name": "David B Beck", - "author_inst": "National Human Genome Research Institute" - }, - { - "author_name": "Priya Duggal", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Derek A.T. Cummings", - "author_inst": "University of Florida" - }, - { - "author_name": "Benjamin D Solomon", - "author_inst": "National Human Genome Research Institute" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.05.31.20118406", "rel_title": "A projection model of COVID-19 pandemic for Belgium", @@ -1382922,6 +1385942,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.30.20117853", + "rel_title": "Evaluating the Efficacy of Stay-At-Home Orders: Does Timing Matter?", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117853", + "rel_abs": "BACKGROUNDThe many economic, psychological, and social consequences of pandemics and social distancing measures create an urgent need to determine the efficacy of non-pharmaceutical interventions (NPIs), and especially those considered most stringent, such as stay-at-home and self-isolation mandates. This study focuses specifically on the efficacy of stay-at-home orders, both nationally and internationally, in the control of COVID-19.\n\nMETHODSWe conducted an observational analysis from April to May 2020 and included countries and US states with known stay-at-home orders. Our primary exposure was the time between the date of the first reported case of COVID-19 to an implemented stay-at-home mandate for each region. Our primary outcomes were the time from the first reported case to the highest number of daily cases and daily deaths. We conducted simple linear regression analyses, controlling for the case rate of the outbreak.\n\nRESULTSFor US states and countries, a larger number of days between the first reported case and stay-at-home mandates was associated with a longer time to reach the peak daily case and death counts. The largest effect was among regions classified as the latest 10% to implement a mandate, which in the US, predicted an extra 35.3 days to the peak number of cases (95 % CI: 18.2, 52.5), and 38.3 days to the peak number of deaths (95 % CI: 23.6, 53.0).\n\nCONCLUSIONSOur study supports the potential beneficial effect of earlier stay-at-home mandates, by shortening the time to peak case and death counts for US states and countries. Regions in which mandates were implemented late experienced a prolonged duration to reaching both peak daily case and death counts.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alexandra Medline, MPH", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Lamar Hayes, MPH", + "author_inst": "David Geffen School of Medicine" + }, + { + "author_name": "Farnoosh Vahedi", + "author_inst": "David Geffen School of Medicine" + }, + { + "author_name": "Katia Valdez", + "author_inst": "Fielding School of Public Health, University of California Los Angeles" + }, + { + "author_name": "Jake Sonnenberg", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Will Capell", + "author_inst": "David Geffen School of Medicine" + }, + { + "author_name": "Ami Hayashi", + "author_inst": "David Geffen School of Medicine" + }, + { + "author_name": "Zoe Glick", + "author_inst": "UC Berkeley" + }, + { + "author_name": "Jeffrey D. Klausner, MD, MPH", + "author_inst": "UCLA David Geffen School of Medicine and Fielding School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.31.20118315", "rel_title": "Cytokine biomarkers of COVID-19", @@ -1383107,101 +1386178,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.01.20118018", - "rel_title": "Continuous positive airway pressure face-mask ventilation to manage massive influx of patients requiring respiratory support during the SARS-CoV-2 outbreak", - "rel_date": "2020-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20118018", - "rel_abs": "BackgroundSince December 2019, a global outbreak of coronavirus disease (COVID-19) is responsible for massive influx of patients with acute respiratory failure in hospitals. We describe the characteristics, clinical course, and outcomes of COVID-19 patients treated with continuous positive airway pressure (CPAP) in a large public hospital in France.\n\nMethodIt is a single centre retrospective observational cohort. From 27th March to 23rd April, consecutive patients who had signs of respiratory failure or were unable to maintain an SpO2 > 90%, despite receiving 10 to 15 l/min of oxygen with a non-rebreather mask, were treated by CPAP with a face-mask unless the ICU physician judged that immediate intubation was indicated. The main outcomes under study were reasons for CPAP discontinuation and mortality.\n\nResultsA total of 585 patients were admitted in Delafontaine hospital for severe COVID-19. ICU was quickly overwhelmed. Fifty-nine out of 159 (37%) patients requiring ICU care had to be referred to other hospitals. CPAP therapy was initiated in 49 patients and performed out of ICU in 41 (84%). SARS-CoV2 pneumonia was confirmed by PCR from respiratory tract in 39 (79%) patients and by thoracic CT scan in the remaining patients. CPAP was performed out of ICU in 41 (84%) cases. Median age was 65 years (IQR=54-71). Median duration of CPAP treatment was 3 days (IQR=1-5). Reasons for discontinuation of CPAP were intubation for invasive ventilation in 25 (51%) patients, improvement in 16 (33%), poor tolerance in 6 (12%) and death in 2 (4%). A decision not to intubate had been taken for the 2 patients who died while on CPAP.\n\nConclusionsTreatment with CPAP is feasible and safe in a non-ICU environment in the context of a massive influx of patients. One third of these patients with high oxygen requirements did not eventually need invasive ventilation.\n\nKey messagesO_ST_ABSWhat is the key question?C_ST_ABSWhat is the best respiratory support strategy to manage a massive influx of patients with hypoxemic respiratory failure despite high-flow oxygen delivered with a non-rebreather mask?\n\nWhat is the bottom line?Continuous positive airway pressure face mask ventilation delivered in non-ICU wards to patients who do not require immediate intubation is feasible and safe.\n\nWhy read on?Face mask ventilation with CPAP should be considered as an option of respiratory support in the context of the on-going COVID-19 pandemic and limited availability of ICU beds.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Sophie Alviset", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Quentin Riller", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Jerome Aboab", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Kelly Dilworth", - "author_inst": "Centre Hospitalier Universitaire Grenoble Alpes" - }, - { - "author_name": "Pierre Alain Billy", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Yannis Lombardi", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Mathilde Azzi", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Luis Ferreira Vargas", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Laurent Laine", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Mathilde Lermuzeaux", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Nathalie Memain", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Daniel Silva", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Tona Tchoubou", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Daria Ushmorova", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Hanane Dabbagh", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Simon Escoda", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Remi Lefrancois", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Annelyse Nardi", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Armand Ngima", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - }, - { - "author_name": "Vincent Ioos", - "author_inst": "Centre Hospitalier de Saint Denis Hopital Delafontaine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.05.30.20118125", "rel_title": "Reduction in stroke patients' referral to the ED in the COVID-19 era: A four-year comparative study", @@ -1384204,6 +1387180,37 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.06.03.129817", + "rel_title": "Closing coronavirus spike glycoproteins by structure-guided design", + "rel_date": "2020-06-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.03.129817", + "rel_abs": "The recent spillover of SARS-CoV-2 in the human population resulted in the ongoing COVID-19 pandemic which has already caused 4.9 million infections and more than 326,000 fatalities. To initiate infection the SARS-CoV-2 spike (S) glycoprotein promotes attachment to the host cell surface, determining host and tissue tropism, and fusion of the viral and host membranes. Although SARS-CoV- 2 S is the main target of neutralizing antibodies and the focus of vaccine design, its stability and conformational dynamics are limiting factors for developing countermeasures against this virus. We report here the design of a prefusion SARS-CoV-2 S ectodomain trimer construct covalently stabilized in the closed conformation. Structural and antigenicity analysis showed we successfully shut S in the closed state without otherwise altering its architecture. Finally, we show that this engineering strategy is applicable to other {beta}-coronavirus S glycoproteins and might become an important tool for vaccine design, structural biology, serology and immunology studies.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Matthew McCallum", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexandra C Walls", + "author_inst": "University of Washington" + }, + { + "author_name": "Davide Corti", + "author_inst": "Humabs Biomed SA, subsidiary of Vir Biotechnology" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.06.02.130955", "rel_title": "Sarbecovirus comparative genomics elucidates gene content of SARS-CoV-2 and functional impact of COVID-19 pandemic mutations", @@ -1384313,29 +1387320,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.06.01.20119388", - "rel_title": "A data driven epidemic model to analyse the lockdown effect and predict the course of COVID-19 progress in India", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119388", - "rel_abs": "We propose a data driven epidemic model using the real data on the infection, recovery and death cases for the analysis of COVID-19 progression in India. The model assumes continuation of existing control measures such as lockdown and quarantines, the suspected and confirmed cases and does not consider the scenario of 2nd surge of the epidemic due to any reason. The model is arrived after least square fitting of epidemic behaviour model based on theoretical formulation to the real data of cumulative infection cases reported between 24 March 2020 and 15 May 2020. The predictive capability of the model has been validated with real data of infection cases reported during May 15-30, 2020. A detailed analysis of model predictions in terms of future trend of COVID-19 progress individually in 18 states of India and India as a whole has been attempted. Infection rate in India as a whole is continuously decreasing with time and has reached 3 times lower than the initial infection rate after 6 weeks of lock down suggesting the effectiveness of the lockdown in containing the epidemic. Results suggest that India as a whole could see the peak and end of the epidemic in the month of July 2020 and January 2021. As per the current trend in the data, active infected cases in India may reach 2 lakhs at the peak time and total infected cases may reach around 14 lakhs. State-wise results have been discussed in the manuscript. However, the prediction may deviate particularly for longer dates, as assumptions of model cannot be met always in a real scenario. In view of this, a real time application (COV-IND Predictor) has been developed which automatically syncs the latest data from COVID19 dash board on daily basis and update the model input parameters and predictions of relevant results on daily basis. This application can serve as a practical tool for epidemic management decisions", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "BK Sahoo", - "author_inst": "Bhabha Atomic Research Centre" - }, - { - "author_name": "BK Sapra", - "author_inst": "Bhabha Atomic Research Centre" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.28.20105692", "rel_title": "Detection of SARS-CoV-2 neutralizing antibodies with a cell-free PCR assay", @@ -1385854,6 +1388838,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.01.20118612", + "rel_title": "Modeling the Covid-19 Epidemic using Time Series Econometrics", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20118612", + "rel_abs": "The classic logistic model has provided a realistic model of the behavior of Covid-19 in China and many East Asian countries. Once these countries passed the peak, the daily case count fell back, mirroring its initial climb in a symmetric way, just as the classic model predicts. However, in Italy and Spain, and now the UK and many other Western countries, the experience has been very different. The daily count has fallen back gradually from the peak but remained stubbornly high. The reason for the divergence from the classical model remain unclear. We take an empirical stance on this issue and develop a model that is based upon the statistical characteristics of the time series. With the possible exception of China, the workhorse logistic model is decisively rejected against more flexible alternatives.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Peter D. Spencer", + "author_inst": "University of York" + }, + { + "author_name": "Adam Golinski", + "author_inst": "University of York" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.01.20118505", "rel_title": "Pulmonary Thromboembolic Disease in Patients with COVID-19 Undergoing Computed Tomography Pulmonary Angiography (CTPA): Incidence and Relationship with Pulmonary Parenchymal Abnormalities", @@ -1385971,53 +1388978,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.05.31.20107276", - "rel_title": "Risk factors for mortality in pregnant women with SARS-CoV-2 infection", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20107276", - "rel_abs": "Since the first case of pneumonia was described, SARS-CoV-2 infection (coronavirus disease [COVID]-19) rapidly spread worldwide With 94,288 infections and more than 10,000 deaths, Mexico is the third Latin-American country in number of confirmed cases and second in mortality1. A major risk factor for adverse outcome in COVID-19 infection is the presence of advance age, co-morbidities including diabetes, hypertension and obesity among other non-communicable diseases2. Epidemiological data from high-prevalence countries reveal that compared to men, women are less likely to die or to require hospital admission to intensive care. This may suggest that pregnant women are not more susceptible to infection or to experience serious complications. However, whether the presence of co-morbidities or advanced maternal age confers a higher risk of adverse outcome in pregnant women with COVID-19 is unknown3.\n\nIn this research letter, we aimed at evaluating the risk factor associated with maternal mortality secondary to COVID-19 infection in a middle-income country.\n\nAdvanced maternal age is linked to an increased risk of mortality, while diabetes is the most important risk factor for maternal death. This is partly explained by an increasing incidence of non-communicable diseases in women of advanced age which is a common feature in most countries4. In the last decades, low- and middle-income countries have experienced accelerated socio-cultural changes associated with its incorporation into the international economic community, which have increased the number of obese and diabetic population, including pregnant women5. This has caused an increased risk for complications and fatality among COVID-19 positive population2,3. Thus, policies for reducing obesity and diabetes in low- and middle-income countries are most needed to reduce the mortality of COVID-19 in pregnant women.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Raigam Jafet Martinez-Portilla", - "author_inst": "University of Barcelona" - }, - { - "author_name": "Alexadros Sotiriadis", - "author_inst": "Second Department of Obstetrics and Gynecology, Faculty of Medicine, Aristotle University of Thessaloniki" - }, - { - "author_name": "Johnatan Torres-Torres", - "author_inst": "Hospital General de Mexico" - }, - { - "author_name": "Charzakis Christos", - "author_inst": "Second Department of Obstetrics and Gynecology, Faculty of Medicine, Aristotle University of Thessaloniki" - }, - { - "author_name": "Ameth Hawkins-Villarreal", - "author_inst": "University of Barcelona" - }, - { - "author_name": "Jose Rafael Villafan-Bernal", - "author_inst": "Catedras CONACYT, Instituto Nacional de Medicina Genomica" - }, - { - "author_name": "Rodolfo A Gurrola-Ochoa", - "author_inst": "Iberoamerican Research Network" - }, - { - "author_name": "Francesc Figueras", - "author_inst": "University of Barcelona" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.26.20112748", "rel_title": "COVID-19 Hospitalization is More Frequent and Severe in Down Syndrome", @@ -1387320,6 +1390280,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.05.29.20114751", + "rel_title": "Syncope at SARS-CoV-2 onset due to impaired baroreflex response", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20114751", + "rel_abs": "We describe clinical and laboratory findings in 35 consecutive patients tested positive for SARS-CoV-2 by reverse transcriptase-polymerase chain reaction on nasopharyngeal swab that presented one or multiple syncopal events at disease onset. Neurological examination and electrocardiographic findings were normal. Chest computed tomography showed findings consistent with interstitial pneumonia. Arterial blood gas analysis showed low pO2, pCO2, and P/F ratio indicating hypocapnic hypoxemia, while patients did not show the expected compensatory heart rate increase. Such mechanism could have led to syncope. We speculate that SARS-CoV-2 could have caused angiotensin-converting enzyme-2 (ACE2) receptor internalization in the nucleus of the solitary tract (NTS), thus altering the baroreflex response and inhibiting the compensatory tachycardia during acute hypocapnic hypoxemia.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Ciro Canetta", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Silvia Accordino", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Elisabetta Buscarini", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Gianpaolo Benelli", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Giuseppe La Piana", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Alessandro Scartabellati", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Giovanni Vigano'", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Roberto Assandri", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Alberto Astengo", + "author_inst": "Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy;" + }, + { + "author_name": "Chiara Benzoni", + "author_inst": "Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy;" + }, + { + "author_name": "Gianfranco Gaudiano", + "author_inst": "Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy;" + }, + { + "author_name": "Daniele Cazzato", + "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan, Italy" + }, + { + "author_name": "Sebastiano Davide Rossi", + "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan, Italy" + }, + { + "author_name": "Susanna Usai", + "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan, Italy" + }, + { + "author_name": "Irene Tramacere", + "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan, Italy" + }, + { + "author_name": "Giuseppe Lauria", + "author_inst": "Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy; Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.05.29.20114199", "rel_title": "Effect of Dry Heat and Autoclave Decontamination Cycles on N95 FFRs", @@ -1388057,25 +1391096,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.28.20115121", - "rel_title": "A Simple, SIR-like but Individual-Based l-i AIR Model: Application in Comparison of COVID-19 in New York City and Wuhan", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115121", - "rel_abs": "COVID-19 has spread around the world with nearly 360,000 deaths from the virus as of today (5/28/2020). Mathematical models have played an important role in many key policy discussions about COVID-19. SIR or SIR-derived models are a common modeling technique. However, the application of these models needs to solve complicated differential equations, enabling use of these models only by professional researchers. In this study, a simple, SIR-like but individual-based model, the l-i AIR model, is presented. The parameters l and i represent the length of the latent period and the infectious period, respectively. The variable A stands for the number of the infected people in the active infectious period, I for the number of cumulative infected people, and R for the number of the people in recovery or death. The nth terms of the three variables are derived, which can be easily calculated in Microsoft Excel, making the program easy to be used in most offices. A transmission coefficient k and a transient incidence rate a of the infected people are induced in the model to examine the effect of social distancing and the testing capacity of coronavirus on the epidemic curves. The simulated daily new cases from this l-i AIR model can fit very well with the reported daily new cases of COVID-19 in Wuhan, China and in New York City, USA, providing important information about latent period, infectious period and lockdown efficiency, and calculating the number of actual infected people who are positive in antibodies.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Xiaoping Liu", - "author_inst": "West Virginia University Health Science Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.31.20114520", "rel_title": "Rapid point of care nucleic acid testing for SARS-CoV-2 in hospitalised patients: a clinical trial and implementation study", @@ -1389506,6 +1392526,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.01.20100461", + "rel_title": "Determining the optimal strategy for reopening schools, work and society in the UK: balancing earlier opening and the impact of test and trace strategies with the risk of occurrence of a secondary COVID-19 pandemic wave", + "rel_date": "2020-06-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20100461", + "rel_abs": "BackgroundIn order to slow down the spread of SARS-CoV-2, the virus causing the COVID-19 pandemic, the UK government has imposed strict physical distancing ( lockdown) measures including school dismissals since 23 March 2020. As evidence is emerging that these measures may have slowed the spread of the pandemic, it is important to assess the impact of any changes in strategy, including scenarios for school reopening and broader relaxation of social distancing. This work uses an individual-based model to predict the impact of a suite of possible strategies to reopen schools in the UK, including that currently proposed by the UK government.\n\nMethodsWe use Covasim, a stochastic agent-based model for transmission of COVID-19, calibrated to the UK epidemic. The model describes individuals contact networks stratified as household, school, work and community layers, and uses demographic and epidemiological data from the UK. We simulate a range of different school reopening strategies with a society-wide relaxation of lockdown measures and in the presence of different non-pharmaceutical interventions, to estimate the number of new infections, cumulative cases and deaths, as well as the effective reproduction number with different strategies. To account for uncertainties within the stochastic simulation, we also simulated different levels of infectiousness of children and young adults under 20 years old compared to older ages.\n\nFindingsWe found that with increased levels of testing of people (between 25% and 72% of symptomatic people tested at some point during an active COVID-19 infection depending on scenarios) and effective contact-tracing and isolation for infected individuals, an epidemic rebound may be prevented across all reopening scenarios, with the effective reproduction number (R) remaining below one and the cumulative number of new infections and deaths significantly lower than they would be if testing did not increase. If UK schools reopen in phases from June 2020, prevention of a second wave would require testing 51% of symptomatic infections, tracing of 40% of their contacts, and isolation of symptomatic and diagnosed cases. However, without such measures, reopening of schools together with gradual relaxing of the lockdown measures are likely to induce a secondary pandemic wave, as are other scenarios for reopening. When infectiousness of <20 year olds was varied from 100% to 50% of that of older ages, our findings remained unchanged.\n\nInterpretationTo prevent a secondary COVID-19 wave, relaxation of social distancing including reopening schools in the UK must be implemented alongside an active large-scale population-wide testing of symptomatic individuals and effective tracing of their contacts, followed by isolation of symptomatic and diagnosed individuals. Such combined measures have a greater likelihood of controlling the transmission of SARS-CoV-2 and preventing a large number of COVID-19 deaths than reopening schools and society with the current level of implementation of testing and isolation of infected individuals.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSSince the onset of COVID-19 pandemic, mathematical modelling has been at the heart of informing decision-making, including the imposing of the lockdown in the UK. As countries are now starting to plan modification of these measures, it is important to assess the impact of different lockdown exit strategies including whether and how to reopen schools and relax other social distancing measures.\n\nAdded value of this studyUsing mathematical modelling, we explored the impact of strategies to reopen schools and society in the UK, including that currently proposed by the UK government. We assessed the impact of opening all schools fully or in a phased way with only some school years going back, with a society-wide relaxation of lockdown measures and in the presence of a different levels of implementation of test-trace-isolate strategies. We projected the number of new COVID-19 infections, cumulative cases and deaths, as well as the temporal distribution in the effective reproduction number (R) across different strategies. Our study is the first to provide quantification of the amount of testing and tracing that would be needed to prevent a second wave of COVID-19 in the UK under different reopening scenarios. To account for uncertainties within the stochastic simulation, we also simulated different levels of infectiousness of children and young adults under 20 years old compared to older ages.\n\nImplications of all the available evidenceEvidence to date points to the need for additional testing, contact tracing, and isolation of individuals who have either been diagnosed with COVID-19, or who are considered to be at high risk of carrying infection due to their contact history or symptoms. Our study supports these conclusions and provides additional quantification of the amount of testing and tracing that would be needed to prevent a second wave of COVID-19 in the UK under different lockdown exit strategies. Reopening schools and society alongside active testing of the symptomatic population (between 25% and 72% of people with symptomatic COVID-19 infection depending on scenarios) and with an effective contact-tracing and rapid isolation of symptomatic and diagnosed individuals, will not only prevent a secondary pandemic wave, but is also likely to be able to control the transmission of SARS-CoV-2, via keeping the R value below 1, thus preventing a large number of COVID-19 cases and deaths. However, in the absence of fully implemented large-scale testing, contact-tracing and isolation strategy, plans for reopening schools, including those currently proposed by the UK government, and the associated increase in work and community contacts, are likely to induce a secondary pandemic wave of COVID-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jasmina Panovska-Griffiths", + "author_inst": "UCL" + }, + { + "author_name": "Cliff Kerr", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Robyn Margaret Stuart", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Dina Mistry", + "author_inst": "Institute for Disease Modelling" + }, + { + "author_name": "Daniel Klein", + "author_inst": "Institute for Disease Modelling" + }, + { + "author_name": "Russell M Viner", + "author_inst": "UCL Great Ormond St. Institute of Child Health" + }, + { + "author_name": "Chris Bonell", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.01.20118885", "rel_title": "Modelling testing frequencies required for early detection of a SARS-CoV-2 outbreak on a university campus", @@ -1389611,41 +1392674,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.29.20097097", - "rel_title": "Population mobility reductions during COVID-19 epidemic in France under lockdown", - "rel_date": "2020-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20097097", - "rel_abs": "On March 17, 2020, French authorities implemented a nationwide lockdown to respond to COVID-19 epidemic and curb the surge of patients requiring critical care, similarly to other countries. Evaluating the impact of lockdown on population mobility is essential to quantify achievable reductions and identify the factors driving the changes in social dynamics that affected viral diffusion. We used temporally resolved travel flows among 1,436 administrative areas of mainland France reconstructed from mobile phone trajectories. We measured mobility changes before and during lockdown at both local and country scales. Lockdown caused a 65% reduction in countrywide number of displacements, and was particularly effective in reducing work-related short-range mobility, especially during rush hours, and recreational trips. Geographical heterogeneities showed anomalous increases in long-range movements even before lockdown announcement that were tightly localized in space. During lockdown, mobility drops were unevenly distributed across regions. They were strongly associated with active population, workers employed in sectors highly impacted by lockdown, and number of hospitalizations per region, and moderately associated with socio-economic level of the region. Major cities largely shrank their pattern of connectivity, reducing it mainly to short-range commuting. Lockdown was effective in reducing population mobility across scales. Caution should be taken in the timing of policy announcements and implementation, as anomalous mobility followed policy announcements that may act as seeding events. On the other hand, risk aversion may be beneficial in further decreasing mobility in largely affected regions. Socio-economic and demographic constraints to the efficacy of restrictions were also identified. The unveiled links between geography, demography, and timing of the response to mobility restrictions may help design interventions that minimize invasiveness while contributing to the current epidemic response.\n\nFundingANR projects EVALCOVID-19 (ANR-20-COVI-0007) and DATAREDUX (ANR-19-CE46-0008-03); EU H2020 grants RECOVER (H2020-101003589) and MOOD (H2020-874850); REACTing COVID-19 modeling grant.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Giulia Pullano", - "author_inst": "INSERM/ORANGE S.A." - }, - { - "author_name": "Eugenio Valdano", - "author_inst": "INSERM" - }, - { - "author_name": "Nicola Scarpa", - "author_inst": "INSERM" - }, - { - "author_name": "Stefania Rubrichi", - "author_inst": "Orange S. A." - }, - { - "author_name": "Vittoria Colizza", - "author_inst": "INSERM" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.29.20065714", "rel_title": "Adaptive policies for use of physical distancing interventions during the COVID-19 pandemic", @@ -1390927,6 +1393955,81 @@ "type": "confirmatory results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.31.116061", + "rel_title": "Origin and cross-species transmission of bat coronaviruses in China", + "rel_date": "2020-05-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.31.116061", + "rel_abs": "Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. We used a Bayesian statistical framework and sequence data from all known bat-CoVs (including 630 novel CoV sequences) to study their macroevolution, cross-species transmission, and dispersal in China. We find that host-switching was more frequent and across more distantly related host taxa in alpha-than beta-CoVs, and more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Alice Latinne", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Ben Hu", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Kevin J Olival", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Guangjian Zhu", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Libiao Zhang", + "author_inst": "Guangdong Institute of Applied Biological Resources" + }, + { + "author_name": "Hongying Li", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Aleksei A Chmura", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Hume E Field", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Carlos Zambrana-Torrelio", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Jonathan H Epstein", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Bei Li", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Wei Zhang", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Lin-Fa Wang", + "author_inst": "Duke-NUS Graduate Medical School" + }, + { + "author_name": "Zhengli Shi", + "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Peter Daszak", + "author_inst": "EcoHealth Alliance" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.05.31.126136", "rel_title": "A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates", @@ -1391084,45 +1394187,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.28.20115899", - "rel_title": "Disparities in Vulnerability to Severe Complications from COVID-19 in the United States", - "rel_date": "2020-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115899", - "rel_abs": "This paper provides the first nationally representative estimates of vulnerability to severe complications from COVID-19 overall and across race-ethnicity and socioeconomic status. We use the Panel Study of Income Dynamics (PSID) to examine the prevalence of specific health conditions associated with complications from COVID-19 and to calculate, for each individual, an index of the risk of severe complications from respiratory infections developed by DeCaprio et al. (2020). We show large disparities across race-ethnicity and socioeconomic status in the prevalence of conditions which are associated with the risk of severe complications from COVID-19. Moreover, we show that these disparities emerge early in life, prior to age 65, leading to higher vulnerability to such complications. While vulnerability is highest among older adults regardless of their race-ethnicity or socioeconomic status, our results suggest particular attention should also be given to the risk of adverse outcomes in midlife for non-Hispanic Blacks, adults with a high school degree or less, and low-income Americans.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Emily E. Wiemers", - "author_inst": "Syracuse University" - }, - { - "author_name": "Scott Abrahams", - "author_inst": "Duke University" - }, - { - "author_name": "Marwa AlFakhri", - "author_inst": "Duke University" - }, - { - "author_name": "V. Joseph Hotz", - "author_inst": "Duke University" - }, - { - "author_name": "Robert F. Schoeni", - "author_inst": "University of Michigan" - }, - { - "author_name": "Judith A. Seltzer", - "author_inst": "University of California, Los Angeles" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.27.20115295", "rel_title": "A control approach to the Covid-19 disease using a SEIHRD dynamical model", @@ -1392521,6 +1395585,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.28.20115584", + "rel_title": "Prognostic value of visual quantification of lesion severity at initial chest CT in confirmed Covid-19 infection: a retrospective analysis on 216 patients", + "rel_date": "2020-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115584", + "rel_abs": "Rationale and ObjectivesStudies suggest an association between chest CT findings assessed with semi-quantitative CT score and gravity of Covid-19. The objective of this work is to analyze potential correlation between visual quantification of lesion severity at initial chest CT and clinical outcome in confirmed Covid-19 patients.\n\nMaterials and MethodsFrom March 5th to March 21st, 2020, all consecutive patients that underwent chest CT for clinical suspicion of Covid-19 at a single tertiary center were retrospectively evaluated for inclusion. Patients with lung parenchyma lesions compatible with Covid-19 and positive RT-PCR were included.\n\nGlobal extensiveness of abnormal lung parenchyma was visually estimated and classified independently by 2 readers, following the European Society of Thoracic Imaging Guidelines. Death and/or mechanical ventilation within 30 days following the initial chest CT was chosen as the primary hard endpoint.\n\nResults216 patients (124 men, 62 years-old {+/-} 16.5, range 22 - 94 yo) corresponding to 216 chest CT were included. Correlation between lesion severity and percentage of patients that met the primary endpoint was high, with a coefficient {rho} of 0.87 (p = 0.05).\n\nA greater than 25% involvement was significantly associated with a higher risk of mechanical ventilation or death at 30 days, with a Risk Ratio of 5.00 (95% CI [3.59-6.99]).\n\nConclusionThis retrospective cohort confirms a correlation between visual evaluation of lesions severity at initial chest CT and the 30 days clinical outcome of Covid-19 patients and suggests using a threshold of greater than 25% involvement to identify patients at risk.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Elias Taieb", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Aissam Labani", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Yvon Ruch", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Francois Danion", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Mathieu Oberlin", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Pascal Bilbault", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Pierre Leyendecker", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Catherine Roy", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Mickael Ohana", + "author_inst": "Hopitaux Universitaires de Strasbourg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.05.29.20116376", "rel_title": "Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report", @@ -1392806,45 +1395921,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2020.05.30.20117572", - "rel_title": "Assessing visible aerosol generation during vitrectomy in the era of Covid-19", - "rel_date": "2020-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117572", - "rel_abs": "ObjectiveTo assess visible aerosol generation during simulated vitrectomy surgery. Methods: A model comprising a human cadaveric corneoscleral rim mounted on an artificial anterior chamber was used. Three-port 25 gauge vitrectomy simulated surgery was performed with any visible aerosol production recorded using high speed 4K camera. The following were assessed: (1) vitrector at maximum cut rate in static and dynamic conditions inside the model, (2) vitrector at air-fluid interface in physical model, (3) passive fluid-air exchange with a backflush hand piece, (4) valved cannulas under air, and (5) defective valved cannula under air.\n\nResultsNo visible aerosol or droplets were identified when the vitrector was used within the model. In the physical model, no visible aerosol or droplets were seen when the vitrector was engaged at the air-fluid interface. Droplets were produced from the opening of backflush hand piece during passive fluid-air exchange. No visible aerosol was produced from the intact valved cannulas under air pressure, but droplets were seen at the beginning of fluid-air exchange when the valved cannula was defective.\n\nConclusionsWe found no evidence of visible aerosol generation during simulated vitrectomy surgery with competent valved cannulas. In the physical model, no visible aerosol was generated by the high-speed vitrector despite cutting at the air-fluid interface.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sidath E Liyanage", - "author_inst": "Bristol Eye Hospital" - }, - { - "author_name": "Pathma Ramasamy", - "author_inst": "Bristol Eye Hospital" - }, - { - "author_name": "Omar Elhaddad", - "author_inst": "Bristol Eye Hospital" - }, - { - "author_name": "Kieren Darcy", - "author_inst": "Bristol Eye Hospital" - }, - { - "author_name": "Andrew Hudson", - "author_inst": "University of Leicester" - }, - { - "author_name": "Johannes Keller", - "author_inst": "Bristol Eye Hospital" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "ophthalmology" - }, { "rel_doi": "10.1101/2020.05.30.20117531", "rel_title": "Remarkable variability in SARS-CoV-2 antibodies across Brazilian regions: nationwide serological household survey in 27 states", @@ -1394051,6 +1397127,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.29.20116921", + "rel_title": "Time courses of COVID-19 infection and local variation in socioeconomic and health disparities in England", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20116921", + "rel_abs": "ObjectiveTo identify factors associated with local variation in the time course of COVID-19 case burden in England.\n\nMethodsWe analyzed laboratory-confirmed COVID-19 case data for 150 upper tier local authorities, from the period from January 30 to May 6, 2020, as reported by Public Health England. Using methods suitable for time-series data, we identified clusters of local authorities with distinct trajectories of daily cases, after adjusting for population size. We then tested for differences in sociodemographic, economic, and health disparity factors between these clusters.\n\nResultsTwo clusters of local authorities were identified: a higher case trajectory that rose faster over time to reach higher peak infection levels, and a lower case trajectory cluster that emerged more slowly, and had a lower peak. The higher case trajectory cluster (79 local authorities) had higher population density (p<0.001), higher proportion of Black and Asian residents (p=0.03; p=0.02), higher multiple deprivation scores (p<0.001), a lower proportions of older adults (p=0.005), and higher preventable mortality rates (p=0.03). Local authorities with higher proportions of Black residents were more likely to belong to the high case trajectory cluster, even after adjusting for population density, deprivation, proportion of older adults and preventable mortality (p=0.04).\n\nConclusionAreas belonging to the trajectory with significantly higher COVID-19 case burden were more deprived, and had higher proportions of ethnic minority residents. A higher proportion of Black residents in regions belonging to the high trajectory cluster was not fully explained by differences in population density, deprivation, and other overall health disparities between the clusters.\n\nWhat is already known on this subject?Emerging evidence suggests that the burden of COVID-19 infection is falling unequally across England, with provisional data suggesting higher overall infection and mortality rates for Black, Asian, and mixed race/ethnicity individuals.\n\nWhat does this study add?We found that regions with greater socioeconomic deprivation and poorer population health measures showed a faster rise in COVID-19 cases, and reached higher peak case levels. Areas with a higher proportion of Black residents were more likely to show this kind of time course, even after adjusting for multiple co-occurring factors, including population density. This finding merits further investigation in terms of the intersecting vulnerability factors Black and other minority ethnic individuals face in England (e.g. proportion of people working in service and caring roles, and the role of structural discrimination), and has implications for the ongoing allocation of public health resources, in order to better mitigate such inequalities.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Shelley H. Liu", + "author_inst": "Icahn School of Medicine at Mount SInai" + }, + { + "author_name": "Bian Liu", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Yan Li", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Agnes Norbury", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.29.20116657", "rel_title": "Loneliness during lockdown: trajectories and predictors during the COVID-19 pandemic in 35,712 adults in the UK", @@ -1394200,29 +1397307,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.27.20100297", - "rel_title": "Automatic Detection of COVID-19 and Pneumonia from Chest X-Ray using Transfer Learning", - "rel_date": "2020-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20100297", - "rel_abs": "In this study, a dataset of X-ray images from patients with common viral pneumonia, bacterial pneumonia, confirmed Covid-19 disease was utilized for the automatic detection of the Coronavirus disease. The point of the investigation is to assess the exhibition of cutting edge convolutional neural system structures proposed over the ongoing years for clinical picture order. In particular, the system called Transfer Learning was received. With transfer learning, the location of different variations from the norm in little clinical picture datasets is a reachable objective, regularly yielding amazing outcomes. The datasets used in this trial. Firstly, a collection of 24000 X-ray images includes 6000 images for confirmed Covid-19 disease,6000 confirmed common bacterial pneumonia and 6000 images of normal conditions. The information was gathered and expanded from the accessible X-Ray pictures on open clinical stores. The outcomes recommend that Deep Learning with X-Ray imaging may separate noteworthy biological markers identified with the Covid-19 sickness, while the best precision, affectability, and particularity acquired is 97.83%, 96.81%, and 98.56% individually.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Sarath Pathari", - "author_inst": "Rajalakshmi Engineering College" - }, - { - "author_name": "Rahul U", - "author_inst": "Rajalakshmi Engineering College" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.05.27.20115303", "rel_title": "A systematic review and meta-analysis of cancer patients affected by a novel coronavirus", @@ -1395221,6 +1398305,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.27.20114819", + "rel_title": "Distinctive trajectories of COVID-19 epidemic by age and gender: a retrospective modeling of the epidemic in South Korea", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114819", + "rel_abs": "ObjectivesElderly people had suffered disproportional burden of COVID-19. We hypothesized that males and females in different age groups might have different epidemic trajectories.\n\nMethodsUsing publicly available data from South Korea, daily new COVID-19 cases were fitted with generalized additive models, assuming Poisson and negative binomial distributions. Epidemic dynamics by age and gender groups were explored with interactions between smoothed time terms and age and gender.\n\nResultsA negative binomial distribution fitted the daily case counts best. Interaction between the dynamic patterns of daily new cases and age groups was statistically significant (p<0.001), but not with gender group. People aged 20-39 years led the epidemic processes in the society with two peaks: one major peak around March 1 and a smaller peak around April 7, 2020. The epidemic process among people aged 60 or above was trailing behind that of younger people with smaller magnitude. After March 15, there was a consistent decline of daily new cases among elderly people, despite large fluctuations of case counts among young adults.\n\nConclusionsAlthough young people drove the COVID-19 epidemic in the whole society with multiple rebounds, elderly people could still be protected from virus infection after the peak of epidemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Xinhua Yu", + "author_inst": "University of Memphis" + }, + { + "author_name": "Jiasong Duan", + "author_inst": "University of Memphis" + }, + { + "author_name": "Yu Jiang", + "author_inst": "University of Memphis" + }, + { + "author_name": "Hongmei Zhang", + "author_inst": "University of Memphis" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.27.20114728", "rel_title": "Lessons from movement ecology for the return to work: modeling contacts and the spread of COVID-19", @@ -1395358,45 +1398473,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.27.20113951", - "rel_title": "Knowledge, attitude, and perceptions towards the 2019 Coronavirus Pandemic: A bi-national survey in Africa", - "rel_date": "2020-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20113951", - "rel_abs": "The current Coronavirus (COVID-19) pandemic has changed and impacted lives on a global scale since its emergence and spread from China in late 2019. It has caused millions of infections, and thousands of deaths worldwide. However, the control of this pandemic still remains unachievable in many African countries including Egypt and Nigeria, despite the application of some strict preventive and control measures. Therefore, this study assessed the knowledge, attitude and perceptions of Egyptians and Nigerians towards COVID-19 pandemic.\n\nA total of 1437 respondents were included in this preliminary cross-sectional survey. The mean knowledge score was 14.7{+/-}2.3. The majority of the respondents (61.6%) had a satisfactory knowledge of the disease. Age (18-39 years), education (College/bachelors) and background of respondents were factors influencing knowledge levels. The attitude of most respondents (68.9%) towards the preventive measures was satisfactory with an average attitude score of 6.9 {+/-} 1.2. The majority of the respondents (96%) practiced self-isolation and social-distancing but only 36% follow all health recommendations. The perception of most respondents (62.1%) on the global efforts at controlling the virus and preventing further spread was satisfactory with an average score of 10.9 {+/-} 2.7. A satisfactory knowledge of COVID-19 was significantly associated with good attitude and perceptions (p < 0.001) of respondents. Only 22% of the respondents were satisfied with their countrys handling of the pandemic.\n\nIt is imperative that to avoid Africa being the next epicenter of the pandemic. Governments need to strengthen health systems, improve their surveillance activities in detecting cases, and effectively apply standard infection prevention and control measures.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Hager Elnadi", - "author_inst": "Infectiologie et Sante Publique, Institut National de la Recherche Agronomique, Nouzilly, France." - }, - { - "author_name": "Ismail A. Odetokun", - "author_inst": "Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Ilorin, Kwara State, Nigeria." - }, - { - "author_name": "Obasanjo Bolarinwa", - "author_inst": "School of Nursing & Public Health Medicine, College of Health Sciences, University of KwaZulu - Natal, Durban, South Africa." - }, - { - "author_name": "Zeinab Ahmed", - "author_inst": "Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Cairo University, Egypt." - }, - { - "author_name": "Ochulor Okechukwu", - "author_inst": "Department of Global Health, Unit of Functional Genetics of Infectious Diseases, Institute Pasteur, France." - }, - { - "author_name": "Ahmad Ibrahim Al-Mustapha", - "author_inst": "University of Helsinki" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.27.20114413", "rel_title": "Determinants of intent to uptake Coronavirus vaccination among respondents in Saudi Arabia: a web-based national survey", @@ -1396495,6 +1399571,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.29.20117069", + "rel_title": "Regression Analysis of COVID-19 Spread in India and its Different States", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20117069", + "rel_abs": "Linear and polynomial regression model has been used to investigate the COVID-19 outbreak in India and its different states using time series epidemiological data up to 26th May 2020. The data driven analysis shows that the case fatality rate (CFR) for India (3.14% with 95% confidence interval of 3.12% to 3.16%) is half of the global fatality rate, while higher than the CFR of the immediate neighbors i.e. Bangladesh, Pakistan and Sri Lanka. Among Indian states, CFR of West Bengal (8.70%, CI: 8.21-9.18%) and Gujrat (6.05%, CI: 4.90-7.19%) is estimated to be higher than national rate, whereas CFR of Bihar, Odisha and Tamil Nadu is less than 1%. The polynomial regression model for India and its different states is trained with data from 21st March 2020 to 19th May 2020 (60 days). The performance of the model is estimated using test data of 7 days from 20th May 2020 to 26th May 2020 by calculating RMSE and % error. The model is then used to predict number of patients in India and its different states up to 16th June 2020 (21 days). Based on the polynomial regression analysis, Maharashtra, Gujrat, Delhi and Tamil Nadu are continue to remain most affected states in India.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Poonam Chauhan", + "author_inst": "Central University of Punjab, Bathinda" + }, + { + "author_name": "Ashok Kumar", + "author_inst": "Central University of Punjab" + }, + { + "author_name": "Pooja Jamdagni", + "author_inst": "Himachal Pradesh University, Shimla" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.28.121533", "rel_title": "Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies", @@ -1396740,37 +1399843,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.05.27.20114447", - "rel_title": "Automated and partially-automated contact tracing: a rapid systematic review to inform the control of COVID-19", - "rel_date": "2020-05-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114447", - "rel_abs": "BackgroundAutomated or partially-automated contact tracing tools are being deployed by many countries to contain SARS-CoV-2; however, the evidence base for their use is not well-established.\n\nMethodsWe undertook a rapid systematic review of automated or partially-automated contact tracing, registered with PROSPERO (CRD42020179822). We searched PubMed, EMBASE, OVID Global Health, EBSCO COVID Portal, Cochrane Library, medRxiv, bioRxiv, arXiv and Google Advanced for articles relevant to COVID-19, SARS, MERS, influenza or Ebola from 1/1/200014/4/2020. Two authors reviewed all full-text manuscripts. One reviewer extracted data using a pre-piloted form; a second independently verified extracted data. Primary outcomes were the number or proportion of contacts (and/or subsequent cases) identified; secondary outcomes were indicators of outbreak control, app/tool uptake, resource use, cost-effectiveness and lessons learnt. The Effective Public Health Practice Project tool or CHEERS checklist were used in quality assessment.\n\nFindings4,033 citations were identified and 15 were included. No empirical evidence of automated contact tracings effectiveness (regarding contacts identified or transmission reduction) was identified. Four of seven included modelling studies suggested that controlling COVID-19 requires high population uptake of automated contact-tracing apps (estimates from 56% to 95%), typically alongside other control measures. Studies of partially-automated contact tracing generally reported more complete contact identification and follow-up, and greater intervention timeliness (0.5-5 hours faster), than previous systems. No meta-analyses were possible.\n\nInterpretationAutomated contact tracing has potential to reduce transmission with sufficient population uptake and usage. However, there is an urgent need for well-designed prospective evaluations as no studies provided empirical evidence of its effectiveness.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Isobel Braithwaite", - "author_inst": "UCL Public Health Data Science Research Group, Institute of Health Informatics, University College London, London, UK" - }, - { - "author_name": "Tom Callender", - "author_inst": "Department of Applied Health Research, University College London, London, UK" - }, - { - "author_name": "Miriam Bullock", - "author_inst": "UCL Collaborative Centre for Inclusion Health, University College London, London UK" - }, - { - "author_name": "Robert W Aldridge", - "author_inst": "UCL Public Health Data Science Group, Institute of Health Informatics, University College London, London UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.27.20114280", "rel_title": "Factors associated with country-variation in COVID-19 morbidity and mortality worldwide: an observational geographic study", @@ -1398049,6 +1401121,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.24.20101238", + "rel_title": "Single-cell RNA-seq and V(D)J profiling of immune cells in COVID-19 patients", + "rel_date": "2020-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20101238", + "rel_abs": "Coronavirus disease 2019 (COVID-19) has caused over 220,000 deaths so far and is still an ongoing global health problem. However, the immunopathological changes of key types of immune cells during and after virus infection remain unclear. Here, we enriched CD3+ and CD19+ lymphocytes from peripheral blood mononuclear cells of COVID-19 patients (severe patients and recovered patients at early or late stages) and healthy people (SARS-CoV-2 negative) and revealed transcriptional profiles and changes in these lymphocytes by comprehensive single-cell transcriptome and V(D)J recombination analyses. We found that although the T lymphocytes were decreased in the blood of patients with virus infection, the remaining T cells still highly expressed inflammatory genes and persisted for a while after recovery in patients. We also observed the potential transition from effector CD8 T cells to central memory T cells in recovered patients at the late stage. Among B lymphocytes, we analyzed the expansion trajectory of a subtype of plasma cells in severe COVID-19 patients and traced the source as atypical memory B cells (AMBCs). Additional BCR and TCR analyses revealed a high level of clonal expansion in patients with severe COVID-19, especially of B lymphocytes, and the clonally expanded B cells highly expressed genes related to inflammatory responses and lymphocyte activation. V-J gene usage and clonal types of higher frequency in COVID-19 patients were also summarized. Taken together, our results provide crucial insights into the immune response against patients with severe COVID-19 and recovered patients and valuable information for the development of vaccines and therapeutic strategies.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Xiaoying Fan", + "author_inst": "Guangzhou Regenerative Medicine and Health Guangdong Laboratory" + }, + { + "author_name": "Xiangyang Chi", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Wenji Ma", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Suijuan Zhong", + "author_inst": "State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University" + }, + { + "author_name": "Yunzhu Dong", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Wei Zhou", + "author_inst": "Guangzhou Regenerative Medicine and Health Guangdong Laboratory" + }, + { + "author_name": "Wenyu Ding", + "author_inst": "State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University" + }, + { + "author_name": "Hongyan Fan", + "author_inst": "Department of Clinical Laboratory, The 940th Hospital of PLA Joint Logistics Support Forces" + }, + { + "author_name": "Chonghai Yin", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Zhentao Zuo", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Yilong Yang", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Mengyao Zhang", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Qiang Ma", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Jianwei Liu", + "author_inst": "Guangzhou Regenerative Medicine and Health Guangdong Laboratory" + }, + { + "author_name": "Ting Fang", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Qian Wu", + "author_inst": "State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University" + }, + { + "author_name": "Wei Chen", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Xiaoqun Wang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.26.20111120", "rel_title": "THE LOW-HARM SCORE FOR PREDICTING MORTALITY IN PATIENTS DIAGNOSED WITH COVID-19: A MULTICENTRIC VALIDATION STUDY", @@ -1398206,33 +1401365,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.26.20110957", - "rel_title": "COVID-19: The unreasonable effectiveness of simple models", - "rel_date": "2020-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20110957", - "rel_abs": "When the novel coronavirus disease SARS-CoV2 (COVID-19) was officially declared a pandemic by the WHO in March 2020, the scientific community had already braced up in the effort of making sense of the fast-growing wealth of data gathered by national authorities all over the world. However, despite the diversity of novel theoretical approaches and the comprehensiveness of many widely established models, the official figures that recount the course of the outbreak still sketch a largely elusive and intimidating picture. Here we show unambiguously that the dynamics of the COVID-19 outbreak belongs to the simple universality class of the SIR model and extensions thereof. Our analysis naturally leads us to establish that there exists a fundamental limitation to any theoretical approach, namely the unpredictable non-stationarity of the testing frames behind the reported figures. However, we show how such bias can be quantified self-consistently and employed to mine useful and accurate information from the data. In particular, we describe how the time evolution of the reporting rates controls the occurrence of the apparent epidemic peak, which typically follows the true one in countries that were not vigorous enough in their testing at the onset of the outbreak. The importance of testing early and resolutely appears as a natural corollary of our analysis, as countries that tested massively at the start clearly had their true peak earlier and less deaths overall.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Timoteo Carletti", - "author_inst": "University of Namur" - }, - { - "author_name": "Duccio Fanelli", - "author_inst": "University of Florence" - }, - { - "author_name": "Francesco Piazza", - "author_inst": "University of Orleans" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.25.20112656", "rel_title": "Association of the Covid-19 lockdown with smoking, drinking, and attempts to quit in England: an analysis of 2019-2020 data", @@ -1399547,6 +1402679,41 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.05.27.119610", + "rel_title": "Assessment of ACE2, CXCL10 and Their co-expressed Genes: An In-silico Approach to Evaluate the Susceptibility and Fatality of Lung Cancer Patients towards COVID-19 Infection", + "rel_date": "2020-05-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.27.119610", + "rel_abs": "BackgroundCOVID-19 is a recent pandemic that started to spread out worldwide from Wuhan, China. This disease is caused by a newly discovered strain of the coronavirus, namely SARS CoV-2. Lung cancer patients are reported to be more susceptible to COVID-19 infection. To evaluate the probable reasons behind the excessive susceptibility and fatality of lung cancer patients to COVID-19 infection, we targeted two most crucial biomarkers of COVID-19, ACE2 and CXCL10. ACE2 plays a vital role in the SARS CoV-2 entry into the host cell while CXCL10 is a cytokine mainly responsible for the lung cell damage involving in a cytokine storm.\n\nMethodsFirstly, we used the TIMER, UALCAN and GEPIA2 databases to analyze the expression and correlation of ACE2 and CXCL10 in LUAD and LUSC. After that, using the cBioPortal database, we performed an analytical study to determine the genetic changes in ACE2 and CXCL10 protein sequences that are responsible for lung cancer development. Finally, we analyzed different functional approaches of ACE2, CXCL10 and their co-expressed genes associated with lung cancer and COVID-19 development by using the PANTHER database.\n\nResultsInitially, we observed that ACE2 and CXCL10 are mostly overexpressed in LUAD and LUSC. We also found the functional significance of ACE2 and CXCL10 in lung cancer development by determining the genetic alteration frequency in their amino acid sequences. Lastly, by doing the functional assessment of the targeted genes, we identified that ACE2 and CXCL10 along with their commonly co-expressed genes are respectively involved in the binding activity and immune responses in case of lung cancer and COVID-19 infection.\n\nConclusionsFinally, on the basis of this systemic analysis, we came to the conclusion that ACE2 and CXCL10 are possible biomarkers responsible for the higher susceptibility and fatality of lung cancer patients towards the COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Tousif Bin Mahmood", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh" + }, + { + "author_name": "Afrin Sultana Chowdhury", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh" + }, + { + "author_name": "Mehedee Hasan", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh" + }, + { + "author_name": "Md. Mezbah-Ul-Islam Aakil", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh" + }, + { + "author_name": "Mohammad Imran Hossan", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.26.20109595", "rel_title": "Efficacy and harms of remdesivir for the treatment of COVID-19: a systematic review and meta-analysis", @@ -1399660,53 +1402827,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.26.20100529", - "rel_title": "Aerosol blocking assessment by different types of fabrics for homemade respiratory masks: spectroscopy and imaging study", - "rel_date": "2020-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20100529", - "rel_abs": "During the COVID-19 pandemic, there is no agreement, until the current date, about the recommendations of homemade face mask use for the general population, and one of the reasons is a lack of information about their real protective rule on spreading aerosols and viruses. This is a comparative study regarding the relative efficiencies of commercial respiratory masks (medical masks) and homemade fabric masks, which may guide authorities across the globe, following the \"Advice on the use of masks in the context of COVID-19\", by the World Health Organization. We described two optical methodologies for charactering respiratory masks. It happens that the aerosol scattering coefficient is linear as a function of its concentration inside the mask chamber. Quantitative optical properties of scattering for a large batch fabrication of masks were demonstrated, making the mask N95 suitable for use as a reference standard.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Mauricio Foschini", - "author_inst": "Federal University ofUberlandia" - }, - { - "author_name": "ADAMO FG MONTE", - "author_inst": "FEDERAL UNIVERSITY OF UBERLANDIA" - }, - { - "author_name": "Ana CM Mendes", - "author_inst": "Federal University ofUberlandia" - }, - { - "author_name": "Renata J Scarabucci", - "author_inst": "Federal University of Uberlandia" - }, - { - "author_name": "Alexandre Maletta", - "author_inst": "Federal University of Uberlandia" - }, - { - "author_name": "Carla D Giuliani", - "author_inst": "Federal University of Uberlandia" - }, - { - "author_name": "Bruna AR Duarte", - "author_inst": "Federal University of Uberlandia" - }, - { - "author_name": "Kleber Del-Claro", - "author_inst": "Federal University of Uberlandia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.26.20099440", "rel_title": "Phenol-chloroform-based RNA purification for detection of SARS-CoV-2 by RT-qPCR: comparison with automated systems", @@ -1401045,6 +1404165,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.26.20104497", + "rel_title": "Knowledge and attitude towards COVID-19 in Bangladesh: Population-level estimation and a comparison of data obtained by phone and online survey methods", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20104497", + "rel_abs": "Peoples adherence to the guidelines and measures suggested in fighting the ongoing COVID-19 pandemic is partly determined by the Knowledge, Attitude, and Practices (KAP) of the population. In this cross-sectional study, we primarily addressed two key issues. First, we tried to determine whether there is a significant difference in the estimated COVID-19 knowledge level from the online and phone survey methods. Second, we tried to quantify the knowledge and attitude of COVID-19 in Bangladeshi adult population. Data were collected through phone calls (April 14-23, 2020) and online survey (April 18-19, 2020) in Bangladesh. The questionnaire had 20 knowledge questions with each correct response getting one point and incorrect/dont know response getting no point (maximum total knowledge score 20). Participants scoring >17 were categorized as having good knowledge. The percentages of good knowledge holders were 57.6%, 75.1%, and 95.8% in the phone (n=1426), online non-medical (n=1097), and online medical participants (n=382), respectively. Comparison between phone and online survey showed that, overall, online survey might overestimate knowledge level than that of phone survey, although there was no difference for elderly, poor, and rural people. Male gender, higher education, living in town/urban areas, good financial condition, and use of internet were positively associated with good knowledge. However, higher knowledge was associated with having less confidence in the final control of COVID-19. Our adult population-level estimates showed that only 32.6% (95% CI 30.1-35.2%) had good knowledge. This study provides crucial information that could be useful for the researchers and policymakers to develop effective strategies.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Anwarul Karim", + "author_inst": "Department of Surgery, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong" + }, + { + "author_name": "Mastura Akter", + "author_inst": "Department of Biomedical Sciences, City University of Hong Kong, Hong Kong" + }, + { + "author_name": "AHM Thafikul Mazid", + "author_inst": "Department of Medicine, Dhaka Medical College and Hospital, Dhaka, Bangladesh" + }, + { + "author_name": "Orindom Shing Pulock", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Tasmiah Tahera Aziz", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Samira Hayee", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Nowrin Tamanna", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "GS Chuwdhury", + "author_inst": "Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong" + }, + { + "author_name": "Afsana Haque", + "author_inst": "Department of Urban Planning and Design, University of Hong Kong, Hong Kong" + }, + { + "author_name": "Farhana Yeasmin", + "author_inst": "Department of Applied Food Science and Nutrition, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh" + }, + { + "author_name": "Mashkura Akter Mitu", + "author_inst": "Faculty of Agriculture, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh" + }, + { + "author_name": "Farjana Yeasmin", + "author_inst": "Department of Zoology, Government Hazi Mohammad Mohsin College, National University, Bangladesh" + }, + { + "author_name": "Humayun Rashid", + "author_inst": "Chattogram International Medical College, Chattogram, Bangladesh" + }, + { + "author_name": "Ashish Kumar Kuri", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Arni Das", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Koushik Majumder", + "author_inst": "Chittagong Medical College and Hospital, Chattogram, Bangladesh" + }, + { + "author_name": "Dipen Barua", + "author_inst": "Centre of Buddhist Studies, Faculty of Arts, University of Hong Kong, Hong Kong" + }, + { + "author_name": "Md Mahabubur Rahaman", + "author_inst": "Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh" + }, + { + "author_name": "Sanjida Akter", + "author_inst": "Department of Social and Preventive Medicine, Faculty of Medicine, University Malaya, Malaysia" + }, + { + "author_name": "Nashid Niaz Munia", + "author_inst": "Chattogram International Medical College, Chattogram, Bangladesh" + }, + { + "author_name": "Jabin Sultana", + "author_inst": "Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangl" + }, + { + "author_name": "Faeeqa Usaila", + "author_inst": "Department of Biomedical Sciences, City University of Hong Kong, Hong Kong" + }, + { + "author_name": "Sabrina Sifat", + "author_inst": "Shaheed Suhrawardy Medical College and Hospital, Dhaka, Bangladesh" + }, + { + "author_name": "Nishat Anjum Nourin", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Md Forhad Uddin", + "author_inst": "Independent Researcher, Chattogram, Bangladesh" + }, + { + "author_name": "Mrinmoy Bhowmik", + "author_inst": "Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh" + }, + { + "author_name": "Tanvir Ahammed", + "author_inst": "Department of Statistics, Shahjalal University of Science and Technology, Sylhet, Bangladesh" + }, + { + "author_name": "Nabil Sharik", + "author_inst": "Upzila Health and Family Planning Office, Sadar, Gopalganj, Bangladesh" + }, + { + "author_name": "Quddus Mehnaz", + "author_inst": "School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong" + }, + { + "author_name": "Md Nur Hossain Bhuiyan", + "author_inst": "Department of Surgery, Chittagong Medical College and Hospital, Chattogram, Bangladesh" + }, + { + "author_name": "Tahmina Banu", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.19.20106492", "rel_title": "A modified SEIR Model with Confinement and Lockdown of COVID-19 for Costa Rica", @@ -1401222,49 +1404481,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.19.20106484", - "rel_title": "Outdoor Air Pollutant Concentration and COVID-19 Infection in Wuhan, China", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20106484", - "rel_abs": "Motivated by earlier findings that exposure to daily outdoor PM2.5 (P) may increase the risk of influenza infection, our study examines if immediate exposure to outdoor P will modify the rate of change in the daily number of COVID-19 infections (R), for (1) the high infection provincial capital cities in China and (2) Wuhan, China, using regression modelling. A multiple linear regression model was constructed to model the statistical relationship between P and R in China and in Wuhan, from 1 January to 20 March 2020. We carefully accounted for potential key confounders and addressed collinearity. The causal relationship between P and R, and the interaction effect between key variables were investigated. A causal relationship between P and R across the high infection provincial capital cities in China was established via matching. A higher P resulted in a higher R in China. A 10 {micro}g/m3 increase in P gave a 1.5% increase in R (p < 0.001). An interaction analysis between P and absolute humidity (AH) showed a statistically significant negative relationship between P x AH and R (p < 0.05). When AH was $ 5.8 g/m3, a higher P and AH gave a higher R. In contrast, when AH [≥] 5.8 g/m3, the effect of a higher P was counteracted by the effect of a higher AH, resulting in a lower R. Given that P can exacerbate R, we recommend the installation of air purifiers and better air ventilation to reduce the effect of P on R. Further, given the increasing discussions/observations that COVID-19 can be airborne, we highly recommend the wearing of surgical masks to keep one from contracting COVID-19 via the viral-particulate transmission pathway.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Yang Han", - "author_inst": "Department of Electrical and Electronic Engineering, The University of Hong Kong" - }, - { - "author_name": "Jacqueline C.K. Lam", - "author_inst": "Department of Electrical and Electronic Engineering, The University of Hong Kong" - }, - { - "author_name": "Victor O.K. Li", - "author_inst": "Department of Electrical and Electronic Engineering, The University of Hong Kong" - }, - { - "author_name": "Jon Crowcroft", - "author_inst": "Department of Computer Science and Technology, The University of Cambridge" - }, - { - "author_name": "Jinqi Fu", - "author_inst": "MRC Cancer Unit, Department of Oncology, The University of Cambridge" - }, - { - "author_name": "Jocelyn Downey", - "author_inst": "Department of Electrical and Electronic Engineering, The University of Hong Kong" - }, - { - "author_name": "Illana Gozes", - "author_inst": "Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Adams Super Center for Brain Studies and Sagol School of Neuroscience, Tel" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.19.20106468", "rel_title": "Estimation of Case Fatality Rate during an Epidemic: an Example from COVID-19 Pandemic", @@ -1402615,6 +1405831,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2020.05.19.20107532", + "rel_title": "COVID-19 Datasets: A Survey and Future Challenges", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20107532", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWIn December 2019, a novel virus named COVID-19 emerged in the city of Wuhan, China. In early 2020, the COVID-19 virus spread in all continents of the world except Antarctica causing widespread infections and deaths due to its contagious characteristics and no medically proven treatment. The COVID-19 pandemic has been termed as the most consequential global crisis after the World Wars. The first line of defense against the COVID-19 spread are the non-pharmaceutical measures like social distancing and personal hygiene. The great pandemic affecting billions of lives economically and socially has motivated the scientific community to come up with solutions based on computer-aided digital technologies for diagnosis, prevention, and estimation of COVID-19. Some of these efforts focus on statistical and Artificial Intelligence-based analysis of the available data concerning COVID-19. All of these scientific efforts necessitate that the data brought to service for the analysis should be open source to promote the extension, validation, and collaboration of the work in the fight against the global pandemic. Our survey is motivated by the open source efforts that can be mainly categorized as (a) COVID-19 diagnosis from CT scans, X-ray images, and cough sounds, (b) COVID-19 case reporting, transmission estimation, and prognosis from epidemiological, demographic, and mobility data, (c) COVID-19 emotional and sentiment analysis from social media, and (d) knowledge-based discovery and semantic analysis from the collection of scholarly articles covering COVID-19. We survey and compare research works in these directions that are accompanied by open source data and code. Future research directions for data-driven COVID-19 research are also debated. We hope that the article will provide the scientific community with an initiative to start open source extensible and transparent research in the collective fight against the COVID-19 pandemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Junaid Shuja", + "author_inst": "Umm Al-Qura University" + }, + { + "author_name": "Eisa Alanazi", + "author_inst": "Umm Al-Qura University" + }, + { + "author_name": "Waleed Alasmary", + "author_inst": "Umm Al-Qura University" + }, + { + "author_name": "Abdulaziz Alashaikh", + "author_inst": "University of Jeddah" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.24.20107193", "rel_title": "Using HoloLens\u2122 to reduce staff exposure to aerosol generating procedures during a global pandemic", @@ -1402712,85 +1405959,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.05.21.20107599", - "rel_title": "Clinical Utility of SARS-CoV-2 Whole Genome Sequencing in Deciphering Source of Infection", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20107599", - "rel_abs": "The novel coronavirus disease (COVID-19) pandemic caused by SARS-CoV-2 is a major threat to humans. Recently, we encountered two seemingly separate COVID-19 clusters in a tertiary care medical center. Whole viral genome sequencing detected the haplotype of the SARS-CoV-2 genome and the two clusters were successfully distinguished by the viral genome haplotype. Concurrently, there were nine COVID-19 patients clinically unlinked to clusters #1 or #2 that necessitated the determination of the source of infection. Such patients had similar haplotypes to those in cluster #2 but were devoid of two rare mutations characteristic to cluster #2. This suggested that these nine cases of \"probable community infection\" indeed had community infection and were not derived from cluster #2. Whole viral genome sequencing of SARS-CoV-2 is a powerful measure not only for monitoring the global trend of SARS-CoV-2 but also for identifying the source of infection of COVID-19 at a level of institution.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Toshiki Takenouchi", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Yuka W. Iwasaki", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Sei Harada", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Hirotsugu Ishizu", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Yoshifumi Uwamino", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Shunsuke Uno", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Asami Osada", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Naoki Hasegawa", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Mitsuru Murata", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Toru Takebayashi", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Koichi Fukunaga", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Hideyuki Saya", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Yuko Kitagawa", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Masayuki Amagai", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Haruhiko Siomi", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Kenjiro Kosaki", - "author_inst": "Keio University School of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.25.20111575", "rel_title": "Effect of socioeconomic and ethnic characteristics on COVID-19 infection: The case of the Ultra-Orthodox and the Arab communities in Israel", @@ -1404041,6 +1407209,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.20.20107755", + "rel_title": "BCG vaccination and socioeconomic variables vs Covid-19 global features: clearing up a controversial issue", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20107755", + "rel_abs": "BackgroundThe Covid-19 pandemic is characterized by extreme variability in the outcome distribution and mortality rates across different countries. Some recent studies suggested an inverse correlation with BCG vaccination at population level, while others denied this hypothesis. In order to address this controversial issue, we performed a strict epidemiological study collecting data available on a global scale, considering additional variables such as cultural-political factors and adherence to other vaccination coverages.\n\nMethodsData on 121 countries, accounting for about 99% of Covid-19 cases and deaths globally, were from Johns Hopkins Coronavirus Resource Center, World Bank, International Monetary Fund, United Nations, Human Freedom Report, and BCG Atlas. Statistical models used were Ordinary Least Squares, Tobit and Fractional Probit, implemented on Stata/MP16 software.\n\nResultsBased on our results, countries where BCG vaccination is or has been mandated in the last decades have seen a drastic reduction in Covid-19 diffusion (-80% on average) and mortality (-50% on average), even controlling for relative wealth of countries and their governmental health expenditure. A significant contribution to this reduction (respectively -50% and -13% on average) was also associated to the outbreak onset during summer, suggesting a possible influence of seasonality. Other variables turned out to be associated, though to a lesser extent.\n\nConclusionsRelying on a very large dataset and a wide array of control variables, our study confirms a strong and robust association between Covid-19 diffusion and mortality with BCG vaccination and a set socio-economic factors, opening new perspectives for clinical speculations and public health policies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Luigi Ventura", + "author_inst": "Department of Economy and Law, Sapienza University of Rome, Rome, Italy" + }, + { + "author_name": "Matteo Vitali", + "author_inst": "Department of Public Health and Infectious Diseases, Sapienza University of Rome, Italy" + }, + { + "author_name": "Vincenzo Romano Spica", + "author_inst": "Department of Movement, Human and Health Sciences, University of Rome \u201cForo Italico\u201d, Rome Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.25.20109470", "rel_title": "Seroprevalence of antibodies against SARS-CoV-2 among public community and health-care workers in Alzintan City of Libya", @@ -1404246,25 +1407441,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2020.05.22.20110064", - "rel_title": "Estimation of the Final Size of the COVID-19 Epidemic inBalochistan, Pakistan.", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20110064", - "rel_abs": "COVID-19 is a new disease that is spreading very fast in Pakistan. Cases have been reported from all the provinces in Pakistan including Balochistan. The first two confirmed cases in Pakistan had travel history from Iran to Pakistan, The some of the initial cases were quarantine at Taftan boarder in Balochistan, hence SIR model is used to predict the magnitude of the disease in Balochistan from May 2020 on wards when lock down and other social distancing measures were loosen up by the government of Balochistan. Our Prediction model shows that about 30,00000 individuals in Balochistan will be infected by 5th of July 2020.Over all 25% of the total population of Balochistan will be affected by this disease with 98% (2940,000) recovery rate by the end of 15th July 2020.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Muhammad Arif", - "author_inst": "FELTP" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.23.20111294", "rel_title": "Predicting COVID-19 spread and public health needs to contain the pandemic in West-Africa", @@ -1405771,6 +1408947,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.05.23.20111310", + "rel_title": "No evidence for allelic association between Covid-19 and ACE2 genetic variants by direct exome sequencing in 99 SARS-CoV-2 positive patients", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20111310", + "rel_abs": "BackgroundCoronaviruses (CoV) are a large family of viruses that are common in people and many animal species. Animal coronaviruses rarely infect humans with the exceptions of the Middle East Respiratory Syndrome (MERS-CoV), the Severe acute respiratory syndrome coronavirus (SARS-CoV), and now SARS-CoV-2, which is the cause of the ongoing pandemic of coronavirus disease 2019 (COVID-19). Many studies suggested that genetic variants in ACE2 gene may influence the host susceptibility/resistance to SARS-CoV-2 virus according to the functional role of ACE2 in human pathophysiology. However, all these studies have been conducted in silico based on epidemiological and population data. We therefore investigated the occurrence of ACE2 variants in a cohort of 99 Italian unrelated individuals clinically diagnosed with coronavirus disease 19 (COVID-19) to experimental demonstrate allelic association with disease severity.\n\nMethodsBy whole-exome sequencing we analysed 99 DNA samples of severely and extremely severely COVID-19 patients hospitalized at the University Hospital of Rome \"Tor Vergata\" and Bambino Gesu Hospital in Rome.\n\nResultsWe identified three different germline variants, one intronic (c.439+4G>A) and two missense (c.2158A>G, p.Asn720Asp; c.1888G>C, p.Asp630His), in 26 patients with a similar frequency between male and female and a not statistically different frequency, except for c.1888G>C, (p.Asp630His) with the ethnically matched populations (EUR).\n\nConclusionsOur results suggest that there is not any ACE2 exonic allelic association with disease severity. It is possible that rare susceptibility alleles are located in the non-coding region of the gene able to control ACE2 gene activity. It is therefore of interest, to explore the existence of ACE2 susceptibility alleles to SARS-Co-V2 in these regulatory regions. In addition, we found no significant evidence that ACE2 alleles is associated with disease severity/sex bias in the Italian population.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Antonio Novelli", + "author_inst": "Laboratory of Medical Genetics, Bambino Ges\u00f9 Children's Hospital, IRCCS, Rome, Italy" + }, + { + "author_name": "Michela Biancolella", + "author_inst": "Department of Biology, Tor Vergata University of Rome, 00133 Rome, Italy" + }, + { + "author_name": "Paola Borgiani", + "author_inst": "Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy" + }, + { + "author_name": "Dario Cocciadiferro", + "author_inst": "Laboratory of Medical Genetics, Bambino Ges\u00f9 Children's Hospital, IRCCS, Rome, Italy" + }, + { + "author_name": "Vito Luigi Colona", + "author_inst": "Medical Genetics Laboratory, Tor Vergata Hospital, Rome, Italy" + }, + { + "author_name": "Maria Rosaria D'Apice", + "author_inst": "Medical Genetics Laboratory, Tor Vergata Hospital, Rome, Italy" + }, + { + "author_name": "Paola Rogliani", + "author_inst": "Unit of Respiratory Medicine, Department of Experimental Medicine, University of Rome \"Tor Vergata\", Rome, Italy" + }, + { + "author_name": "Salvatore Zaffina", + "author_inst": "Occupational Medicine, Bambino Ges\u00f9 Children's Hospital, IRCCS, Rome, Italy" + }, + { + "author_name": "Francesca Leonardis", + "author_inst": "Intensive Care Unit, Tor Vergata University Hospital, Rome, Italy" + }, + { + "author_name": "Andrea Campana", + "author_inst": "Department of Pediatrics, IRCCS Bambino Ges\u00f9 Children's Hospital, Rome, Italy" + }, + { + "author_name": "Massimiliano Raponi", + "author_inst": "Medical Directorate, IRCCS Bambino Ges\u00f9 Children's Hospital, Rome, Italy" + }, + { + "author_name": "Massimo Andreoni", + "author_inst": "Infectious Diseases Clinic, Policlinico Tor Vergata, Rome, Italy" + }, + { + "author_name": "Sandro Grelli", + "author_inst": "Dept. of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, Italy" + }, + { + "author_name": "Giuseppe Novelli", + "author_inst": "Tor Vergata University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.05.25.20112938", "rel_title": "What Can We Learn from the Time Evolution of COVID-19 Epidemic in Slovenia?", @@ -1405848,73 +1409095,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.23.20111468", - "rel_title": "Containing the Spread of Coronavirus Disease 2019 (COVID-19): Meteorological Factors and Control Strategies", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20111468", - "rel_abs": "The novel coronavirus disease 2019 (COVID-19) has spread globally and the meteorological factors vary greatly across the world. Understanding the effect of meteorological factors and control strategies on COVID-19 transmission is critical to contain the epidemic. Using individual-level data in mainland China, Hong Kong, and Singapore, and the number of confirmed cases in other regions, we explore the effect of temperature, relative humidity, and control measures on the spread of COVID-19. We found that high temperature mitigates the transmission of the disease. High relative humidity promotes COVID-19 transmission when temperature is low, but tends to reduce transmission when temperature is high. Implementing classical control measures can dramatically slow the spread of the disease. However, due to the occurrence of pre-symptomatic infections, the effect of the measures to shorten onset-to-isolation time is markedly reduced and the importance of contact tracing and quarantine and social distancing increases. The analytic results also highlight the importance of early intervention to contain the spread of COVID-19.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Jun Lin", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Weihao Huang", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Muchen Wen", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Shuyi Ma", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Jiawen Hua", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Hang Hu", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Dehong Li", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Shan Yin", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Yanjun Qian", - "author_inst": "Northwestern Polytechnical University" - }, - { - "author_name": "Peiling Chen", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Qiao Zhang", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Ningbo Yuan", - "author_inst": "Chang'an University" - }, - { - "author_name": "Shaolong Sun", - "author_inst": "Xi'an Jiaotong University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.05.25.20113092", "rel_title": "Finding Tentative Causes for the reduced impact of Covid-19 on the Health Systems of poorer and developing nations: An ecological study of the effect of demographic, climatological and health-related factors on the global spread of Covid-19", @@ -1406905,6 +1410085,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.23.112284", + "rel_title": "SciSight: Combining faceted navigation and research group detection for COVID-19 exploratory scientific search", + "rel_date": "2020-05-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.23.112284", + "rel_abs": "The COVID-19 pandemic has sparked unprecedented mobilization of scientists, generating a deluge of papers that makes it hard for researchers to keep track and explore new directions. Search engines are designed for targeted queries, not for discovery of connections across a corpus. In this paper, we present SciSight, a system for exploratory search of COVID-19 research integrating two key capabilities: first, exploring associations between biomedical facets automatically extracted from papers (e.g., genes, drugs, diseases, patient outcomes); second, combining textual and network information to search and visualize groups of researchers and their ties. SciSight1 has so far served over 15K users with over 42K page views and 13% returns.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Tom Hope", + "author_inst": "Allen Institute for AI" + }, + { + "author_name": "Jason Portenoy", + "author_inst": "University of Washington" + }, + { + "author_name": "Kishore Vasan", + "author_inst": "University of Washington" + }, + { + "author_name": "Jonathan Borchardt", + "author_inst": "Allen Institute for AI" + }, + { + "author_name": "Eric Horvitz", + "author_inst": "Microsoft Research" + }, + { + "author_name": "Daniel S. Weld", + "author_inst": "Allen Institute for AI" + }, + { + "author_name": "Marti A. Hearst", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Jevin West", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.23.20111443", "rel_title": "COVID-19 in Latin America: Contrasting phylodynamic inference with epidemiological surveillance.", @@ -1407014,25 +1410241,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.25.115774", - "rel_title": "Alveolar early progenitors in the aged human lung have increased expression of ACE2 accompanied with genes involved in beta-amyloid clearance: Indication of SARS-CoV-2 also using soluble ACE2 in aged-lungs to enter ACE2-negative cells", - "rel_date": "2020-05-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.25.115774", - "rel_abs": "COVID-19 is the current pandemic caused by severe acute respiratory syndrome virus 2 (SARS-CoV-2) that uses ACE2 protein on the cell surface. By analyzing publicly available datasets, I uncovered that alveolar early progenitors (AEP), a subset of the type-2 pneumocytes, showed increased ACE2 expression in the older lungs. AEPs co-express TMPRSS2, CTSL. Aged AEP-gene expression signature suggested an active response to beta-amyloid-induced ACE2 shedding, to limit the intercellular beta-amyloid accumulation in otherwise healthy human lungs. Susceptibility of AEP to SARS-CoV2 and ACE2 secretory capacity of these cells makes aged human lung sensitive for rapid-infection, by a possible in-solution ACE2 binding and entry into ACE2-negative cells, thereby increasing the target cell diversity and numbers. Single-cell analysis of COVID19 patients with moderate and severe infections, clearly showed that severe infections showed SARS-CoV-2 transcript in ACE2-negative TMPRSS-negative but CTSL-positive cell types in their bronchoalveolar lavage fluid, validating in-solution ACE2-binding enabling infection.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Virendra K Chaudhri", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.05.20.20078915", "rel_title": "Total and Stroke Related Imaging Utilization Patterns During the COVID-19 Pandemic", @@ -1408339,6 +1411547,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.24.20104414", + "rel_title": "Risk of infection and hospitalization by Covid-19 in Mexico: a case-control study", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20104414", + "rel_abs": "ObjectiveDuring the onset of a novel epidemic, there are public health priorities that need to be estimated, such as risk factors for infection, hospitalization, and clinical severity to allocate resources and issue health policies. In this work we calculate the risk of infection and hospitalization by Covid-19 conferred by demographic, lifestyle, and co-morbidity factors.\n\nMaterial and methodsThis is a case-control study including the tested individuals for SARS-Cov-2 by RT-PCR officially reported by the Health Secretary of Mexico from January 01 to May 8, 2020 (102,875 subjects). Demographic (sex, age, foreign and immigrant status, native speaking, place of residence), life-style (smoking), and co-morbidities [diabetes, obesity, high blood pressure (HBP), asthma, immunosuppression, chronic obstructive pulmonary disease (COPD), cardiovascular disease other than HBP, chronic kidney disease (CKD), and other not specified diseases (other diseases)] variables were included in this study. The risk of infection and hospitalization conferred by each variable was calculated with univariate (ULR) and multivariate (MLR) logistic regression models.\n\nResultsThe place of residence (OR=4.91 living in Tijuana City), followed by advanced age (OR=6.71 in 61-70 years-old), suffering from diabetes (OR=1.87) or obesity (OR=1.61), being male (OR=1.55), having HBP (OR=1.52), and notoriously being indigenous (OR=1.49) conferred a higher risk of becoming infected by SARS-CoV-2 in Mexico. Unexpectedly, we found that having asthma (OR=0.63), immunosuppression (OR=0.65) or smoking (OR=0.85) are protective factors against infection, while suffering from COPD does not increase the risk for SARS-CoV-2 infection. In contrast, advanced age (OR=11.6 in [≥] 70 years-old) is the main factor for hospitalization due to Covid-19, followed by some co-morbidities, mainly diabetes (OR=3.69) and HBP (OR=2.79), being indigenous (OR=1.89), male sex (OR=1.67) and the place of residence (OR=4.22 for living in Juarez City). Unlike the protective risk against infection, immunosuppression (OR=2.69) and COPD (OR=3.63), contribute to the risk of being hospitalized, while having asthma (OR=0.7) also provides protection against hospitalization.\n\nConclusionsIn addition to confirming that older age, diabetes, HBP and obesity are the main risk of infection and hospitalization by Covid-19, we found that being indigenous, immunosuppression, smoking and asthma protect against infection, and the latter also against hospitalization.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jaime Berumen", + "author_inst": "Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" + }, + { + "author_name": "Max Schmulson", + "author_inst": "Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" + }, + { + "author_name": "Jesus Alegre", + "author_inst": "Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" + }, + { + "author_name": "Guadalupe Guerrero", + "author_inst": "Hospital General de Mexico, Dr. Eduardo Liceaga, Mexico City, Mexico" + }, + { + "author_name": "Gustavo Olaiz", + "author_inst": "Centro de Investigacion en politicas, poblacion y salud, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" + }, + { + "author_name": "Rosa M. Wong-Chew", + "author_inst": "Division de Investigacion, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" + }, + { + "author_name": "Jorge Larriva-Sahd", + "author_inst": "Instituto de Neurobiologia, Universidad Nacional Autonoma de Mexico, Campus Juriquilla, Queretaro Mexico" + }, + { + "author_name": "Carlos Cantu-Brito", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico." + }, + { + "author_name": "Ana Ochoa-Guzman", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico." + }, + { + "author_name": "Adrian Garcilazo-Avila", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico." + }, + { + "author_name": "Carlos Gonzalez-Carballo", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico." + }, + { + "author_name": "Erwin Chiquete", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.22.20102525", "rel_title": "Study on the expression levels of antibodies against SARS-CoV-2 at different period of disease and its related factors in 192 cases of COVID-19 patients", @@ -1408472,57 +1411743,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.24.20100990", - "rel_title": "Performance evaluation of the point-of-care SAMBA II SARS-CoV-2 Test for detection of SARS-CoV-2", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20100990", - "rel_abs": "Nucleic acid amplification for the detection of SARS-CoV-2 RNA in respiratory samples is the standard method for diagnosis. These tests are centralised and therefore turnaround times can be 2-5 days. Point-of-care testing with rapid turnaround times would allow more effective triage in settings where patient management and infection control decisions need to be made rapidly.\n\nInclusivity and specificity of the SAMBA II SARS-CoV-2 assay was determined by in silico analyses of the primers and probes. Analytical and clinical sensitivity and specificity of the SAMBA II SARS-CoV-2 Test was evaluated for analytical sensitivity and specificity. Clinical performance was evaluated in residual clinical samples compared to the Public Health England reference tests.\n\nThe limit of detection of the SAMBA II SARS-CoV-2 Test is 250 cp/mL and is specific for detection of 2 regions of the SARS-CoV-2 genome. The clinical sensitivity was evaluated in 172 clinical samples provided by the Clinical Microbiology and Public Health Laboratory, Addenbrookes Hospital, Cambridge (CMPHL), which showed a sensitivity of 98.9% (95% CI 94.03-99.97%), specificity of 100% (95% CI 95.55-100%), PPV of 100% and NPV of 98.78% (92.02-99.82%) compared to testing by CMPHLSAMBA detected 3 positive samples that were initially negative by PHE Test. The data shows that the SAMBA II SARS-CoV-2 Test performs equivalently to the centralised testing methods with a much quicker turnaround time. Point of care testing, such as SAMBA, should enable rapid patient management and effective implementation of infection control measures.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sonny M Assennato", - "author_inst": "Diagnostics for the Real World Europe Ltd" - }, - { - "author_name": "Allyson V Ritchie", - "author_inst": "Diagnostics for the Real World Europe Ltd" - }, - { - "author_name": "Cesar Nadala", - "author_inst": "Diagnostics for the Real World Ltd" - }, - { - "author_name": "Neha Goel", - "author_inst": "Diagnostics for the Real World Europe Ltd" - }, - { - "author_name": "Hongyi Zhang", - "author_inst": "Public Health England" - }, - { - "author_name": "Rawlings Datir", - "author_inst": "Division of Infection and Immunity, University College London, London, UK" - }, - { - "author_name": "Ravindra K Gupta", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Martin D Curran", - "author_inst": "Public Health England" - }, - { - "author_name": "Helen H Lee", - "author_inst": "Diagnostics for the Real World EU Ltd" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.25.20109058", "rel_title": "Prioritizing COVID-19 tests based in Participatory Surveillance and Spatial Scanning.", @@ -1409557,6 +1412777,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.19.20107425", + "rel_title": "A Modelling Analysis of Strategies for Relaxing COVID-19 Social Distancing", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20107425", + "rel_abs": "BackgroundThe ability of countries to contain and control COVID-19 virus transmission via social distancing is critical in the absence of a vaccine. Early activation of robust measures has been shown to control the daily infection rate, and consequential pressure on the health care system. As countries begin to control COVID-19 spread an understanding of how to ease social distancing measures to prevent a rebound in cases and deaths is required.\n\nMethodsUsing COVID-19 transmission data from the outbreak source in Hubei Province, China prior to activation of containment measures, we adapted an established individual-based simulation model of the city of Newcastle, Australia. Simulation of virus transmission in this model, with and without, social distancing measures activated permitted us to quantify social distancing effectiveness. Optimal strategies for relaxing social distancing were determined under two settings: with high numbers of daily cases, as in New York; and where early social distancing activation resulted in limited ongoing transmission, as in Perth, Australia.\n\nFindingsIn countries where strong social distancing measures were activated after the COVID-19 virus had spread widely, our study found these measures are required to be maintained for significant periods before being eased, to return to a situation where daily case numbers become low. In countries where early responses to the COVID-19 pandemic have been highly successful, as in Australia, we show that a staged relaxation of social distancing prevents a rebound in cases.\n\nInterpretationModelling studies and direct observation have shown that robust and timely social distancing have the most effect in containing the spread of the COVID-19 virus. Questions arise as to the duration of strong social distancing measures, given they are highly disruptive to society and economic activity. This study demonstrates the necessity of holding robust social distancing in place until COVID-19 virus transmission has significantly decreased, and how they may then be safely eased.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "George J Milne", + "author_inst": "University of Western Australia" + }, + { + "author_name": "Simon Xie", + "author_inst": "the University of Western Australia" + }, + { + "author_name": "Dana Poklepovich", + "author_inst": "University of Western Australia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.20.20107573", "rel_title": "Modelling information-dependent social behaviors in response to lockdowns: the case of COVID-19 epidemic in Italy", @@ -1409726,117 +1412973,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.20.20107813", - "rel_title": "SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T-cell receptors", - "rel_date": "2020-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20107813", - "rel_abs": "Understanding the hallmarks of the adaptive immune response to SARS-CoV-2 is critical for fighting the COVID-19 pandemic. We assessed the antibody and T-cell reactivity in COVID-19 convalescent patients and healthy donors sampled both prior to and during the pandemic. The numbers of SARS-CoV-2-specific T cells were increased in healthy donors examined during COVID-19. Combined with the absence of symptoms and humoral response across that group, this finding suggests that some individuals might be protected by T-cell cross-reactivity. In convalescent patients we observed public and diverse T-cell response to SARS-CoV-2 epitopes, revealing T-cell receptor motifs with germline-encoded features. Bulk CD4+ and CD8+ T-cell responses to Spike glycoprotein were mediated by groups of homologous T-cell receptors, some of them shared across multiple donors. Overall, our results demonstrate that T-cell response to SARS-CoV-2, including the identified set of specific T-cell receptors, can serve as a useful biomarker for surveying viral exposure and immunity.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Alina S Shomuradova", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Murad S Vagida", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Savely A Sheetikov", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Ksenia V Zornikova", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Dmitry Kiryukhin", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Aleksei Titov", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Iuliia O Peshkova", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Alexandra Khmelevskaya", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Dmitry V Dianov", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Maria Malasheva", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Anton Shmelev", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Yana Serdyuk", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Dmitry V Bagaev", - "author_inst": "Eindhoven University of Technology, Eindhoven, Netherlands" - }, - { - "author_name": "Anastasia Pivnyuk", - "author_inst": "Center of Life Sciences, Skolkovo Institute of Science and Technology" - }, - { - "author_name": "Dmitrii S Shcherbinin", - "author_inst": "Pirogov Russian Medical State University, Moscow, Russia; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia" - }, - { - "author_name": "Alexandra V Maleeva", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Naina T Shakirova", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Artem Pilunov", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Dmitry B Malko", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Ekaterina G Khamaganova", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Bella Biderman", - "author_inst": "National Research Center for Hematology, Moscow, Russian Federation" - }, - { - "author_name": "Alexander V Ivanov", - "author_inst": "Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Ru" - }, - { - "author_name": "Mikhail Shugay", - "author_inst": "Center of Life Sciences, Skolkovo Institute of Science and Technology; Pirogov Russian Medical State University, Moscow, Russia; Shemyakin and Ovchinnikov Insti" - }, - { - "author_name": "Grigory A Efimov", - "author_inst": "National Research Center for Hematology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.19.20107524", "rel_title": "Can a herd immunity strategy become a viable option against COVID-19? A model-based analysis on social acceptability and feasibility", @@ -1411235,6 +1414371,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.05.22.20109959", + "rel_title": "CLINICAL CHARACTERISTICS AND PROGNOSTIC FACTORS FOR ICU ADMISSION OF PATIENTS WITH COVID-19 USING MACHINE LEARNING AND NATURAL LANGUAGE PROCESSING", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20109959", + "rel_abs": "There remain many unknowns regarding the onset and clinical course of the ongoing COVID-19 pandemic. We used a combination of classic epidemiological methods, natural language processing (NLP), and machine learning (for predictive modeling), to analyse the electronic health records (EHRs) of patients with COVID-19.\n\nWe explored the unstructured free text in the EHRs within the SESCAM Healthcare Network (Castilla La-Mancha, Spain) from the entire population with available EHRs (1,364,924 patients) from January 1st to March 29th, 2020. We extracted related clinical information upon diagnosis, progression and outcome for all COVID-19 cases, focusing in those requiring ICU admission.\n\nA total of 10,504 patients with a clinical or PCR-confirmed diagnosis of COVID-19 were identified, 52.5% males, with age of 58.2{+/-}19.7 years. Upon admission, the most common symptoms were cough, fever, and dyspnoea, but all in less than half of cases. Overall, 6% of hospitalized patients required ICU admission. Using a machine-learning, data-driven algorithm we identified that a combination of age, fever, and tachypnoea was the most parsimonious predictor of ICU admission: those younger than 56 years, without tachypnoea, and temperature <39{degrees}C, (or >39{degrees}C without respiratory crackles), were free of ICU admission. On the contrary, COVID-19 patients aged 40 to 79 years were likely to be admitted to the ICU if they had tachypnoea and delayed their visit to the ER after being seen in primary care.\n\nOur results show that a combination of easily obtainable clinical variables (age, fever, and tachypnoea with/without respiratory crackles) predicts which COVID-19 patients require ICU admission.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jose Luis Izquierdo", + "author_inst": "Hospital Universitario de Guadalajara, Guadalajara, Spain" + }, + { + "author_name": "Julio Ancochea", + "author_inst": "Hospital Universitario de La Princesa, Madrid, Spain" + }, + { + "author_name": "- Savana COVID-19 Research Group", + "author_inst": "" + }, + { + "author_name": "Joan B Soriano", + "author_inst": "Hospital Universitario de La Princesa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.05.21.20108969", "rel_title": "ASSESSMENT OF WORKERS PERSONAL VULNERABILITY TO COVID-19 USING COVID-AGE", @@ -1411392,33 +1414559,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.21.20109041", - "rel_title": "Rising evidence of COVID-19 transmission potential to and between animals: do we need to be concerned?", - "rel_date": "2020-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20109041", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)--the virus that causes coronavirus disease (COVID-19)--has been detected in domestic dogs and cats, raising concerns of transmission from, to, or between these animals. There is currently no indication that feline- or canine-to-human transmission can occur, though there is rising evidence of the reverse. To explore the extent of animal-related transmission, we aggregated 17 case reports on confirmed SARS-CoV-2 infections in animals as of 15 May 2020. All but two animals fully recovered and had only mild respiratory or digestive symptoms. Using data from probable cat-to-cat transmission in Wuhan, China, we estimated the basic reproduction number R0 under this scenario at 1.09 (95% confidence interval: 1.05, 1.13). This value is much lower than the R0 reported for humans and close to one, indicating that the sustained transmission between cats is unlikely to occur. Our results support the view that the pet owners and other persons with COVID-19 in close contact with animals should be cautious of the way they interact with them.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Andrei R. Akhmetzhanov", - "author_inst": "Graduate School of Medicine, Hokkaido University" - }, - { - "author_name": "Natalie M. Linton", - "author_inst": "Graduate School of Medicine, Hokkaido University" - }, - { - "author_name": "Hiroshi Nishiura", - "author_inst": "Graduate School of Medicine, Hokkaido University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.21.20108993", "rel_title": "Comparison of renin-angiotensin-aldosterone system inhibitors with other antihypertensives in association with coronavirus disease-19 clinical outcomes: systematic review and meta-analysis", @@ -1412673,6 +1415813,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.22.20110502", + "rel_title": "Conditions for a second wave of COVID-19 due to interactions between disease dynamics and social processes", + "rel_date": "2020-05-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20110502", + "rel_abs": "In May 2020, many jurisdictions around the world began lifting physical distancing restrictions against the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), giving rise to concerns about a possible second wave of coronavirus disease 2019 (COVID-19). These restrictions were imposed as a collective population response to the presence of COVID-19 in communities. However, lifting restrictions is also a population response to their socio-economic impacts, and is expected to increase COVID-19 cases, in turn. This suggests that the COVID-19 pandemic exemplifies a coupled behaviour-disease system. Here we develop a minimal mathematical model of the interaction between social support for school and workplace closure and the transmission dynamics of SARS-CoV-2. We find that a second wave of COVID-19 occurs across a broad range of plausible model input parameters, on account of instabilities generated by behaviour-disease interactions. We conclude that second waves of COVID-19-should they materialize-can be interpreted as the outcomes of nonlinear interactions between disease dynamics and population behaviour.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sansao A Pedro", + "author_inst": "Universidade Eduardo Mondlane, Departamento de Matematica e Informatica, Maputo, Mozambique" + }, + { + "author_name": "Frank T Ndjomatchoua", + "author_inst": "International Rice Research Institute, Sustainable Impact Platform, Geospatial Science and Modelling cluster, DAPO Box 7777-1301, Metro Manila, Philippines" + }, + { + "author_name": "Peter Jentsch", + "author_inst": "University of Guelph, School of Environmental Sciences, Guelph, N1G 2W1, Canada and University of Waterloo, Department of Applied Mathematics, Waterloo, N2L 3G1" + }, + { + "author_name": "Jean M Tcheunche", + "author_inst": "Avenir Health, Glastonbury, CT, USA" + }, + { + "author_name": "Madhur Anand", + "author_inst": "University of Guelph, School of Environmental Sciences, Guelph, N1G 2W1, Canada" + }, + { + "author_name": "Chris T Bauch", + "author_inst": "University of Waterloo, Department of Applied Mathematics, Waterloo, N2L 3G1, Canada" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.22.20110551", "rel_title": "Anti-SARS-CoV-2 IgG antibodies are associated with reduced viral load", @@ -1412802,53 +1415981,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.23.20110882", - "rel_title": "SARS-CoV-2 lethality decreased over time in two Italian Provinces", - "rel_date": "2020-05-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20110882", - "rel_abs": "BackgroundSome experts recently reported that SARS-CoV-2 lethality decreased considerably, but no evidence is yet available. This retrospective cohort study aimed to evaluate whether SARS-CoV-2 case-fatality rate decreased with time, adjusting for several potential confounders.\n\nMethodsWe included all subjects diagnosed with SARS-CoV-2 infection in Ferrara and Pescara provinces, Italy. Information were collected from local registries, clinical charts, and electronic health records. We compared the case-fatality rate (after [≥]28 days of follow-up) of the subjects diagnosed during April and March, 2020. We used Cox proportional hazards analysis and random-effect logistic regression, adjusting for age, gender, hypertension, type II diabetes, major cardiovascular diseases (CVD), chronic obstructive pulmonary diseases (COPD), cancer and renal disease.\n\nResultsThe sample included 2493 subjects (mean age 58.6y; 47.7% males). 258 persons deceased, after a mean of 16.1 days of follow-up. The mean age of those who died substantially increased from March (78.1{+/-}11.0y) to April (84.3{+/-}10.2y). From March to April, the case-fatality rate did not decrease in the total sample (9.5% versus 12.1%; adjusted hazard ratio 0.93; 95% Confidence Interval: 0.71-1.21; p=0.6), and in any age-class.\n\nConclusionsIn this sample, SARS-CoV-2 case-fatality rate did not decrease over time, in contrast with recent claims of a substantial improvement of SARS-CoV-2 clinical management. The findings require confirmation from larger datasets.\n\nAuthor summaryO_ST_ABSWhy was this study done?C_ST_ABSO_LISome experts recently reported that SARS-CoV-2 lethality decreased considerably, but no evidence is yet available.\nC_LI\n\nWhat did the researchers do and find?O_LIWe carried out a retrospective cohort study on 2493 SARS-CoV-2 infected subjects from two Italian provinces, evaluating the potential variation of the case-fatality rate over time.\nC_LIO_LIFrom March to April, SARS-CoV-2 case-fatality rate did not decrease, overall and in any age-class.\nC_LI\n\nWhat do these findings mean?O_LIThe therapies and clinical management of SARS-CoV-2 infected subjects did not determine a substantial change of the clinical course of the disease from March to April, 2020.\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Maria Elena Flacco", - "author_inst": "Department of Medical Sciences, University of Ferrara, Italy" - }, - { - "author_name": "Cecilia Acuti Martellucci", - "author_inst": "Department of Biomedical Sciences and Public Health, University of the Marche Region, Ancona, Italy" - }, - { - "author_name": "Francesca Bravi", - "author_inst": "\"Sant'Anna\" University Hospital of Ferrara, Italy" - }, - { - "author_name": "Giustino Parruti", - "author_inst": "Local Health Authority of Pescara, Italy" - }, - { - "author_name": "Alfonso Mascitelli", - "author_inst": "Regional Healthcare Agency of Abruzzo, Pescara, Italy" - }, - { - "author_name": "Lorenzo Mantovani", - "author_inst": "School of Medicine and Surgery, University Bicocca, Milan, Italy" - }, - { - "author_name": "Stefania Boccia", - "author_inst": "Catholic University of the Sacred Heart, Rome" - }, - { - "author_name": "Lamberto Manzoli", - "author_inst": "University of Ferrara" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.21.20108647", "rel_title": "Psychological Impact of COVID-19 on Pakistani University Students and How They Are Coping", @@ -1414067,6 +1417199,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.23.107334", + "rel_title": "Lung epithelial stem cells express SARS-CoV-2 entry factors: implications for COVID-19", + "rel_date": "2020-05-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.23.107334", + "rel_abs": "SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, we analyzed published RNA-seq datasets and demonstrated that cells of four different lung epithelial stem cell types express SARS-CoV-2 entry factors, including Ace2. Thus, stem cells can be potentially infected by SARS-CoV-2, which may lead to defects in regeneration capacity partially accounting for the severity of SARS-CoV-2 infection and its consequences.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anna A. Valyaeva", + "author_inst": "Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University" + }, + { + "author_name": "Anastasia A. Zharikova", + "author_inst": "Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University" + }, + { + "author_name": "Artem S. Kasianov", + "author_inst": "The Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute)" + }, + { + "author_name": "Yegor S. Vassetzky", + "author_inst": "CNRS, UMR 9018, Universite Paris-Saclay, Institut Gustave Roussy" + }, + { + "author_name": "Eugene V. Sheval", + "author_inst": "Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2020.05.21.109322", "rel_title": "The emergence of SARS-CoV-2 in Europe and the US", @@ -1414448,69 +1417615,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.05.22.111237", - "rel_title": "Biophysical modeling of the SARS-CoV-2 viral cycle reveals ideal antiviral targets", - "rel_date": "2020-05-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.22.111237", - "rel_abs": "Effective therapies for COVID-19 are urgently needed. Presently there are more than 800 COVID-19 clinical trials globally, many with drug combinations, resulting in an empirical process with an enormous number of possible combinations. To identify the most promising potential therapies, we developed a biophysical model for the SARS-CoV-2 viral cycle and performed a sensitivity analysis for individual model parameters and all possible pairwise parameter changes (162 = 256 possibilities). We found that model-predicted virion production is fairly insensitive to changes in most viral entry, assembly, and release parameters, but highly sensitive to some viral transcription and translation parameters. Furthermore, we found a cooperative benefit to pairwise targeting of transcription and translation, predicting that combined targeting of these processes will be especially effective in inhibiting viral production.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Brian T Castle", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Carissa Dock", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Mahya Hemmat", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Susan Kline", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Christopher Tignanelli", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Radha Rajasingham", - "author_inst": "University of Minnesota" - }, - { - "author_name": "David Masopust", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Paolo Provenzano", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Ryan Langlois", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Timothy Schacker", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Ashley Haase", - "author_inst": "University of Minnesota" - }, - { - "author_name": "David J Odde", - "author_inst": "University of Minnesota" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.05.22.20109793", "rel_title": "Changes in premature birth rates during the Danish nationwide COVID-19 lockdown: a nationwide register-based prevalence proportion study", @@ -1415681,6 +1418785,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.05.18.20105874", + "rel_title": "Early experiences with antibody testing in a Flemish nursing home during an acute COVID-19 outbreak: a retrospective cohort study.", + "rel_date": "2020-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20105874", + "rel_abs": "objectivesto assess the prevalence of COVID-19 (PCR-test) in residents and staff of a nursing home. To examine the presence of IgM and IgG antibodies in the sample and the relation between PCR and antibody test results.\n\ndesigncross-sectional and (retrospective) cohort study\n\nsettinga nursing home for the elderly Bessemerberg in Lanaken (Belgium) with up to 130 beds. Lanaken is situated in the Belgian province with the highest COVID-19 prevalence.\n\nparticipantsresidents (N=108) and staff members (N=93) of the nursing home\n\noutcomesPCR, IgM and IgG\n\nresultsthe prevalence of COVID-19, based on PCR test was 34% (N=40) for residents and 13% (N=11) for staff members, respectively. Of the residents, 13% showed positive IgM results and 15% positive IgG results. In 17% of the residents, at least one of the antibodies was positive. In total 13% of the staff members had positive IgM and 16% had a positive IgG. In 20% of the staff members at least one of these antibody tests was positive. In PCR positive residents, the percentage of IgM positive, IgG positive, and at least one of both was 28%, 34%, and 41%. In PCR positive staff, we found 30%, 60%, and 60%. Additional antibody tests were performed in nine residents between day 11 and 14 after the positive PCR test. Of those, 7 (78%) tested positive on at least one antibody. When retesting three weeks later, all remaining residents also tested positive.\n\nconclusionsRecently it was reported that in Belgium antibodies are present in 3-4% of the general population. Although, the prevalence in our residents is higher, the number is largely insufficient for herd immunity. In staff members of the regional hospital the prevalence of antibodies was 6%. The higher prevalence in nursing home staff (21%) may be related to the complete absence of good quality protection in the first weeks of the outbreak.\n\nArticle summaryO_LSTStrengths and limitations of this studyC_LST- This is the first study in Belgium examining the prevalence of COVID-19 and the presence of antibodies in residents and staff members of a nursing home\n- The internal procedural control was positive -with one exception- in all tests, which suggests good quality sampling and testing.\n- Some degree of selection bias should be assumed in residents, since some residents were absent; mostly from hospitalisation or death which can be related to the presence of COVID-related disease.\n- The study was set up in one nursing home and is consequently not representative for the whole of the Flemish community", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Frank Buntinx", + "author_inst": "University of Leuven, Department of Public Health and Primary Care, Leuven, Belgium" + }, + { + "author_name": "Peter Claes", + "author_inst": "Woonzorgcentrum Bessemerberg, Lanaken, Belgium." + }, + { + "author_name": "Marjo Gulikers", + "author_inst": "Woonzorgcentrum Bessemerberg, Lanaken, Belgium." + }, + { + "author_name": "Jan Y Verbakel", + "author_inst": "University of Leuven, Department of Public Health and Primary Care, Leuven, Belgium" + }, + { + "author_name": "Jan De Lepeleire", + "author_inst": "University of Leuven, Department of Public Health and Primary Care, Leuven, Belgium" + }, + { + "author_name": "Michael Van der Elst", + "author_inst": "University of Leuven, Department of Public Health and Primary Care, Leuven, Belgium" + }, + { + "author_name": "Marc Van Ranst", + "author_inst": "University of Leuven, Laboratory of Clinical and Epidemiological Virology (Rega Institute), Leuven, Belgium" + }, + { + "author_name": "Pieter Vermeersch", + "author_inst": "Department of cardiovascular Sciences, KU Leuven, Leuven Belgium" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.18.20104703", "rel_title": "COVID-19 in China: Risk Factors and R0 Revisited", @@ -1415802,61 +1418953,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.18.20097444", - "rel_title": "Diagnostic power of chest CT for COVID-19: to screen or not to screen", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20097444", - "rel_abs": "Structured abstractO_ST_ABSBackgroundC_ST_ABSchest CT is increasingly used for COVID-19 screening in healthcare systems with limited SARS-CoV-2 PCR capacity. Its diagnostic value was supported by studies with methodological concerns and its use is controversial. Here we investigated its potential to diagnose COVID-19 in symptomatic patients and to screen asymptomatic patients in a prospective study with minimal selection bias.\n\nMethodsFrom March 19, 2020 to April 20, 2020 we performed parallel SARS-CoV-2 PCR and CT with categorization of COVID-19 suspicion by CO-RADS, in 859 patients with COVID-19 symptoms and 1138 controls admitted to the hospital for COVID-19 unrelated medical urgencies. CT-CORADS was categorized on a 5-point scale from 1 (very low suspicion) to 5 (very high suspicion). AUC under ROC curve were calculated in symptomatic versus asymptomatic patients to predict positive SARS-CoV-2 positive PCR and likelihood ratios for each CO-RADS score were used for rational selection of diagnostic thresholds.\n\nFindingsCT-CORADS had significant (P<0.0001) diagnostic power in both symptomatic (AUC=0.891) and asymptomatic (AUC=0.700) patients hospitalized during SARS-CoV-2 peak prevalence. In symptomatic patients (41.7% PCR+), CO-RADS [≥] 3 detected positive PCR with high sensitivity (89.1%) and 72.5% specificity. In asymptomatic patients (5.3% PCR+), a CO-RADS score [≥] 3 detected SARS-CoV-2 infection with low sensitivity (45.0%) but high specificity (88.8%).\n\nInterpretationCT-CORADS has meaningful diagnostic power in symptomatic patients, supporting its application for time-sensitive triage. Sensitivity in asymptomatic patients is insufficient to justify its use as screening approach. Incidental detection of CO-RADS [≥] 3 in asymptomatic patients should trigger reflex testing for respiratory pathogens.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Kristof De Smet", - "author_inst": "AZ Delta General Hospital, Department of Radiology" - }, - { - "author_name": "Dieter De Smet", - "author_inst": "AZ Delta General Hospital, AZ Delta Medical Laboratories" - }, - { - "author_name": "Ingel Demedts", - "author_inst": "AZ Delta General Hospital, Department of Pulmonary Diseases" - }, - { - "author_name": "Bernard Bouckaert", - "author_inst": "AZ Delta General Hospital, Department of Pulmonary Diseases" - }, - { - "author_name": "Thomas Ryckaert", - "author_inst": "AZ Delta General Hospital, Department of Radiology" - }, - { - "author_name": "Emanuel Laridon", - "author_inst": "AZ Delta General Hospital, Department of Radiology" - }, - { - "author_name": "Birgit Heremans", - "author_inst": "AZ Delta General Hospital, Department of Radiology" - }, - { - "author_name": "Ruben Vandenbulcke", - "author_inst": "AZ Delta General Hospital, Department of Radiology" - }, - { - "author_name": "Stefaan Gryspeerdt", - "author_inst": "AZ Delta General Hospital, Department of Radiology" - }, - { - "author_name": "Geert Antoine Martens", - "author_inst": "AZ Delta General Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.05.18.20105502", "rel_title": "Almitrine as a non ventilatory strategy to improve intrapulmonary shunt in COVID-19 patients", @@ -1417251,6 +1420347,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.21.109280", + "rel_title": "A previously uncharacterized gene in SARS-CoV-2 illuminates the functional dynamics and evolutionary origins of the COVID-19 pandemic", + "rel_date": "2020-05-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.21.109280", + "rel_abs": "Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics, but are still widely overlooked. We identify and characterize ORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of ORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of Severe acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). ORF3d has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene ORF3b, leading to confusion. Our results liken ORF3d to other accessory genes in emerging viruses and highlight the importance of OLGs.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Chase W. Nelson", + "author_inst": "American Museum of Natural History" + }, + { + "author_name": "Zachary Ardern", + "author_inst": "Chair for Microbial Ecology, Technical University of Munich, Freising, Germany" + }, + { + "author_name": "Tony L. Goldberg", + "author_inst": "Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI" + }, + { + "author_name": "Chen Meng", + "author_inst": "Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany" + }, + { + "author_name": "Chen-Hao Kuo", + "author_inst": "Biodiversity Research Center, Academia Sinica, Taipei, Taiwan" + }, + { + "author_name": "Christina Ludwig", + "author_inst": "Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany" + }, + { + "author_name": "Sergios-Orestis Kolokotronis", + "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Health Sciences University, Brooklyn, NY" + }, + { + "author_name": "Xinzhu Wei", + "author_inst": "Departments of Integrative Biology and Statistics, University of California, Berkeley, CA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.05.21.109298", "rel_title": "Recombinant SARS-CoV-2 spike proteins for sero-surveillance and epitope mapping", @@ -1417420,109 +1420563,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.19.20101832", - "rel_title": "Serologic responses to SARS-CoV-2 infection among hospital staff with mild disease in eastern France", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20101832", - "rel_abs": "BackgroundThe serologic response of individuals with mild forms of SARS-CoV-2 infection is poorly characterized.\n\nMethodsHospital staff who had recovered from mild forms of PCR-confirmed SARS-CoV-2 infection were tested for anti-SARS-CoV-2 antibodies using two assays: a rapid immunodiagnostic test (99.4% specificity) and the S-Flow assay ([~]99% specificity).The neutralizing activity of the sera was tested with a pseudovirus-based assay.\n\nResultsOf 162 hospital staff who participated in the investigation, 160 reported SARS-CoV-2 infection that had not required hospital admission and were included in these analyses. The median time from symptom onset to blood sample collection was 24 days (IQR: 21-28, range 13-39). The rapid immunodiagnostic test detected antibodies in 153 (95.6%) of the samples and the S-Flow assay in 159 (99.4%), failing to detect antibodies in one sample collected 18 days after symptom onset (the rapid test did not detect antibodies in that patient). Neutralizing antibodies (NAbs) were detected in 79%, 92% and 98% of samples collected 13-20, 21-27 and 28-41 days after symptom onset, respectively (P=0.02).\n\nConclusionAntibodies against SARS-CoV-2 were detected in virtually all hospital staff sampled from 13 days after the onset of COVID-19 symptoms. This finding supports the use of serologic testing for the diagnosis of individuals who have recovered from SARS-CoV-2 infection. The neutralizing activity of the antibodies increased overtime. Future studies will help assess the persistence of the humoral response and its associated neutralization capacity in recovered patients.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Samira Fafi-Kremer", - "author_inst": "CHRU Strasbourg" - }, - { - "author_name": "Timothee Bruel", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Yoann Madec", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Rebecca Grant", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Laura Tondeur", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Ludivine Grzelak", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Isabelle Staropoli", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Francois Anna", - "author_inst": "Pasteur-Theravectys" - }, - { - "author_name": "Philippe Souque", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Catherine Mutter", - "author_inst": "CHRU Strasbourg" - }, - { - "author_name": "Nicolas Collongues", - "author_inst": "CHRU Strasbourg" - }, - { - "author_name": "Alexandre Bolle", - "author_inst": "CHRU Strasbourg" - }, - { - "author_name": "Aurelie Velay", - "author_inst": "CHRU Strasbourg" - }, - { - "author_name": "Nicolas Lefebvre", - "author_inst": "CHRU Strasbourg" - }, - { - "author_name": "Marie Mielcarek", - "author_inst": "CHRU Strasbourg" - }, - { - "author_name": "Nicolas Meyer", - "author_inst": "CHRU Strasbourg" - }, - { - "author_name": "David Rey", - "author_inst": "CHRU Strasbourg" - }, - { - "author_name": "Pierre Charneau", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Bruno Hoen", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Jerome De Seze", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Olivier Schwartz", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Arnaud Fontanet", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.18.20101709", "rel_title": "Risk stratification of hospitalized COVID-19 patients through comparative studies of laboratory results with influenza", @@ -1418949,6 +1421989,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.05.17.20104687", + "rel_title": "A DISSYMMETRY IN THE FIGURES RELATED TO THE COVID-19 PANDEMIC IN THE WORLD: WHAT FACTORS EXPLAIN THE DIFFERENCE BETWEEN AFRICA AND THE REST OF THE WORLD?", + "rel_date": "2020-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104687", + "rel_abs": "Humanity has experienced outbreaks for millennia, from epidemics limited to pandemics that have claimed many victims and changed the course of civilizations. The advent of vaccines has eradicated some of the serious pathogens and reduced many others. However, pandemics are still part of our modern world, as we continue to have pandemics as devastating as HIV and as alarming as severe acute respiratory syndrome, Ebola and the Middle East respiratory syndrome. The Covid-19 epidemic with 0-exponential contamination curves reaching 3 million confirmed cases should not have come as a surprise, nor should it have been the last pandemic in the world. In this article, we try to summarize the lost opportunities as well as the lessons learned, hoping that we can do better in the future. The objective of this study is to relate the situation of Covid-19 in African countries with those of the countries most affected by the pandemic. It also allows us to verify how, according to the observed situation, the African ecosystem seems to be much more resilient compared to that of other continents where the number of deaths is in the thousands. To verify this, the diagnosed morbidity and mortality reported for different states of the world are compared to the ages of life and the average annual temperature of these states. The results show that the less dramatic balance of the African continent compared to other continents is partly linked to the relatively high temperatures on the continent but also to the relatively young character of its population.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Cheikh Faye Sr.", + "author_inst": "Assane Seck University of Ziguinchor" + }, + { + "author_name": "CheikhTidiane Wade Sr.", + "author_inst": "Assane Seck University of Ziguinchor" + }, + { + "author_name": "Ibrahima Demba Dione Sr.", + "author_inst": "Assane Seck University of Ziguinchor" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.05.20.20103200", "rel_title": "The Hybrid Forecasting Method SVR-ESAR forCovid-19", @@ -1419058,77 +1422125,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.20.20104398", - "rel_title": "Erythrocytes Reveal Complement Activation in Patients with COVID-19", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20104398", - "rel_abs": "COVID-19, the disease caused by the SARS-CoV-2 virus, can progress to multi-organ failure characterized by respiratory insufficiency, arrhythmias, thromboembolic complications and shock 1-5. The mortality of patients hospitalized with COVID-19 is unacceptably high and new strategies are urgently needed to rapidly identify and treat patients at risk for organ failure. Clinical epidemiologic studies demonstrate that vulnerability to organ failure is greatest after viral clearance from the upper airway 6-8, which suggests that dysregulation of the host immune response is a critical mediator of clinical deterioration and death. Autopsy and pre-clinical evidence implicate aberrant complement activation in endothelial injury and organ failure 9,10. A potential therapeutic strategy warranting investigation is to inhibit complement, with case reports of successful treatment of COVID-19 with inhibitors of complement 10-13. However, this approach requires careful balance between the host protective and potential injurious effects of complement activation, and biomarkers to identify the optimal timing and candidates for therapy are lacking. Here we report the presence of complement activation products on circulating erythrocytes from hospitalized COVID-19 patients using flow cytometry. These findings suggest that novel erythrocyte-based diagnostics provide a method to identify patients with dysregulated complement activation.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "LK Metthew Lam", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Sophie J. Murphy", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Leticia Kuri-Cervantes", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Ariel R. Weisman", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Caroline A. G. Ittner", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "John P. Reilly", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "M. Betina Pampena", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Michael R. Betts", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "E. John Wherry", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Wen-Chao Song", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "John D. Lambris", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Douglas B. Cines", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Nuala J. Meyer", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Nilam S. Mangalmurti", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.20.20103887", "rel_title": "COVID-19 case forecasting model for Sri Lanka based on Stringency Index", @@ -1420371,6 +1423367,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.17.20104968", + "rel_title": "Fuzzy Autocatalytic analysis of Covid-19 outbreak in Malaysia", + "rel_date": "2020-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104968", + "rel_abs": "The objective of this research is to demonstrate a mathematical technique to analyze the Covid-19 outbreak, particularly with respect to Malaysia. The technique is able to accommodate scarcity, quantity, and availability of the data set. The obtained results can offer descriptive insight for reflecting and strategizing actions in combating the pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tahir Ahmad", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Azmirul Ashaari", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Siti Rahmah Awang", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Siti Salwana Mamat", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Wan Munirah Wan Mohamad", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Amirul Aizad Ahmad Fuad", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Nurfarhana Hassan", + "author_inst": "Universiti Teknologi Malaysia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.18.20105155", "rel_title": "The Dynamic Changes of Antibodies against SARS-CoV-2 during the Infection and Recovery of COVID-19", @@ -1420560,53 +1423599,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.18.20105510", - "rel_title": "Development and Validation of Two In-house, Low-Cost SARS-CoV-2 Detection Assays", - "rel_date": "2020-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20105510", - "rel_abs": "BackgroundOne major challenge for detecting the virus that causes COVID-19 is commercial SARS-CoV-2 testing kit or reagent availability. To allow every laboratory or hospital access to an in-house assay, we developed two low-cost SARS-CoV-2 detection assay protocols using in-house primers and reagents/equipment on hand in most biology or diagnostic laboratories: a SYBR Green-based RT-PCR and PCR assays. RNA extraction has also become a major bottleneck due to limited supplies and the required labor. Thus, we validated alternative RNA extraction protocols.\n\nMethodsSARS-CoV-2 genome sequences deposited into the GISAID database were retrieved to design and synthesize in-house primers. Forty patient samples were collected by nasopharyngeal swab, coded, and used to develop and validate the assay protocols. Both assays used TRIzol and heat-processing techniques to extract RNA from patient samples and to inactivate the virus; thus, testing was conducted in a conventional biosafety level 2 laboratory.\n\nResultsThe sensitivity and specificity of the primers were evaluated using samples previously confirmed positive for SARS-CoV-2. The positive amplicons were sequenced to confirm the results. The assay protocols were developed, and the specificity of each PCR product was confirmed using melting curve analyses. The most accurate heat-processing technique for primers with short amplicon lengths was 95 {degrees}C for 15 mins. Of 40 samples, both the SYBR Green-based quantitative RT-PCR assay and the PCR assay detected SARS-CoV-2 target genes in 28 samples, with no false-positive or false-negative results. These findings were 100% concordant with those of the diagnostic laboratory that tested the same samples using a Rotor-Gene PCR cycler with an Altona Diagnostics SARS-CoV-2 kit (R2=0.889).\n\nConclusionsThese approaches are reliable, repeatable, specific, sensitive, simple, and low-cost tools for the detection of SARS-CoV-2 in a conventional biosafety level 2 laboratory, offering alternative approaches when commercial kits are unavailable or cost ineffective.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Fatimah Alhamlan", - "author_inst": "King Faisal Specialist Hospital and Research Centre" - }, - { - "author_name": "Ahmed Alqahtani", - "author_inst": "King Faisal Specialist Hospital and Research Centre" - }, - { - "author_name": "Dana Bakheet", - "author_inst": "King Faisal Specialist Hospital and Research Centre" - }, - { - "author_name": "Marie Bohol", - "author_inst": "King Faisal Specialist Hospital and Research Centre" - }, - { - "author_name": "Sahar Althawadi", - "author_inst": "King Faisal Specialist Hospital and Research Centre" - }, - { - "author_name": "Maysoon Mutabagani", - "author_inst": "King Faisal Specialist Hospital and Research Centre" - }, - { - "author_name": "Reem Almaghrabi", - "author_inst": "King Faisal Specialist Hospital and Research Centre" - }, - { - "author_name": "Dalia Obeid", - "author_inst": "King Faisal Specialist Hospital and Research Centre" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.17.20104877", "rel_title": "COVID-19: the key role of pulmonary capillary leakage. An observational cohort study", @@ -1421929,6 +1424921,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.18.20103283", + "rel_title": "Search for asymptomatic carriers of SARS-CoV-2 in healthcare workers during the pandemic: a Spanish experience", + "rel_date": "2020-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20103283", + "rel_abs": "Objectivedetermine the percentage of healthcare workers (HCW) carrying SARS-CoV-2 in high exposure areas of the hospital.\n\nDesigncross-sectional study during April 15-24th in Hospital Costa del Sol (Marbella, Spain), excluding HCW with previous COVID19.\n\nSettinghospital based, focused on patient care areas COVID19.\n\nParticipants498 subjects, 80% women. Participation was offered to all the HCW of Emergencies, Intensive Care and Anesthesia, Internal Medicine and Pneumology. Other units not directly involved in the care of these patients were offered to participate.\n\nInterventionnaso and oropharyngeal PCR determination was performed together with IgG and IgM antibody determination by immunochromatography. On the day of sampling, a health questionnaire was answered, reporting symptoms on the same day and in the previous fourteen days.\n\nMain outcome measurespercentage of HCW with positive PCR for SARS-CoV-2, percentage of HCW with positive IgG for SARS-CoV-2.\n\nResultsTwo individuals were detected with PCR for SARS-CoV-2 positive (0.4%). Both were asymptomatic on the day of sampling, but one of them had had a CoVID-19 compatible picture in the previous two weeks and had positive IgG and IgM; therefore, only one subject was truly asymptomatic carrier (0.2%). 9 workers with positive IgG (1.8%) were detected.\n\nConclusionsthe prevalence of asymptomatic carriers among health workers of the services directly involved in the care of patients with CoVID-19 was very low in our center. This type of strategy can be one more tool in controlling the pandemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Julian Olalla", + "author_inst": "Unidad de Medicina Interna. Hospital Costa del Sol" + }, + { + "author_name": "Ana M Correa", + "author_inst": "Unidad de Microbiologia. Hospital Costa del Sol." + }, + { + "author_name": "Maria Dolores Martin-Escalante", + "author_inst": "Unidad de Medicina Interna. Hospital Costa del Sol." + }, + { + "author_name": "Maria Luisa Hortas", + "author_inst": "Area de Laboratorio. Hospital Costa del Sol." + }, + { + "author_name": "Maria Jesus Martin-Sendarrubias", + "author_inst": "Salud Laboral. Hospital Costa del Sol." + }, + { + "author_name": "Victor Fuentes", + "author_inst": "Medicina Preventiva. Hospital Costa del Sol." + }, + { + "author_name": "Gabriel Sena", + "author_inst": "Unidad de Microbiologia. Hospital Costa del Sol." + }, + { + "author_name": "Javier Garcia-Alegria", + "author_inst": "Unidad de Medicina Interna. Hospital Costa del Sol." + }, + { + "author_name": "ROBLE Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.15.20103531", "rel_title": "IL6 inhibition in critically ill COVID-19 patients is associated with increased secondary infections", @@ -1422066,45 +1425109,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2020.05.16.20104240", - "rel_title": "When Can Elimination of SARS-CoV-2 Infection be Assumed? Simulation Modelling in a Case Study Island Nation", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20104240", - "rel_abs": "AimsWe aimed to determine the length of time from the last detected case of SARS-CoV-2 infection before elimination can be assumed at a country level in an island nation.\n\nMethodsA stochastic version of the SEIR model Covid SIM v1.1 designed specifically for COVID-19 was utilised. It was populated with data for the case study island nation of New Zealand (NZ) along with relevant parameters sourced from the NZ and international literature. This included a testing level for symptomatic cases of 7,800 tests per million people per week.\n\nResultsIt was estimated to take between 27 and 33 days of no new detected cases for there to be a 95% probability of epidemic extinction. This was for effective reproduction numbers (Re) in the range of 0.50 to 1.0, which encompass such controls as case isolation (the shorter durations relate to low Re values). For a 99% probability of epidemic extinction, the equivalent time period was 37 to 44 days. In scenarios with lower levels of symptomatic cases seeking medical attention and lower levels of testing, the time period was up to 53 to 91 days (95% level).\n\nConclusionsIn the context of a high level of testing, a period of around one month of no new notified cases of COVID-19 would give 95% certainty that elimination of SARS-CoV-2 transmission had been achieved.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Nick Wilson", - "author_inst": "University of Otago, Wellington" - }, - { - "author_name": "Matthew Parry", - "author_inst": "University of Otago, Dunedin" - }, - { - "author_name": "Ayesha J Verrall", - "author_inst": "University of Otago, Wellington" - }, - { - "author_name": "Michael G Baker", - "author_inst": "University of Otago, Wellington" - }, - { - "author_name": "Markus Schwehm", - "author_inst": "ExploSYS GmbH" - }, - { - "author_name": "Martin Eichner", - "author_inst": "Epimos GmbH" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.16.20104117", "rel_title": "The role of age distribution, time lag between reporting and death and healthcare system capacity on case fatality estimates of COVID-19", @@ -1423207,6 +1426211,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.19.105445", + "rel_title": "Clinical And Analytical Performance Of An Automated Serological Test That Identifies S1/S2 Neutralizing IgG In Covid-19 Patients Semiquantitatively.", + "rel_date": "2020-05-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.19.105445", + "rel_abs": "BACKGROUNDIn the Covid-19 pandemic, highly selective serological testing is essential to define exposure to SARS-CoV-2 virus. Many tests have been developed, yet with variable speed to first result, and of unknown quality, particularly when considering the prediction of neutralizing capacity.\n\nOBJECTIVES/METHODSThe LIAISON(R) SARS-CoV-2 S1/S2 IgG assay was designed to measure antibodies against the SARS-CoV-2 native S1/S2 proteins in a standardized automated chemiluminescent assay. Clinical and analytical performance of the test were validated in an observational study using residual samples (>1500) with positive or negative Covid-19 diagnosis.\n\nRESULTSThe LIAISON(R) SARS-CoV-2 S1/S2 IgG assay proved highly selective and specific, and offers semiquantitative measures of serum or plasma levels of anti-S1/S2 IgG with neutralizing activity. The diagnostic sensitivity was 91.3% and 95.7% at >5 or [≥]15 days from diagnosis respectively, and 100% when assessed against a neutralizing assay. The specificity ranged between 97% and 98.5%. The average imprecision of the assay was <5 % coefficient of variation. Assay performance at 2 different cut-offs was evaluated to optimize predictive values in settings with different % disease prevalence. CONCLUSIONS. The automated LIAISON(R) SARS-CoV-2 S1/S2 IgG assay brings efficient, sensitive, specific, and precise serological testing to the laboratory, with the capacity to test large amounts of samples per day: first results are available within 35 minutes with a throughput of 170 tests/hour. The test also provides a semiquantitative measure to identify samples with neutralizing antibodies, useful also for a large scale screening of convalescent plasma for safe therapeutic use.\n\nIMPORTANCEWith the worldwide advance of the COVID-19 pandemic, efficient, reliable and accessible diagnostic tools are needed to support public health officials and healthcare providers in their efforts to deliver optimal medical care, and articulate sound demographic policy. DiaSorin has developed an automated serology based assay for the measurement of IgG specific to SARS CoV-2 Spike protein, and tested its clinical performance in collaboration with Italian health care professionals who provided access to large numbers of samples from infected and non-infected individuals. The assay delivers excellent sensitivity and specificity, and is able to identify samples with high levels of neutralizing antibodies. This will provide guidance in assessing the true immune status of subjects, as well as meeting the pressing need to screen donors for high titer convalescent sera for subsequent therapeutic and prophylactic use.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Fabrizio Bonelli", + "author_inst": "DiaSorin" + }, + { + "author_name": "Antonella Sarasini", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Claudia Zierold", + "author_inst": "DiaSorin" + }, + { + "author_name": "Mariella Calleri", + "author_inst": "DiaSorin" + }, + { + "author_name": "Alice Bonetti", + "author_inst": "Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Frank A Blocki", + "author_inst": "DiaSorin" + }, + { + "author_name": "Luca Pallavicini", + "author_inst": "DiaSorin" + }, + { + "author_name": "Alberto Chinali", + "author_inst": "DiaSorin" + }, + { + "author_name": "Daniela Campisi", + "author_inst": "ASST Niguarda Hospital" + }, + { + "author_name": "Elena Percivalle", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Anna Pia DiNapoli", + "author_inst": "Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Carlo Federico Perno", + "author_inst": "University of Milan" + }, + { + "author_name": "Fausto Balldanti", + "author_inst": "Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.05.20.105247", "rel_title": "A replication-competent vesicular stomatitis virus for studies of SARS-CoV-2 spike-mediated cell entry and its inhibition", @@ -1423536,101 +1426607,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.05.20.106294", - "rel_title": "Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures", - "rel_date": "2020-05-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.20.106294", - "rel_abs": "Deep sequencing of B cell receptor (BCR) heavy chains from a cohort of 19 COVID-19 patients from the UK reveals a stereotypical naive immune response to SARS-CoV-2 which is consistent across patients and may be a positive indicator of disease outcome. Clonal expansion of the B cell memory response is also observed and may be the result of memory bystander effects. There was a strong convergent sequence signature across patients, and we identified 777 clonotypes convergent between at least four of the COVID-19 patients, but not present in healthy controls. A subset of the convergent clonotypes were homologous to known SARS and SARS-CoV-2 spike protein neutralising antibodies. Convergence was also demonstrated across wide geographies by comparison of data sets between patients from UK, USA and China, further validating the disease association and consistency of the stereotypical immune response even at the sequence level. These convergent clonotypes provide a resource to identify potential therapeutic and prophylactic antibodies and demonstrate the potential of BCR profiling as a tool to help understand and predict positive patient responses.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Jacob D. Galson", - "author_inst": "Alchemab Therapeutics Ltd" - }, - { - "author_name": "Sebastian Schaetzle", - "author_inst": "Alchemab Therapeutics Ltd" - }, - { - "author_name": "Rachael J.M. Bashford-Rogers", - "author_inst": "Wellcome Centre for Human Genetics" - }, - { - "author_name": "Matthew I.J. Raybould", - "author_inst": "Oxford University" - }, - { - "author_name": "Aleksandr Kovaltsuk", - "author_inst": "Oxford University" - }, - { - "author_name": "Gavin J. Kilpatrick", - "author_inst": "Alchemab Therapeutics Ltd" - }, - { - "author_name": "Ralph Minter", - "author_inst": "Alchemab Therapeutics Ltd" - }, - { - "author_name": "Donna K. Finch", - "author_inst": "Alchemab Therapeutics Ltd" - }, - { - "author_name": "Jorge Dias", - "author_inst": "Alchemab Therapeutics Ltd" - }, - { - "author_name": "Louisa James", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Gavin Thomas", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Wing-Yiu Jason Lee", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Jason Betley", - "author_inst": "Illumina" - }, - { - "author_name": "Olivia Cavlan", - "author_inst": "Alchemab Therapeutics Ltd" - }, - { - "author_name": "Alex Leech", - "author_inst": "Alchemab Therapeutics Ltd" - }, - { - "author_name": "Charlotte M. Deane", - "author_inst": "Oxford University" - }, - { - "author_name": "Carlos Caldas", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Dan Pennington", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Paul Pfeffer", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Jane Osbourn", - "author_inst": "Alchemab Therapeutics Ltd" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.05.20.106658", "rel_title": "Kidney and Lung ACE2 expression after an ACE inhibitor or an Ang II receptor blocker: implications for COVID-19", @@ -1424597,6 +1427573,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.18.20101501", + "rel_title": "The impact of physical distancing measures against COVID-19 transmission on contacts and mixing patterns in the Netherlands: repeated cross-sectional surveys", + "rel_date": "2020-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20101501", + "rel_abs": "BackgroundDuring the current pandemic of coronavirus (COVID-19) many countries have taken drastic measures to reduce transmission of SARS-CoV2. The measures often include physical distancing that aims to reduce the number of contacts in the population. Little is known about the actual reduction in number of contacts as a consequence of physical distancing measures.\n\nMethodsIn the Netherlands, a cross-sectional survey was carried out in 2016/2017 in which 8179 participants retrospectively reported the number, age and gender of different persons they had contacted (spoken to in person or touched) during the previous day. The survey was repeated among 2830 of the original participants, using the same questionnaire, in March and April 2020 after physical distancing measures had been implemented.\n\nResultsThe average number of contacts in the community was reduced from on average 12.5 (interquartile range: 2-17) to 3.7 (interquartile range: 0-4) different persons per participant, a reduction of 71% (95% confidence interval: 71-71). The reduction in the number of community contacts was highest for children and adolescents (between 5 and 20 years) and smallest for elderly persons of 80 years and older. The reduction in the effective number of total contacts, measured as the largest eigenvalue of the matrix with community and household contacts, was 62% (95% confidence interval: 48 - 72).\n\nConclusionThe substantial reduction in contacts has contributed greatly in halting the COVID-19 epidemic. This reduction was unevenly distributed over age groups, household sizes and occupations. These findings offer guidance for the lifting of age-group targeted measures.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jantien A. Backer", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Liesbeth Mollema", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Eric R. A. Vos", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Don Klinkenberg", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Fiona R.M. van der Klis", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Hester E. de Melker", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Susan van den Hof", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Jacco Wallinga", + "author_inst": "National Institute for Public Health and the Environment" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.15.20103077", "rel_title": "Mathematical Modeling and Simulation of SIR Model for COVID-2019 Epidemic Outbreak: A Case Study of India", @@ -1424674,41 +1427697,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.15.20102954", - "rel_title": "A Human-Pathogen SEIR-P Model for COVID-19 Outbreak under different intervention scenarios in Kenya", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20102954", - "rel_abs": "This work describes the mathematical modelling and dynamics of a novel Coronavirus disease 2019 (COVID-19) in Kenya. The mathematical model assumes Human-Human infection as well as Human-Pathogen interaction. Using the SEIR (Susceptible-Exposed-Infected-Recovered) compartmental model with additional component of the pathogen,we simulated the dynamics of COVID-19 outbreak and impact of different control measures. The resulting system of ordinary differential equations (ODEs) are directly solved using a combination of fourth and fifth-order Runge-Kutta methods. Simulation results indicate that non-pharmaceutical measures such as school closure, social distancing and movement restriction emphatically flatten the epidemic peak curve hence leading to a smaller number of overall disease cases.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Viona Nakhulo Ojiambo", - "author_inst": "Jomo Kenyatta University of Agriculture and Technology" - }, - { - "author_name": "Mark Kimathi", - "author_inst": "Machakos University" - }, - { - "author_name": "Samuel Mwalili", - "author_inst": "Jomo Kenyatta University of Agriculture and Technology" - }, - { - "author_name": "Duncan Gathungu", - "author_inst": "Jomo Kenyatta University of Agriculture and Technology" - }, - { - "author_name": "Rachel Mbogo", - "author_inst": "Strathmore University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.16.20104158", "rel_title": "Extended Storage of SARS-CoV2 Nasopharyngeal Swabs Does Not Negatively Impact Results of Molecular-Based Testing", @@ -1426091,6 +1429079,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.13.20100495", + "rel_title": "Risk factors for adverse clinical outcomes in patients with COVID-19: A systematic review and meta-analysis", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100495", + "rel_abs": "ImportanceCOVID-19 is a clinically heterogeneous disease of varying severity and prognosis. Clinical characteristics that impact disease course could offer guidance for clinical decision making and future research endeavors and unveil disease pathways.\n\nObjectiveTo examine risk factors associated with adverse clinical outcomes in patients with COVID-19.\n\nData sourcesWe performed a systematic review in PubMed from January 1 until April 19, 2020.\n\nStudy selectionObservational studies that examined the association of any clinical characteristic with an adverse clinical outcome were considered eligible. We scrutinized studies for potential overlap.\n\nData extraction and synthesisInformation on the effect of clinical factors on clinical endpoints of patients with COVID-19 was independently extracted by two researchers. When an effect size was not reported, crude odds ratios were calculated based on the available information from the eligible articles. Study-specific effect sizes from non-overlapping studies were synthesized applying the random-effects model.\n\nMain outcome and measureThe examined outcomes were severity and progression of disease, admission to ICU, need for mechanical ventilation, mortality, or a composite outcome.\n\nResultsWe identified 88 eligible articles, and we performed a total of 256 meta-analyses on the association of 98 unique risk factors with five clinical outcomes. Seven meta-analyses presented the strongest epidemiological evidence in terms of statistical significance (P-value <0.005), between-study heterogeneity (I2 <50%), sample size (more than 1000 COVID-19 patients), 95% prediction interval excluded the null value, and absence of small-study effects. Elevated C-reactive protein (OR, 6.46; 95% CI, 4.85 - 8.60), decreased lymphocyte count (OR, 4.16; 95% CI, 3.17 - 5.45), cerebrovascular disease (OR, 2.84; 95% CI, 1.55 - 5.20), chronic obstructive pulmonary disease (OR, 4.44; 95% CI, 2.46 - 8.02), diabetes mellitus (OR, 2.04; 95% CI, 1.54 - 2.70), hemoptysis (OR, 7.03; 95% CI, 4.57 - 10.81), and male sex (OR, 1.51; 95% CI, 1.30 - 1.75) were associated with risk of severe COVID-19.\n\nConclusions and relevanceOur results highlight factors that could be useful for prognostic model building, help guide patients selection for randomized clinical trials, as well as provide alternative treatment targets by shedding light to disease pathophysiology.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vanesa Bellou", + "author_inst": "University of Ioannina Medical School" + }, + { + "author_name": "Ioanna Tzoulaki", + "author_inst": "University of Ioannina Medical School" + }, + { + "author_name": "Evangelos Evangelou", + "author_inst": "University of Ioannina Medical School" + }, + { + "author_name": "Lazaros Belbasis", + "author_inst": "University of Ioannina Medical School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.13.20100404", "rel_title": "Clinical characteristics and early outcomes in patients with COVID-19 treated with tocilizumab at a United States academic center", @@ -1426272,45 +1429291,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.13.20100743", - "rel_title": "Detecting the Emergent or Re-Emergent COVID-19 Pandemic in a Country: Modelling Study of Combined Primary Care and Hospital Surveillance", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100743", - "rel_abs": "AimsWe aimed to determine the effectiveness of surveillance using testing for SARS-CoV-2 to identify an outbreak arising from a single case of border control failure at a country level.\n\nMethodsA stochastic version of the SEIR model CovidSIM v1.1 designed specifically for COVID-19 was utilised. It was seeded with New Zealand (NZ) population data and relevant parameters sourced from the NZ and international literature.\n\nResultsFor what we regard as the most plausible scenario with an effective reproduction number of 2.0, the results suggest that 95% of outbreaks from a single imported case would be detected in the period up to day 33 after introduction. At the time point of detection, there would be a median number of 6 infected cases in the community (95%UI: 1-68). To achieve this level of detection, an on-going programme of 7,800 tests per million people per week for the NZ population would be required. The vast majority of this testing (96%) would be of symptomatic cases in primary care settings and the rest in hospitals. Despite the large number of tests required, there are plausible strategies to enhance testing yield and cost-effectiveness eg, (i) adjusting the eligibility criteria via symptom profiles; (ii) and pooling of test samples.\n\nConclusionsThis model-based analysis suggests that a surveillance system with a very high level of routine testing is probably required to detect an emerging or re-emerging SARS-CoV-2 outbreak within one month of a border control failure in a nation.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Nick Wilson", - "author_inst": "University of Otago, Wellington" - }, - { - "author_name": "Markus Schwehm", - "author_inst": "ExploSYS" - }, - { - "author_name": "Ayesha J Verrall", - "author_inst": "University of Otago, Wellington" - }, - { - "author_name": "Matthew Parry", - "author_inst": "University of Otago, Dunedin" - }, - { - "author_name": "Michael G Baker", - "author_inst": "University of Otago, Wellington" - }, - { - "author_name": "Martin Eichner", - "author_inst": "Epimos" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.13.20101089", "rel_title": "Making sense of publicly available data on COVID-19 in Ireland", @@ -1427253,6 +1430233,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.14.20101824", + "rel_title": "Changing travel patterns in China during the early stages of the COVID-19 pandemic", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20101824", + "rel_abs": "Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigated the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020 and discussed their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower access to care. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and have not yet led to structural reorganisation of the transportation network at the time of this study.\n\nOne sentence summaryUnderstanding travel before, during, and after the introduction of travel restrictions in China in response to the COVID-19 Pandemic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Hamish Gibbs", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Yang Liu", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Carl AB Pearson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Christopher I Jarvis", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Chris Grundy", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Billy J Quilty", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Charlie Diamond", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Rosalind M Eggo", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.14.20101873", "rel_title": "COVID Faster R-CNN: A Novel Framework to Diagnose Novel Coronavirus Disease (COVID-19) in X-Ray Images", @@ -1427358,45 +1430385,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.14.20099234", - "rel_title": "Off-Label Real World Experience Using Tocilizumab for Patients Hospitalized with COVID-19 Disease in a Regional Community Health System: A Case-Control Study", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20099234", - "rel_abs": "ObjectiveTo determine if Tocilizumab treatment in patients hospitalized with laboratory confirmed SARS-CoV-2 infection and subsequent COVID-19 disease provides short-term survival benefit.\n\nDesignCase-control, observational study that includes an observation period from arrival to discharge or inpatient death. Both Cox proportional hazards and average treatment effects models were used to determine survival and treatment benefits.\n\nSettingThree Cone Health acute care hospitals including one COVID dedicated facility.\n\nPatientsPatients admitted with confirmed SARS-CoV-2 from March 16, 2020 through April 22, 2020.\n\nExposureTocilizumab dosed at either 400 mg fixed dose or 8 mg/kg weight-based dose with maximum single dose of 800mg.\n\nMeasurements and Main ResultsOverall, 86 patients were admitted during the observation period with confirmed COVID-19 disease. Of these, 21 received Tocilizumab during the hospital stay. Both the Cox model and treatment effects models showed short-term survival benefit. There was an associated 75% reduction in the risk of inpatient death when treated (HR 0.25; 95% CI 0.07-0.90) in the Cox model. This association was confirmed in the treatment effects model where we found a 52.7% reduced risk of dying while hospitalized compared to those not treated (RR 0.472; 95% CI 0.449-0.497). In both models, we show short-term survival benefit in patients with severe COVID-19 illness.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Murali Ramaswamy", - "author_inst": "PulmonIx, LLC and Cone Health Division of Critical Care & Pulmonary Medicine" - }, - { - "author_name": "Praveen Mannam", - "author_inst": "Cone Health Division of Critical Care & Pulmonary Medicine" - }, - { - "author_name": "Robert Comer", - "author_inst": "Cone Health Division of Infectious Diseases Medicine" - }, - { - "author_name": "Emily Sinclair", - "author_inst": "Cone Health Antimicrobial Stewardship Program" - }, - { - "author_name": "Douglas Brent McQuaid", - "author_inst": "Cone Health Division of Critical Care & Pulmonary Medicine" - }, - { - "author_name": "Monica L Schmidt", - "author_inst": "Cone Health Enterprise Analytics" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.05.13.20101113", "rel_title": "Temporal and spatial characteristics of the spread of COVID-19 in Rio de Janeiro state and city", @@ -1428931,6 +1431919,97 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.18.101493", + "rel_title": "SARS-CoV2 infection in farmed mink, Netherlands, April 2020", + "rel_date": "2020-05-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.18.101493", + "rel_abs": "In April 2020, respiratory disease and increased mortality were observed in farmed mink on two farms in the Netherlands. In both farms, at least one worker had been found positive for SARS-CoV-2. Necropsies of the mink revealed interstitial pneumonia, and organ and swab samples tested positive for SARS-CoV-2 RNA by qPCR. Variations in viral genomes point at between-mink transmission on the farms and lack of infection link between the farms. Inhalable dust in the mink houses contained viral RNA, indicating possible exposure of workers.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Nadia Oreshkova", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Robert-Jan Molenaar", + "author_inst": "GD Animal Health, Deventer, The Netherlands" + }, + { + "author_name": "Sandra Vreman", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Frank Harders", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands WBVR" + }, + { + "author_name": "Bas B. Oude Munnink", + "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Renate W. Hakze-vd Honing", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Nora Gerhards", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Paulien Tolsma", + "author_inst": "Regional Public Health Service Brabant-Zuid-Oost, Eindhoven, The Netherlands" + }, + { + "author_name": "Ruth Bouwstra", + "author_inst": "GD Animal Health, Deventer, The Netherlands" + }, + { + "author_name": "Reina Sikkema", + "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Mirriam Tacken", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Myrna M.T. de Rooij", + "author_inst": "Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands" + }, + { + "author_name": "Eefke Weesendorp", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Marc Engelsma", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Christianne Bruschke", + "author_inst": "Ministry of Agriculture, Nature and Food Quality, The Hague, The Netherlands" + }, + { + "author_name": "Lidwien A.M. Smit", + "author_inst": "Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands" + }, + { + "author_name": "Marion Koopmans", + "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Wim H.M. van der Poel", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "JA Stegeman", + "author_inst": "Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, The Netherlands" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.18.102038", "rel_title": "Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2.", @@ -1429164,33 +1432243,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.12.20076794", - "rel_title": "COVID-19 outbreak in Italy: estimation of reproduction numbers over two months toward the Phase 2", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20076794", - "rel_abs": "After two months from the first case in COVID-19 outbreak, Italy counts more than 190,000 confirmed positive cases. From the beginning of April 2020, the nationwide lockdown started to show early effects by reducing the total cumulative incidence reached by the epidemic wave. This allows the government to program the measures to loosen lockdown restrictions for the so called \"Phase 2\". Here we provided the reproduction number estimation both in space and in time from February 24th to April 24th, 2020 across two months into the epidemic. Our estimates suggest basic reproduction number averaged over all the regions of 3.29, confirming that epidemiological figures of the SARS-CoV-2 epidemic in Italy are higher than those observed at the early stage of Wuhan (China) outbreak. Based on the SARS-CoV-2 transmission dynamics reported here, we gave a quantitative evaluation of the efficiency of the government measures to low the reproduction number under the unity (control regime). We estimated that among the worst hit regions in Italy, Lombardy reached the control regime on March 22nd followed by Emilia-Romagna (March 23th), Veneto (March 25th) and Piemonte (March 26th). Overall, we found that the mean value of time to reach the control regime in all the country is about 31 days from the February 24th and about 14 days from the first day of nationwide lockdown (March 12th). Finally, we highlighted the interplay between the reproduction number and two demographic indices in order to probe the \"state of activity\" of the epidemic for each Italian region in the control regime. We believe that this approach can provide a tool in the management of \"Phase 2\", potentially helping in challenging decision to continue, ease or tighten up restrictions.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mattia Allieta", - "author_inst": "independent researcher" - }, - { - "author_name": "Andrea Allieta", - "author_inst": "Universita del Piemonte Orientale A. Avogadro Dipartimento di Medicina Traslazionale Anestesia e Rianimazione" - }, - { - "author_name": "Davide Rossi Sebastiano", - "author_inst": "Neurophysiology Unit , IRCCS-Neurological Institute Carlo Besta" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.08.20090464", "rel_title": "Mining Twitter Data on COVID-19 for Sentiment analysis and frequent patterns Discovery", @@ -1430881,6 +1433933,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.05.14.20096602", + "rel_title": "Decline in Emergent and Urgent Care during the COVID-19 Pandemic", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20096602", + "rel_abs": "Due to the ongoing coronavirus disease (COVID-19) pandemic, there are concerns that patients may be avoiding care for emergent and urgent health conditions due to fear of contagion or as an unintentional consequence of government orders to postpone \"non-essential\" services. We therefore sought to evaluate the effect of the COVID-19 pandemic on the number of patient encounters for select emergent or urgent diagnoses at a large tertiary-care academic medical center in Boston. Inpatient diagnoses included acute myocardial infarction (MI) and stroke, and outpatient but urgent diagnoses included new referrals for breast and hematologic malignancies. For each condition, we used a \"difference-in-differences\" approach to estimate the proportional change in number of encounters during the pandemic (March - April 2020) compared with earlier in the same year (January - February 2020), using equivalent periods in 2019 as a control. After the onset of the pandemic, we observed significant reductions in hospitalizations for MI (difference-in-differences estimate, 0.67; 95%CI, 0.46-0.96; P=0.04) and stroke (difference-in-differences estimate, 0.42; 95%CI, 0.28-0.65; P<0.001) (Table). In the ambulatory setting, there was a reduction in referrals for breast cancer and hematologic cancers, but this did not reach statistical significance until the month after the onset of the pandemic. Our findings suggest an urgent need for public health messaging to ensure that patients continue to seek care for acute emergencies. In addition, decisions by health systems regarding when to reinitiate non-emergent care should carefully factor in the harms of delayed diagnosis and treatment occurring during the COVID-19 pandemic.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Dhruv S Kazi", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Rishi K Wadhera", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Changyu Shen", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Kalon K.L. Ho", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Rushad Patell", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Magdy H. Selim", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "John H. Urwin", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Mark L. Zeidel", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Peter Zimetbaum", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Kevin Tabb", + "author_inst": "Beth Israel Lahey Health, Cambridge, MA" + }, + { + "author_name": "Robert W. Yeh", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.05.11.20098053", "rel_title": "Parasites and their protection against COVID-19- Ecology or Immunology?", @@ -1430998,101 +1434109,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.12.20097105", - "rel_title": "Distributions and risks of SARS-CoV-2 in hospital outdoor environment", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20097105", - "rel_abs": "The outbreak of coronavirus infectious disease-2019 (COVID-19) pandemic has rapidly spread throughout over 200 countries, posing a global threat to human health. Till 15th May 2020, there are over 4.5 million confirmed cases, with roughly 300,000 death1. To date, most studies focus on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in indoor environment owing to its main transmission routes via human respiratory droplets and direct contact2,3. It remains unclear whether SARS-CoV-2 can spill over and impose transmission risks to outdoor environments despite potential threats to people and communities. Here, we investigated the presence of SARS-CoV-2 by measuring viral RNA in 73 samples from outdoor environment of three hospitals in Wuhan. We detected SARS-CoV-2 in soils (205-550 copies/g), aerosols (285-1,130 copies/m3) and wastewaters (255 to 18,744 copies/L) in locations close to hospital departments receiving COVID-19 patients or in wastewater treatment sectors. These findings reveal significant viral spillover in hospital outdoor environments that was possibly caused by respiratory droplets from patients or aerosolized particles from wastewater containing SARS-CoV-2. In contrast, SARS-CoV-2 was not detected in other areas or on surfaces with regular disinfection implemented. Soils may behave as viral warehouse through deposition and serve as a secondary source spreading SARS-CoV-2 for a prolonged time. For the first time, our findings demonstrate that there are high-risk areas in hospital outdoor environments to spread SARS-CoV-2, calling for sealing of wastewater treatment unit and complete sanitation to prevent COVID-19 transmission risks.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Dayi Zhang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Yunfeng Yang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Xia Huang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Jingkun Jiang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Miao Li", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Xian Zhang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Haibo Ling", - "author_inst": "Hubei Academy of Environmental Sciences" - }, - { - "author_name": "Jing Li", - "author_inst": "Hubei Center for Disease Control and Prevention" - }, - { - "author_name": "Yi Liu", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Guanghe Li", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Weiwei Li", - "author_inst": "Hubei Academy of Environmental Sciences" - }, - { - "author_name": "Chuan Yi", - "author_inst": "Hubei Academy of Environmental Sciences" - }, - { - "author_name": "Ting Zhang", - "author_inst": "Hubei Center for Disease Control and Prevention" - }, - { - "author_name": "Yongzhong Jiang", - "author_inst": "Hubei Center for Disease Control and Prevention" - }, - { - "author_name": "Yan Xiong", - "author_inst": "Wuhan Center for Control & Prevention" - }, - { - "author_name": "Zhenyu Hu", - "author_inst": "Wuhan Center for Control & Prevention" - }, - { - "author_name": "Xinzi Wang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Songqiang Deng", - "author_inst": "Research Institute for Environmental Innovation (Tsinghua-Suzhou)" - }, - { - "author_name": "Peng Zhao", - "author_inst": "Research Institute for Environmental Innovation (Tsinghua-Suzhou)" - }, - { - "author_name": "Jiuhui Qu", - "author_inst": "Tsinghua University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.15.20102640", "rel_title": "Forecasting COVID-19 pandemic Severity in Asia", @@ -1432083,6 +1435099,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2020.05.11.20098392", + "rel_title": "Forecasting Covid-19 dynamics in Brazil: a data driven approach", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20098392", + "rel_abs": "This paper has a twofold contribution. The first is a data driven approach for predicting the Covid-19 pandemic dynamics, based on data from more advanced countries. The second is to report and discuss the results obtained with this approach for Brazilian states, as of May 4th, 2020. We start by presenting preliminary results obtained by training an LSTM-SAE network, which are somewhat disappointing. Then, our main approach consists in an initial clustering of the world regions for which data is available and where the pandemic is at an advanced stage, based on a set of manually engineered features representing a countrys response to the early spread of the pandemic. A Modified Auto-Encoder network is then trained from these clusters and learns to predict future data for Brazilian states. These predictions are used to estimate important statistics about the disease, such as peaks. Finally, curve fitting is carried out on the predictions in order to find the distribution that best fits the outputs of the MAE, and to refine the estimates of the peaks of the pandemic. Results indicate that the pandemic is still growing in Brazil, with most states peaks of infection estimated between the 25th of April and the 19th of May 2020. Predicted numbers reach a total of 240 thousand infected Brazilians, distributed among the different states, with Sao Paulo leading with almost 65 thousand estimated, confirmed cases. The estimated end of the pandemics (with 97% of cases reaching an outcome) starts as of May 28th for some states and rests through August 14th, 2020.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Igor Gadelha Pereira", + "author_inst": "Universidade Federal do Rio Grande do Norte" + }, + { + "author_name": "Joris M Guerin", + "author_inst": "Universidade Federal do Rio Grande do Norte" + }, + { + "author_name": "Andouglas Goncalves Silva Jr.", + "author_inst": "Instituto Federal do Rio Grande do Norte" + }, + { + "author_name": "Cosimo Distante", + "author_inst": "CNR" + }, + { + "author_name": "Gabriel Santos Garcia", + "author_inst": "Universidade de Brasilia" + }, + { + "author_name": "Luiz M.G. Goncalves", + "author_inst": "Universidade Federal do Rio Grande do Norte" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.05.11.20098459", "rel_title": "Distinct systems serology features in children, elderly and COVID patients", @@ -1432292,61 +1435347,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.12.20098236", - "rel_title": "Anti-Spike, anti-Nucleocapsid and neutralizing antibodies in SARS-CoV-2 hospitalized patients and asymptomatic carriers", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20098236", - "rel_abs": "ObjectiveThe objective of this study was to monitor the anti-SARS-CoV-2 antibody response in infected patients.\n\nMethodsIn order to assess the time of seroconversion, we used 151 samples from 30 COVID-19 inpatients and monitored the detection kinetics of anti-S1, anti-S2, anti-RBD and anti-N antibodies with in-house ELISAs. We also monitored the presence of neutralizing antibodies in these samples as well as 25 asymptomatic carrier samples using retroviral particles pseudotyped with the spike of the SARS-CoV-2.\n\nResultsWe observed that specific antibodies were detectable in all inpatients two weeks post-symptom onset. The detection of the SARS-CoV-2 Nucleocapsid and RBD was more sensitive than the detection of the S1 or S2 subunits. Neutralizing antibodies reached a plateau two weeks post-symptom onset and then declined in the majority of inpatients. Furthermore, neutralizing antibodies were undetectable in 56% of asymptomatic carriers.\n\nConclusionsOur results raise questions concerning the role played by neutralizing antibodies in COVID-19 cure and protection against secondary infection. They also suggest that induction of neutralizing antibodies is not the only strategy to adopt for the development of a vaccine. Finally, they imply that anti-SARS-CoV-2 neutralizing antibodies should be titrated to optimize convalescent plasma therapy.\n\nHighlightsO_LISpecific antibodies are detectable in 100% COVID-19 inpatients two weeks post-symptom onset.\nC_LIO_LIThe detection of the SARS-CoV-2 Nucleocapsid and Receptor Binding Domain is more sensitive than the detection of the S1 or S2 subunits.\nC_LIO_LINeutralizing antibodies reach a plateau two weeks post-symptom onset and then decline in the majority of inpatients.\nC_LIO_LINeutralizing antibodies are undetectable in the majority of asymptomatic carriers.\nC_LI", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Etienne Brochot", - "author_inst": "CHU Amiens, France" - }, - { - "author_name": "Baptiste Demey", - "author_inst": "CHU Amiens, France" - }, - { - "author_name": "Antoine Touze", - "author_inst": "University of Tours, France" - }, - { - "author_name": "Sandrine Belouzard", - "author_inst": "Center for Infection and Immunity of Lille, France" - }, - { - "author_name": "Jean Dubuisson", - "author_inst": "Center for Infection and Immunity of Lille, France" - }, - { - "author_name": "Jean-Luc Schmit", - "author_inst": "CHU Amiens, France" - }, - { - "author_name": "Gilles Duverlie", - "author_inst": "CHU Amiens, France" - }, - { - "author_name": "Catherine Francois", - "author_inst": "CHU Amiens, France" - }, - { - "author_name": "Sandrine Castelain", - "author_inst": "CHU Amiens, France" - }, - { - "author_name": "Francois Helle", - "author_inst": "University of Picardie Jules Verne, France" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.11.20098202", "rel_title": "Adjusting Coronavirus prevalence estimates for laboratory test kit error", @@ -1433381,6 +1436381,121 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.05.18.099507", + "rel_title": "Afucosylated immunoglobulin G responses are a hallmark of enveloped virus infections and show an exacerbated phenotype in COVID-19", + "rel_date": "2020-05-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.18.099507", + "rel_abs": "IgG antibodies are crucial for protection against invading pathogens. A highly conserved N-linked glycan within the IgG-Fc-tail, essential for IgG function, shows variable composition in humans. Afucosylated IgG variants are already used in anti-cancer therapeutic antibodies for their elevated binding and killing activity through Fc receptors (Fc{gamma}RIIIa). Here, we report that afucosylated IgG which are of minor abundance in humans ([~]6% of total IgG) are specifically formed against surface epitopes of enveloped viruses after natural infections or immunization with attenuated viruses, while protein subunit immunization does not elicit this low fucose response. This can give beneficial strong responses, but can also go awry, resulting in a cytokine-storm and immune-mediated pathologies. In the case of COVID-19, the critically ill show aggravated afucosylated-IgG responses against the viral spike protein. In contrast, those clearing the infection unaided show higher fucosylation levels of the anti-spike protein IgG. Our findings indicate antibody glycosylation as a potential factor in inflammation and protection in enveloped virus infections including COVID-19.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Mads D. Larsen", + "author_inst": "Sanquin Reseach" + }, + { + "author_name": "Erik L de Graaf", + "author_inst": "Sanquin Reseach" + }, + { + "author_name": "Myrthe E. Sonneveld", + "author_inst": "Sanquin Research" + }, + { + "author_name": "H. Rosina Plomp", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Federica Linty", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Remco Visser", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Maximilian Brinkhaus", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Tonci Sustic", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Steven W. deTaeye", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Arthur E.H. Bentlage", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Jan Nouta", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Suvi Natunen", + "author_inst": "Finnish Red Cross Blood Service" + }, + { + "author_name": "Carolien A.M. Koeleman", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Susanna Sainio", + "author_inst": "Finnish Red Cross Blood Service" + }, + { + "author_name": "Neeltje A. Kootstra", + "author_inst": "University of Amsterdam" + }, + { + "author_name": "Philip J.M. Brouwer", + "author_inst": "Amsterdam University Medical Centers" + }, + { + "author_name": "Rogier W. Sanders", + "author_inst": "Amsterdam University Medical Centers" + }, + { + "author_name": "Marit J. van Gils", + "author_inst": "Amsterdam University Medical Centers" + }, + { + "author_name": "Sanne de Bruin", + "author_inst": "Amsterdam University Medical Centers" + }, + { + "author_name": "Alexander P.J. Vlaar", + "author_inst": "Amsterdam University Medical Centers" + }, + { + "author_name": "Amsterdam UMC COVID-19 biobank study group", + "author_inst": "" + }, + { + "author_name": "Hans L. Zaaijer", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Manfred Wuhrer", + "author_inst": "Leiden University Medical Center," + }, + { + "author_name": "C. Ellen van der Schoot", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Gestur Vidarsson", + "author_inst": "Sanquin Research" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.05.12.20099085", "rel_title": "Understanding the indoor pre-symptomatic transmission mechanism of COVID-19", @@ -1433494,45 +1436609,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2020.05.16.099499", - "rel_title": "SARS-CoV-2 amino acid substitutions widely spread in the human population are mainly located in highly conserved segments of the structural proteins", - "rel_date": "2020-05-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.16.099499", - "rel_abs": "The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic offers a unique opportunity to study the introduction and evolution of a pathogen into a completely naive human population. We identified and analysed the amino acid mutations that gained prominence worldwide in the early months of the pandemic. Eight mutations have been identified along the viral genome, mostly located in conserved segments of the structural proteins and showing low variability among coronavirus, which indicated that they might have a functional impact. At the moment of writing this paper, these mutations present a varied success in the SARS-CoV-2 virus population; ranging from a change in the spike protein that becomes absolutely prevalent, two mutations in the nucleocapsid protein showing frequencies around 25%, to a mutation in the matrix protein that nearly fades out after reaching a frequency of 20%.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Marti Cortey", - "author_inst": "Universitat Autonoma de Barcelona Facultat de Veterinaria" - }, - { - "author_name": "Yanli Li", - "author_inst": "Universitat Autonoma de Barcelona, Facultat de Veterinaria" - }, - { - "author_name": "Ivan Diaz", - "author_inst": "Centre de Recerca en Sanitat Animal (CReSA-IRTA-UAB)" - }, - { - "author_name": "Hepzibar Clilverd", - "author_inst": "Universitat Autonoma de Barcelona, Facultat de Veterinaria" - }, - { - "author_name": "Laila Darwich", - "author_inst": "Universitat Autonoma de Barcelona, Facultat de Veterinaria" - }, - { - "author_name": "Enric Mateu", - "author_inst": "Universitat Autonoma de Barcelona, Facultat de Veterinaria" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2020.05.16.088989", "rel_title": "Robust computational design and evaluation of peptide vaccines for cellular immunity with application to SARS-CoV-2", @@ -1434575,6 +1437651,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.14.20102483", + "rel_title": "Early and massive testing saves lives: COVID-19 related infections and deaths in the United States during March of 2020", + "rel_date": "2020-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20102483", + "rel_abs": "To optimize epidemiologic interventions, predictors of mortality should be identified. The US COVID-19 epidemic data -reported up to 3-31-2020- were analyzed using kernel regularized least squares regression. Six potential predictors of mortality were investigated: (i) the number of diagnostic tests performed in testing week I; (ii) the proportion of all tests conducted during week I of testing; (iii) the cumulative number of (test-positive) cases through 3-31-2020, (iv) the number of tests performed/million citizens; (v) the cumulative number of citizens tested; and (vi) the apparent prevalence rate, defined as the number of cases/million citizens. Two metrics estimated mortality: the number of deaths and the number of deaths/million citizens. While both expressions of mortality were predicted by the case count and the apparent prevalence rate, the number of deaths/million citizens was {approx}3.5 times better predicted by the apparent prevalence rate than the number of cases. In eighteen states, early testing/million citizens/population density was inversely associated with the cumulative mortality reported by 31 March, 2020. Findings support the hypothesis that early and massive testing saves lives. Other factors -e.g., population density-may also influence outcomes. To optimize national and local policies, the creation and dissemination of high-resolution geo-referenced, epidemic data is recommended.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "James B. Hittner", + "author_inst": "Department of Psychology, College of Charleston, Charleston, South Carolina, United States of America" + }, + { + "author_name": "Folorunso O. Fasina", + "author_inst": "Food and Agriculture Organization, Dar es Salam, Tanzania" + }, + { + "author_name": "Almira L. Hoogesteijn", + "author_inst": "Human Ecology, Centro de Investigacion y de Estudios Avanzados (CINVESTAV), Merida, Mexico" + }, + { + "author_name": "Renata Piccinini", + "author_inst": "Department of Veterinary Medicine, University of Milan, Milan, Italy" + }, + { + "author_name": "Prakasha Kempaiah", + "author_inst": "Loyola University Chicaco Stritch School of Medicine, Chicago, USA" + }, + { + "author_name": "Stephen D. Smith", + "author_inst": "Institute for Resource Information Science, College of Agriculture, Cornell University, Ithaca, United States of America" + }, + { + "author_name": "Ariel L. Rivas", + "author_inst": "Center for Global Health, Department of Internal Medicine, Medical School, University of New Mexico, Albuquerque, New Mexico, United States of America" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.13.20099614", "rel_title": "Dynamic liver function indexes monitoring and clinical characteristics in three types of COVID-19 patients", @@ -1434776,37 +1437895,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.05.16.097238", - "rel_title": "Mechanistic modeling of the SARS-CoV-2 and immune system interplay unravels design principles for diverse clinicopathological outcomes", - "rel_date": "2020-05-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.16.097238", - "rel_abs": "The disease caused by SARS-CoV-2 is a global pandemic that threatens to bring long-term changes worldwide. Approximately 80% of infected patients are asymptomatic or have mild symptoms such as fever or cough, while rest of the patients have varying degrees of severity of symptoms, with 3-4% mortality rate. Severe symptoms such as pneumonia and Acute Respiratory Distress Syndrome can be caused by tissue damage mostly due to aggravated and unresolved innate and adaptive immune response, often resulting from a cytokine storm. However, the mechanistic underpinnings of such responses remain elusive, with an incomplete understanding of how an intricate interplay among infected cells and cells of innate and adaptive immune system can lead to such diverse clinicopathological outcomes. Here, we use a dynamical systems approach to dissect the emergent nonlinear intra-host dynamics among virally infected cells, the immune response to it and the consequent immunopathology. By mechanistic analysis of cell-cell interactions, we have identified key parameters affecting the diverse clinical phenotypes associated with COVID-19. This minimalistic yet rigorous model can explain the various phenotypes observed across the clinical spectrum of COVID-19, various co-morbidity risk factors such as age and obesity, and the effect of antiviral drugs on different phenotypes. It also reveals how a fine-tuned balance of infected cell killing and resolution of inflammation can lead to infection clearance, while disruptions can drive different severe phenotypes. These results will help further the case of rational selection of drug combinations that can effectively balance viral clearance and minimize tissue damage simultaneously.\n\nSignificance StatementThe SARS-CoV-2 pandemic has already infected millions of people, and thousands of lives have been lost to it. The pandemic has already tested the limits of our public healthcare systems with a wide spectrum of clinicopathological symptoms and outcomes. The mechanistic underpinnings of the resultant immunopathology caused by the viral infection still remains to be elucidated. Here we propose a minimalistic but rigorous description of the interactions of the virus infected cells and the core components of the immune system that can potentially explain such diversity in the observed clinical outcomes. Our proposed framework could enable a platform to determine the efficacy of various treatment combinations and can contributes a conceptual understanding of dynamics of disease pathogenesis in SARS-CoV-2 infections.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Sarthak Sahoo", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Kishore Hari", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Siddharth Jhunjhunwala", - "author_inst": "Indian Institute of Science" - }, - { - "author_name": "Mohit Kumar Jolly", - "author_inst": "Indian Institute of Science" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.05.16.099176", "rel_title": "A comprehensive germline variant and expression analyses of ACE2, TMPRSS2 and SARS-CoV-2 activator FURIN genes from the Middle East: Combating SARS-CoV-2 with precision medicine", @@ -1435973,6 +1439061,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.13.20100370", + "rel_title": "Derivation and validation of a prognostic model for predicting in-hospital mortality in patients admitted with COVID-19 in Wuhan, China: the PLANS (Platelet Lymphocyte Age Neutrophil Sex) model", + "rel_date": "2020-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100370", + "rel_abs": "OBJECTIVETo develop and validate a prognostic model for in-hospital mortality in COVID-19 patients using routinely collected demographic and clinical characteristics.\n\nDESIGNMulticenter, retrospective cohort study.\n\nSETTINGJinyintan Hospital, Union Hospital, and Tongji Hosptial in Wuhan, China.\n\nPARTICIPANTSA pooled derivation cohort of 1008 COVID-19 patients from Jinyintan Hospital, Union Hospital in Wuhan and an external validation cohort of 1031 patients from Tongji Hospital in Wuhan, China.\n\nMAIN OUTCOME MEASURESOutcome of interest was in-hospital mortality, treating discharged alive from hospital as the competing event. Fine-Gray models, using backward elimination for inclusion of predictor variables and allowing non-linear effects of continuous variables, were used to derive a prognostic model for predicting in-hospital mortality among COVID-19 patients. Internal validation was implemented to check model overfitting using bootstrap approach. External validation to a separate hospital was implemented to evaluate the generalizability of the model.\n\nRESULTSThe derivation cohort was a case-mix of mild-to-severe hospitalized COVID-19 patients (n=1008, 43.6% females, median age 55). The final model (PLANS), including five predictor variables of platelet count, lymphocyte count, age, neutrophil count, and sex, had an excellent predictive performance (optimism-adjusted C-index: 0.85, 95% CI: 0.83 to 0.87; averaged calibration slope: 0.95, 95% CI: 0.82 to 1.08). Internal validation showed little overfitting. External validation using an independent cohort (n=1031, 47.8% female, median age 63) demonstrated excellent predictive performance (C-index: 0.87, 95% CI: 0.85 to 0.89; calibration slope: 1.02, 95% CI: 0.92 to 1.12). The averaged predicted survival curves were close to the observed survival curves across patients with different risk profiles.\n\nCONCLUSIONSThe PLANS model based on the five routinely collected demographic and clinical characteristics (platelet count, lymphocyte count, age, neutrophil count, and sex) showed excellent discriminative and calibration accuracy in predicting in-hospital mortality in COVID-19 patients. This prognostic model would assist clinicians in better triaging patients and allocating healthcare resources to reduce COVID-19 fatality.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jiong Li", + "author_inst": "Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine" + }, + { + "author_name": "Yuntao Chen", + "author_inst": "Department of Epidemiology, University Medical Center Groningen, Groningen, The Netherlands" + }, + { + "author_name": "Shujing Chen", + "author_inst": "Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China" + }, + { + "author_name": "Sihua Wang", + "author_inst": "Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" + }, + { + "author_name": "Dingyu Zhang", + "author_inst": "Department of Tuberculosis and Respiratory Disease, Jinyintan Hospital, Wuhan, China" + }, + { + "author_name": "Junfeng Wang", + "author_inst": "Julius Center for Health Science and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands" + }, + { + "author_name": "Douwe Postmus", + "author_inst": "Department of Epidemiology, University Medical Center Groningen, Groningen, The Netherlands" + }, + { + "author_name": "Hesong Zeng", + "author_inst": "Department of Cardiology, Tongji Hospital, School of Medicine, Huazhong University of Science and Technology, Wuhan, China." + }, + { + "author_name": "Guoyou Qin", + "author_inst": "Department of Biostatistics, School of Public Health, and The Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China" + }, + { + "author_name": "Yin Shen", + "author_inst": "Eye Center, Medical Research Institute, Wuhan University Renmin Hospital, Wuhan University, Wuhan, China" + }, + { + "author_name": "Jinjun Jiang", + "author_inst": "Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China" + }, + { + "author_name": "Yongfu Yu", + "author_inst": "Department of Biostatistics, School of Public Health, and The Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.13.20101006", "rel_title": "Loss of Taste and Smell as Distinguishing Symptoms of COVID-19", @@ -1436190,69 +1439341,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.14.20102491", - "rel_title": "COVID-19 infection results in alterations of the kynurenine pathway and fatty acid metabolism that correlate with IL-6 levels and renal status", - "rel_date": "2020-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20102491", - "rel_abs": "Previous studies suggest a role for systemic reprogramming of host metabolism during viral pathogenesis to fuel rapidly expanding viral proliferation, for example by providing free amino acids and fatty acids as building blocks. In addition, general alterations in metabolism can provide key understanding of pathogenesis. However, little is known about the specific metabolic effects of SARS-COV-2 infection. The present study evaluated the serum metabolism of COVID-19 patients (n=33), identified by a positive nucleic acid test of a nasopharyngeal swab, as compared to COVID-19-negative control patients (n=16). Targeted and untargeted metabolomics analyses specifically identified alterations in the metabolism of tryptophan into the kynurenine pathway, which is well-known to be involved in regulating inflammation and immunity. Indeed, the observed changes in tryptophan metabolism correlated with serum interleukin-6 (IL-6) levels. Metabolomics analysis also confirmed widespread dysregulation of nitrogen metabolism in infected patients, with decreased circulating levels of most amino acids, except for tryptophan metabolites in the kynurenine pathway, and increased markers of oxidant stress (e.g., methionine sulfoxide, cystine), proteolysis, and kidney dysfunction (e.g., creatine, creatinine, polyamines). Increased circulating levels of glucose and free fatty acids were also observed, consistent with altered carbon homeostasis in COVID-19 patients. Metabolite levels in these pathways correlated with clinical laboratory markers of inflammation and disease severity (i.e., IL-6 and C-reactive protein) and renal function (i.e., blood urea nitrogen). In conclusion, this initial observational study of the metabolic consequences of COVID-19 infection in a clinical cohort identified amino acid metabolism (especially kynurenine and cysteine/taurine) and fatty acid metabolism as correlates of COVID-19, providing mechanistic insights, potential markers of clinical severity, and potential therapeutic targets.\n\nKey pointsO_LIMetabolism of tryptophan into the kynurenine pathway is increased in COVID-19 patients\nC_LIO_LICOVID-19 infection is significantly associated with dysregulated nitrogen and carbon metabolism\nC_LIO_LICOVID-19 infection induces increased circulating levels of free fatty acids and glucose\nC_LI", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Tiffany Thomas", - "author_inst": "Columbia University, New York, NY, USA" - }, - { - "author_name": "Davide Stefanoni", - "author_inst": "University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA" - }, - { - "author_name": "Julie A Reisz", - "author_inst": "University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA" - }, - { - "author_name": "Travis Nemkov", - "author_inst": "University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA" - }, - { - "author_name": "Lorenzo Bertolone", - "author_inst": "University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA" - }, - { - "author_name": "Richard O Francis", - "author_inst": "Columbia University, New York, NY, USA" - }, - { - "author_name": "Krystalyn E Hudson", - "author_inst": "Columbia University, New York, NY, USA" - }, - { - "author_name": "James C Zimring", - "author_inst": "University of Virginia, Charlottesville, VA, USA" - }, - { - "author_name": "Kirk C Hansen", - "author_inst": "University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA" - }, - { - "author_name": "Eldad A Hod", - "author_inst": "Columbia University, New York, NY, USA" - }, - { - "author_name": "Steven L Spitalnik", - "author_inst": "Columbia University, New York, NY, USA" - }, - { - "author_name": "Angelo D'Alessandro", - "author_inst": "University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.13.20101071", "rel_title": "Estimation of the true infection rate and infection fatality rate of COVID-19 in the whole population of each country", @@ -1437719,6 +1440807,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.11.20095158", + "rel_title": "SARS-CoV-2 antibody seroprevalence in industry workers in Split-Dalmatia and Sibenik-Knin County, Croatia", + "rel_date": "2020-05-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20095158", + "rel_abs": "BACKGROUNDAs a result of global spread, COVID-19 has also affected the Republic of Croatia in the last week of February. Although official data show that the number of newly infected is declining, it is still unknown what proportion of the population has been affected by the disease.\n\nAIMTo examine seroprevalence of SARS-CoV-2 antibodies in industry workers population sample.\n\nMETHODSFrom 23 to 28 April 2020, we conducted serological testing for antibodies (IgG and IgM) on 1494 factory employees living in the Split-Dalmatia and [S]ibenik-Knin County (Croatia). We analysed antibody seroprevalence on the level of the company, county, and separately for employees living at the factory premises with limited mobility during the lockdown measures.\n\nRESULTSIn a total sample of tested company employees, we detected antibodies in 1.27% of participants (95% CI 0.77-1.98%). In Split facility 13/1316 (0.99%, 95% CI 0.53-1.68%) of participants were tested positive, of which 13/1079 (1.20%, 95% CI 0.64-2.05%) of those living outside the facility and 0/237 (0%, 95% CI 0-1.26%) of those living inside the facility. In Knin facility, 6/178 (3.37%, 95% CI 1.25-7.19%) participants were tested positive for antibodies. The difference between Split (no mobility restrictions) and Knin, was not statistically significant ({chi}2 = 3.47, P = 0.062).\n\nCONCLUSIONSThe study showed relatively small SARS-CoV-2 antibody seroprevalence in the DIV Group population sample. When the study findings are interpreted on the county levels, they could indicate that most of the counties population was not exposed to the virus.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ivan Jerkovic", + "author_inst": "University Department of Forensic Sciences University of Split" + }, + { + "author_name": "Toni Ljubic", + "author_inst": "University Department of Forensic Sciences University of Split" + }, + { + "author_name": "Zeljana Basic", + "author_inst": "University Department of Forensic Sciences" + }, + { + "author_name": "Ivana Kruzic", + "author_inst": "University Deparment ofForensic Sciences" + }, + { + "author_name": "Nenad Kunac", + "author_inst": "Clinical Department for Pathology, Forensic Medicine and Cytology, University Hospital Center Split" + }, + { + "author_name": "Josko Bezic", + "author_inst": "Clinical Department for Pathology, Forensic Medicine and Cytology, University Hospital Center Split" + }, + { + "author_name": "Arijana Vuko", + "author_inst": "Clinical Department for Pathology, Forensic Medicine and Cytology, University Hospital Center Split" + }, + { + "author_name": "Alemka Markotic", + "author_inst": "Dr. Fran Mihaljevic University Hospital for Infectious Diseases, Zagreb, Croatia; Catholic University of Croatia, Zagreb, Croatia; University of Rijeka School o" + }, + { + "author_name": "Simun Andjelinovic", + "author_inst": "Clinical Department for Pathology, Forensic Medicine and Cytology, University Hospital Center Split, Split, Croatia; University of Split, School of Medicine, Sp" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.10.20097543", "rel_title": "Estimating the extent of true asymptomatic COVID-19 and its potential for community transmission: systematic review and meta-analysis", @@ -1437804,20 +1440943,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.15.077313", - "rel_title": "CoV-AbDab: the Coronavirus Antibody Database", - "rel_date": "2020-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.15.077313", - "rel_abs": "The emergence of a novel strain of betacoronavirus, SARS-CoV-2, has led to a pandemic that has been associated with hundreds of thousands of deaths. Research is ongoing around the world to create vaccines and therapies to minimise rates of disease spread and mortality. Crucial to these efforts are molecular characterisations of neutralising antibodies to SARS-CoV-2. Such antibodies would be valuable for measuring vaccine efficacy, diagnosing exposure, and developing effective biotherapeutics. Here, we describe our new database, CoV-AbDab, which already contains data on over 380 published/patented antibodies and nanobodies known to bind to at least one betacoronavirus. This database is the first consolidation of antibodies known to bind SARS-CoV-2 and other betacoronaviruses such as SARS-CoV-1 and MERS-CoV. We supply relevant metadata such as evidence of cross-neutralisation, antibody/nanobody origin, full variable domain sequence (where available) and germline assignments, epitope region, links to relevant PDB entries, homology models, and source literature. Our preliminary analysis exemplifies a spectrum of potential applications for the database, including identifying characteristic germline usage biases in receptor-binding domain antibodies and contextualising the diagnostic value of the SARS-CoV binding CDRH3s through comparison to over 500 million antibody sequences from SARS-CoV serologically naive individuals. Community submissions are invited to ensure CoV-AbDab is efficiently updated with the growing body of data analysing SARS-CoV-2. CoV-AbDab is freely available and downloadable on our website at http://opig.stats.ox.ac.uk/webapps/coronavirus.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.05.09.20096800", "rel_title": "Estimation of the incubation period of SARS-CoV-2 in Vietnam", @@ -1439316,6 +1442441,45 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.05.14.097204", + "rel_title": "Expression of ACE2 and TMPRSS2 proteins in the upper and lower aerodigestive tracts of rats", + "rel_date": "2020-05-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.097204", + "rel_abs": "Objective Patients with coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), exhibit not only respiratory symptoms but also symptoms of chemo-sensitive disorders and kidney failure. Cellular entry of SARS-CoV-2 depends on the binding of its spike protein to a cellular receptor named angiotensin-converting enzyme 2 (ACE2), and the subsequent spike protein-priming by host cell proteases, including transmembrane protease serine 2 (TMPRSS2). Thus, high expression of ACE2 and TMPRSS2 are considered to enhance the invading capacity of SARS-CoV-2.Methods To elucidate the underlying histological mechanisms of the aerodigestive disorders caused by SARS-CoV-2, we investigated the expression of ACE2 and TMPRSS2 proteins in the aerodigestive tracts of the tongue, hard palate with partial nasal tissue, larynx with hypopharynx, trachea, esophagus, lung, and kidney of rats through immunohistochemistry.Results Strong co-expression of ACE2 and TMPRSS2 proteins was observed in the nasal respiratory epithelium, trachea, bronchioles, alveoli, kidney, and taste buds of the tongue. Remarkably, TMPRSS2 expression was much stronger in the peripheral alveoli than in the central alveoli. These results coincide with the reported clinical symptoms of COVID-19, such as the loss of taste, loss of olfaction, respiratory dysfunction, and acute nephropathy.Conclusions A wide range of organs have been speculated to be affected by SARS-CoV-2 depending on the expression levels of ACE2 and TMPRSS2. Differential distribution of TMPRSS2 in the lung indicated the COVID-19 symptoms to possibly be exacerbated by TMPRSS2 expression. This study might provide potential clues for further investigation of the pathogenesis of COVID-19.Level of Evidence NACompeting Interest StatementThe authors have declared no competing interest.View Full Text", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Rumi Ueha", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Taku Sato", + "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" + }, + { + "author_name": "Takao Goto", + "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" + }, + { + "author_name": "Akihito Yamauchi", + "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" + }, + { + "author_name": "Kenji Kondo", + "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" + }, + { + "author_name": "Tatsuya Yamasoba", + "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.05.15.097501", "rel_title": "Traffic-derived particulate matter and angiotensin-converting enzyme 2 expression in human airway epithelial cells", @@ -1439421,89 +1442585,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.15.096719", - "rel_title": "IgA MAb blocks SARS-CoV-2 Spike-ACE2 interaction providing mucosal immunity", - "rel_date": "2020-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.15.096719", - "rel_abs": "COVID-19 caused by SARS-CoV-2 has become a global pandemic requiring the development of interventions for the prevention or treatment to curtail mortality and morbidity. No vaccine to boost mucosal immunity or as a therapeutic has yet been developed to SARS-CoV-2. In this study we discover and characterize a cross-reactive human IgA monoclonal antibody, MAb362. MAb362 binds to both SARS-CoV and SARS-CoV-2 spike proteins and competitively blocks hACE2 receptor binding, by completely overlapping the hACE2 structural binding epitope. Furthermore, MAb362 IgA neutralizes both pseudotyped SARS-CoV and SARS-CoV-2 in human epithelial cells expressing hACE2. SARS-CoV-2 specific IgA antibodies, such as MAb362, may provide effective immunity against SARS-CoV-2 by inducing mucosal immunity within the respiratory system, a potentially critical feature of an effective vaccine.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Monir Ejemel", - "author_inst": "MassBiologics of the University of Massachusetts Medical School, Boston, Massachusetts, USA" - }, - { - "author_name": "Qi Li", - "author_inst": "MassBiologics of the University of Massachusetts Medical School, Boston, Massachusetts, USA" - }, - { - "author_name": "Shurong Hou", - "author_inst": "Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA" - }, - { - "author_name": "Zachary A. Schiller", - "author_inst": "MassBiologics of the University of Massachusetts Medical School, Boston, Massachusetts, USA" - }, - { - "author_name": "Aaron L. Wallace", - "author_inst": "MassBiologics of the University of Massachusetts Medical School, Boston, Massachusetts, USA" - }, - { - "author_name": "Alla Amcheslavsky", - "author_inst": "MassBiologics of the University of Massachusetts Medical School, Boston, Massachusetts, USA" - }, - { - "author_name": "Nese Kurt Yilmaz", - "author_inst": "Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA" - }, - { - "author_name": "Jacqueline R. Toomey", - "author_inst": "MassBiologics of the University of Massachusetts Medical School, Boston, Massachusetts, USA" - }, - { - "author_name": "Ryan Schneider", - "author_inst": "MassBiologics of the University of Massachusetts Medical School, Boston, Massachusetts, USA" - }, - { - "author_name": "Brianna J. Close", - "author_inst": "National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA" - }, - { - "author_name": "Da-Yuan Chen", - "author_inst": "National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA" - }, - { - "author_name": "Hashan L. Conway", - "author_inst": "National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA" - }, - { - "author_name": "Mohsan Saeed", - "author_inst": "National Emerging Infectious Diseases Laboratories, Boston University, Boston, Massachusetts, USA" - }, - { - "author_name": "Lisa A. Cavacini", - "author_inst": "MassBiologics of the University of Massachusetts Medical School, Boston, Massachusetts, USA" - }, - { - "author_name": "Mark S. Klempner", - "author_inst": "MassBiologics of the University of Massachusetts Medical School, Boston, Massachusetts, USA" - }, - { - "author_name": "Celia A. Schiffer", - "author_inst": "Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA" - }, - { - "author_name": "Yang Wang", - "author_inst": "MassBiologics of the University of Massachusetts Medical School, Boston, Massachusetts, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.14.097287", "rel_title": "Recommendations for sample pooling on the Cepheid GeneXpert(R) system using the Cepheid Xpert(R) Xpress SARS-CoV-2 assay", @@ -1441294,6 +1444375,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.14.096081", + "rel_title": "Crystal structures of SARS-CoV-2 ADP-ribose phosphatase (ADRP): from the apo form to ligand complexes", + "rel_date": "2020-05-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.096081", + "rel_abs": "Among 15 nonstructural proteins (Nsps), the newly emerging SARS-CoV-2 encodes a large, multidomain Nsp3. One of its units is ADP-ribose phosphatase domain (ADRP, also known as macrodomain) which is believed to interfere with the host immune response. Such a function appears to be linked to the proteins ability to remove ADP-ribose from ADP-ribosylated proteins and RNA, yet the precise role and molecular targets of the enzyme remains unknown. Here, we have determined five, high resolution (1.07 - 2.01 [A]) crystal structures corresponding to the apo form of the protein and complexes with 2-(N-morpholino)ethanesulfonic acid (MES), AMP and ADPr. We show that the protein undergoes conformational changes to adapt to the ligand in a manner previously observed before for in close homologs from other viruses. We also identify a conserved water molecule that may participate in hydrolysis. This work builds foundations for future structure-based research of the ADRP, including search for potential antiviral therapeutics.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Karolina Michalska", + "author_inst": "Argonne National Laboratory/University of Chicago" + }, + { + "author_name": "Youngchang Kim", + "author_inst": "Argonne National Laboratory/University of Chicago" + }, + { + "author_name": "Robert Jedrzejczak", + "author_inst": "Argonne National Laboratory/University of Chicago" + }, + { + "author_name": "Natalia I. Maltseva", + "author_inst": "Argonne National Laboratory/University of Chicago" + }, + { + "author_name": "Lucy Stols", + "author_inst": "University of Chicago" + }, + { + "author_name": "Michael Endres", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Andrzej Joachimiak", + "author_inst": "Argonne National Laboratory" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.05.14.092767", "rel_title": "ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study", @@ -1441399,85 +1444523,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.05.11.20097808", - "rel_title": "Prevalence of Hospital PCR Confirmed Covid-19 Cases in Patients with Chronic Inflammatory and Autoimmune Rheumatic Diseases", - "rel_date": "2020-05-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20097808", - "rel_abs": "BackgroundThe susceptibility of patients with rheumatic diseases, and the risks or benefits of immunosuppressive therapies for COVID-19 are unknown.\n\nMethodsWe performed a retrospective study with patients under follow-up in rheumatology departments from seven hospitals in Spain. We matched updated databases of rheumatology patients with SARS-CoV-2 positive PCR tests performed in the hospital to the same reference populations. Rates of PCR+ confirmed COVID-19 were compared among groups.\n\nResultsPatients with chronic inflammatory diseases had 1.32-fold higher prevalence of hospital PCR+ COVID-19 than the reference population (0.76% vs 0.58%). Systemic autoimmune or immune mediated diseases (AI/IMID) patients showed a significant increase, whereas inflammatory arthritis (IA) or systemic lupus erythematosus (SLE) patients did not. COVID-19 cases in some but not all diagnostic groups had older ages than cases in the reference population. IA patients on targeted-synthetic or biological disease-modifying antirheumatic drugs (ts/bDMARD), but not those on conventional-synthetic (csDMARD), had a greater prevalence despite a similar age distribution.\n\nConclusionPatients with AI/IMID show a variable risk of hospital diagnosed COVID-19. Interplay of aging, therapies, and disease specific factors seem to contribute. These data provide a basis to improve preventive recommendations to rheumatic patients and to analyze the specific factors involved in COVID-19 susceptibility.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Jos\u00e9 L. Pablos", - "author_inst": "Servicio de Reumatologia, Instituto de Investigacion Hospital 12 de Octubre (imas12), Universidad Complutense de Madrid, Madrid, Spain." - }, - { - "author_name": "Lydia Abasolo-Alc\u00e1zar", - "author_inst": "Servicio de Reumatologia, Hospital Cl\u00ednico San Carlos, Instituto de Investigacion Sanitaria San Carlos (IdISSC), Madrid, Spain." - }, - { - "author_name": "Jos\u00e9 M. \u00c1lvaro-Gracia", - "author_inst": "Servicio de Reumatologia, Hospital General Universitario Gregorio Mara\u00f1on, Instituto de Investigacion Sanitaria Gregorio Mara\u00f1on (IiSGM), Madrid, Spain." - }, - { - "author_name": "Francisco J. Blanco", - "author_inst": "Servicio de Reumatologia, INIBIC-Complejo Hospitalario Universitario A Coru\u00f1a, Universidad de A Coru\u00f1a, A Coru\u00f1a, Spain." - }, - { - "author_name": "Ricardo Blanco", - "author_inst": "Servicio de Reumatologia, Hospital Universitario Marqu\u00e9s de Valdecilla-IDIVAL, Santander, Spain." - }, - { - "author_name": "Isabel Castrej\u00f3n", - "author_inst": "Servicio de Reumatologia, Hospital General Universitario Gregorio Mara\u00f1on, Instituto de Investigacion Sanitaria Gregorio Mara\u00f1on (IiSGM), Madrid, Spain." - }, - { - "author_name": "David Fern\u00e1ndez-Fern\u00e1ndez", - "author_inst": "Servicio de Reumatologia, Hospital Cl\u00ednico Universitario de Santiago, Instituto de Investigacion Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain." - }, - { - "author_name": "Benjam\u00edn Fern\u00e1ndez-Gutierrez", - "author_inst": "Servicio de Reumatologia, Hospital Cl\u00ednico San Carlos, Instituto de Investigacion Sanitaria San Carlos (IdISSC), Madrid, Spain." - }, - { - "author_name": "Mar\u00eda Galindo", - "author_inst": "Servicio de Reumatologia, Instituto de Investigacion Hospital 12 de Octubre (imas12), Universidad Complutense de Madrid, Madrid, Spain." - }, - { - "author_name": "Miguel A. Gonz\u00e1lez-Gay", - "author_inst": "Servicio de Reumatologia, Hospital Universitario Marqu\u00e9s de Valdecilla-IDIVAL, Santander, Spain." - }, - { - "author_name": "Sara Manrique-Arija", - "author_inst": "UGC de Reumatologia, Hospital Regional Universitario de M\u00e1laga, Instituto de Investigacion Biom\u00e9dica de M\u00e1laga (IBIMA), M\u00e1laga, Spain." - }, - { - "author_name": "Natalia Mena-V\u00e1zquez", - "author_inst": "UGC de Reumatologia, Hospital Regional Universitario de M\u00e1laga, Instituto de Investigacion Biom\u00e9dica de M\u00e1laga (IBIMA), M\u00e1laga, Spain." - }, - { - "author_name": "Antonio Mera-Varela", - "author_inst": "Servicio de Reumatologia, Hospital Cl\u00ednico Universitario de Santiago, Instituto de Investigacion Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain." - }, - { - "author_name": "Miriam Retuerto", - "author_inst": "Servicio de Reumatologia, Instituto de Investigacion Hospital 12 de Octubre (imas12), Universidad Complutense de Madrid, Madrid, Spain." - }, - { - "author_name": "\u00c1lvaro Seijas-Lopez", - "author_inst": "Servicio de Reumatologia, INIBIC-Complejo Hospitalario Universitario A Coru\u00f1a, Universidad de A Coru\u00f1a, A Coru\u00f1a, Spain." - }, - { - "author_name": "- RIER investigators group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "rheumatology" - }, { "rel_doi": "10.1101/2020.05.11.20098004", "rel_title": "COVID-19 Pandemic in Pakistan: Stages and Recommendations", @@ -1442672,6 +1445717,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.05.10.20097154", + "rel_title": "The Estimated Time-Varying Reproduction Numbers during the Ongoing Pandemic of the Coronavirus Disease 2019 (COVID-19) in 12 Selected Countries outside China", + "rel_date": "2020-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20097154", + "rel_abs": "BackgroundHow can we anticipate the progression of the ongoing pandemic of the coronavirus disease 2019 (COVID-19)? As a measure of transmissibility, we aimed to estimate concurrently the time-varying reproduction number, R0(t), over time during the COVID-19 pandemic for each of the following 12 heavily-attacked countries: Singapore, South Korea, Japan, Iran, Italy, Spain, Germany, France, Belgium, United Kingdom, the United States of America, and South Africa.\n\nMethodsWe downloaded the publicly available COVID-19 pandemic data from the WHO COVID-19 Dashboard website (https://covid19.who.int/) for the duration of January 11, 2020 and May 1, 2020. Then, we specified two plausible distributions of serial interval to apply the novel estimation method implemented in the incidence and EpiEstim packages to the data of daily new confirmed cases for robustly estimating R0(t) in the R software.\n\nResultsWe plotted the epidemic curves of daily new confirmed cases for the 12 selected countries. A clear peak of the epidemic curve appeared in 10 of the 12 selected countries at various time points, and then the epidemic curve declined gradually. However, the United States of America and South Africa happened to have two or more peaks and their epidemic curves either reached a plateau or still climbed up. Almost all curves of the estimated R0(t) monotonically went down to be less than or close to 1.0 up to April 30, 2020 except Singapore, South Korea, Japan, Iran, and South Africa, of which the curves surprisingly went up and down at various time periods during the COVID-19 pandemic. Finally, the United States of America and South Africa were the two countries with the approximate R0(t) [≥] 1.0 at the end of April, and thus they were now facing the harshest battles against the coronavirus among the 12 selected countries. By contrast, Spain, Germany, and France with smaller values of the estimated R0(t) were relatively better than the other 9 countries.\n\nConclusionSeeing the estimated R0(t) going downhill speedily is more informative than looking for the drops in the daily number of new confirmed cases during an ongoing epidemic of infectious disease. We urge public health authorities and scientists to estimate R0(t) routinely during an epidemic of infectious disease and to report R0(t) daily to the public until the end of the epidemic.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Fu-Chang Hu", + "author_inst": "National Taiwan University, College of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.12.091314", "rel_title": "Meta-analysis of transcriptomes of SARS-Cov2 infected human lung epithelial cells identifies transmembrane serine proteases co-expressed with ACE2 and biological processes related to viral entry, immunity, inflammation and cellular stress.", @@ -1442789,73 +1445853,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.08.20094755", - "rel_title": "Beneficial effect of corticosteroids in severe COVID-19 pneumonia: a propensity score matching analysis.", - "rel_date": "2020-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20094755", - "rel_abs": "BackgroundSince December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), responsible for Coronavirus Disease 2019 (COVID-19), is spreading worldwide, causing significant morbidity and mortality. No specific treatment has yet clearly shown to improve the diseases evolution. Validated therapeutic options are urgently needed.\n\nMethodsIn this retrospective study, we aimed to evaluate determinants of the prognosis of the disease in 70 patients with COVID-19 severe pneumonia (i.e. requiring at least 3 liters of oxygen) hospitalized between 10 March and 9 April, 2020, in the Centre Hospitalier Alpes Leman, France. The main outcome was oro-tracheal intubation and the exposure of interest was corticotherapy. Since this was not a randomized trial, we used propensity score matching to estimate average treatment effect.\n\nResultsThere was evidence that corticotherapy lowered the risk of intubation with a risk difference of -47.1% (95% confidence interval -71.8% to -22.5%).\n\nConclusionCorticosteroid, a well-known, easily available, and cheap treatment, could be an important tool in management of severe COVID-19 patients with respiratory failure. Not only could it provide an individual benefit, but also, in the setting of the COVID-19 ongoing pandemic, lower the burden on our vulnerable healthcare systems.\n\nKey pointsBy propensity score matching analysis, the average treatment effect of corticosteroids on 70 patients with severe COVID-19 pneumonia was estimated. Corticosteroid therapy lowered the risk of intubation with a risk difference of -47.1% (95% confidence interval -71.8% to -22.5%).", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Tomasz Chroboczek", - "author_inst": "Centre Hospitalier Alpes Leman" - }, - { - "author_name": "Marie Lacoste", - "author_inst": "Centre Hospitalier Alpes Leman" - }, - { - "author_name": "Chloe Wackenheim", - "author_inst": "Centre Hospitalier Alpes Leman" - }, - { - "author_name": "Thibaut Challan-Belval", - "author_inst": "Centre Hospitalier Alpes Leman" - }, - { - "author_name": "Benjamin Amar", - "author_inst": "Centre Hospitalier Alpes Leman" - }, - { - "author_name": "Thomas Boisson", - "author_inst": "Centre Hospitalier Alpes Leman" - }, - { - "author_name": "Jason Hubac", - "author_inst": "Centre Hospitalier Alpes Leman" - }, - { - "author_name": "Dominique Leduc", - "author_inst": "Centre Hospitalier Alpes Leman" - }, - { - "author_name": "Colleen Masse", - "author_inst": "Centre Hospitalier Alpes Leman" - }, - { - "author_name": "Victor Dechaene", - "author_inst": "Centre Hospitalier Alpes Leman" - }, - { - "author_name": "Laetitia Touhiri-Maximin", - "author_inst": "Centre Hospitalier Alpes Leman" - }, - { - "author_name": "Sandrine Megessier", - "author_inst": "Centre Hospitalier Alpes Leman" - }, - { - "author_name": "Camille Lassale", - "author_inst": "Hospital del Mar Medical Research Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.05.20092452", "rel_title": "Identification of Immune complement function as a determinant of adverse SARS-CoV-2 infection outcome", @@ -1444110,6 +1447107,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.09.20096420", + "rel_title": "Timing of non-pharmaceutical interventions to mitigate COVID-19 transmission and their effects on mobility: A cross-country analysis", + "rel_date": "2020-05-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096420", + "rel_abs": "Non-pharmaceutical interventions (NPIs) that encourage physical distancing can decrease and delay the transmission of COVID-19. They have been implemented globally during the pandemic, however, the specific NPIs implemented and the timing of interventions has varied widely. We validated two published datasets on the implementation of NPIs globally. The health and socioeconomic factors associated with delay in implementation of NPIs was analyzed using fractional logit and probit models, and beta regression models. The probability of timely NPI implementation by a country was analyzed using a probit model. The effects of these interventions on mobility changes using Google social mobility reports, were analyzed with propensity score matching methods. Three NPIs were analyzed: national school closure, national lockdown, and global travel ban. Countries with higher incomes, larger populations, and better health preparedness measures had greater delays in implementation. Countries with greater population density, more democratic political systems, lower case detection capacity, and later arrival of first cases were more likely to implement NPIs. Implementation of lockdowns significantly reduced physical mobility. Mobility was further reduced when lockdowns were enforced with curfews or fines, or were more strictly defined. National school closures did not significantly change mobility. The implementation of NPIs is a global public good during pandemics, and the international community needs to address constraints and design incentives so countries implement NPIs in a timely manner. Further analysis is needed on the effect of NPI variations on mobility and transmission, and their associated costs.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Amit Summan", + "author_inst": "Center for Disease Dynamics, Economics, and Policy" + }, + { + "author_name": "Arindam Nandi", + "author_inst": "The Center for Disease Dynamics, Economics & Policy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.09.20096099", "rel_title": "Healthcare workers preparedness for COVID-19 pandemic in the occupied Palestinian territory: a cross-sectional survey", @@ -1444231,45 +1447251,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.09.20096255", - "rel_title": "Effect of preventive actions and health care factors in controlling the outbreaks of COVID-19 pandemic", - "rel_date": "2020-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096255", - "rel_abs": "With the insurgence of the COVID-19 pandemic, a large number of people died in the past several months, and the situation is ongoing with increasing health, social and economic panic and vulnerability. Due to the lack of drugs and prophylaxis against COVID-19, most of the countries are now relying on maintaining social distance as preventative actions. However, this social distancing can create global socio-economic crisis and psychological disorders. Therefore, these control measures need to have an assessment to evaluate their value in containing the situation. In this study, we analyzed the outcome of COVID-19 in response to different control measures, health care facilities, and prevalent diseases. Based on our findings, the number of COVID-19 deaths found to be reduced with increased medical personnel and hospital beds. We found 0.23, 0.16, and 0.21 as the measurement of significant non-linear relationship between COVID-19 case fatality and number of physicians (p-value [≤] 7.1x10-6), nurses and midwives (p-value [≤] 4.6x10-3), and hospital beds (p-value [≤] 1.9x10-2). Importantly, we observed a significant correlation between the reduction of COVID-19 cases and the earliness of preventive initiation. As a result, enhancing health care facilities as well as imposing the control measures in a short time could be valuable to prevent the currently raging COVID-19 pandemic. The apathy of taking nation-wide immediate precaution measure has identified as one of the critical reasons to make the circumstances worst. Notably, countries including Gambia, Nicaragua, Burundi, Namibia, and Nepal have marked in a state of danger. Interestingly, no association between the comorbidities and severity of COVID-19 was found except for few diseases including cancer, which warranted further investigation at the pathobiological level. We believe that this study could be useful in developing a control strategy in COVID-19 as well as future pandemics.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Faruq Abdulla", - "author_inst": "Department of Statistics, Faculty of Sciences, Islamic University, Kushtia-7003, Bangladesh." - }, - { - "author_name": "Zulkar Nain", - "author_inst": "Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia-7003, Bangladesh." - }, - { - "author_name": "Md. Karimuzzaman", - "author_inst": "Department of Statistics, Faculty of Mathematical and Physical Sciences, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh." - }, - { - "author_name": "Md. Moyazzem Hossain", - "author_inst": "School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, UK." - }, - { - "author_name": "Utpal Kumar Adhikari", - "author_inst": "School of Medicine, Western Sydney University, Campbelltown, NSW-2560, Australia." - }, - { - "author_name": "Azizur Rahman", - "author_inst": "School of Computing and Mathematics, Charles Sturt University, Wagga Wagga, NSW-2678, Australia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.08.20095943", "rel_title": "Epidemiological, socio-demographic and clinical features of the early phase of the COVID-19 epidemic in Ecuador", @@ -1445728,6 +1448709,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.12.092163", + "rel_title": "A Computational Toolset for Rapid Identification of SARS-CoV-2, other Viruses, and Microorganisms from Sequencing Data", + "rel_date": "2020-05-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.092163", + "rel_abs": "In this paper, we present a toolset and related resources for rapid identification of viruses and microorganisms from short-read or long-read sequencing data. We present fastv as an ultra-fast tool to detect microbial sequences present in sequencing data, identify target microorganisms, and visualize coverage of microbial genomes. This tool is based on the k-mer mapping and extension method. K-mer sets are generated by UniqueKMER, another tool provided in this toolset. UniqueKMER can generate complete sets of unique k-mers for each genome within a large set of viral or microbial genomes. For convenience, unique k-mers for microorganisms and common viruses that afflict humans have been generated and are provided with the tools. As a lightweight tool, fastv accepts FASTQ data as input, and directly outputs the results in both HTML and JSON formats. Prior to the k-mer analysis, fastv automatically performs adapter trimming, quality pruning, base correction, and other pre-processing to ensure the accuracy of k-mer analysis. Specifically, fastv provides built-in support for rapid SARS-CoV-2 identification and typing. Experimental results showed that fastv achieved 100% sensitivity and 100% specificity for detecting SARS-CoV-2 from sequencing data; and can distinguish SARS-CoV-2 from SARS, MERS, and other coronaviruses. This toolset is available at: https://github.com/OpenGene/fastv.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Shifu Chen", + "author_inst": "HaploX Biotechnology" + }, + { + "author_name": "Changshou He", + "author_inst": "HaploX Biotechnology" + }, + { + "author_name": "Yingqiang Li", + "author_inst": "HaploX Biotechnology" + }, + { + "author_name": "Zhicheng Li", + "author_inst": "Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Charles E Melancon III", + "author_inst": "HaploX Biotechnology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.13.092577", "rel_title": "Lung Disease Network Reveals the Impact of Comorbidity on SARS-CoV-2 infection", @@ -1445841,81 +1448857,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.05.12.092171", - "rel_title": "Structure of SARS-CoV-2 main protease in the apo state reveals the inactive conformation", - "rel_date": "2020-05-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.092171", - "rel_abs": "Mpro is of considerable interest as a drug target in the treatment of COVID-19 since the proteolytic activity of this viral protease is essential for viral replication. Here we report the first insight of the structure Mpro for SARS-CoV-2 in the inactive conformation under conditions close to the physiological state (pH 7.5) to an overall resolution of 1.9 [A]. The comparisons of Mpro in different states reveal that substrate binding site and the active site are more flexible in the inactive conformation than that in the active conformations. Notably, compared with the active conformation of the apo state structure in pH7.6 of SARS, the SARS-CoV-2 apo state is in the inactive conformation under condition close to physiological state (pH7.5). Two water molecules are present in the oxyanion hole in our apo state structure, whereas in the ligand-bound structure, water molecular is absence in the same region. This structure provides novel and important insights that have broad implications for understanding the structural basis underlying enzyme activity, and can facilitate rational, structure-based, approaches for the design of specific SARS-CoV-2 ligands as new therapeutic agents.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Xuelan Zhou", - "author_inst": "School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China." - }, - { - "author_name": "Fanglin Zhong", - "author_inst": "College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, Jiangxi, PR, China." - }, - { - "author_name": "Cheng Lin", - "author_inst": "Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen, Guangdong, 518118, China" - }, - { - "author_name": "Xiaohui Hu", - "author_inst": "School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China." - }, - { - "author_name": "Yan Zhang", - "author_inst": "The Second Affliated Hospital Of Nanchang University" - }, - { - "author_name": "Bing Xiong", - "author_inst": "Department of Medicinal Chemistry , Shanghai Institute of Materia Medica,Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China." - }, - { - "author_name": "Xiushan Yin", - "author_inst": "Shenyang University of Chemical Technology" - }, - { - "author_name": "Jinheng Fu", - "author_inst": "Jiangxi-OAI Joint Research Institution, Nanchang University, Nanchang, 330047, China." - }, - { - "author_name": "Wei He", - "author_inst": "College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, Jiangxi, PR,China." - }, - { - "author_name": "Jingjing Duan", - "author_inst": "Human Aging Research Institute (HARI), School of Life Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China" - }, - { - "author_name": "Yang Fu", - "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China 518055" - }, - { - "author_name": "Huan Zhou", - "author_inst": "Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute,Chinese Academy of Sciences 239 Zhangheng Road, Pudong District, Shanghai 201204, " - }, - { - "author_name": "Qisheng Wang", - "author_inst": "Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute,Chinese Academy of Sciences 239 Zhangheng Road, Pudong District, Shanghai 201204, " - }, - { - "author_name": "Jian Li", - "author_inst": "College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou, 341000, Jiangxi, PR,China." - }, - { - "author_name": "Jin Zhang", - "author_inst": "School of Basic Medical Sciences, Nanchang University, Nanchang, Jiangxi, 330031, China." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.05.07.20094151", "rel_title": "The British Thoracic Society survey of rehabilitation to support recovery of the Post Covid -19 population.", @@ -1447022,6 +1449963,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2020.05.08.20095463", + "rel_title": "Using epidemic simulators for monitoring an ongoing epidemic", + "rel_date": "2020-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095463", + "rel_abs": "Prediction of infection trends, estimating the efficacy of contact tracing, testing or impact of influx of infected are of vital importance for administration during an ongoing epidemic. Most effective methods currently are empirical in nature and their relation to parameters of interest to administrators are not evident. We thus propose a modified SEIRD model that is capable of modeling effect of interventions and in migrations on the progress of an epidemic. The tunable parameters of this model bear relevance to monitoring of an epidemic. This model was used to show that some of the commonly seen features of cumulative infections in real data can be explained by piece wise constant changes in interventions and population influx. We also show that the data of cumulative infections from twelve Indian states between mid March and mid April 2020 can be generated from the model by applying interventions according to a set of heuristic rules. Prediction for the next ten days based on this model, reproduced real data very well. In addition, our model also reproduced the time series of recoveries and deaths. Our work constitutes an important first step towards an effective dashboard for the monitoring of epidemic by the administration, especially in an Indian context.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mohan Raghavan", + "author_inst": "Indian Institute of Technology Hyderabad" + }, + { + "author_name": "Kousik Sarathy Sridharan", + "author_inst": "Indian Institute of Technology Hyderabad" + }, + { + "author_name": "Yashaswini M R", + "author_inst": "Indian Institute of Technology Hyderabad" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.08.20093229", "rel_title": "Placental pathology in COVID-19", @@ -1447239,73 +1450207,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.05.11.089375", - "rel_title": "The SARS-CoV-2 conserved macrodomain is a highly efficient ADP-ribosylhydrolase enzyme", - "rel_date": "2020-05-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.11.089375", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-like-CoVs encode 3 tandem macrodomains within non-structural protein 3 (nsp3). The first macrodomain, Mac1, is conserved throughout CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. Mac1 likely counters host-mediated anti-viral ADP-ribosylation, a posttranslational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Here we report the crystal structure of SARS-CoV-2 Mac1 in complex with ADP-ribose. SARS-CoV-2, SARS-CoV and MERS-CoV Mac1 exhibit similar structural folds and all 3 proteins bound to ADP-ribose with low M affinities. Importantly, using ADP-ribose detecting binding reagents in both a gel-based assay and novel ELISA assays, we demonstrated de-MARylating activity for all 3 CoV Mac1 proteins, with the SARS-CoV-2 Mac1 protein leading to a more rapid loss of substrate compared to the others. In addition, none of these enzymes could hydrolyze poly-ADP-ribose. We conclude that the SARS-CoV-2 and other CoV Mac1 proteins are MAR-hydrolases with similar functions, indicating that compounds targeting CoV Mac1 proteins may have broad anti-CoV activity.\n\nIMPORTANCESARS-CoV-2 has recently emerged into the human population and has led to a worldwide pandemic of COVID-19 that has caused greater than 900 thousand deaths worldwide. With, no currently approved treatments, novel therapeutic strategies are desperately needed. All coronaviruses encode for a highly conserved macrodomain (Mac1) that binds to and removes ADP-ribose adducts from proteins in a dynamic post-translational process increasingly recognized as an important factor that regulates viral infection. The macrodomain is essential for CoV pathogenesis and may be a novel therapeutic target. Thus, understanding its biochemistry and enzyme activity are critical first steps for these efforts. Here we report the crystal structure of SARS-CoV-2 Mac1 in complex with ADP-ribose, and describe its ADP-ribose binding and hydrolysis activities in direct comparison to SARS-CoV and MERS-CoV Mac1 proteins. These results are an important first step for the design and testing of potential therapies targeting this unique protein domain.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Yousef M.O. Alhammad", - "author_inst": "University of Kansas" - }, - { - "author_name": "Maithri M. Kashipathy", - "author_inst": "University of Kansas" - }, - { - "author_name": "Anuradha Roy", - "author_inst": "University of Kansas" - }, - { - "author_name": "Jean-Philippe Gagne", - "author_inst": "Laval University" - }, - { - "author_name": "Peter McDonald", - "author_inst": "University of Kansas" - }, - { - "author_name": "Philip Gao", - "author_inst": "University of Kansas" - }, - { - "author_name": "Louis Nonfoux", - "author_inst": "Laval University" - }, - { - "author_name": "Kevin P. Battaile", - "author_inst": "New York Structural Biology Center" - }, - { - "author_name": "David K. Johnson", - "author_inst": "University of Kansas" - }, - { - "author_name": "Erik D Holmstrom", - "author_inst": "University of Kansas" - }, - { - "author_name": "Guy G Poirier", - "author_inst": "Laval University" - }, - { - "author_name": "Scott W. Lovell", - "author_inst": "University of Kansas" - }, - { - "author_name": "Anthony R. Fehr", - "author_inst": "University of Kansas" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.05.12.088088", "rel_title": "A putative new SARS-CoV protein, 3a*, encoded in an ORF overlapping ORF3a", @@ -1448611,6 +1451512,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.06.20093419", + "rel_title": "Evidence of Protective Role of Ultraviolet-B (UVB) Radiation in Reducing COVID-19 Deaths", + "rel_date": "2020-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093419", + "rel_abs": "BackgroundResearch is ongoing to identify an effective way to prevent or treat COVID-19, but thus far these efforts have not yet identified a possible solution. Prior studies indicate the protective role of Ultraviolet-B (UVB) radiation in human health, mediated by vitamin D synthesis. In this study, we empirically outline a negative association of UVB radiation as measured by ultraviolet index (UVI) with the number of deaths attributed to COVID-19 (COVID- 19 deaths).\n\nMethodsWe carry out an observational study, applying a fixed-effect log-linear regression model to a panel dataset of 152 countries over a period of 108 days (n=6524). We use the cumulative number of COVID-19 deaths and case-fatality rate (CFR) as the main dependent variables to test our hypothesis and isolate UVI effect from potential confounding factors such as underlying time trends, country-specific time-constant and time-varying factors such as weather.\n\nFindingsAfter controlling for time-constant and time-varying factors, we find that a permanent unit increase in UVI is associated with a 1.2 percentage points decline in daily growth rates of cumulative COVID-19 deaths [p < 0.01] as well as a 1.0 percentage points decline in the daily growth rates of CFR [p < 0.05]. These results represent a significant percentage reduction in terms of the daily growth rates of cumulative COVID-19 deaths (-11.88%) and CFR (-38.46%). Our results are consistent across different model specifications.\n\nInterpretationWe find a significant negative association between UVI and COVID-19 deaths, indicating evidence of the protective role of UVB in mitigating COVID-19 deaths. If confirmed via clinical studies, then the possibility of mitigating COVID-19 deaths via sensible sunlight exposure or vitamin D intervention will be very attractive because it is cost-effective and widely available.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rahul Kalippurayil Moozhipurath", + "author_inst": "Goethe University Frankfurt am Main" + }, + { + "author_name": "Lennart Kraft", + "author_inst": "Goethe University Frankfurt am Main" + }, + { + "author_name": "Bernd Skiera", + "author_inst": "Goethe University Frankfurt am Main" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.07.20094888", "rel_title": "SARS-CoV-2 Infection Associated Hemophagocytic Lymphohistiocytosis: An autopsy series with clinical and laboratory correlation.", @@ -1448736,29 +1451664,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.05.07.20094466", - "rel_title": "Text Mining Approach to Analyze Coronavirus Impact: Mexico City as Case of Study", - "rel_date": "2020-05-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094466", - "rel_abs": "The epidemiological outbreak of a novel coronavirus (2019-nCoV or Covid-19) in China, and its rapid spread, gave rise to the first pandemic in the digital age. Derived from this fact that has surprised humanity, many countries started with different strategies in order to stop the infection. In this context, one of the greatest challenges for the scientific community is monitoring (real time) the global population to get immediate feedback of what is happening with the people during this public health contingency. An alternative interesting and affordable for the materialization of the aforementioned are the social networks. In a social network, the persons can act as sensors/information not only of personal data but also data derived from their behavior. This paper aims to analyze the publications of people in Mexico using a Text Mining approach. Specifically, Mexico City is presented as a case study to help understand the impact on society of the spread of Covid-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Josimar E. Chire Saire", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Anabel Pineda-Briseno", - "author_inst": "Tecnologico Nacional del Mexico / Instituto Tecnologico de Matamoros" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.06.20093773", "rel_title": "Psychological Distress Among People Losing Work During the COVID-19 Pandemic in Australia", @@ -1450285,6 +1453190,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.05.20092445", + "rel_title": "Smoking and the risk of COVID-19 infection in the UK Biobank Prospective Study", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092445", + "rel_abs": "Several studies suggest a lower prevalence of smoking than expected among adults with coronavirus disease (COVID-19). We conducted logistic regression analyses of the UK Biobank prospective study of 0.5 million adults followed for an average of 11 years. Compared to women, men were more likely to be tested and to test positive. In sex-stratified analyses, current smokers had higher adjusted Odds Ratios (OR) for being tested (male OR 1.60, 95%CI 1.32-1.95 and female OR 1.50,1.21-.1.86). Current smokers were more slightly more likely than never smokers to test positive for COVID-19. Further examination of smoking as a risk factor for COVID-19 is required. These must take into account reverse causality, where smokers quit to avoid disease as well as prior diseases.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Eo Rin Cho", + "author_inst": "Centre for Global Health Research, St. Michael's Hospital, University of Toronto" + }, + { + "author_name": "Arthur S Slutsky", + "author_inst": "Centre for Global Health Research, St. Michael's Hospital, University of Toronto" + }, + { + "author_name": "Prabhat Jha", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.06.20092957", "rel_title": "Associations with covid-19 hospitalisation amongst 406,793 adults: the UK Biobank prospective cohort study", @@ -1450382,29 +1453314,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.06.20093138", - "rel_title": "A study on the relationship between BCG vaccination and Covid-19 prevalence: Do other confounders warrant investigation?", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093138", - "rel_abs": "The Covid-19 pandemic, which originated from Wuhan, Hubei province, China, and quickly spread to the rest of the globe is caused by SARS-CoV-2, a single-stranded RNA virus. Preliminary data suggest a relationship between the BCG vaccine and the prevalence of Covid-19. The BCG vaccine is used in the prevention of tuberculosis, a disease that is most prevalent in developing countries. To determine the potential protective role of BCG vaccination, this study investigated the occurrence of Covid-19 and the relationship between the spread of Covid-19 in countries that offer BCG vaccination and those that do not. The study also performed a phylogenetic analysis of the strains involved in the Covid-19 outbreak from the representative countries. To achieve the objectives, the study utilized publicly available data on population size, vaccination coverage, and Covid-19 cases. Phylogenetic analysis was used to determine if some SARS-CoV-2 strains were more prevalent than others. The study revealed a significant negative trend between countries that offer the BCG vaccine to the general population and the reported cases of Covid-19. The study proposes future molecular and immunological analyses to determine the potential role of BCG vaccination in protection against Covid-19. This will determine if BCG has antiviral properties, with the possibility of recommending it for widespread use if supported by scientific data.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Richard M Mariita", - "author_inst": "Microbial BioSolutions" - }, - { - "author_name": "Jonathan M Musila", - "author_inst": "Fayetteville State University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.05.20088757", "rel_title": "Hydroxychloroquine plus azithromycin: a potential interest in reducing in-hospital morbidity due to COVID-19 pneumonia (HI-ZY-COVID)?", @@ -1451915,6 +1454824,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.07.20094177", + "rel_title": "Clinical and behavioural characteristics of self-isolating healthcare workers during the COVID-19 pandemic: a single-centre observational study", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094177", + "rel_abs": "ObjectivesTo describe a cohort of self-isolating healthcare workers (HCWs) with presumed COVID-19.\n\nDesignA cross-sectional, single-centre study.\n\nSettingA large, teaching hospital based in Central London with tertiary infection services.\n\nParticipants236 HCWs completed a survey distributed by internal staff email bulletin. 167 were female and 65\n\nMeasuresInformation on symptomatology, exposures and health-seeking behaviour were collected from participants by self-report.\n\nResultsThe 236 respondents reported illness compatible with COVID-19 and there was an increase in illness reporting during March 2020. Diagnostic swabs were not routinely performed.. Cough (n=179, 75.8%), fever (n=138, 58.5%), breathlessness (n=84, 35.6%) were reported. Anosmia was reported in 42.2%. Fever generally settled within 1 week (n=110, 88%). Several respondents remained at home and did not seek formal medical attention despite reporting severe breathlessness and measuring hypoxia (n=5/9, 55.6%). 2 patients required hospital admission but recovered following oxygen therapy. 84 respondents (41.2%) required greater than the obligated 7 days off work and 9 required greater than 3 weeks off.\n\nConclusionThere was a significant increase in staff reporting illness compatible with possible COVID-19 during March 2020. Conclusions cannot be drawn about exact numbers of confirmed cases due to lack of diagnostic swabbing. There were significant numbers of respondents reporting anosmia; as well as early non-specific illness prior to onset of cough and fever. This may represent pre-symptomatic HCWs who are likely to be infectious and thus criteria for isolation and swabbing should be broadened. The study also revealed concerning lack of healthcare seeking in respondents with significant red flag symptoms (severe breathlessness, hypoxia). This should be addressed urgently to reduce risk of severe disease being detected late. Finally, this study should inform trusts that HCWs may require longer than 7 days off work to recover from illness.\n\nO_LSTStrengths and limitations of this studyC_LSTO_LITo the authors knowledge, this study presents one of the first descriptive data analysis of self-reported healthcare worker (HCW) COVID-19 exposures and symptomatology in the UK.\nC_LIO_LIStudy respondents represented a broad range of job roles, including both frontline clinical and non-patient facing staff.\nC_LIO_LIThe inclusion of questions focusing on health-seeking behaviour allows results to be used to inform human resource management in the developing pandemic, and provides concerning but important data around late healthcare seeking in HCWs\nC_LIO_LIData were self-reported, cross-sectional and retrospective, which may be subject to recall bias, and the lack of diagnostic swabbing in the majority of respondents limits interpretation of the data\nC_LIO_LIFull demographic data were not collected on participants and certain staff groups may have been over-represented in the sample, which may introduce sampling bias.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Angus de Wilton", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust; Hospital of Tropical Diseases, London" + }, + { + "author_name": "Eliz Kilich", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust; Hospital of Tropical Diseases, London" + }, + { + "author_name": "Zain Chaudhry", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust; Hospital of Tropical Diseases, London" + }, + { + "author_name": "Lucy CK Bell", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust; Hospital of Tropical Diseases, London" + }, + { + "author_name": "Joshua Gahir", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust; Hospital of Tropical Diseases, London" + }, + { + "author_name": "Jane Cadman", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Robert A Lever", + "author_inst": "Hospital of Tropical Diseases, London; University College London" + }, + { + "author_name": "Sarah Logan", + "author_inst": "Hospital of Tropical Diseases, London; COVID-19 Response Team, University College London Hospitals NHS Foundation Trust;" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.07.20094276", "rel_title": "Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy", @@ -1452048,89 +1455004,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.07.20093963", - "rel_title": "Serological signatures of SARS-CoV-2 infection: Implications for antibody-based diagnostics", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20093963", - "rel_abs": "BackgroundInfection with SARS-CoV-2 induces an antibody response targeting multiple antigens that changes over time. This complexity presents challenges and opportunities for serological diagnostics.\n\nMethodsA multiplex serological assay was developed to measure IgG and IgM antibody responses to seven SARS-CoV-2 spike or nucleoprotein antigens, two antigens for the nucleoproteins of the 229E and NL63 seasonal coronaviruses, and three non-coronavirus antigens. Antibodies were measured in serum samples from patients in French hospitals with RT-qPCR confirmed SARS-CoV-2 infection (n = 259), and negative control serum samples collected before the start of the SARS-CoV-2 epidemic (n = 335). A random forests algorithm was trained with the multiplex data to classify individuals with previous SARS-CoV-2 infection. A mathematical model of antibody kinetics informed by prior information from other coronaviruses was used to estimate time-varying antibody responses and assess the potential sensitivity and classification performance of serological diagnostics during the first year following symptom onset. A statistical estimator is presented that can provide estimates of seroprevalence in very low transmission settings.\n\nResultsIgG antibody responses to trimeric Spike protein identified individuals with previous RT-qPCR confirmed SARS-CoV-2 infection with 91.6% sensitivity (95% confidence interval (CI); 87.5%, 94.5%) and 99.1% specificity (95% CI; 97.4%, 99.7%). Using a serological signature of IgG and IgM to multiple antigens, it was possible to identify infected individuals with 98.8% sensitivity (95% CI; 96.5%, 99.6%) and 99.3% specificity (95% CI; 97.6%, 99.8%). Informed by prior data from other coronaviruses, we estimate that one year following infection a monoplex assay with optimal anti-Stri IgG cutoff has 88.7% sensitivity (95% CI: 63.4%, 97.4%), and that a multiplex assay can increase sensitivity to 96.4% (95% CI: 80.9%, 100.0%). When applied to population-level serological surveys, statistical analysis of multiplex data allows estimation of seroprevalence levels less than 1%, below the false positivity rate of many other assays.\n\nConclusionSerological signatures based on antibody responses to multiple antigens can provide accurate and robust serological classification of individuals with previous SARS-CoV-2 infection. This provides potential solutions to two pressing challenges for SARS-CoV-2 serological surveillance: classifying individuals who were infected greater than six months ago, and measuring seroprevalence in serological surveys in very low transmission settings.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Jason Rosado", - "author_inst": "Malaria: Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France" - }, - { - "author_name": "Stephane Pelleau", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Charlotte Cockram", - "author_inst": "Spatial Regulation of Genomes Unit, Department of Genomes and Genetics, Institut Pasteur, Paris, France" - }, - { - "author_name": "Sarah Helene Merkling", - "author_inst": "Insect-Virus Interactions Unit, Department of Virology, Institut Pasteur, Paris, France" - }, - { - "author_name": "Narimane Nekkab", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Caroline Demeret", - "author_inst": "Molecular Genetics of RNA Viruses Unit, Department of Virology, Institut Pasteur, Paris, France" - }, - { - "author_name": "Annalisa Meola", - "author_inst": "Structural Virology Unit, Department of Virology and CNRS UMR 3569, Institut Pasteur, Paris, France" - }, - { - "author_name": "Solen Kerneis", - "author_inst": "Equipe Mobile d Infectiologie, APHP Centre-Universite de Paris, Paris, France" - }, - { - "author_name": "Benjamin Terrier", - "author_inst": "Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hopitaux de Paris-Centre (APHP-CUP), Univer" - }, - { - "author_name": "Samira Fafi-Kremer", - "author_inst": "CHU de Strasbourg, Laboratoire de Virologie, F-67091 Strasbourg, France" - }, - { - "author_name": "Jerome de Seze", - "author_inst": "Centre d'Investigation Clinique - INSERM CIC-1434, Strasbourg, France" - }, - { - "author_name": "Francois Dejardin", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Stephane Petres", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Rhea Longley", - "author_inst": "Walter and Eliza Hall Institute of Medical Research" - }, - { - "author_name": "Marija Backovic", - "author_inst": "Structural Virology Unit, Department of Virology and CNRS UMR 3569, Institut Pasteur, Paris, France" - }, - { - "author_name": "Ivo Mueller", - "author_inst": "Division of Population Health and Immunity, The Walter and Eliza Hall Institute, Melbourne, Australia" - }, - { - "author_name": "Michael T White", - "author_inst": "Malaria: Parasites and Hosts Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.08.20094870", "rel_title": "Estimating pre-symptomatic transmission of COVID-19: a secondary analysis using published data", @@ -1453341,6 +1456214,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.06.20093492", + "rel_title": "Metapopulation modeling of COVID-19 advancing into the countryside: an analysis of mitigation strategies for Brazil", + "rel_date": "2020-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093492", + "rel_abs": "Since the first case of COVID-19 was confirmed in Brazil on 19 February 2020, this epidemic has spread throughout all states and at least 2142 of 5570 municipalities up to 30 April 2020. In order to understand this spreading, we investigate a stochastic epidemic model using a metapopulation approach. Simulations are supplied with real data for mobility, demography, and confirmed cases of COVID-19 extracted from public sources. Contagion follows a compartmental epidemic model for each municipality; the latter, in turn, interact with each other through recurrent mobility. Considering the number of municipalities with confirmed COVID-19 cases, simulations can infer the level of mitigation (strong, moderate, or none) that each state is effectively adopting. Properties of the epidemic curves such as time and value of epidemic peak and outbreak duration have very broad distributions across different geographical locations. This outbreak variability is observed on several scales from state, passing through intermediate, immediate down to municipality levels. The epidemic waves start from several foci concentrated in highly populated regions and propagate towards the countryside. Correlations between delay of the epidemic outbreak and distance from the respective capital cities are strong in several states, showing propagation towards the countryside, and weak in others, signaling strong influences of multiple centers, not necessarily within the same state. Our take home message is that the responses of different regions to the same mitigation protocol can vary enormously such that the policies of combating COVID-19, such as quarantine or lockdown, must be engineered according to the region specificity but integrated with the overall situation. Even though we restricted our study to Brazil, we believe that these ideas can be generalized to other countries with continental scales and heterogeneous demographic distributions.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Guilherme S Costa", + "author_inst": "Departamento de Fisica, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil" + }, + { + "author_name": "Wesley Cota", + "author_inst": "Departamento de Fisica, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil" + }, + { + "author_name": "Silvio C Ferreira", + "author_inst": "Departamento de Fisica, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil and National Institute of Science and Technology for Complex Systems, Rio d" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.06.20093476", "rel_title": "Sensitivity and specificity of a rapid test for assessment of exposure to SARS-CoV-2 in a community-based setting in Brazil", @@ -1453450,37 +1456350,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.06.20093344", - "rel_title": "Who can go back to work when the COVID-19 pandemic remits?", - "rel_date": "2020-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093344", - "rel_abs": "This paper seeks to determine which workers affected by lockdown measures can return to work when a government decides to apply lockdown exit strategies. This system, which we call Sequential Selective Multidimensional Decision (SSMD), involves deciding sequentially, by geographical areas, sectors of activity, age groups and immunity, which workers can return to work at a given time according to the epidemiological criteria of the country as well as that of a group of reference countries, used as a benchmark, that have suffered a lower level of lockdown de-escalation strategies. We apply SSMD to Spain, based on affiliation to the Social Security system prior to the COVID-19 pandemic, and conclude that 98.37% of the population could be affected. The proposed system makes it possible to accurately identify the target population for serological IgG antibody tests in the work field, as well as those affected by special income replacement measures due to lockdown being maintained over a longer period.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Luis Angel Hierro", - "author_inst": "University of Seville" - }, - { - "author_name": "David Cantarero", - "author_inst": "University of Cantabria-IDIVAL" - }, - { - "author_name": "David Patino", - "author_inst": "University of Seville" - }, - { - "author_name": "Daniel Rodriguez-Perez", - "author_inst": "University of Seville" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.06.20092601", "rel_title": "Perceived Stress and Psychological (Dis)Stress among Indian Endodontists During COVID19 Pandemic Lock down", @@ -1455127,6 +1457996,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.05.20092122", + "rel_title": "Indian communitys Knowledge, Attitude & Practice towards COVID-19", + "rel_date": "2020-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092122", + "rel_abs": "As COVID-19 pandemic has caused unprecedented human health consequences. Knowledge, attitude, perception of general population of India towards the transmission and prevention plays vital role for effective control measures. The study was conducted to assess the knowledge, attitude and practice of the general public of India on COVID-19. In this study, a web-based cross-sectional survey was conducted between 10th March to 18th April 2020. A 19-item questionnaire was generated, Cronbachs alpha was used to measure the internal consistency of the questionnaire & randomly distributed among the public using Google forms through social media networks. The chi-square test or Fischer exact test was used to compare categorical data and multiple linear regression was used to identify factor influencing KAP. Among 7978 participants, the overall knowledge, attitude and practice score was 80.64%, 97.33% and 93.8% consecutively. Majority of Indian population demonstrated preceded good knowledge, positive attitude and good practice regarding COVID-19 pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Balvir Singh Tomar", + "author_inst": "Institute of Gastroenterology Hepatology & Transplant" + }, + { + "author_name": "Pratima Singh", + "author_inst": "Department of Pharmacy Practice, Nims University Rajasthan, Jaipur India" + }, + { + "author_name": "Deepak Nathiya", + "author_inst": "Department of Pharmacy Practice, Nims University Rajasthan Jaipur India" + }, + { + "author_name": "Supriya Suman", + "author_inst": "Department of Pharmacy Practice, Nims University Rajasthan, Jaipur India" + }, + { + "author_name": "Preeti Raj", + "author_inst": "Department of Pharmacy Practice, Nims University Rajasthan, Jaipur, India" + }, + { + "author_name": "Sandeep Tripathi", + "author_inst": "National Institute of Medical Sciences & Research, Nims University Rajasthan, Jaipur, India" + }, + { + "author_name": "Dushyant Singh Chauhan", + "author_inst": "Institute of Advance Sciences, Nims University Rajasthan, Jaipur, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.05.20092254", "rel_title": "County-level factors influence the trajectory of Covid-19 incidence", @@ -1455224,29 +1458136,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.05.20091520", - "rel_title": "Epidemic Situation and Forecasting of COVID-19 in Saudi Arabia using the SIR model", - "rel_date": "2020-05-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091520", - "rel_abs": "BackgroundSaudi Arabia is one of the countries affected by COVID-19 pandemic. This will lead to negative impacts in many sectors. Saudi Arabia not only plays an important role on the economical side because it is the leading country in oil production, but also because it is considered the heart of the Islamic countries. Although protective measures have been implemented in Saudi Arabia, the number of COVID-19 cases has increased.\n\nAims of the studyThis study aimed to employ SIR model to forecast the peak of COVID-19 progression and an estimation of it is end in Saudi Arabia.\n\nMethodBased on the World Health Organization data on COVID-19 progression in Saudi Arabia from March 3rd to April 29th, 2020, we reliably estimate the constant parameters and make predictions on the inflection point and potential ending time. Susceptible, Infected, and Recovered are the main components of the SIR model that were used to run the analysis.\n\nResultThe data showed an interesting result about the peak of the disease progression. It is projected to occur around the 20th day after running the model. According to the model, the peak time will be around the 20th of May. Then the cases will decrease until the 55th day, which is around June 20th.\n\nConclusionThe result predicts a second peak and an estimation end of COVID-19 in Saudi Arabia. This data can inform the policy makers, who should try to contain the virus, to be prepared for what is coming next.\n\nKey Messages:", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "haitham khoj", - "author_inst": "Knig Abdulaziz University" - }, - { - "author_name": "Alaa F Mujallad", - "author_inst": "University of Jeddah" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.05.05.20091967", "rel_title": "Risk Stratification for Healthcare workers during the CoViD-19 Pandemic; using demographics, co-morbid disease and clinical domain in order to assign clinical duties", @@ -1456609,6 +1459498,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.05.20091637", + "rel_title": "Application-oriented mathematical algorithms for group testing", + "rel_date": "2020-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091637", + "rel_abs": "Group testing is a widely used protocol which aims to test a small group of people to identify whether at least one of them is infected. It is particularly efficient if the infection rate is low, because it only requires a single test if everybody in the group is negative. The most efficient use of group testing is a complex mathematical question. However, the answer highly depends on practical parameters and restrictions, which are partially ignored by the mathematical literature. This paper aims to offer practically efficient group testing algorithms, focusing on the current COVID-19 epidemic.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Endre Csoka", + "author_inst": "Alfred Renyi Institute of Mathematics" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.08.083816", "rel_title": "Intra-genome variability in the dinucleotide composition of SARS-CoV-2", @@ -1456714,49 +1459622,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.05.08.084996", - "rel_title": "Elevated ACE2 expression in the olfactory neuroepithelium: implications for anosmia and upper respiratory SARS-CoV-2 entry and replication", - "rel_date": "2020-05-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.08.084996", - "rel_abs": "The site of SARS-CoV-2 entry and replication critically impacts strategies for COVID-19 diagnosis, transmission mitigation, and treatment. We determined the cellular location of the SARS-CoV-2 target receptor protein, ACE2, in the human upper airway, finding striking enrichment (200-700 folds) in the olfactory neuroepithelium relative to nasal respiratory or tracheal epithelial cells. This cellular tropism of SARS-CoV-2 may underlie its high transmissibility and association with olfactory dysfunction, while suggesting a viral reservoir potentially amenable to intranasal therapy.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Mengfei Chen", - "author_inst": "Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine" - }, - { - "author_name": "Wenjuan Shen", - "author_inst": "Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine" - }, - { - "author_name": "Nicholas Rowan", - "author_inst": "Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine" - }, - { - "author_name": "Heather Kulaga", - "author_inst": "Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine" - }, - { - "author_name": "Alexander Hillel", - "author_inst": "Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine" - }, - { - "author_name": "Murugappan Ramanathan", - "author_inst": "Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine" - }, - { - "author_name": "Andrew P Lane", - "author_inst": "Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.05.08.084236", "rel_title": "Knowledge, attitude and practice of secondary school students toward COVID-19 epidemic in Italy: a cross selectional study", @@ -1458331,6 +1461196,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2020.05.04.20090316", + "rel_title": "Early postmortem brain MRI findings in COVID-19 non-survivors", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090316", + "rel_abs": "ImportanceThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is considered to have potential neuro-invasiveness that might lead to acute brain disorders or contribute to respiratory distress in patients with coronavirus disease 2019 (COVID-19). Brain magnetic resonance imaging (MRI) data in COVID-19 patients are scarce due to difficulties to obtain such examination in infected unstable patients during the COVID-19 outbreak.\n\nObjectiveTo investigate the occurrence of structural brain abnormalities in non-survivors of COVID-19 in a virtopsy framework.\n\nDesignProspective, case series study with postmortem brain MRI obtained early (<24h) after death.\n\nSettingMonocentric study.\n\nParticipantsFrom 31/03/2020 to 24/04/2020, consecutive decedents who fulfilled the following inclusion criteria were included: death <24 hours, SARS-CoV-2 detection on nasopharyngeal swab specimen, chest computerized tomographic (CT) scan suggestive of COVID-19, absence of known focal brain lesion, and MRI compatibility.\n\nMain Outcome(s) andMeasure(s)Signs of acute brain injury and MRI signal abnormalities along the olfactory tract and brainstem were searched independently by 3 neuroradiologists, then reviewed with neurologists and clinicians.\n\nResultsAmong the 62 patients who died from COVID-19 during the inclusion period, 19 decedents fulfilled inclusion criteria. Subcortical micro- and macro-bleeds (2 decedents), cortico-subcortical edematous changes evocative of posterior reversible encephalopathy syndrome (PRES, one decedent), and nonspecific deep white matter changes (one decedent) were observed. Asymmetric olfactory bulbs were found in 4 other decedents without downstream olfactory tract abnormalities. No brainstem MRI signal abnormality.\n\nConclusions and RelevancePostmortem brain MRI demonstrates hemorrhagic and PRES-related brain lesions in non-survivors of COVID-19 that might be triggered by the virus-induced endothelial disturbances. SARS-CoV-2-related olfactory impairment seems to be limited to olfactory bulbs. The absence of brainstem MRI abnormalities does not support a brain-related contribution to respiratory distress in COVID-19.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSIs there common brain MRI abnormalities patterns in non-survivors of coronavirus disease 2019 ?\n\nFindingsIn a case series of 19 non-survivors of severe COVID-19 disease, early postmortem brain MRI demonstrated patterns evocative of intracranial vasculopathy in 4 decedents: subcortical micro- and macro-bleeds (2 decedents), cortico-subcortical edematous changes evocative of posterior reversible encephalopathy syndrome (PRES, one decedent), and nonspecific deep white matter changes (one decedent). Asymmetric olfactory bulbs were found in 4 other decedents but without downstream olfactory tract abnormalities.\n\nMeaningPostmortem brain MRI demonstrates hemorrhagic and PRES-related brain lesions in non-survivors of COVID-19 that might be triggered by virus-induced endothelial disturbances.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Tim Coolen", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Valentina Lolli", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Niloufar Sadeghi", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Antonin Rovai", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Nicola Trotta", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Fabio S Taccone", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Jacques Creteur", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Sophie Henrard", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Jean-Christophe Goffard", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Olivier Dewitte", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Gilles Naeije", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Serge Goldman", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Xavier De Tiege", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.05.04.20091041", "rel_title": "The Social and Economic Factors Underlying the Impact of COVID-19 Cases and Deaths in US Counties", @@ -1458440,77 +1461372,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.05.20091728", - "rel_title": "Suboptimal biological sampling as a probable cause of false-negative COVID-19 diagnostic test results", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091728", - "rel_abs": "Improper nasopharyngeal swab collection could contribute to false-negative COVID-19 results. In support of this, specimens from confirmed or suspected COVID-19 cases that tested negative or indeterminate (i.e. suspected false-negatives) contained less human DNA (a stable molecular marker of sampling quality) compared to a representative pool of specimens submitted for testing.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Natalie N. Kinloch", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Gordon Ritchie", - "author_inst": "Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Chanson J. Brumme", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada." - }, - { - "author_name": "Winnie Dong", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada." - }, - { - "author_name": "Weiyan Dong", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada." - }, - { - "author_name": "Tanya Lawson", - "author_inst": "Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada" - }, - { - "author_name": "R. Brad Jones", - "author_inst": "Infectious Diseases Division, Department of Medicine, Weill Cornell Medical College, New York, USA" - }, - { - "author_name": "Julio S.G. Montaner", - "author_inst": "British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada." - }, - { - "author_name": "Victor Leung", - "author_inst": "Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Marc G. Romney", - "author_inst": "Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Aleksandra Stefanovic", - "author_inst": "Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Nancy Matic", - "author_inst": "Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Christopher F. Lowe", - "author_inst": "Division of Medical Microbiology and Virology, St Paul's Hospital, Vancouver, British Columbia, Canada" - }, - { - "author_name": "Zabrina Brumme", - "author_inst": "Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.05.20091413", "rel_title": "Global genetic diversity patterns and transmissions of SARS-CoV-2", @@ -1460189,6 +1463050,61 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.05.08.084061", + "rel_title": "Comparison of SARS-CoV-2 spike protein binding to human, pet, farm animals, and putative intermediate hosts ACE2 and ACE2 receptors", + "rel_date": "2020-05-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.08.084061", + "rel_abs": "The emergence of a novel coronavirus, SARS-CoV-2, resulted in a pandemic. Here, we used recently released X-ray structures of human ACE2 bound to the receptor-binding domain (RBD) of the spike protein (S) from SARS-CoV-2 to predict its binding to ACE2 proteins from different animals, including pets, farm animals, and putative intermediate hosts of SARS-CoV-2. Comparing the interaction sites of ACE2 proteins known to serve or not serve as receptor allows to define residues important for binding. From the 20 amino acids in ACE2 that contact S up to seven can be replaced and ACE2 can still function as the SARS-CoV-2 receptor. These variable amino acids are clustered at certain positions, mostly at the periphery of the binding site, while changes of the invariable residues prevent S-binding or infection of the respective animal. Some ACE2 proteins even tolerate the loss or the acquisition of N-glycosylation sites located near the S-interface. Of note, pigs and dogs which are not or not effectively infected, respectively, have only a few changes in the binding site have relatively low levels of ACE2 in the respiratory tract. Comparison of the RBD of S of SARS-CoV-2 with viruses from bat and pangolin revealed that the latter contains only one substitution, whereas the bat virus exhibits five. However, ACE2 of pangolin exhibit seven changes relative to human ACE2, a similar number of substitutions is present in ACE2 of bats, raccoon, and civet suggesting that SARS-CoV-2 may not especially adapted to ACE2 of any of its putative intermediate hosts. These analyses provide new insight into the receptor usage and animal source/origin of SARS-COV-2.\n\nIMPORTANCESARS-CoV-2 is threatening people worldwide and there are no drugs or vaccines available to mitigate its spread. The origin of the virus is still unclear and whether pets and livestock can be infected and transmit SARS-CoV-2 are important and unknown scientific questions. Effective binding to the host receptor ACE2 is the first prerequisite for infection of cells and determines the host range. Our analysis provides a framework for the prediction of potential hosts of SARS-CoV-2. We found that ACE2 from species known to support SARS-CoV-2 infection tolerate many amino acid changes indicating that the species barrier might be low. However, the lower expression of ACE2 in the upper respiratory tract of some pets and livestock means more research and monitoring should be done to explore the animal source of infection and the risk of potential cross-species transmission. Finally, the analysis also showed that SARS-CoV-2 may not specifically adapted to any of its putative intermediate hosts.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Xiaofeng Zhai", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Jiumeng Sun", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Ziqing Yan", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Jie Zhang", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Jin Zhao", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Zongzheng Zhao", + "author_inst": "Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China." + }, + { + "author_name": "Qi Gao", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Wan-Ting He", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Michael Veit", + "author_inst": "Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin, Germany." + }, + { + "author_name": "Shuo Su", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.08.084384", "rel_title": "ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity", @@ -1460422,41 +1463338,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.05.06.081026", - "rel_title": "Epigenetic regulator miRNA pattern differences among SARS-CoV, SARS-CoV-2 and SARS-CoV-2 world-wide isolates delineated the mystery behind the epic pathogenicity and distinct clinical characteristics of pandemic COVID-19", - "rel_date": "2020-05-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.06.081026", - "rel_abs": "Detailed molecular mechanism of SARS-CoV-2 pathogenesis is still elusive to address its deadlier nature and to design effective theraputics. Here, we present our study elucidating the interplay between the SARS-CoV and SARS-CoV-2 viruses; and hosts miRNAs, an epigenetic regulator, as a mode of pathogenesis, and enlightened how the SARS-CoV and SARS-CoV-2 infections differ in terms of their miRNA mediated interactions with host and its implications in the disease complexity. We have utilized computational approaches to predict potential host and viral miRNAs, and their possible roles in different important functional pathways. We have identified several putative host antiviral miRNAs that can target the SARS viruses, and also SARS viruses encoded miRNAs targeting host genes. In silico predicted targets were also integrated with SARS infected human cells microarray and RNA-seq gene expression data. Comparison of the host miRNA binding profiles on 67 different SARS-CoV-2 genomes from 24 different countries with respective countrys normalized death count surprisingly uncovered some miRNA clusters which are associated with increased death rates. We have found that induced cellular miRNAs can be both a boon and a bane to the host immunity, as they have possible roles in neutralizing the viral threat, parallelly, they can also function as proviral factors. On the other hand, from over representation analysis, interestingly our study revealed that although both SARS-CoV and SARS-CoV-2 viral miRNAs could target broad immune signaling pathways; only some of the SARS-CoV-2 miRNAs are found to uniquely target some immune signaling pathways like-autophagy, IFN-I signaling etc, which might suggest their immune-escape mechanisms for prolonged latency inside some hosts without any symptoms of COVID-19. Further, SARS-CoV-2 can modulate several important cellular pathways which might lead to the increased anomalies in patients with comorbidities like-cardiovascular diseases, diabetes, breathing complications, etc. This might suggest that miRNAs can be a key epigenetic modulator behind the overcomplications amongst the COVID-19 patients. Our results support that miRNAs of host and SARS-CoV-2 can indeed play a role in the pathogenesis which can be further concluded with more experiments. These results will also be useful in designing RNA therapeutics to alleviate the complications from COVID-19.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Md. Abdullah-Al-Kamran Khan", - "author_inst": "Department of Mathematics and Natural Sciences, BRAC University" - }, - { - "author_name": "Md. Rabi Us Sany", - "author_inst": "Department of Genetic Engineering and Biotechnology, University of Dhaka" - }, - { - "author_name": "Md. Shafiqul Islam", - "author_inst": "Department of Genetic Engineering and Biotechnology, University of Dhaka" - }, - { - "author_name": "Md. Saheb Mehebub", - "author_inst": "Department of Genetic Engineering and Biotechnology, University of Dhaka" - }, - { - "author_name": "Abul B.M.M.K. Islam", - "author_inst": "Department of Genetic Engineering and Biotechnology, University of Dhaka" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.05.08.084103", "rel_title": "AI334 and AQ806 antibodies recognize the spike S protein from SARS-CoV-2 by ELISA", @@ -1461663,6 +1464544,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2020.05.04.20090076", + "rel_title": "Infection fatality rate of SARS-CoV-2 infection in a German community with a super-spreading event", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090076", + "rel_abs": "The world faces an unprecedented SARS-CoV2 pandemic where many critical factors still remain unknown. The case fatality rates (CFR) reported in the context of the SARS-CoV-2 pandemic substantially differ between countries. For SARS-CoV-2 infection with its broad clinical spectrum from asymptomatic to severe disease courses, the infection fatality rate (IFR) is the more reliable parameter to predict the consequences of the pandemic. Here we combined virus RT-PCR testing and assessment for SARS-CoV2 antibodies to determine the total number of individuals with SARS-CoV-2 infections in a given population.\n\nMethodsA sero-epidemiological GCP- and GEP-compliant study was performed in a small German town which was exposed to a super-spreading event (carnival festivities) followed by strict social distancing measures causing a transient wave of infections. Questionnaire-based information and biomaterials were collected from a random, household-based study population within a seven-day period, six weeks after the outbreak. The number of present and past infections was determined by integrating results from anti-SARS-CoV-2 IgG analyses in blood, PCR testing for viral RNA in pharyngeal swabs and reported previous positive PCR tests.\n\nResultsOf the 919 individuals with evaluable infection status (out of 1,007; 405 households) 15.5% (95% CI: [12.3%; 19.0%]) were infected. This is 5-fold higher than the number of officially reported cases for this community (3.1%). Infection was associated with characteristic symptoms such as loss of smell and taste. 22.2% of all infected individuals were asymptomatic. With the seven SARS-CoV-2-associated reported deaths the estimated IFR was 0.36% [0.29%; 0.45%]. Age and sex were not found to be associated with the infection rate. Participation in carnival festivities increased both the infection rate (21.3% vs. 9.5%, p<0.001) and the number of symptoms in the infected (estimated relative mean increase 1.6, p=0.007). The risk of a person being infected was not found to be associated with the number of study participants in the household this person lived in. The secondary infection risk for study participants living in the same household increased from 15.5% to 43.6%, to 35.5% and to 18.3% for households with two, three or four people respectively (p<0.001).\n\nConclusionsWhile the number of infections in this high prevalence community is not representative for other parts of the world, the IFR calculated on the basis of the infection rate in this community can be utilized to estimate the percentage of infected based on the number of reported fatalities in other places with similar population characteristics. Whether the specific circumstances of a super-spreading event not only have an impact on the infection rate and number of symptoms but also on the IFR requires further investigation. The unexpectedly low secondary infection risk among persons living in the same household has important implications for measures installed to contain the SARS-CoV-2 virus pandemic.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Hendrik Streeck", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Bianca Schulte", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Beate Kuemmerer", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Enrico Richter", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Tobias Hoeller", + "author_inst": "Clinical Study Core Unit, Study Centre Bonn (SZB), University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Christine Fuhrmann", + "author_inst": "Clinical Study Core Unit, Study Centre Bonn (SZB), University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Eva Bartok", + "author_inst": "Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Ramona Dolscheid", + "author_inst": "Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Moritz Berger", + "author_inst": "Institute for Medical Biometry, Informatics and Epidemiology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Lukas Wessendorf", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Monika Eschbach-Bludau", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Angelika Kellings", + "author_inst": "Clinical Study Core Unit, Study Centre Bonn (SZB), University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Astrid Schwaiger", + "author_inst": "Biobank Core Unit, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Martin Coenen", + "author_inst": "Clinical Study Core Unit, Study Centre Bonn (SZB), University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Per Hoffmann", + "author_inst": "Institute of Human Genetics, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Markus Noethen", + "author_inst": "Institute of Human Genetics, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Anna-Maria Eis-Huebinger", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Martin Exner", + "author_inst": "Institute for Hygiene and Public Health, University Hospital, University of Bonn" + }, + { + "author_name": "Ricarda Schmithausen", + "author_inst": "Institute for Hygiene and Public Health, University Hospital, University of Bonn" + }, + { + "author_name": "Matthias Schmid", + "author_inst": "Institute for Medical Biometry, Informatics and Epidemiology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Gunther Hartmann", + "author_inst": "Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Germany; German Center for Infection Research (DZIF), partne" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.04.20090555", "rel_title": "Laboratory findings associated with mechanical ventilation requirement and mortality among hospitalized individuals with Covid-19 in Eastern Massachusetts", @@ -1461804,81 +1464784,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.04.20090027", - "rel_title": "Detection of SARS-CoV-2 antibodies using commercial assays and seroconversion patterns in hospitalized patients", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090027", - "rel_abs": "SARS-CoV-2 antibody assays are needed for serological surveys and as a complement to molecular tests to confirm COVID-19. However, the kinetics of the humoral response against SARS-CoV-2 remains poorly described and relies on the performance of the different serological tests.\n\nIn this study, we evaluated the performance of six CE-marked point-of-care tests (POC) and three ELISA assays for the diagnosis of COVID-19 by exploring seroconversions in hospitalized patients who tested positive for SARS-CoV-2 RNA.\n\nBoth the ELISA and POC tests were able to detect SARS-CoV-2 antibodies in at least half of the samples collected seven days or more after the onset of symptoms. After 15 days, the rate of detection rose to over 80% but without reaching 100%, irrespective of the test used. More than 90% of the samples collected after 15 days tested positive using the iSIA and Accu-Tell(R) POC tests and the ID.Vet IgG ELISA assay. Seroconversion was observed 5 to 12 days after the onset of symptoms. Three assays suffer from a specificity below 90% (EUROIMMUN IgG and IgA, UNscience, Zhuhai Livzon).\n\nThe second week of COVID-19 seems to be the best period for assessing the sensitivity of commercial serological assays. To achieve an early diagnosis of COVID-19 based on antibody detection, a dual challenge must be met: the immunodiagnostic window period must be shortened and an optimal specificity must be conserved.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Edouard TUAILLON", - "author_inst": "Montpellier University" - }, - { - "author_name": "Karine Bollore", - "author_inst": "University of Montpellier" - }, - { - "author_name": "Amandine Pisoni", - "author_inst": "Montpellier University Hospital" - }, - { - "author_name": "Segolene Debiesse", - "author_inst": "Inserm U1058" - }, - { - "author_name": "Constance Renault", - "author_inst": "University of Montpellier" - }, - { - "author_name": "Sylvain Marie", - "author_inst": "Montpellier University Hospital" - }, - { - "author_name": "Soraya Groc", - "author_inst": "Montpellier University Hospital" - }, - { - "author_name": "Clemence Niels", - "author_inst": "Montpellier University Hospital" - }, - { - "author_name": "Nathalie Pansu", - "author_inst": "Montpellier University Hospital" - }, - { - "author_name": "Anne-Marie Dupuy", - "author_inst": "Montpellier University Hospital" - }, - { - "author_name": "David Morquin", - "author_inst": "Montpellier University Hospital" - }, - { - "author_name": "Vincent Foulongne", - "author_inst": "University of Montpellier" - }, - { - "author_name": "Arnaud Bourdin", - "author_inst": "University of Montpellier" - }, - { - "author_name": "Vincent Le Moing", - "author_inst": "University of Montpellier" - }, - { - "author_name": "Philippe Van de Perre", - "author_inst": "University of Montpellier" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.03.20089920", "rel_title": "Cocooning is essential to relaxing social distancing", @@ -1463413,6 +1466318,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.05.06.20092858", + "rel_title": "Spatial Network based model forecasting transmission and control of COVID-19", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20092858", + "rel_abs": "The SARS-CoV-2 driven infectious novel coronavirus disease (COVID-19) has been declared a pandemic by virtue of its brutal impact on the world in terms of loss on human life, health, economy, and other crucial resources. With the aim to explore more about its aspects, we adopted the SEIQRD (Susceptible-Exposed-Infected-Quarantine-Recovered-Death) pandemic spread with a time delay on the heterogeneous population and geography in this work. Focusing on the spatial heterogeneity, the entire population of interest in a region is divided into small distinct geographical sub regions, which interact by means of migration networks across boundaries. Utilizing the estimations of the time delay differential equations based model, we analyzed the spread dynamics of disease in a region and its sub regions. The model based numerical outcomes are validated from real time available data for India. We computed the approximate peak infection in forward time and relative timespan when disease outspread halts. To further evaluate the influence of the delay on the long term system dynamics, the sensitivity analysis is performed on time delay. The most crucial parameter, basic reproduction number R0 and its time-dependent generalization, has been estimated at both regional and sub regional levels. The impact of the most significant lockdown measure that has been implemented in India to contain the pandemic spread has been extensively studied by considering no lockdown scenario. A suggestion based on outcomes, for a bit relaxed lockdown, followed by an extended period of strict social distancing as one of the most effective control measures to manage COVID-19 spread is provided for India.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Arvind Kumar Gupta", + "author_inst": "Indian Institute of Technology Ropar" + }, + { + "author_name": "Natasha Sharma", + "author_inst": "Kanya Maha Vidyalaya, Jalandhar" + }, + { + "author_name": "Atul Kumar Verma", + "author_inst": "Indian Institute of Technology, Ropar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.03.20089938", "rel_title": "Protocol for a systematic review of qualitative and quantitative effects of cardiovascular disease risk communication using heart age concepts", @@ -1463518,25 +1466450,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2020.05.04.20091009", - "rel_title": "A mathematical assessment of the efficiency of quarantining and contact tracing in curbing the COVID-19 epidemic", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20091009", - "rel_abs": "In our model of the COVID-19 epidemic, infected individuals can be of four types, according whether they are asymptomatic (A) or symptomatic (I), and use a contact tracing mobile phone app (Y) or not (N). We denote by f the fraction of As, by y the fraction of Ys and by R0 the average number of secondary infections from a random infected individual.\n\nWe investigate the effect of non-electronic interventions (voluntary isolation upon symptom onset, quarantining private contacts) and of electronic interventions (contact tracing thanks to the app), depending on the willingness to quarantine, parameterized by four cooperating probabilities.\n\nFor a given effective R0 obtained with non-electronic interventions, we use nonnegative matrix theory and stopping line techniques to characterize mathematically the minimal fraction y0 of app users needed to curb the epidemic. We show that under a wide range of scenarios, the threshold y0 as a function of R0 rises steeply from 0 at R0 = 1 to prohibitively large values (of the order of 60 - 70% up) whenever R0 is above 1.3. Our results show that moderate rates of adoption of a contact tracing app can reduce R0 but are by no means sufficient to reduce it below 1 unless it is already very close to 1 thanks to non-electronic interventions.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Amaury Lambert", - "author_inst": "College de France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.04.20090431", "rel_title": "Significance of neutrophil-to-lymphocyte ratio, platelet-to-lymphocyte ratio for predicting clinical outcomes in COVID-19", @@ -1464886,6 +1467799,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.06.074039", + "rel_title": "The heterogeneous landscape and early evolution of pathogen-associated CpG and UpA dinucleotides in SARS CoV-2", + "rel_date": "2020-05-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.06.074039", + "rel_abs": "COVID-19 can lead to acute respiratory syndrome, which can be due to dysregulated immune signaling. We analyze the distribution of CpG dinucleotides, a pathogen-associated molecular pattern, in the SARS-CoV-2 genome. We find that the CpG content, which we characterize by a force parameter that accounts for statistical constraints acting on the genome at the nucleotidic and amino-acid levels, is, on average, low compared to other pathogenic betacoronaviruses. However, the CpG force widely fluctuates along the genome, with a particularly low value, comparable to the circulating seasonal HKU1, in the spike coding region and a greater value, comparable to SARS and MERS, in the highly expressed nucleocapside coding region (N ORF), whose transcripts are relatively abundant in the cytoplasm of infected cells and present in the 3UTRs of all subgenomic RNA. This dual nature of CpG content could confer to SARS-CoV-2 the ability to avoid triggering pattern recognition receptors upon entry, while eliciting a stronger response during replication. We then investigate the evolution of synonymous mutations since the outbreak of the COVID-19 pandemic, finding a signature of CpG loss in regions with a greater CpG force. Sequence motifs preceding the CpG-loss-associated loci in the N ORF match recently identified binding patterns of the Zinc finger Anti-viral Protein. Using a model of the viral gene evolution under human host pressure, we find that synonymous mutations seem driven in the SARS-CoV-2 genome, and particularly in the N ORF, by the viral codon bias, the transition-transversion bias and the pressure to lower CpG content.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Andrea Di Gioacchino", + "author_inst": "Ecole Normale Superieure, PSL and CNRS" + }, + { + "author_name": "Petr Sulc", + "author_inst": "Arizona State University" + }, + { + "author_name": "Anastassia V Komarova", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Benjamin D Greenbaum", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Remi Monasson", + "author_inst": "Ecole Normale Superieure, PSL and CNRS" + }, + { + "author_name": "Simona Cocco", + "author_inst": "Ecole Normale Superieure, PSL and CNRS" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.05.07.082487", "rel_title": "COVID-19: Viral-host interactome analyzed by network based-approach model to study pathogenesis of SARS-CoV-2 infection.", @@ -1465111,37 +1468063,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.05.06.080630", - "rel_title": "In Silico Trial to test COVID-19 candidate vaccines: a case study with UISS platform", - "rel_date": "2020-05-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.06.080630", - "rel_abs": "SARS-CoV-2 is a severe respiratory infection that infects humans. Its outburst entitled it as a pandemic emergence. To get a grip on this outbreak, specific preventive and therapeutic interventions are urgently needed. It must be said that, until now, there are no existing vaccines for coronaviruses. To promptly and rapidly respond to pandemic events, the application of in silico trials can be used for designing and testing medicines against SARS-CoV-2 and speed-up the vaccine discovery pipeline, predicting any therapeutic failure and minimizing undesired effects. Here, we present an in silico platform that showed to be in very good agreement with the latest literature in predicting SARS-CoV-2 dynamics and related immune system host response. Moreover, it has been used to predict the outcome of one of the latest suggested approach to design an effective vaccine, based on monoclonal antibody. Universal Immune System Simulator (UISS) in silico platform is potentially ready to be used as an in silico trial platform to predict the outcome of vaccination strategy against SARS-CoV-2.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Giulia Russo", - "author_inst": "University of Catania" - }, - { - "author_name": "Marzio Pennisi", - "author_inst": "Universita Piemonte Orientale" - }, - { - "author_name": "Marco Viceconti", - "author_inst": "Alma Mater Studiorum - University of Bologna" - }, - { - "author_name": "Francesco Pappalardo", - "author_inst": "University of Catania" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.05.07.082925", "rel_title": "A Combined approach of MALDI-TOF Mass Spectrometry and multivariate analysis as a potential tool for the detection of SARS-CoV-2 virus in nasopharyngeal swabs.", @@ -1466256,6 +1469177,109 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.06.080119", + "rel_title": "Multiple SARS-CoV-2 introductions shaped the early outbreak in Central Eastern Europe: comparing Hungarian data to a worldwide sequence data-matrix", + "rel_date": "2020-05-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.06.080119", + "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus 2 is the third highly pathogenic human coronavirus in history. Since the emergence in Hubei province, China, during late 2019 the situation evolved to pandemic level. Following China, Europe was the second epicenter of the pandemic. To better comprehend the detailed founder mechanisms of the epidemic evolution in Central-Eastern Europe, particularly in Hungary, we determined the full-length SARS-CoV-2 genomes from 32 clinical samples collected from laboratory confirmed COVID-19 patients over the first month of disease in Hungary. We applied a haplotype network analysis on all available complete genomic sequences of SARS-CoV-2 from GISAID database as of the 21th of April, 2020. We performed additional phylogenetic and phylogeographic analyses to achieve the recognition of multiple and parallel introductory events into our region. Here we present a publicly available network imaging of the worldwide haplotype relations of SARS-CoV-2 sequences and conclude the founder mechanisms of the outbreak in Central-Eastern Europe.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Gabor Kemenesi", + "author_inst": "University of Pecs" + }, + { + "author_name": "Safia Zeghbib", + "author_inst": "University of Pecs" + }, + { + "author_name": "Balazs Somogyi", + "author_inst": "University of Pecs" + }, + { + "author_name": "Gabor E Toth", + "author_inst": "University of Pecs" + }, + { + "author_name": "Krisztian Banyai", + "author_inst": "Centre for Agricultural Research, Hungary" + }, + { + "author_name": "Norbert Solymosi", + "author_inst": "University of Veterinary Medicine Budapest" + }, + { + "author_name": "Peter M Szabo", + "author_inst": "Stromal Biology, Bristol-Myers Squibb, Princeton" + }, + { + "author_name": "Istvan Szabo", + "author_inst": "National Food Safety Office, Budapest" + }, + { + "author_name": "Adam Balint", + "author_inst": "National Food Safety Office, Budapest" + }, + { + "author_name": "Peter Urban", + "author_inst": "Szentagothai Research Centre, Bioinformatics Research Group" + }, + { + "author_name": "Robert Herczeg", + "author_inst": "Szentagothai Research Centre, Bioinformatics Research Group" + }, + { + "author_name": "Attila Gyenesei", + "author_inst": "Szentagothai Research Centre, Bioinformatics Research Group" + }, + { + "author_name": "Agnes Nagy", + "author_inst": "Hungarian Defense Forces, Military Medical Centre" + }, + { + "author_name": "Csaba I Pereszlenyi", + "author_inst": "Hungarian Defense Forces, Military Medical Centre" + }, + { + "author_name": "Gergely Babinszky", + "author_inst": "Hungarian Defense Forces, Military Medical Centre" + }, + { + "author_name": "Gabor Dudas", + "author_inst": "Hungarian Defense Forces, Military Medical Centre" + }, + { + "author_name": "Gabriella Terhes", + "author_inst": "Institute of Clinical Microbiology, University of Szeged" + }, + { + "author_name": "Viktor Zoldi", + "author_inst": "Independent researcher, Vantaa, Finland" + }, + { + "author_name": "Robert Lovas", + "author_inst": "Institute for Computer Science and Control, Hungarian Academy of Sciences" + }, + { + "author_name": "Szabolcs Tenczer", + "author_inst": "Institute for Computer Science and Control, Hungarian Academy of Sciences" + }, + { + "author_name": "Laszlo Kornya", + "author_inst": "Central Hospital of Southern Pest, Budapest" + }, + { + "author_name": "Ferenc Jakab", + "author_inst": "University of Pecs" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.05.079202", "rel_title": "Neutralization of SARS-CoV-2 by destruction of the prefusion Spike", @@ -1466433,57 +1469457,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.05.06.077883", - "rel_title": "Coronavirus activates a stem cell-mediated defense mechanism that accelerates the activation of dormant tuberculosis: implications for the COVID-19 pandemic", - "rel_date": "2020-05-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.06.077883", - "rel_abs": "We postulate that similar to bacteria, adult stem cells may also exhibit an innate defense mechanism to protect their niche. Here, we provide preliminary data on stem cell based innate defense against a mouse model of coronavirus, murine hepatitis virus-1 (MHV-1) infection. In a mouse model of mesenchymal stem cell (MSC) mediated Mycobacterium tuberculosis (Mtb) dormancy, MHV-1 infection in the lung exhibited 20 fold lower viral loads than the healthy control mice, suggesting the potential enhancement of an anti-MHV-1 defense by Mtb. This defense mechanism involves the in vivo expansion and reprogramming of CD271+MSCs in the lung to an enhanced stemness phenotype. The reprogrammed MSCs facilitate the activation of stemness genes, intracellular Mtb replication, and extracellular release of Mtb. The conditioned media of the reprogrammed MSCs exhibit direct anti-viral activity in an in vitro model of MHV-1 induced toxicity to type II alveolar epithelial cells. Thus, our data suggest that reprogrammed MSCs exert a unique innate defense against MHV-1 by activating dormant Mtb. The molecular details of this anti-viral defense mechanism against coronavirus could be further studied to develop a vaccine against COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Lekhika Pathak", - "author_inst": "KaviKrishna Laboratory, Guwahati Biotech Park, Indian Institute of Technology, Guwahati, India" - }, - { - "author_name": "Sukanya Gayan", - "author_inst": "KaviKrishna Laboratory, Guwahati Biotech Park, Indian Institute of Technology, Guwahati, India" - }, - { - "author_name": "Bidisha Pal", - "author_inst": "Thoreau Laboratory for Global Health, M2D2, University of Massachusetts, Lowell" - }, - { - "author_name": "Joyeeta Talukdar", - "author_inst": "KaviKrishna Laboratory, Guwahati Biotech Park, Indian Institute of Technology, Guwahati, India" - }, - { - "author_name": "Seema Bhuyan", - "author_inst": "KaviKrishna Laboratory, Guwahati Biotech Park, Indian Institute of Technology, Guwahati, India" - }, - { - "author_name": "Sorra Sandhya", - "author_inst": "KaviKrishna Laboratory, Guwahati Biotech Park, Indian Institute of Technology, Guwahati, India" - }, - { - "author_name": "Herman Yeger", - "author_inst": "Hospital for Sick Children, Toronto" - }, - { - "author_name": "Debabrat Baishya", - "author_inst": "Gauhati University, Assam, India" - }, - { - "author_name": "Bikul Das", - "author_inst": "KaviKrishna Laboratory, Guwahati Biotech Park, Indian Institute of Technology, Guwahati, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.05.079939", "rel_title": "Identification of novel mutations in RNA-dependent RNA polymerases of SARS-CoV-2 and their implications", @@ -1467826,6 +1470799,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.05.01.20086801", + "rel_title": "Efficient prevalence estimation and infected sample identification with group testing for SARS-CoV-2", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20086801", + "rel_abs": "Extensive virological testing is central to SARS-CoV-2 containment, but many settings face severe limitations on testing. Group testing offers a way to increase throughput by testing pools of combined samples; however, most proposed designs have not yet addressed key concerns over sensitivity loss and implementation feasibility. Here, we combine a mathematical model of epidemic spread and empirically derived viral kinetics for SARS-CoV-2 infections to identify pooling designs that are robust to changes in prevalence, and to ratify losses in sensitivity against the time course of individual infections. Using this framework, we show that prevalence can be accurately estimated across four orders of magnitude using only a few dozen pooled tests without the need for individual identification. We then exhaustively evaluate the ability of different pooling designs to maximize the number of detected infections under various resource constraints, finding that simple pooling designs can identify up to 20 times as many positives compared to individual testing with a given budget. We illustrate how pooling affects sensitivity and overall detection capacity during an epidemic and on each day post infection, finding that sensitivity loss is mainly attributed to individuals sampled at the end of infection when detection for public health containment has minimal benefit. Crucially, we confirm that our theoretical results can be accurately translated into practice using pooled human nasopharyngeal specimens. Our results show that accounting for variation in sampled viral loads provides a nuanced picture of how pooling affects sensitivity to detect epidemiologically relevant infections. Using simple, practical group testing designs can vastly increase surveillance capabilities in resource-limited settings.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Brian Cleary", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "James A Hay", + "author_inst": "Harvard T H Chan School of Public Health" + }, + { + "author_name": "Brendan Blumenstiel", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Maegan Harden", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Michelle Cipicchio", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Jon Bezney", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Brooke Simonton", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "David Hong", + "author_inst": "Wharton Statistics, University of Pennsylvania" + }, + { + "author_name": "Madikay Senghore", + "author_inst": "Harvard School of Public Health" + }, + { + "author_name": "Abdul K Sesay", + "author_inst": "MRC Unit The Gambia at London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Stacey Gabriel", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Aviv Regev", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Michael J Mina", + "author_inst": "Harvard School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.02.20084947", "rel_title": "Voluntary Cyclical Distancing: A potential alternative to constant level mandatory social distancing, relying on an 'infection weather report'", @@ -1467923,33 +1470963,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.01.20087155", - "rel_title": "Asymptomatic infection and herd immunity of COVID-19 in Wuhan and Japan", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087155", - "rel_abs": "BackgroundIn Japan, as a measure to inhibit the COVID-19 outbreak, voluntary restrictions against going out (VRG) have been applied.\n\nObjectMobility information provided by Apple Inc. and NTT Docomo were assessed in terms of its usefulness in predicting conditions exacerbating an outbreak.\n\nMethodA polynomial function was applied to daily Apple and Docomo data to calculate the observed R(t).\n\nResultsThe correlation coefficient among Apple and Docomo data was 0.91. The adjusted coefficient of determination for R(t) for the whole study period was higher using Docomo data than when Apple data were used. When we regressed R(t) on daily Apple and Docomo data simultaneously, the estimated coefficient of Docomo data was not significant.\n\nDiscussion and ConclusionWe demonstrated that Apple mobility data might be superior to Docomo data for explaining the entire course of the COVID-19 outbreak in Japan.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Junko Kurita", - "author_inst": "Department of Nursing , Tokiwa University, Ibaraki, Japan" - }, - { - "author_name": "Tamie Sugawara", - "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" - }, - { - "author_name": "Yasushi Ohkusa", - "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.01.20087064", "rel_title": "The use of facemasks by the general population to prevent transmission of Covid 19 infection: A systematic review.", @@ -1469028,6 +1472041,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.01.20087833", + "rel_title": "Early Evidence of Disparities in COVID-19 Testing in US Cities", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087833", + "rel_abs": "BackgroundPreliminary evidence has shown inequities in COVID-19 related cases and deaths in the US.\n\nObjectiveWe explored the emergence of spatial inequities in COVID-19 testing, positivity, confirmed cases, and mortality in New York City, Philadelphia, and Chicago during the first six months of the pandemic.\n\nDesignEcological, observational study at the zip code tabulation area (ZCTA) level from March to September 2020.\n\nSettingChicago, New York City and Philadelphia.\n\nParticipantsAll populated ZCTAs in the three cities.\n\nMeasuresOutcomes were ZCTA-level COVID-19 testing, positivity, confirmed cases, and mortality cumulatively through the end of September. Predictors were the CDC social vulnerability index and its four domains, obtained from the 2014-2018 American Community Survey. We examined the spatial autocorrelation of COVID-19 outcomes using global and local Morans I and estimated associations using spatial conditional autoregressive negative binomial models.\n\nResultsWe found spatial clusters of high and low positivity, confirmed cases and mortality, co-located with clusters of low and high social vulnerability. We also found evidence for the existence of spatial inequities in testing, positivity, confirmed cases and mortality for the three cities. Specifically, neighborhoods with higher social vulnerability had lower testing rates, higher positivity ratios, confirmed case rates and mortality rates.\n\nLimitationsZCTAs are imperfect and heterogeneous geographical units of analysis. We rely on surveillance data, which may be incomplete.\n\nConclusionWe found spatial inequities in COVID-19 testing, positivity, confirmed cases, and mortality in three large cities of the US.\n\nRegistrationN/A\n\nFunding sourceNIH (DP5OD26429) and RWJF (77644)", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Usama Bilal", + "author_inst": "Drexel University" + }, + { + "author_name": "Loni P Tabb", + "author_inst": "Drexel University" + }, + { + "author_name": "Sharrelle Barber", + "author_inst": "Drexel University" + }, + { + "author_name": "Ana V Diez-Roux", + "author_inst": "Drexel University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.01.20087460", "rel_title": "Prediction of Spreads of COVID-19 in India from Current Trend", @@ -1469117,93 +1472161,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.02.20087221", - "rel_title": "Evaluating efficiency of pooling specimens for PCR-based detection of COVID-19", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20087221", - "rel_abs": "In the age of a pandemic, such as the ongoing one caused by SARS-CoV-2, the world faces limited supply of tests, PPE and reagents, and factories are struggling to meet the growing demands. This study aimed to evaluate the efficacy of pooling specimen for testing of SARS-CoV-2 virus, to determine whether costs and resource savings could be achieved without impacting the sensitivity of the testing. Ten specimens were pooled for testing, containing either one or two known positive specimen of varying viral concentrations. Pooling specimens did not affect the sensitivity of detecting SARS-CoV-2, and the PCR cycle threshold (Ct) between testing of pooling specimen and subsequent individual testing was not significantly different using paired t-test. This study also identified cost savings garnered from pooling of specimen for testing at 4 differing prevalence rates, ranging from 0.1-10%. Pooling specimens to test for COVID-19 infection in low prevalence areas or in low risk population can dramatically decrease the resources burden on lab operations by up to 80%. This paves the possibility for large-scale population screening, allowing for assured policy decisions by governmental bodies to ease lockdown restrictions in areas with low incidence of infection, or with lower risk populations.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Supaporn Wacharapluesadee", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, K" - }, - { - "author_name": "Thongchai Kaewpom", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, K" - }, - { - "author_name": "Weenassarin Ampoot", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, K" - }, - { - "author_name": "Siriporn Ghai", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, K" - }, - { - "author_name": "Worrawat Khamhang", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, K" - }, - { - "author_name": "Kanthita Worachotsueptrakun", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, K" - }, - { - "author_name": "Phanni Wanthong", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, K" - }, - { - "author_name": "Chatchai Nopvichai", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, K" - }, - { - "author_name": "Thirawat Supharatpariyakorn", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, K" - }, - { - "author_name": "Opass Putcharoen", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Clinical Centre, King Chulalongkorn Memorial Hospital, Division of Infectious Diseases, Department of Medicine, Facu" - }, - { - "author_name": "Leilani Paitoonpong", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Clinical Centre, King Chulalongkorn Memorial Hospital, Division of Infectious Diseases, Department of Medicine, Facu" - }, - { - "author_name": "Gompol Suwanpimolkul", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Clinical Centre, King Chulalongkorn Memorial Hospital, Division of Infectious Diseases, Department of Medicine, Facu" - }, - { - "author_name": "Watsamon Jantarabenjakul", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Clinical Centre, King Chulalongkorn Memorial Hospital, Department of Pediatrics, Faculty of Medicine, Chulalongkorn " - }, - { - "author_name": "Pasin Hemachudha", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, K" - }, - { - "author_name": "Artit Krichphiphat", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, K" - }, - { - "author_name": "Rome Buathong", - "author_inst": "Department of Disease Control, Ministry of Public Health, Nonthaburi, TH" - }, - { - "author_name": "Tanarak Plipat", - "author_inst": "Department of Disease Control, Ministry of Public Health, Nonthaburi, TH" - }, - { - "author_name": "Thiravat Hemachudha", - "author_inst": "Thai Red Cross Emerging Infectious Diseases Health Science Centre, World Health Organization Collaborating Centre for Research and Training on Viral Zoonoses, K" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.02.20086231", "rel_title": "Trends in excess cancer and cardiovascular deaths in Scotland during the COVID-19 pandemic 30 December 2019 to 20 April 2020", @@ -1470570,6 +1473527,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.29.20084376", + "rel_title": "A novel deterministic forecast model for COVID-19 epidemic based on a single ordinary integro-differential equation", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20084376", + "rel_abs": "In this paper we present a new approach to deterministic modelling of COVID-19 epidemic. Our model dynamics is expressed by a single prognostic variable which satisfies an integro-differential equation. All unknown parameters are described with a single, time-dependent variable R(t). We show that our model has similarities to classic compartmental models, such as SIR, and that the variable R(t) can be interpreted as a generalized effective reproduction number. The advantages of our approach are the simplicity of having only one equation, the numerical stability due to an integral formulation and the reliability since the model is formulated in terms of the most trustable statistical data variable: the number of cumulative diagnosed positive cases of COVID-19. Once this dynamic variable is calculated, other non-dynamic variables, such as the number of heavy cases (hospital beds), the number of intensive-care cases (ICUs) and the fatalities, can be derived from it using a similarly stable, integral approach. The formulation with a single equation allows us to calculate from real data the values of the sample effective reproduction number, which can then be fitted. Extrapolated values of R(t) can be used in the model to make reliable forecasts, though under the assumption that measures for reducing infections are maintained. We have applied our model to more than 15 countries and the ongoing results are available on a web-based platform [1]. In this paper, we focus on the data for two exemplary countries, Italy and Germany, and show that the model is capable of reproducing the course of the epidemic in the past and forecasting its course for a period of four to five weeks with a reasonable numerical stability.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Felix Koehler-Rieper", + "author_inst": "Goethe-Universtitaet Frankfurt, Germany" + }, + { + "author_name": "Claudius H. F. Roehl", + "author_inst": "Universitaet Leipzig, Germany" + }, + { + "author_name": "Enrico De Micheli", + "author_inst": "IBF - Consiglio Nazionale Delle Ricerche, Genova, Italy" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.01.20084384", "rel_title": "A Susceptible-Infected-Removed (SIR) model of COVID-19 epidemic trend in Malaysia under Movement Control Order (MCO) using a data fitting approach", @@ -1470683,65 +1473667,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.29.20085068", - "rel_title": "Antibody Profiling and Prevalence in the US population during the SARS-CoV2 Pandemic", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20085068", - "rel_abs": "BackgroundAntibody diagnostics play an important role in disease detection and can potentially aid in monitoring of the immune responses to see if an individual has developed immunity. Developing high throughput diagnostics which does not involve handling of infectious material becomes imperative in the case of pandemics such as the recent outbreak of SARS-CoV2.\n\nMethodsA protein microarray technology was used to detect the plurality of antibody response to four novel antigens namely S1 glycoprotein, Receptor binding domain (RBD), S2 glycoprotein and Nucleoprotein of the novel coronavirus named SARS-CoV2 using serum samples. A DBS card was additionally used to compare its performance with a venipuncture-based serum separator tube (SST) draw.\n\nResultsThe three main subclasses of antibodies IgM, IgA and IgG were analyzed to see the variations in immune responses in the affected population and compared to their microbial RT-PCR based NP swab results. The clinical sensitivity and specificity were determined to be 98.1% and 98.6%. In the matrix comparison study, which would enable patients to test without risk of transmitting the virus, DBS matched with higher than 98% accuracy to a venipuncture-based SST collection.\n\nConclusionMultiplex testing enables higher sensitivity and specificity which is essential while establishing exposure on a population scale. This flexible platform along with a discrete collection methodology would be crucial and broadly useful to scale up testing in current and future pandemics. Minimum sample volume that can be collected using DBS cards can be processed in this multiplex pillar plate format enabling the capacity to provide the reliability of high throughput analyzers while having the ease of collection similar to rapid tests.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Hari K Krishnamurthy", - "author_inst": "Vibrant Sciences" - }, - { - "author_name": "Vasanth Jayaraman", - "author_inst": "Vibrant Sciences" - }, - { - "author_name": "Karthik Krishna", - "author_inst": "Vibrant Sciences" - }, - { - "author_name": "Karenah E Rajasekaran", - "author_inst": "Vibrant America" - }, - { - "author_name": "Tianhao Wang", - "author_inst": "Vibrant Sciences" - }, - { - "author_name": "Kang Bei", - "author_inst": "Vibrant Sciences" - }, - { - "author_name": "John J Rajasekaran", - "author_inst": "Vibrant Sciences" - }, - { - "author_name": "Inna Yaskin", - "author_inst": "Elite Medical Center" - }, - { - "author_name": "Alex J Rai", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Rok Seon Choung", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Joseph A Murray", - "author_inst": "Mayo Clinic" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.29.20085233", "rel_title": "The Utility of rRT-PCR in Diagnosis and Assessment of Case-fatality rates of COVID-19 In the Iranian Population. Positive Test Results are a Marker for Illness Severity", @@ -1472128,6 +1475053,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, + { + "rel_doi": "10.1101/2020.04.30.20086462", + "rel_title": "Kidney Allograft Recipients Diagnosed with Coronavirus Disease-2019: A Single Center Report", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086462", + "rel_abs": "BackgroundOrgan graft recipients receiving immunosuppressive therapy are likely to be at heightened risk for the Coronavirus Disease 2019 (Covid-19) and adverse outcomes including death. It is therefore important to characterize the clinical course and outcome of Covid-19 in this vulnerable population and identify therapeutic strategies that are safe.\n\nMethodsWe performed a retrospective chart review of 54 adult kidney transplant patients diagnosed with Covid-19 and all managed in New York State, the epicenter of Covid-19 pandemic. All 54 patients were evaluated by video visits, or phone interviews, and referred to our Fever Clinic or Emergency Room for respiratory illness symptoms consistent with Covid-19 and admitted if deemed necessary from March 13, 2020 to April 20, 2020. Characteristics of the patients were stratified by hospitalization status and disease severity. Clinical course including alterations in immunosuppressive therapy were retrieved from their electronic medical records. Primary outcomes included recovery from Covid-19 symptoms, acute kidney injury, graft failure, and case fatality rate.\n\nResultsOf the 54 SARS-Cov-2 positive kidney transplant recipients, 39 with moderate to severe symptoms were admitted and 15 with mild symptoms were managed at home. Hospitalized patients compared to non-hospitalized patients were more likely to be male, of Hispanic ethnicity, and to have cardiovascular disease. At baseline, all but 2 were receiving tacrolimus, mycophenolate mofetil (MMF) and 32 were on a steroid free immunosuppression regimen. Tacrolimus dosage was reduced in 46% of hospitalized patients and maintained at baseline level in the non-hospitalized cohort. Mycophenolate mofetil (MMF) dosage was maintained at the baseline dosage in 11% of hospitalized patients and 64% of non-hospitalized patients and was stopped in 61% hospitalized patients and 0% in the non-hospitalized cohort. Azithromycin or doxycycline were prescribed at a similar rate among hospitalized and non-hospitalized patients (38% vs. 40%). In addition, 50% of hospitalized patients were treated for concurrent bacterial infections including pneumonia, urinary tract infections and sepsis. Hydroxychloroquine was prescribed in 79% of hospitalized patients and only one of 15 non-hospitalized patients. Acute kidney injury occurred in 51% of hospitalized patients. Patients with severe disease were more likely to have elevations in inflammatory biomarkers at presentation. At a median of 21 days follow up, 67% of patients have had their symptoms resolved or improved and 33% have persistent symptoms. Graft failure requiring hemodialysis occurred in 3 of 39 hospitalized patients (8%). Three of 39 (8%) hospitalized patients expired and none of the 15 non-hospitalized patients expired.\n\nConclusionsClinical presentation of Covid-19 in kidney transplant recipients was similar to what has been described in the general population. The case fatality rate in our entire cohort of 54 kidney transplant recipients was reassuringly low and patients with mild symptomology could be successfully managed at home. Data from the our study suggest that a strategy of systematic screening and triage to outpatient or inpatient care, close monitoring, early management of concurrent bacterial infections and judicious use of immunosuppressive drugs rather than cessation is beneficial.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Michelle Lubetzky", + "author_inst": "New York Presbyterian, Weill Cornell" + }, + { + "author_name": "Meredith Aull", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Rebecca Craig-Shapiro", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Jun Lee", + "author_inst": "New York Presbyterian" + }, + { + "author_name": "John Lee", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Samuel Sultan", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Jehon Marku-Podvorica", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Laura Gingras", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Rosy Priya Kodiyanplakkal", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Choli Hartono", + "author_inst": "New York Presbyterian" + }, + { + "author_name": "Stuart Saal", + "author_inst": "New York Presbyterian" + }, + { + "author_name": "Thangamani Muthukumar", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Sandip Kapur", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Manikkam Suthanthiran", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Darshana Dadhania", + "author_inst": "New York Presbyterian-Weill Cornell" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "transplantation" + }, { "rel_doi": "10.1101/2020.04.30.20086447", "rel_title": "Evaluation of effects of public health interventions on COVID-19 transmission for Pakistan: A mathematical simulation study", @@ -1472249,37 +1475249,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.30.20086538", - "rel_title": "Novel Spatiotemporal Feature Extraction Parallel Deep Neural Network for Forecasting Confirmed Cases of Coronavirus Disease 2019", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086538", - "rel_abs": "The coronavirus disease 2019 pandemic continues as of March 26 and spread to Europe on approximately February 24. A report from April 29 revealed 1.26 million confirmed cases and 125 928 deaths in Europe. This study proposed a novel deep neural network framework, COVID-19Net, which parallelly combines a convolutional neural network (CNN) and bidirectional gated recurrent units (GRUs). Three European countries with severe outbreaks were studied--Germany, Italy, and Spain--to extract spatiotemporal feature and predict the number of confirmed cases. The prediction results acquired from COVID-19Net were compared to those obtained using a CNN, GRU, and CNN-GRU. The mean absolute error, mean absolute percentage error, and root mean square error, which are commonly used model assessment indices, were used to compare the accuracy of the models. The results verified that COVID-19Net was notably more accurate than the other models. The mean absolute percentage error generated by COVID-19Net was 1.447 for Germany, 1.801 for Italy, and 2.828 for Spain, which were considerably lower than those of the other models. This indicated that the proposed framework can accurately predict the accumulated number of confirmed cases in the three countries and serve as a crucial reference for devising public health strategies.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Chiou-Jye Huang", - "author_inst": "Jiangxi University of Science and Technology" - }, - { - "author_name": "Yamin Shen", - "author_inst": "Jiangxi University of Science and Technology" - }, - { - "author_name": "Ping-Huan Kuo", - "author_inst": "National Pingtung University" - }, - { - "author_name": "Yung-Hsiang Chen", - "author_inst": "National Pingtung University of Science and Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.05.20075507", "rel_title": "Clinical and Genetic Characteristics of Covid-19 Patients from UK Biobank", @@ -1473310,6 +1476279,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.30.20081828", + "rel_title": "Modeling COVID-19 on a network: super-spreaders, testing and containment", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20081828", + "rel_abs": "To model COVID-19 spread, we use an SEIR agent-based model on a graph, which takes into account several important real-life attributes of COVID-19: super-spreaders, realistic epidemiological parameters of the disease, testing and quarantine policies. We find that mass-testing is much less effective than testing the symptomatic and contact tracing, and some blend of these with social distancing is required to achieve suppression. We also find that the fat tail of the degree distribution matters a lot for epidemic growth, and many standard models do not account for this. Additionally, the average reproduction number for individuals, equivalent in many models to R0, is not an upper bound for the effective reproduction number, R. Even with an expectation of less than one new case per person, our model shows that exponential spread is possible. The parameter which closely predicts growth rate is the ratio between 2nd to 1st moments of the degree distribution. We provide mathematical arguments to argue that certain results of our simulations hold in more general settings.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ofir Reich", + "author_inst": "Google" + }, + { + "author_name": "Guy Shalev", + "author_inst": "Google" + }, + { + "author_name": "Tom Kalvari", + "author_inst": "Tel Aviv University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.30.20077594", "rel_title": "Early transmission dynamics and control of COVID-19 in a southern hemisphere setting: Lima-Peru, February 29th-March 30th, 2020 .", @@ -1473435,25 +1476431,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2020.04.28.20082990", - "rel_title": "A simple model to show the relative risk of viral aerosol infection and the benefit of wearing masks in different settings with implications for Covid-19 .", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20082990", - "rel_abs": "BackgroundWidespread use of masks in the general population is being used in many countries for control of Covid-19. There has been reluctance on the part of the WHO and some governments to recommend this.\n\nMethodologyA basic model has been constructed to show the relative risk of aerosol from normal breathing in various situations together with the relative benefit from use of different masks.\n\nResultsThe benefit from mask use between individuals is multiplicative not additive and although social distancing at 2 meters appears beneficial with regards to aerosol infectivity, in confined areas this is time limited requiring additional measures such as masks. The model shows the relative benefit of masks when social distancing is not possible at all times, or when in confined areas which can also be aided by efficient ventilation. Where a person is in one place for a prolonged period there is more risk requiring protection.\n\nConclusionsMasks should be used in the above situations especially at an early stage of an outbreak. Public health planning requires stockpiling of masks and encouraging everyone to have suitable masks in their household when supplies are normalised. In the absence of widely available good quality masks the use of a cloth mask will be better than no protection at all.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Gerald D Barr", - "author_inst": "Independent Health Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.30.20079657", "rel_title": "Geospatial Correlation Between COVID-19 Health Misinformation on Social Media and Poisoning with Household Cleaners", @@ -1474972,6 +1477949,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.29.20084244", + "rel_title": "Are COVID-19 infected children with gastrointestinal symptoms different from those without symptoms? A comparative study of the clinical characteristics and epidemiological trend of 244 pediatric cases from Wuhan", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20084244", + "rel_abs": "ObjectiveCOVID-19 patients presenting with gastrointestinal (GI) symptoms occur in both adults and children. To date, however, no large sample size study focusing on gastrointestinal symptoms in pediatric cases has been published. We analyzed COVID-19 infected children in Wuhan who presented with initial GI symptoms to determine the GI characteristics and epidemiological trend of the disease.\n\nDesignWe retrospectively analyzed 244 children patients confirmed with COVID-19 at Wuhan Childrens Hospital from 21 Jan to 20 Mar 2020. Symptomatic cases were divided into two groups according to whether the patients presented with or without GI symptoms on admission. Demographic, epidemiological, symptoms, and laboratory data were compared. We also analyzed the respective trends of case number changes of GI cases and asymptomatic cases.\n\nResults34 out of 193 symptomatic children had GI symptoms. They had lower median age and weight, a higher rate of fever, a longer length of stay and more hematological and biochemical abnormalities than patients without GI symptoms. There was no significant difference in chest CT findings or stool SARS-CoV-2 test positive percentages between the two groups. The number of patients admitted with GI symptoms showed an overall downward trend with time. At the time of writing, 242 patients were discharged, one died, and one critically ill patient was still in the intensive care unit.\n\nConclusionCOVID-19 infected children with GI symptoms are prone to presenting with more clinical and laboratory abnormalities than patients without GI symptoms. More attention and timely hospital admission are needed for these patients.\n\nSignificance of this studyO_LSTWhat is already known on this subject?C_LSTO_LICOVID-19 is now a pandemic with more than 1.6 million people infected worldwide\nC_LIO_LIAlthough attacking the respiratory tract mostly, both adult and children infected with COVID-19 can present with GI symptoms\nC_LI\n\nO_LSTWhat are the new findings?C_LSTO_LIInfants younger than two years old and presence of fever are the two risk factors of presenting with GI symptoms\nC_LIO_LIA high proportion of patients without GI symptoms and asymptomatic patients will have positive RT-PCR for the virus in stool\nC_LIO_LIEarlier testing through contact screening of family members means more COVID-19 infected children are diagnosed when completely asymptomatic\nC_LI\n\nO_LSTHow might it impact on clinical practice in the foreseeable future?C_LSTO_LIThe presence of COVID-19 in stool in infected children will have a major implication for parents and carers of young infants\nC_LIO_LIIncreasing number of asymptomatic COVID-19 patients who are detected through screening could provide a useful lesson for other countries still experiencing the rise and peak of the pandemic\nC_LI", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Xiaoli Xiong", + "author_inst": "Wuhan Children's Hospital" + }, + { + "author_name": "Kenenth Kak-Yuen Wong", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Shuiqing Chi", + "author_inst": "Union Hospital, Wuhan" + }, + { + "author_name": "Aifen Zhou", + "author_inst": "Wuhan Children's Hospital" + }, + { + "author_name": "Jianqiao Tang", + "author_inst": "Wuhan Children's Hospital" + }, + { + "author_name": "Lishan Zhou", + "author_inst": "Wuhan Children's Hospital" + }, + { + "author_name": "Patrick Ho-yu Chung", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Gilbert Chua", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Keith TS Tung", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Ian CK Wong", + "author_inst": "The Univeristy of Hong Kong" + }, + { + "author_name": "Celine SL Chui", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Xue Li", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Mike Yat-wah Kwan", + "author_inst": "Princess Margaret Hospital, Hong Kong" + }, + { + "author_name": "Wilfred HS Wong", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Marco Hok-kung Ho", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Godfrey CF Chan", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Guoqing Cao", + "author_inst": "Union Hospital, Wuhan" + }, + { + "author_name": "Kang Li", + "author_inst": "Union Hospital, Wuhan" + }, + { + "author_name": "Patrick Ip", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Peng Chen", + "author_inst": "Wuhan Children's Hospital" + }, + { + "author_name": "Shaotao Tang", + "author_inst": "Union Hospital, Wuhan" + }, + { + "author_name": "Paul KH Tam", + "author_inst": "The University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.04.30.20083881", "rel_title": "Associations between psychiatric disorders, COVID-19 testing probability and COVID-19 testing results: Findings from a population-based study", @@ -1475101,33 +1478181,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.04.29.20084236", - "rel_title": "Battling the COVID-19 Pandemic: Is Bangladesh Prepared?", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20084236", - "rel_abs": "Following detection of the first few COVID-19 cases in early March, Bangladesh has stepped up its efforts to strengthen capacity of the healthcare system to avert a crisis in the event of a surge in the number of cases. This paper sheds light on the preparedness of the healthcare system by examining the spatial distribution of isolation beds across districts and divisions, forecasting the number of ICU units that may be required in the short term and analyzing the availability of frontline healthcare workers to combat the pandemic. As of May 2, COVID-19 cases have been found in 61 of the 64 districts in Bangladesh with Dhaka District being the epicenter. Seventy-one percent of the cases have been identified in 6 neighboring districts, namely, Dhaka, Narayanganj, Gazipur, Narsingdi, Munsiganj and Kishoreganj, which appear to form a spatial cluster. However, if one takes into account the population at risk, the prevalence appears to be highest in Dhaka, followed by Narayanganj, Gazipur, Kishorganj, Narsingdi and Munshiganj. These regions may therefore be flagged as the COVID-19 hotspots in Bangladesh. Among the eight divisions, prevalence is highest in Dhaka Division followed by Mymensingh. The number of cases per million exceeds the number of available isolation beds per million in the major hotspots indicating that there is a risk of the healthcare system becoming overwhelmed should the number of cases rise. This is especially true for Dhaka Division, where the ratio of COVID-19 patients to doctors appears to be alarmingly high. My-mensingh Division also has a disproportionately small number of doctors relative to the number of COVID-19 patients. Using second order polynomial regression, the analysis predicts that even if all ICU beds are allocated to COVID-19 patients, Bangladesh may run out of ICU beds soon after May 15, 2020. We conclude that in spite of a significant increase in hospital capacity during 2005-15 and a 57 % rise in the number of doctors during the same period, the healthcare system in Bangladesh and Dhaka Division in particular, may not be fully prepared to handle the COVID-19 crisis. Thus, further steps need to be taken to flatten the curve and improve healthcare capacity.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Hasinur Rahaman Khan", - "author_inst": "ISRT, University of Dhaka, Bangladesh" - }, - { - "author_name": "Tamanna Howlader", - "author_inst": "ISRT, University of Dhaka, Bangladesh" - }, - { - "author_name": "Md. Mazharul Islam", - "author_inst": "Bangladesh Institute of Governance and Management" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2020.04.28.20084079", "rel_title": "Patient-Led COVID-19 Triage Systems and Case Fatality Rates: A Comparative Study Between Singapore, Japan, Norway, the USA and the UK.", @@ -1476718,6 +1479771,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.05.03.073080", + "rel_title": "Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication", + "rel_date": "2020-05-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.03.073080", + "rel_abs": "The COVID-19 pandemic, attributed to the SARS-CoV-2 coronavirus infection, resulted in millions infected worldwide and an immediate need for antiviral treatments. The main protease (Mpro) in SARS-CoV-2 is a viable drug target because of its essential role in the cleavage of the virus polypeptide and subsequent viral replication. Feline infectious peritonitis, a fatal infection in cats caused by a coronavirus, was successfully treated previously with a dipeptide-based protease inhibitor. Here we show this drug, GC376, and its analog GC373, are effective inhibitors of the Mpro from both SARS-CoV and SARS-CoV-2 with IC50 values in the nanomolar range. Crystal structures of the SARS-CoV and SARS-CoV-2 Mpro with these inhibitors have a covalent modification of the nucleophilic Cys145. NMR analysis reveals that inhibition proceeds via reversible formation of a hemithioacetal. GC373 and GC376 are potent inhibitors of SARS-CoV-2 in cell culture, with EC50 values near one micromolar and little to no toxicity. These protease inhibitors are soluble, non-toxic, and bind reversibly. They are strong drug candidates for the treatment of human coronavirus infections because they have already been successful in animals (cats). The work here lays the framework for their use in human trials for the treatment of COVID-19.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Wayne Vuong", + "author_inst": "University of Alberta" + }, + { + "author_name": "Muhammad Bashir Khan", + "author_inst": "University of Alberta" + }, + { + "author_name": "Conrad Fischer", + "author_inst": "University of Alberta" + }, + { + "author_name": "Elena Arutyunova", + "author_inst": "University of Alberta" + }, + { + "author_name": "Tess Lamer", + "author_inst": "University of Alberta" + }, + { + "author_name": "Justin Shields", + "author_inst": "University of Alberta" + }, + { + "author_name": "Holly A Saffran", + "author_inst": "University of Alberta" + }, + { + "author_name": "Ryan T McKay", + "author_inst": "University of Alberta" + }, + { + "author_name": "Marco J van Belkum", + "author_inst": "University of Alberta" + }, + { + "author_name": "Michael Joyce", + "author_inst": "University of Alberta" + }, + { + "author_name": "Howard S Young", + "author_inst": "University of Alberta" + }, + { + "author_name": "D. Lorne Tyrrell", + "author_inst": "University of Alberta" + }, + { + "author_name": "John C Vederas", + "author_inst": "University of Alberta" + }, + { + "author_name": "M Joanne Lemieux", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.05.02.043554", "rel_title": "Catalytic cleavage of HEAT and subsequent covalent binding of the tetralone moiety by the SARS-CoV-2 main protease", @@ -1477179,41 +1480303,6 @@ "type": "confirmatory results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.05.03.074971", - "rel_title": "Pathogen Reduction Of SARS-CoV-2 Virus In Plasma And Whole Blood Using Riboflavin And UV Light", - "rel_date": "2020-05-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.03.074971", - "rel_abs": "BACKGROUNDSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has recently been identified as the causative agent for Coronavirus Disease 2019 (COVID-19). The ability of this agent to be transmitted by blood transfusion has not been documented, although viral RNA has been detected in serum. Exposure to treatment with riboflavin and ultraviolet light (R + UV) reduces blood-borne pathogens while maintaining blood product quality. Here, we report on the efficacy of R + UV in reducing SARS-CoV-2 infectivity when tested in human plasma and whole blood products.\n\nSTUDY DESIGN AND METHODSSARS-CoV-2 (isolate USA-WA1/2020) was used to inoculate plasma and whole blood units that then underwent treatment with riboflavin and UV light (Mirasol Pathogen Reduction Technology System, Terumo BCT, Lakewood, CO). The infectious titers of SARS-CoV-2 in the samples before and after R + UV treatment were determined by plaque assay on Vero cells. Each plasma pool (n=9) underwent R + UV treatment performed in triplicate using individual units of plasma and then repeated using individual whole blood donations (n=3).\n\nRESULTSRiboflavin and UV light reduced the infectious titer of SARS-CoV-2 below the limit of detection for plasma products at 60-100% of the recommended energy dose. At the UV light dose recommended by the manufacturer, the mean log reductions in the viral titers were [≥] 4.79 {+/-} 0.15 Logs in plasma and 3.30 {+/-} 0.26 in whole blood units.\n\nCONCLUSIONRiboflavin and UV light effectively reduced the titer of SARS-CoV-2 to the limit of detection in human plasma and by 3.30 {+/-} 0.26 on average in whole blood. Two clades of SARS-CoV-2 have been described and questions remain about whether exposure to one strain confers strong immunity to the other. Pathogen-reduced blood products may be a safer option for critically ill patients with COVID-19, particularly those in high-risk categories.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Izabela Ragan", - "author_inst": "Colorado State University" - }, - { - "author_name": "Lindsay Hartson", - "author_inst": "Colorado State University" - }, - { - "author_name": "Heather Pidcoke", - "author_inst": "Colorado State University" - }, - { - "author_name": "Richard Bowen", - "author_inst": "Colorado State University" - }, - { - "author_name": "Raymond P. Goodrich", - "author_inst": "Colorado State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.04.077511", "rel_title": "Complexity in SARS-CoV-2 genome data: Price theory of mutant isolates", @@ -1478432,6 +1481521,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2020.04.27.20081794", + "rel_title": "Predicting community mortality risk due to CoVID-19 using machine learning and development of a prediction tool", + "rel_date": "2020-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081794", + "rel_abs": "BackgroundThe recent pandemic of CoVID-19 has emerged as a threat to global health security. There are a very few prognostic models on CoVID-19 using machine learning.\n\nObjectivesTo predict mortality among confirmed CoVID-19 patients in South Korea using machine learning and deploy the best performing algorithm as an open-source online prediction tool for decision-making.\n\nMaterials and methodsMortality for confirmed CoVID-19 patients (n=3,299) between January 20, 2020 and April 30, 2020 was predicted using five machine learning algorithms (logistic regression, support vector machine, K nearest neighbor, random forest and gradient boosting). Performance of the algorithms was compared, and the best performing algorithm was deployed as an online prediction tool.\n\nResultsThe random forest algorithm was the best performer in terms of predictive ability (accuracy=0.981), discrimination (area under ROC curve=0.886), calibration (Matthews Correlation Coefficient=0.459; Brier Score=0.063) and. The best performer algorithm (random forest) was deployed as the online CoVID-19 Community Mortality Risk Prediction tool named CoCoMoRP (https://ashis-das.shinyapps.io/CoCoMoRP/).\n\nConclusionsWe describe the development and deployment of an open-source machine learning tool to predict mortality risk among CoVID-19 confirmed patients using publicly available surveillance data. This tool can be utilized by potential stakeholders such as health providers and policy makers to triage patients at the community level in addition to other approaches.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "ASHIS DAS", + "author_inst": "The World Bank" + }, + { + "author_name": "Shiba Mishra", + "author_inst": "Credit Suisse Private Limited" + }, + { + "author_name": "Saji Saraswathy Gopalan", + "author_inst": "The World Bank Group" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.04.27.20081539", "rel_title": "An ARIMA Model to Forecast the Spread and the Final Size of COVID-2019 Epidemic in Italy", @@ -1478677,45 +1481793,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.28.20083311", - "rel_title": "Anosmia in COVID-19 patients", - "rel_date": "2020-05-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083311", - "rel_abs": "ObjectivesCoronaviruses (CoVs) have a neuroinvasive propensity, and the frequently reported symptoms of smelling and taste dysfunction in many COVID-19 patients may be related to the respective capability of SARS-CoV2, the cause of the current pandemic. In this study we objectified and quantified the magnitude and underreporting of the smelling dysfunction caused by COVID-19 using a standardized test.\n\nMethodsWe conducted a prospective cross-sectional study comparing the proportion of anosmia using Sniffin-sticks in those reporting a loss of smell, in those who did not as well as in uninfected controls. The outcome of anosmic versus not anosmic patients were recorded during hospital stay and at day 15 on a six-category ordinal scale. The study was approved by the institutional review board, all participants consented to the study.\n\nResults40% of 45 consecutive hospitalized COVID-19 patients and 0% of 45 uninfected controls consenting were diagnosed with anosmia. 44% of anosmic and 50% of hyposmic patients did not report having smelling problems. Anosmia or hyposmia was not predictive of a severe COVID-19 manifestation.\n\nConclusionsThe majority of COVID-19 patients have an objective anosmia and hyposmia, which often occurs unnoticed. These symptoms may be related to the neuroinvasive propensity of SARS-COV-2 and the unusual presentation of COVID-19 disease manifestations.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Daniel Hornuss", - "author_inst": "Section of Infectious Diseases, Department of Internal Medicine II, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Germany" - }, - { - "author_name": "Berit Lange", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Nils Schroeter", - "author_inst": "Department of Neurology and Neurophysiology, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Germany" - }, - { - "author_name": "Siegbert Rieg", - "author_inst": "Section of Infectious Diseases, Department of Internal Medicine II, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Germany" - }, - { - "author_name": "Winfried V. Kern", - "author_inst": "Section of Infectious Diseases, Department of Internal Medicine II, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Germany" - }, - { - "author_name": "Dirk Wagner", - "author_inst": "Section of Infectious Diseases, Department of Internal Medicine II, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.28.20083337", "rel_title": "Failure of the cobas(R) SARS-CoV-2 (Roche) E-gene assay is associated with a C-to-T transition at position 26340 of the SARS-CoV-2 genome", @@ -1480306,6 +1483383,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.27.20081893", + "rel_title": "Individual variation in susceptibility or exposure to SARS-CoV-2 lowers the herd immunity threshold", + "rel_date": "2020-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081893", + "rel_abs": "Individual variation in susceptibility and exposure is subject to selection by natural infection, accelerating the acquisition of immunity, and reducing herd immunity thresholds and epidemic final sizes. This is a manifestation of a wider population phenomenon known as \"frailty variation\". Despite theoretical understanding, public health policies continue to be guided by mathematical models that leave out considerable variation and as a result inflate projected disease burdens and overestimate the impact of interventions. Here we focus on trajectories of the coronavirus disease (COVID-19) pandemic in England and Scotland until November 2021. We fit models to series of daily deaths and infer relevant epidemiological parameters, including coefficients of variation and effects of non-pharmaceutical interventions which we find in agreement with independent empirical estimates based on contact surveys. Our estimates are robust to whether the analysed data series encompass one or two pandemic waves and enable projections compatible with subsequent dynamics. We conclude that vaccination programmes may have contributed modestly to the acquisition of herd immunity in populations with high levels of pre-existing naturally acquired immunity, while being critical to protect vulnerable individuals from severe outcomes as the virus becomes endemic.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC=\"FIGDIR/small/20081893v5_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (19K):\norg.highwire.dtl.DTLVardef@aeb87forg.highwire.dtl.DTLVardef@d2c441org.highwire.dtl.DTLVardef@152aeceorg.highwire.dtl.DTLVardef@1526779_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIVariation in susceptibility/exposure responds to selection by natural infection\nC_LIO_LISelection on susceptibility/exposure flattens epidemic curves\nC_LIO_LIModels with incomplete heterogeneity overestimate intervention impacts\nC_LIO_LIIndividual variation lowered the natural herd immunity threshold for SARS-CoV-2\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "M. Gabriela M. Gomes", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Marcelo U. Ferreira", + "author_inst": "Universidade de Sao Paulo, Brazil" + }, + { + "author_name": "Rodrigo M. Corder", + "author_inst": "Universidade de Sao Paulo, Brazil" + }, + { + "author_name": "Jessica G. King", + "author_inst": "University of Edinburgh, UK" + }, + { + "author_name": "Caetano Souto-Maior", + "author_inst": "National Institutes of Health, USA" + }, + { + "author_name": "Carlos Penha-Goncalves", + "author_inst": "Instituto Gulbenkian de Ciencia, Portugal" + }, + { + "author_name": "Guilherme Goncalves", + "author_inst": "Universidade do Porto, Portugal" + }, + { + "author_name": "Maria Chikina", + "author_inst": "University of Pittsburgh, USA" + }, + { + "author_name": "Wesley Pegden", + "author_inst": "Carnegie Mellon University, USA" + }, + { + "author_name": "Ricardo Aguas", + "author_inst": "University of Oxford, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.27.20074849", "rel_title": "Performance verification of detecting COVID-19 specific antibody by using four chemiluminescence immunoassay systems", @@ -1480471,145 +1483603,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.02.073411", - "rel_title": "Rapid adaptation of SARS-CoV-2 in BALB/c mice: Novel mouse model for vaccine efficacy", - "rel_date": "2020-05-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.02.073411", - "rel_abs": "Coronavirus disease 2019 (COVID-19) threatens global public health and economy. In order to develop safe and effective vaccines, suitable animal models must be established. Here we report the rapid adaption of SARS-CoV-2 in BALB/c mice, based on which a convenient, economical and effective animal model was developed. Specifically, we found that mouse-adapted SARS-CoV-2 at passage 6 (MACSp6) efficiently infected both aged and young wild-type BALB/c mice, resulting in moderate pneumonia as well as inflammatory responses. The elevated infectivity of MACSp6 in mice could be attributed to the substitution of a key residue (N501Y) in the receptorbinding domain (RBD). Using this novel animal model, we further evaluated the in vivo protective efficacy of an RBD-based SARS-CoV-2 subunit vaccine, which elicited highly potent neutralizing antibodies and conferred full protection against SARS-CoV-2 MACSp6 challenge. This novel mouse model is convenient and effective in evaluating the in vivo protective efficacy of SARS-CoV-2 vaccine.\n\nSummaryThis study describes a unique mouse model for SARS-CoV-2 infection and confirms protective efficacy of a SARS-CoV-2 RBD subunit vaccine.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Hongjing Gu", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Qi Chen", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Guan Yang", - "author_inst": "Beijing Institute of Biotechnology" - }, - { - "author_name": "Lei He", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Hang Fan", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Yong-qiang Deng", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Yanxiao Wang", - "author_inst": "Beijing Institute of Biotechnology" - }, - { - "author_name": "Yue Teng", - "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Zhongpeng Zhao", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Yujun Cui", - "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Yuchang Li", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Xiao-Feng Li", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Jiangfan Li", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Nana Zhang", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Xiaolan Yang", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Shaolong Chen", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Guangyu Zhao", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Xiliang Wang", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Deyan Luo", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Hui Wang", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Xiao Yang", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Yan Li", - "author_inst": "Institute of Military Cognition and Brain Sciences" - }, - { - "author_name": "Gencheng Han", - "author_inst": "Institute of Military Cognition and Brain Sciences" - }, - { - "author_name": "Yuxian He", - "author_inst": "Chinese Academy of Medical Sciences" - }, - { - "author_name": "Xiaojun Zhou", - "author_inst": "Laboratory Animal Center, Academy of Military Medical Sciences" - }, - { - "author_name": "Shusheng Geng", - "author_inst": "Beijing Joinn Biologics Co. Ltd, Beijing" - }, - { - "author_name": "Xiaoli Sheng", - "author_inst": "Beijing Joinn Biologics Co. Ltd, Beijing" - }, - { - "author_name": "Bojiang Shi", - "author_inst": "Shang-Hai Medical College, Fudan University" - }, - { - "author_name": "Shihui Sun", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Cheng-Feng Qin", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Yusen Zhou", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.01.073171", "rel_title": "Functional pathways in respiratory tract microbiome separate COVID-19 from community-acquired pneumonia patients", @@ -1481884,6 +1484877,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.04.28.20083089", + "rel_title": "A possible role of immunopathogenesis in COVID-19 progression", + "rel_date": "2020-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083089", + "rel_abs": "BackgroundThe role of cellular immunity in pathogenesis of COVID-19 is unclear and conflicting data points to insufficient or pathogenic immunity as drivers of COVID-19 progression. Here we aimed to delineate the phenotype and function of the immune system in patients with moderate, severe, and critical COVID-19.\n\nMethodsIn this prospective study, we included 53 patients with moderate (n=21), severe (n=18), and critical (n=14) COVID-19 manifestations. Using multiparametric flow cytometry we compared quantitative, phenotypic, and functional characteristics of circulating immune cells, SARS-CoV-2 antigen-reactive T-cells, and humoral immunity.\n\nResultsDeep phenotypic profiling revealed a depletion of circulating bulk CD8+ T-cells, CD4+ and CD8+ T-cell subsets with activated memory/effector T-cells expressing CD57+, HLA-DR+, and the key activation and migration molecule CD11a++ in critical COVID-19. Importantly, survival from acute respiratory distress syndrome was accompanied by a recovery of the depleted CD11++ T-cell subsets including T-cells expressing CD28, CD57, HLA-DR activation/effector molecules. We further observed a stronger response of S-protein specific T-cells producing inflammatory cytokines in critical COVID-19 cases. This seemingly contradictory observation is in fact confirmation of the underlying immunopathogenesis in patients with critical COVID-19.\n\nConclusionOur findings suggest a CD11a-based immune signature as a possible prognostic marker for disease development. Our data further reveal that increased rather than decreased SARS-CoV-2 specific T cell immunity is associated with adverse outcome in COVID-19. Tissue migration of activated effectors T-cells may constitute a crucial cornerstone in the immunopathogenesis of SARS-CoV-2 associated tissue injury.\n\nTrial registrationThis is a prospective observational study without a trial registration number.\n\nFundingThis work was supported by grants from Mercator Foundation, the BMBF e:KID (01ZX1612A), and BMBF NoChro (FKZ 13GW0338B).\n\n25 Word summaryStronger S-protein reactivity and decreased frequency of activated memory/effector T-cells expressing CD11a++ suggests immunopathogenesis in critical COVID-19 mediated by tissue migration of activated effector T-cells.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Moritz Anft", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Krystallenia Paniskaki", + "author_inst": "Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Germany" + }, + { + "author_name": "Arturo Blazquez-Navarro", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Adrian Atila Nicolas Doevelaar", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Felix Seibert", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Bodo Hoelzer", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Sarah Skrzypczyk", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Eva Kohut", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Julia Kurek", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Jan Zapka", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Patrizia Wehler", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Sviatlana Kaliszczyk", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Sharon Bajda", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Constantin Thieme", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Toralf Roch", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Margarethe Justine Konik", + "author_inst": "Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Germany" + }, + { + "author_name": "Thorsten Brenner", + "author_inst": "Department of Anesthesiology, University Hospital Essen, University Duisburg-Essen, Germany" + }, + { + "author_name": "Clemens Tempfer", + "author_inst": "Department of Gynecology and Obstetrics, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Hoelkeskampring 40, 44625 Herne, Germany" + }, + { + "author_name": "Carsten Watzl", + "author_inst": "Department of Immunology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund (IfADo), Ardeystrasse 67, 44139" + }, + { + "author_name": "Sebastian Dolff", + "author_inst": "Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Germany" + }, + { + "author_name": "Ulf Dittmer", + "author_inst": "Germany Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany" + }, + { + "author_name": "Timm Westhoff", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Oliver Witzke", + "author_inst": "Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Germany" + }, + { + "author_name": "Ulrik Stervbo", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Nina Babel", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2020.04.26.20080341", "rel_title": "How the COVID-19 pandemic is favoring the adoption of digital technologies in healthcare: a rapid literature review", @@ -1482085,65 +1485193,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.26.20079822", - "rel_title": "Estimation of seroprevalence of novel coronavirus disease (COVID-19) using preserved serum at an outpatient setting in Kobe, Japan: A cross-sectional study.", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20079822", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 has been affecting many people on earth and our society. Japan is known to have relatively less number of infections as well as deaths among developed nations. However, accurate prevalence of COVID-19 in Japan remains unknown. Therefore, we conducted a cross-sectional study to estimate seroprevalence of SARS-CoV-2 infection.\n\nMethodsWe conducted a cross-sectional serologic testing for SARS-CoV-2 antibody using 1,000 samples from patients at outpatient settings who visited the clinic from March 31 to April 7, 2020, stratified by the decade of age and sex.\n\nResultsThere were 33 positive IgG among 1,000 serum samples (3.3%, 95%CI: 2.3-4.6%). By applying this figure to the census of Kobe City (population: 1,518,870), it is estimated that the number of people with positive IgG be 50,123 (95%CI: 34,934-69,868). Age and sex adjusted prevalence of positivity was calculated 2.7% (95%CI: 1.8-3.9%), and the estimated number of people with positive IgG was 40,999 (95%CI: 27,333-59,221). These numbers were 396 to 858 fold more than confirmed cases with PCR testing in Kobe City.\n\nConclusionsOur cross-sectional serological study suggests that the number of people with seropositive for SARS-CoV-2 infection in Kobe, Japan is far more than the confirmed cases by PCR testing.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Asako Doi", - "author_inst": "Kobe City Medical Center General Hospital" - }, - { - "author_name": "Kentaro Iwata", - "author_inst": "Kobe University Graduate School of Medicine" - }, - { - "author_name": "Hirokazu Kuroda", - "author_inst": "Kobe City Medical Center General Hospital" - }, - { - "author_name": "Toshikazu Hasuike", - "author_inst": "Kobe City Medical Center General Hospital" - }, - { - "author_name": "Seiko Nasu", - "author_inst": "Kobe City Medical Center General Hospital" - }, - { - "author_name": "Aya Kanda", - "author_inst": "Kobe City Medical Center General Hospital" - }, - { - "author_name": "Tomomi Nagao", - "author_inst": "Kobe City Medical Center General Hospital" - }, - { - "author_name": "Hiroaki Nishioka", - "author_inst": "Kobe City Medical Center General Hospital" - }, - { - "author_name": "Keisuke Tomii", - "author_inst": "Kobe City Medical Center General Hospital" - }, - { - "author_name": "Takeshi Morimoto", - "author_inst": "Hyogo Medical College" - }, - { - "author_name": "Yasuki Kihara", - "author_inst": "Kobe City Medical Center General Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.26.20080101", "rel_title": "High frequency of SARS-CoV-2 RNAemia and association with severe disease", @@ -1483454,6 +1486503,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.26.20080770", + "rel_title": "A first study on the impact of containment measure on COVID-19 spread in Morocco", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20080770", + "rel_abs": "BackgroundSince the appearance of the first case of COVID-19 in Morocco, the cumulative number of reported infectious cases continues to increase and, consequently, the government imposed the containment measure within the country. Our aim is to predict the impact of the compulsory containment on COVID-19 spread. Earlier knowledge of the epidemic characteristics of COVID-19 transmission related to Morocco will be of great interest to establish an optimal plan-of-action to control the epidemic.\n\nMethodUsing a Susceptible-Asymptomatic-Infectious model and the data of reported cumulative confirmed cases in Morocco from March 2nd to April 9, 2020, we determined the basic and control reproduction numbers and we estimated the model parameter values. Furthermore, simulations of different scenarios of containment are performed.\n\nResultsEpidemic characteristics are predicted according to different rates of containment. The basic reproduction number is estimated to be 2.9949, with CI(2.6729-3.1485). Furthermore, a threshold value of containment rate, below which the epidemic duration is postponed, is determined.\n\nConclusionOur findings show that the basic reproduction number reflects a high speed of spread of the epidemic. Furthermore, the compulsory containment can be efficient if more than 73% of population are confined. However, even with 90% of containment, the end-time is estimated to happen on July 4th which can be harmful and lead to consequent social-economic damages. Thus, containment need to be accompanied by other measures such as mass testing to reduce the size of asymptomatic population. Indeed, our sensitivity analysis investigation shows that the COVID-19 dynamics depends strongly on the asymptomatic duration as well as the contact and containment rates. Our results can help the Moroccan government to anticipate the spread of COVID-19 and avoid human loses and consequent social-economic damages as well.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Aayah Hammoumi", + "author_inst": "Cadi Ayyad University" + }, + { + "author_name": "Redouane Qesmi", + "author_inst": "USMBA University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.27.20076000", "rel_title": "The effect of a national lockdown in response to COVID-19 pandemic on the prevalence of clinical symptoms in the population", @@ -1483631,25 +1486703,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.04.26.20081042", - "rel_title": "Fitting SIR model to COVID-19 pandemic data and comparative forecasting with machine learning", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20081042", - "rel_abs": "In this work, we use a classical SIR model to study COVID-19 pandemic. We aim, to deal with the SIR model fitting to COVID-19 data by using different technics and tools. We particularly use two ways: the first one start by fitting the total number of the confirmed cases and the second use a parametric solver tool. Finally a comparative forecasting, machine learning tools, is given.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Mouhamadou Aliou Mountaga Tall Bald\u00e9", - "author_inst": "Universite Cheikh Anta Diop(UCAD)-FASEG" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.28.20075481", "rel_title": "Preparedness and response to Pediatric CoVID-19 in European Emergency Departments: a survey of the REPEM and PERUKI networks", @@ -1484700,6 +1487753,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.30.069922", + "rel_title": "Broad-spectrum antiviral activity of naproxen: from Influenza A to SARS-CoV-2 Coronavirus", + "rel_date": "2020-05-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.30.069922", + "rel_abs": "There is an urgent need for specific antiviral drugs directed against SARS-CoV-2 both to prevent the most severe forms of COVID-19 and to reduce viral excretion and subsequent virus dissemination; in the present pandemic context, drug repurposing is a priority. Targeting the nucleoprotein N of the SARS-CoV-2 coronavirus in order to inhibit its association with viral RNA could be a strategy to impeding viral replication and possibly other essential functions associated with viral N. The antiviral properties of naproxen, belonging to the NSAID family, previously demonstrated against Influenza A virus, were evaluated against SARS-CoV-2. Naproxen binding to the nucleoprotein of SARS-CoV2 was shown by molecular modeling. In VeroE6 cells and reconstituted human primary respiratory epithelium models of SARS-CoV-2 infection, naproxen inhibited viral replication and protected the bronchial epithelia against SARS-CoV-2 induced-damage. The benefit of naproxen addition to the standard of care is tested in an on-going clinical study.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Olivier Terrier", + "author_inst": "Centre International de Recherche en Infectiologie" + }, + { + "author_name": "Sebastien Dilly", + "author_inst": "INSERM and Sorbonne University, CRSA UMR S_938" + }, + { + "author_name": "Mario-Andres Pizzorno", + "author_inst": "Lyon I University, CIRI, INSERM 1111, CNRS UMR 5308, Ens de Lyon" + }, + { + "author_name": "Julien Henri", + "author_inst": "Institut de Biologie Physico-Chimique CNRS UMR 8226" + }, + { + "author_name": "Francis Berenbaum", + "author_inst": "Sorbonne University, INSERM, CRSA UMR S_938, AP-HP" + }, + { + "author_name": "Bruno Lina", + "author_inst": "Lyon I University, CIRI, INSERM U 1111, CNRS UMR 5308, Ens de Lyon" + }, + { + "author_name": "Bruno Feve", + "author_inst": "INSERM and Sorbonne Universitu CRSA UMR S_938, AP-HP, ICAN" + }, + { + "author_name": "Frederic Adnet", + "author_inst": "AP-HP, SAMU, Avicenne Hospital" + }, + { + "author_name": "Michele Sabbah", + "author_inst": "INSERM and Sorbonne University, CRSA UMR S_938" + }, + { + "author_name": "Manuel Rosa-Calavatra", + "author_inst": "University Lyon I, CIRI, INSERM U1111, CNRS UMR 5308, Ens de Lyon" + }, + { + "author_name": "Vincent Marechal", + "author_inst": "INSERM and Sorbonne University, CRSA UMR S_938" + }, + { + "author_name": "Anny Slama-Schwok", + "author_inst": "INSERM and Sorbonne University, CRSA UMR S_938" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.30.071175", "rel_title": "Electrostatic Characteristics of SARS-CoV-2 Spike and Human ACE2 Protein Variations Predict Mutable Binding Efficacy", @@ -1484857,89 +1487973,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.30.071290", - "rel_title": "Potent antiviral effect of protoporphyrin IX and verteporfin on SARS-CoV-2 infection", - "rel_date": "2020-05-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.30.071290", - "rel_abs": "The SARS-CoV-2 infection is spreading rapidly worldwide. Efficacious antiviral therapeutics against SARS-CoV-2 is urgently needed. Here, we discovered that protoporphyrin IX (PpIX) and verteporfin, two FDA-approved drugs, completely inhibited the cytopathic effect produced by SARS-CoV-2 infection at 1.25 M and 0.31 M respectively, and their EC50 values of reduction of viral RNA were at nanomolar concentrations. The selectivity indices of PpIX and verteporfin were 952.74 and 368.93, respectively, suggesting broad margin of safety. Importantly, PpIX and verteporfin prevented SARS-CoV-2 infection in mice adenovirally transduced with human ACE2. The compounds, sharing a porphyrin ring structure, were shown to bind viral receptor ACE2 and interfere with the interaction between ACE2 and the receptor-binding domain of viral S protein. Our study suggests that PpIX and verteporfin are potent antiviral agents against SARS-CoV-2 infection and sheds new light on developing novel chemoprophylaxis and chemotherapy against SARS-CoV-2.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Chenjian Gu", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Yang Wu", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Huimin Guo", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Yuanfei Zhu", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Wei Xu", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Yuyan Wang", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Yu Zhou", - "author_inst": "CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Sha" - }, - { - "author_name": "Zhiping Sun", - "author_inst": "BSL-3 laboratory of Fudan University, School of Basic Medical Sciences, Shanghai Medical College, Fudan University" - }, - { - "author_name": "Xia Cai", - "author_inst": "BSL-3 laboratory of Fudan University, School of Basic Medical Sciences, Shanghai Medical College, Fudan University" - }, - { - "author_name": "Yutang Li", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Jing Liu", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Zhong Huang", - "author_inst": "Institut Pasteur of Shanghai" - }, - { - "author_name": "Zhenghong Yuan", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Rong Zhang", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Qiang Deng", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Di Qu", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Youhua Xie", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.30.069039", "rel_title": "SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms", @@ -1486198,6 +1489231,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.27.20078329", + "rel_title": "Population-scale testing can suppress the spread of COVID-19", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20078329", + "rel_abs": "We propose an additional intervention that would contribute to the control of the COVID-19 pandemic, offer more protection for people working in essential jobs, and help guide an eventual reopening of society. The intervention is based on: (1) testing every individual (2) repeatedly, and (3) self-quarantine of infected individuals. Using a standard epidemiological model (SIR), we show here that by identification and isolation of the majority of infectious individuals, including those who may be asymptomatic, the reproduction number R0 of SARS-CoV-2 would be reduced well below 1.0, and the epidemic would collapse. We replicate these observations in a more complex stochastic dynamic model on a social network graph. We also find that the testing regime would be additive to other interventions, and be effective at any level of prevalence. If adopted as a policy, any industrial society could sustain the regime for as long as it takes to find a safe and effective cure or vaccine. Our model also indicates that unlike sampling-based tests, population-scale testing does not need to be very accurate: false negative rates up to 15% could be tolerated if 80% comply with testing every ten days, and false positives can be almost arbitrarily high when a high fraction of the population is already effectively quarantined. Testing at the required scale would be feasible if existing qPCR-based methods are scaled up and multiplexed. A mass produced, low throughput field test kit could also be carried out at home. Economic analysis also supports the feasibility of the approach: current reagent costs for tests are in the range of a dollar or less, and the estimated benefits for population-scale testing are so large that the policy would be cost-effective even if the costs were larger by more than two orders of magnitude. To identify both active and previous infections, both viral RNA and antibodies could be tested. All technologies to build such test kits, and to produce them in the scale required to test the entire worlds population exist already. Integrating them, scaling up production, and implementing the testing regime will require resources and planning, but at a scale that is very small compared to the effort that every nation would devote to defending itself against a more traditional foe.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jussi Taipale", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Paul Romer", + "author_inst": "New York University" + }, + { + "author_name": "Sten Linnarsson", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.24.20078717", "rel_title": "Full lockdown policies in Western Europe countries have no evident impacts on the COVID-19 epidemic.", @@ -1486259,53 +1489319,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.26.20079756", - "rel_title": "Racial, Economic and Health Inequality and COVID-19 Infection in the United States", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20079756", - "rel_abs": "BackgroundThere is preliminary evidence of racial and social-economic disparities in the population infected by and dying from COVID-19. The goal of this study is to report the associations of COVID-19 with respect to race, health and economic inequality in the United States.\n\nMethodsWe performed a cross-sectional study of the associations between infection and mortality rate of COVID-19 and demographic, socioeconomic and mobility variables from 369 counties (total population: 102,178,117 [median: 73,447, IQR: 30,761-256,098]) from the seven most affected states (Michigan, New York, New Jersey, Pennsylvania, California, Louisiana, Massachusetts).\n\nFindingsThe risk factors for infection and mortality are different. Our analysis shows that counties with more diverse demographics, higher population, education, income levels, and lower disability rates were at a higher risk of COVID-19 infection. However, counties with higher disability and poverty rates had a higher death rate. African Americans were more vulnerable to COVID-19 than other ethnic groups (1,981 African American infected cases versus 658 Whites per million). Data on mobility changes corroborate the impact of social distancing.\n\nInterpretationThe observed inequality might be due to the workforce of essential services, poverty, and access to care. Counties in more urban areas are probably better equipped at providing care. The lower rate of infection, but a higher death rate in counties with higher poverty and disability could be due to lower levels of mobility, but a higher rate of comorbidities and health care access.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Vida Abedi", - "author_inst": "Geisinger Health System; Virginia Tech" - }, - { - "author_name": "Oluwaseyi Olulana", - "author_inst": "Geisinger Commonwealth School of Medicine" - }, - { - "author_name": "Venkatesh Avula", - "author_inst": "Geisinger Health System" - }, - { - "author_name": "Durgesh Chaudhary", - "author_inst": "Geisinger Health System" - }, - { - "author_name": "Ayesha Khan", - "author_inst": "Geisinger Health System" - }, - { - "author_name": "Shima Shahjouei", - "author_inst": "Geisinger Health System" - }, - { - "author_name": "Jiang Li", - "author_inst": "Geisinger Health System" - }, - { - "author_name": "Ramin Zand", - "author_inst": "Geisinger Health System" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.24.20078576", "rel_title": "Modeling serological testing to inform relaxation of social distancing for COVID-19 control", @@ -1487400,6 +1490413,85 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.04.29.069054", + "rel_title": "Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2", + "rel_date": "2020-04-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.29.069054", + "rel_abs": "We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. To date we have identified thirteen mutations in Spike that are accumulating. Mutations are considered in a broader phylogenetic context, geographically, and over time, to provide an early warning system to reveal mutations that may confer selective advantages in transmission or resistance to interventions. Each one is evaluated for evidence of positive selection, and the implications of the mutation are explored through structural modeling. The mutation Spike D614G is of urgent concern; it began spreading in Europe in early February, and when introduced to new regions it rapidly becomes the dominant form. Also, we present evidence of recombination between locally circulating strains, indicative of multiple strain infections. These finding have important implications for SARS-CoV-2 transmission, pathogenesis and immune interventions.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Bette Korber", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Will Fischer", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "S. Gnana Gnanakaran", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Heyjin Yoon", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "James Theiler", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Werner Abfalterer", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Brian Foley", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Elena E Giorgi", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Tanmoy Bhattacharya", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Matthew D Parker", + "author_inst": "The University of Sheffield" + }, + { + "author_name": "David G Partridge", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Cariad M Evans", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Thushan de Silva", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Celia C LaBranche", + "author_inst": "Duke Univerisity" + }, + { + "author_name": "David C Montefiori", + "author_inst": "Duke University" + }, + { + "author_name": "- Sheffield COVID-19 Genomics Group", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.04.30.029736", "rel_title": "Susceptibility of tree shrew to SARS-CoV-2 infection", @@ -1487621,85 +1490713,6 @@ "type": "confirmatory results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.04.30.071027", - "rel_title": "Identification of variable sites in Sars-CoV-2 and their abundance profiles in time", - "rel_date": "2020-04-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.30.071027", - "rel_abs": "The SARS-CoV-2 pandemic that we are currently experiencing is exerting a massive toll both in human lives and economic impact. One of the challenges we must face is to try to understand if and how different variants of the virus emerge and change their frequency in time. Such information can be extremely valuable as it may indicate shifts in aggressiveness, and it could provide useful information to trace the spread of the virus in the population. In this work we identified and traced over time 7 amino acid variants that are present with high frequency in Italy and Europe, but that were absent or present at very low frequencies during the first stages of the epidemic in China and the initial reports in Europe. The analysis of these variants helps defining 6 phylogenetic clades that are currently spreading throughout the world with changes in frequency that are sometimes very fast and dramatic. In the absence of conclusive data at the time of writing, we discuss whether the spread of the variants may be due to a prominent founder effect or if it indicates an adaptive advantage.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Francesco Comandatore", - "author_inst": "University of Milano" - }, - { - "author_name": "Alice Chiodi", - "author_inst": "University of Milano" - }, - { - "author_name": "Paolo Gabrieli", - "author_inst": "University of Milano" - }, - { - "author_name": "Gherard Batisti Biffignandi", - "author_inst": "University of Pavia" - }, - { - "author_name": "Matteo Perini", - "author_inst": "University of Milano" - }, - { - "author_name": "Stefano Ricagno", - "author_inst": "University of Milano" - }, - { - "author_name": "Elia Mascolo", - "author_inst": "University of Milano" - }, - { - "author_name": "Greta Petazzoni", - "author_inst": "University of Milano" - }, - { - "author_name": "Matteo Ramazzotti", - "author_inst": "University of Firenze" - }, - { - "author_name": "Sara Giordana Rimoldi", - "author_inst": "ASST Fatebenefratelli Sacco" - }, - { - "author_name": "Mariarita Gismondo", - "author_inst": "ASST Fatebenefratelli Sacco" - }, - { - "author_name": "Valeria Micheli", - "author_inst": "ASST Fatebenefratelli Sacco" - }, - { - "author_name": "Davide Sassera", - "author_inst": "University of Pavia" - }, - { - "author_name": "Stefano Gaiarsa", - "author_inst": "Policlinico San Matteo Pavia Fondazione IRCCS" - }, - { - "author_name": "Claudio Bandi", - "author_inst": "University of Milano" - }, - { - "author_name": "Matteo Brilli", - "author_inst": "University of Milano" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.04.27.20081695", "rel_title": "COVID-19 and depressive symptoms in students before and during lockdown", @@ -1488742,6 +1491755,29 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.04.24.20078824", + "rel_title": "Estimating COVID-19 Antibody Seroprevalence in Santa Clara County, California. A re-analysis of Bendavid et al.", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078824", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWA recent study by Bendavid et al. claimed that the rate of infection of COVID-19 in Santa Clara county was between 2.49% and 4.16%, 50-85 times higher than the number of officially confirmed cases. The statistical methodology used in that study overestimates of rate of infection given the available data. We jointly estimate the sensitivity and specificity of the test kit along with rate of infection with a simple Bayesian model, arriving at lower estimates of the rate of COVID-19 in Santa Clara county. Re-analyzing their data, we find that the rate of infection was likely between 0.27% and 3.21%.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Stephen T Bennett", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Mark Steyvers", + "author_inst": "University of California, Irvine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.24.20078808", "rel_title": "Reacting to outbreaks at neighboring localities", @@ -1488831,29 +1491867,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.24.20078550", - "rel_title": "The impact of the COVID19 pandemic and initial period of lockdown on the mental health and wellbeing of UK adults", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078550", - "rel_abs": "Mental health and wellbeing impacts of COVID19 were assessed in a convenience sample of 600 UK adults using a cross-sectional design. Recruited over a two-week period during the initial phase of the government lockdown, participants completed an online survey that included COVID19-related questions, the Hospital Anxiety and Depression Scale, the WHO-5 and the OXCAP-MH. Self-isolating prior to lockdown, increased feelings of isolation since the lockdown, and having COVID19-related livelihood concerns, were associated with poorer mental health, wellbeing and quality of life. Perceiving increased kindness, community connectedness, and being an essential worker were associated with better mental health and wellbeing outcomes.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ross G White", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Catharina Van Der Boor", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.04.24.20079012", "rel_title": "Validating a Widely Implemented Deterioration Index Model Among Hospitalized COVID-19 Patients", @@ -1490180,6 +1493193,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.24.20078774", + "rel_title": "State-by-State prediction of likely COVID-19 scenarios in the United States and assessment of the role of testing and control measures", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078774", + "rel_abs": "Due to the heterogeneity among the States in the US, predicting COVID-19 trends and quantitatively assessing the effects of government testing capability and control measures need to be done via a State-by-State approach. We develop a comprehensive model for COVID-19 incorporating time delays and population movements. With key parameter values determined by empirical data, the model enables the most likely epidemic scenarios to be predicted for each State, which are indicative of whether testing services and control measures are vigorous enough to contain the disease. We find that government control measures play a more important role than testing in suppressing the epidemic. The vast disparities in the epidemic trends among the States imply the need for long-term placement of control measures to fully contain COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Zheng-Meng Zhai", + "author_inst": "East China Normal University" + }, + { + "author_name": "Yong-Shang Long", + "author_inst": "East China Normal University" + }, + { + "author_name": "Jie Kang", + "author_inst": "East China Normal University" + }, + { + "author_name": "Yi-Lin Li", + "author_inst": "East China Normal University" + }, + { + "author_name": "Lang Zeng", + "author_inst": "East China Normal University" + }, + { + "author_name": "Li-Lei Han", + "author_inst": "East China Normal University" + }, + { + "author_name": "Zhao-Hua Lin", + "author_inst": "East China Normal University" + }, + { + "author_name": "Yin-Qi Zeng", + "author_inst": "East China Normal University" + }, + { + "author_name": "Da-Yu Wu", + "author_inst": "East China Normal University" + }, + { + "author_name": "Ming Tang", + "author_inst": "East China Normal University" + }, + { + "author_name": "Di Xu", + "author_inst": "Fudan University" + }, + { + "author_name": "Zonghua Liu", + "author_inst": "East China Normal University" + }, + { + "author_name": "Ying-Cheng Lai", + "author_inst": "Arizona State University - Tempe Campus" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.28.066977", "rel_title": "Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world", @@ -1490277,49 +1493357,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.28.066985", - "rel_title": "Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India", - "rel_date": "2020-04-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.28.066985", - "rel_abs": "India has recently started sequencing SARS-CoV2 genome from clinical isolates. Currently only few sequences are available from three states in India. Kerala was the first state to deposit complete sequence from two isolates followed by one from Gujarat. On April 27, 2020, the first five sequences from the state of West Bengal (Eastern India) were deposited on a global initiative on sharing avian flu data (GISAID) platform. In this paper we have analysed the spike protein sequences from all these five isolates and also compared for their similarities or differences with other sequences reported in India and with isolates of Wuhan origin. We report one unique mutation at position 723 and the other at 1124 in the S2 domain of spike protein of the isolates from West Bengal only and one mutation downstream of the receptor binding domain at position 614 in S1 domain which was common with the sequence from Gujarat (a state of western part of India). Mutation in the S2 domain showed changes in the secondary structure of the spike protein at region of mutation. We also studied molecular dynamics using normal mode analyses and found that this mutation decreases the flexibility of S2 domain. Since both S1 and S2 are important in receptor binding followed by entry in the host cells, such mutations may define the affinity or avidity of receptor binding.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "FEROZA BEGUM", - "author_inst": "CSIR-Indian Institute of Chemical Biology" - }, - { - "author_name": "DEBICA MUKHERJEE", - "author_inst": "CSIR-Indian Institute of Chemical Biology" - }, - { - "author_name": "DLUYA THAKRIKI", - "author_inst": "CSIR-Indian Institute of Chemical Biology" - }, - { - "author_name": "SANDEEPAN DAS", - "author_inst": "CSIR-Indian Institute of Chemical Biology" - }, - { - "author_name": "PREM PRAKASH TRIPATHI", - "author_inst": "CSIR-Indian Institute of Chemical Biology" - }, - { - "author_name": "ARUP KUMAR BANERJEE", - "author_inst": "North Bengal Medical College and Hospital" - }, - { - "author_name": "UPASANA RAY", - "author_inst": "CSIR-Indian Institute of Chemical Biology" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.04.28.051789", "rel_title": "A collection of designed peptides to target SARS-Cov-2 - ACE2 interaction: PepI-Covid19 database.", @@ -1491638,6 +1494675,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.23.20077230", + "rel_title": "Analysis of national and international guidelines on respiratory protection equipment for COVID-19 in healthcare settings.", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20077230", + "rel_abs": "BackgroundConsistent guidelines on respiratory protection for healthcare professionals combined with improved global supply chains are critical to prevent COVID-19. We analysed the guidelines published by national and international societies/organizations on facemasks and respirators to prevent COVID-19 in healthcare settings.\n\nMethodsFrom the 1st January to the 2nd April 2020, guidelines published in four countries (France, Germany, United States, United Kingdom), and two international organizations (US and European Centre for Diseases Control, and World Health Organization) were reviewed to analyse the mask and respirators recommended for healthcare settings during the COVID-19 outbreak. The aerosol generating procedures (AGP) definitions and the strategy recommended for optimizing supplies and overcoming shortages were collected.\n\nFindingsThe recommendation of respirator was universally recommended for AGP across countries, although the type of respirators and what constituted an AGP was variable. Some guidance maintained the use of N95/99 for all contact with confirmed COVID-19 cases (i.e. Germany) whereas others, recommended a surgical mask (i.e. WHO, UK, France). Most guidelines were published in March with either downgraded (US and European CDC), relatively stable (WHO, Germany, and UK), or a mixing of high and low level equipment (France). The strategies to overcome shortage of respiratory protection equipment were based on minimizing the need and rationalizing the use, but also prolonging their use, reusing them after cleaning/sterilization, or using cloth masks.\n\nInterpretationsIn a crisis context, stable and consistent guidelines clearly detailing the respiratory protection type, and their indications, may prevent the confusion and anxiety among frontline staff, and avoid shortage.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Gabriel Birgand", + "author_inst": "Imperial College London" + }, + { + "author_name": "Nico T. Mutters", + "author_inst": "Heidelberg University Hospital" + }, + { + "author_name": "Jonathan Otter", + "author_inst": "Imperial College London" + }, + { + "author_name": "Vanessa M. Eichel", + "author_inst": "Heidelberg University Hospital" + }, + { + "author_name": "Didier Lepelletier", + "author_inst": "CHU de Nantes" + }, + { + "author_name": "Daniel J. Morgan", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Jean Christophe Lucet", + "author_inst": "AP-HP, Hopital Bichat Claude Bernard" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.25.20074856", "rel_title": "Test performance evaluation of SARS-CoV-2 serological assays", @@ -1492011,37 +1495091,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.23.20077651", - "rel_title": "Characterizing COVID-19 case detection utilizing influenza surveillance data in the United States, January-March, 2020", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20077651", - "rel_abs": "COVID-19 reached the US in January, 2020, but state and local case detection efforts varied in timing and scale. We conducted a state-level ecological analysis of COVID-19 epidemiology alongside CDC influenza surveillance data and policy timelines. Our findings show wide variation in COVID-19 case detection and influenza-like-illness activity between states.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Micaela Sandoval", - "author_inst": "UTHealth School of Public Health" - }, - { - "author_name": "Adam W Hair", - "author_inst": "Texas A&M University Department of Computer Science" - }, - { - "author_name": "Shreela V Sharma", - "author_inst": "UTHealth School of Public Health" - }, - { - "author_name": "Catherine L Troisi", - "author_inst": "UTHealth School of Public Health, Houston, Texas, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.23.20077677", "rel_title": "A new design of an adaptive model of infectious diseases based on artificial intelligence approach: monitoring and forecasting of COVID-19 epidemic cases", @@ -1493004,6 +1496053,217 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.26.20073411", + "rel_title": "Machine Learning to Predict Mortality and Critical Events in COVID-19 Positive New York City Patients", + "rel_date": "2020-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20073411", + "rel_abs": "Coronavirus 2019 (COVID-19), caused by the SARS-CoV-2 virus, has become the deadliest pandemic in modern history, reaching nearly every country worldwide and overwhelming healthcare institutions. As of April 20, there have been more than 2.4 million confirmed cases with over 160,000 deaths. Extreme case surges coupled with challenges in forecasting the clinical course of affected patients have necessitated thoughtful resource allocation and early identification of high-risk patients. However, effective methods for achieving this are lacking. In this paper, we use electronic health records from over 3,055 New York City confirmed COVID-19 positive patients across five hospitals in the Mount Sinai Health System and present a decision tree-based machine learning model for predicting in-hospital mortality and critical events. This model is first trained on patients from a single hospital and then externally validated on patients from four other hospitals. We achieve strong performance, notably predicting mortality at 1 week with an AUC-ROC of 0.84. Finally, we establish model interpretability by calculating SHAP scores to identify decisive features, including age, inflammatory markers (procalcitonin and LDH), and coagulation parameters (PT, PTT, D-Dimer). To our knowledge, this is one of the first models with external validation to both predict outcomes in COVID-19 patients with strong validation performance and identify key contributors in outcome prediction that may assist clinicians in making effective patient management decisions.\n\nOne-Sentence SummaryWe identify clinical features that robustly predict mortality and critical events in a large cohort of COVID-19 positive patients in New York City.", + "rel_num_authors": 49, + "rel_authors": [ + { + "author_name": "Akhil Vaid", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sulaiman Somani", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adam J Russak", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jessica K De Freitas", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Fayzan F Chaudhry", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ishan Paranjpe", + "author_inst": "Ican School of Medicine at Mount Sinai" + }, + { + "author_name": "Kipp W Johnson", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Samuel J Lee", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Riccardo Miotto", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Shan Zhao", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Noam Beckmann", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Nidhi Naik", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kodi Arfer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Arash Kia", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Prem Timsina", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Anuradha Lala", + "author_inst": "Icahn School of Medicine Mount Sinai" + }, + { + "author_name": "Manish Paranjpe", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Patricia Glowe", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Eddye Golden", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Matteo Danieletto", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Manbir Singh", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Dara Meyer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Paul F O'Reilly", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Laura H Huckins", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Patricia Kovatch", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Joseph Finkelstein", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Robert M Freeman", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Edgar Argulian", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Andrew Kasarskis", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Bethany Percha", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Judith A Aberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Emilia Bagiella", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Carol R Horowitz", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Barbara Murphy", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Eric J Nestler", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Eric E Schadt", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Judy H Cho", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Carlos Cordon-Cardo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Valentin Fuster", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Dennis S Charney", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "David L Reich", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Erwin P Bottinger", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Matthew A Levin", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jagat Narula", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Zahi A Fayad", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Allan Just", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alexander W Charney", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Girish N Nadkarni", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Benjamin S Glicksberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.04.22.20074351", "rel_title": "Resilient SARS-CoV-2 diagnostics workflows including viral heat inactivation", @@ -1493397,73 +1496657,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.24.20073957", - "rel_title": "The incubation period of COVID-19: A rapid systematic review and meta-analysis of observational research", - "rel_date": "2020-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20073957", - "rel_abs": "BackgroundReliable estimates of the incubation period are important for decision making around the control of infectious diseases. Knowledge of the incubation period distribution can be used directly to inform decision-making or as inputs into mathematical models.\n\nObjectivesThe aim of this study was to conduct a rapid systematic review and meta-analysis of estimates of the incubation periods of COVID-19.\n\nDesignRapid systematic review and meta-analysis of observational research\n\nData sourcesPublications on the electronic databases PubMed, Google Scholar, MedRxiv and BioRxiv were searched. The search was not limited to peer-reviewed published data, but also included pre-print articles.\n\nStudy appraisal and synthesis methodsStudies were selected for meta-analysis if they reported either the parameters and confidence intervals of the distributions fit to the data, or sufficient information to facilitate calculation of those values. The majority of studies suitable for inclusion in the final analysis modelled incubation period as a lognormal distribution. We conducted a random effects meta-analysis of the parameters of this distribution.\n\nResultsThe incubation period distribution may be modelled with a lognormal distribution with pooled mu and sigma parameters of 1.63 (1.51, 1.75) and 0.50 (0.45, 0.55) respectively. The corresponding mean was 5.8 (5.01, 6.69 days). It should be noted that uncertainty increases towards the tail of the distribution: the pooled parameter estimates resulted in a median incubation period of 5.1 (4.5, 5.8) days, whereas the 95th percentile was 11.6 (9.5, 14.2) days.\n\nConclusions and implicationsThe choice of which parameter values are adopted will depend on how the information is used, the associated risks and the perceived consequences of decisions to be taken. These recommendations will need to be revisited once further relevant information becomes available. Finally, we present an RShiny app that facilitates updating these estimates as new data become available.\n\nARTICLE SUMMARYO_ST_ABSStrengths and limitations of this studyC_ST_ABSO_LIThis study provides a pooled estimate of the distribution of incubation periods which may be used in subsequent modelling studies or to inform decision-making\nC_LIO_LIThis estimate will need to be revisited as subsequent data become available. We present an RShiny app to allow the meta-analysis to be updated with new estimates\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Conor G McAloon", - "author_inst": "University College Dublin" - }, - { - "author_name": "Aine Collins", - "author_inst": "University College Dublin" - }, - { - "author_name": "Kevin Hunt", - "author_inst": "University College Dublin" - }, - { - "author_name": "Ann Barber", - "author_inst": "University College Dublin" - }, - { - "author_name": "Andrew Byrne", - "author_inst": "Department of Agriculture, Food and the Marine" - }, - { - "author_name": "Francis Butler", - "author_inst": "University College Dublin" - }, - { - "author_name": "Miriam Casey", - "author_inst": "University College Dublin" - }, - { - "author_name": "John M Griffin", - "author_inst": "Straffan, Co. Kildare" - }, - { - "author_name": "Elizabeth Lane", - "author_inst": "Department of Agriculture, Food and the Marine" - }, - { - "author_name": "David McEvoy", - "author_inst": "University College Dublin" - }, - { - "author_name": "Patrick Wall", - "author_inst": "University College Dublin" - }, - { - "author_name": "Martin J Green", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Simon J More", - "author_inst": "University College Dublin" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.24.20073148", "rel_title": "Racial and Ethnic Disparities in SARS-CoV-2 Pandemic: Analysis of a COVID-19 Observational Registry for a Diverse U.S. Metropolitan Population", @@ -1494634,6 +1497827,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.28.066761", + "rel_title": "Heparin inhibits cellular invasion by SARS-CoV-2: structural dependence of the interaction of the surface protein (spike) S1 receptor binding domain with heparin.", + "rel_date": "2020-04-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.28.066761", + "rel_abs": "The dependence of the host on the interaction of hundreds of extracellular proteins with the cell surface glycosaminoglycan heparan sulphate (HS) for the regulation of homeostasis is exploited by many microbial pathogens as a means of adherence and invasion. The closely related polysaccharide heparin, the widely used anticoagulant drug, which is structurally similar to HS and is a common experimental proxy, can be expected to mimic the properties of HS. Heparin prevents infection by a range of viruses if added exogenously, including S-associated coronavirus strain HSR1. Heparin prevents infection by a range of viruses if added exogenously, including S-associated coronavirus strain HSR1. Here, we show that the addition of heparin to Vero cells between 6.25 - 200 g.ml-1, which spans the concentration of heparin in therapeutic use, and inhibits invasion by SARS-CoV-2 at between 44 and 80%. We also demonstrate that heparin binds to the Spike (S1) protein receptor binding domain and induces a conformational change, illustrated by surface plasmon resonance and circular dichroism spectroscopy studies. The structural features of heparin on which this interaction depends were investigated using a library of heparin derivatives and size-defined fragments. Binding is more strongly dependent on the presence of 2-O or 6-O sulphation, and the consequent conformational consequences in the heparin structure, than on N-sulphation. A hexasaccharide is required for conformational changes to be induced in the secondary structure that are comparable to those that arise from heparin binding. Enoxaparin, a low molecular weight clinical anticoagulant, also binds the S1 RBD protein and induces conformational change. These findings have implications for the rapid development of a first-line therapeutic by repurposing heparin as well as for next-generation, tailor-made, GAG-based antiviral agents against SARS-CoV-2 and other members of the Coronaviridae.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Courtney Mycroft-West", + "author_inst": "Keele University" + }, + { + "author_name": "Dunhao Su", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Isabel Pagani", + "author_inst": "IRCCS San Raffaele Scientific Institute" + }, + { + "author_name": "Timothy Rudd", + "author_inst": "National Institute for Biological Standards and Control" + }, + { + "author_name": "Stefano Elli", + "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" + }, + { + "author_name": "Scott Guimond", + "author_inst": "Keele University" + }, + { + "author_name": "Gavin Miller", + "author_inst": "Keele University" + }, + { + "author_name": "Maria Meneghetti", + "author_inst": "Universidade Federal de Sao Paulo" + }, + { + "author_name": "Helena Nader", + "author_inst": "Universidade Federal de Sao Paulo" + }, + { + "author_name": "Yong Li", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Quentin Nunes", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Patricia Procter", + "author_inst": "Keele University" + }, + { + "author_name": "Nicasio Mancini", + "author_inst": "Universita Vita-Salute San Raffaele" + }, + { + "author_name": "Massimo Clementi", + "author_inst": "Universita Vita-Salute San Raffaele" + }, + { + "author_name": "Antonella Bisio", + "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" + }, + { + "author_name": "Nicholas Forsyth", + "author_inst": "Keele University" + }, + { + "author_name": "Jeremy Turnbull", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Marco Guerrini", + "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" + }, + { + "author_name": "David Fernig", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Elisa Vicenzi", + "author_inst": "San Raffaele Scientific Institute" + }, + { + "author_name": "Edwin Yates", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Marcelo Lima", + "author_inst": "Keele University" + }, + { + "author_name": "Mark A Skidmore", + "author_inst": "Keele University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.04.27.064139", "rel_title": "A Modular Framework for Multiscale Spatial Modeling of Viral Infection and Immune Response in Epithelial Tissue", @@ -1494767,41 +1498067,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.23.20076513", - "rel_title": "Intention to participate in a COVID-19 vaccine clinical trial and to get vaccinated against COVID-19 in France during the pandemic", - "rel_date": "2020-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076513", - "rel_abs": "BackgroundThe world is facing the COVID-19 pandemic. Development of vaccine is challenging.\n\nAimTo determine the proportion of people who intend to get vaccinated against COVID-19 in France or to participate in a vaccine clinical trial.\n\nMethodsWe conducted an anonymous on-line survey from the 26th of March to the 20th of April 2020. Primary endpoints were the intention to get vaccinated against COVID-19 if a vaccine was available or participate in a vaccine clinical trial.\n\nResultsThree thousand two hundred and fifty nine individuals answered the survey; women accounted for 67.4 % of the responders, 670 (20.6 %) were under 30 years of age, 1,502 (46.1 %) between 30-49 years, 803 (24.6 %) between 50-64 years, 271 (8.3%) between 65-80 years, 13 (0.4%) over 80 years of age. According to their statements, 2.512 participants (77.6%, 95 % CI 76.2-79 %) will certainly or probably agree to get vaccinated against COVID-19. Older age, male gender, fear about COVID-19, being healthcare workers and individual perceived risk were associated with COVID-19 vaccine acceptance Vaccine hesitancy was associated with a decrease in COVID-19 vaccine acceptance. One thousand and five hundred and fifty responders (47.6 % 95 % CI 45.9-49.3 %) will certainly or probably agree to participate in a COVID-19 vaccine clinical trial.\n\nConclusions and RelevanceNearly 75 % and 48 % of the survey responders were likely to accept vaccination or participation in a clinical trial against COVID-19. Vaccine hesitancy will be the major barrier to COVID-19 vaccine uptake.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Maelle Detoc", - "author_inst": "CHU de Saint-Etienne" - }, - { - "author_name": "Sebastien Bruel", - "author_inst": "Faculte de Medecine Jacques Lisfranc, Saint-Etienne" - }, - { - "author_name": "Paul Frappe", - "author_inst": "Faculte de medecine Jacques Lisfranc" - }, - { - "author_name": "Elisabeth Botelho-Nevers", - "author_inst": "CHU de Saint-Etienne" - }, - { - "author_name": "Amandine Gagneux-Brunon", - "author_inst": "CHU de Saint-Etienne" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.23.20076679", "rel_title": "Metropolitan Wastewater Analysis for COVID-19 Epidemiological Surveillance", @@ -1496048,6 +1499313,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.21.20074450", + "rel_title": "The dynamics of Covid-19: weather, demographics and infection timeline", + "rel_date": "2020-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20074450", + "rel_abs": "We study the effects of temperature, absolute humidity, population density and when country/U.S. state reached 100 cases on early pace of Covid-19 expansion, for all 50 U.S. states and 110 countries with enough data. For U.S. states, weather variables show opposite effects when compared to the case of countries: higher temperature or absolute humidity imply faster early outbreak. The higher the population density or the earlier the date when state reached 100th case, the faster the pace of outbreak. When all variables are considered, only population density and the timeline variable show statistical significance. Discounting the effect of the timeline variable, we obtain an estimate for the initial growth rate of Covid-19, which can be also used to estimate the basic reproduction number for a region, in terms of population density. This has policy implications regarding how to control the pace of Covid-10 outbreak in a particular area, and we discuss some of them. In the case of countries, for which we did not have demographic information, weather variables lose statistical significance once the timeline variable is added. Relaxing CI requirements, absolute humidity contributes mildly to the reduction of growth rate of cases for the countries studied. Our results suggest that population density should be employed as a control variable and that analysis should have a local character, for subregions and countries separately, in studies involving the dynamics of Covid-19 and similar infectious diseases.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Renato H.L. Pedrosa", + "author_inst": "Unicamp" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.22.20075762", "rel_title": "Proactive social distancing mitigates COVID-19 outbreaks within a month across 58 mainland China cities", @@ -1496257,61 +1499541,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.22.20075804", - "rel_title": "Assessing suppression strategies against epidemic outbreaks like COVID-19: the SPQEIR model", - "rel_date": "2020-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20075804", - "rel_abs": "Against the current COVID-19 pandemic, governments worldwide have devised a variety of non-pharmaceutical interventions to suppress it, but the efficacy of distinct measures is not yet well quantified. In this paper, we propose a novel tool to achieve this quantification. In fact, this paper develops a new extended epidemic SEIR model, informed by a socio-political classification of different interventions, to assess the value of several suppression approaches. First, we inquire the conceptual effect of suppression parameters on the infection curve. Then, we illustrate the potential of our model on data from a number of countries, to perform cross-country comparisons. This gives information on the best synergies of interventions to control epidemic outbreaks while minimising impact on socio-economic needs. For instance, our results suggest that, while rapid and strong lock-down is an effective pandemic suppression measure, a combination of social distancing and contact tracing can achieve similar suppression synergistically. This quantitative understanding will support the establishment of mid- and long-term interventions, to prepare containment strategies against further outbreaks. This paper also provides an online tool that allows researchers and decision makers to interactively simulate diverse scenarios with our model.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Daniele Proverbio", - "author_inst": "University of Luxembourg" - }, - { - "author_name": "Francoise Kemp", - "author_inst": "University of Luxembourg" - }, - { - "author_name": "Stefano Magni", - "author_inst": "University of Luxembourg" - }, - { - "author_name": "Andreas Dominik Husch", - "author_inst": "University of Luxembourg" - }, - { - "author_name": "Atte Aalto", - "author_inst": "University of Luxembourg" - }, - { - "author_name": "Laurent Mombaerts", - "author_inst": "University of Luxembourg" - }, - { - "author_name": "Alexander Skupin", - "author_inst": "University of Luxembourg" - }, - { - "author_name": "Jorge Goncalves", - "author_inst": "University of Luxembourg" - }, - { - "author_name": "Jose Ameijeiras-Alonso", - "author_inst": "KU Leuven" - }, - { - "author_name": "Christophe Ley", - "author_inst": "Ghent University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.22.20075705", "rel_title": "COVID-19: One-month impact of the French lockdown on the epidemic burden", @@ -1497066,6 +1500295,53 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.04.26.062406", + "rel_title": "How did SARS-CoV-19 spread in India from Italy, Iran and China? Genetic surveillance of early cases and virus demography", + "rel_date": "2020-04-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.26.062406", + "rel_abs": "SARS-CoV-19 after emerging from Wuhan, drastically devastated all sectors of human life by crushing down the global economy and increased psychological burden on public, government, and healthcare professionals. We manifested by analyzing 35 early coronavirus cases of India, that virus introduction in India, occurred from Italy, Iran and China and population demography apparently revealed a rapid population expansion after the outbreak with a present steady growth. We depicted nucleotide substitutions in structural genes, drove for the adaptive selection and plead for sequencing more genomes to facilitate identification of new emerged mutants, genetic evolution and disease transmission caused by coronavirus.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Mukesh Thakur", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Abhishek Singh", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Bheem Dutt Joshi", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Avijit Ghosh", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Sujeet Kumar Singh", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Neha Singh", + "author_inst": "University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Lalit Kumar Sharma", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Kailash Chandra", + "author_inst": "Zoological Survey of India, Kolkata" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.04.23.20076612", "rel_title": "A systematic review of Anakinra, Tocilizumab, Sarilumab and Siltuximab for coronavirus-related infections", @@ -1497203,33 +1500479,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.24.059527", - "rel_title": "A transcriptional regulatory atlas of coronavirus infection of human cells", - "rel_date": "2020-04-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.24.059527", - "rel_abs": "Establishing consensus around the transcriptional interface between coronavirus (CoV) infection and human cellular signaling pathways can catalyze the development of novel anti-CoV therapeutics. Here, we used publicly archived transcriptomic datasets to compute consensus regulatory signatures, or consensomes, that rank human genes based on their rates of differential expression in MERS-CoV (MERS), SARS-CoV-1 (SARS1) and SARS-CoV-2 (SARS2)-infected cells. Validating the CoV consensomes, we show that high confidence transcriptional targets (HCTs) of CoV infection intersect with HCTs of signaling pathway nodes with known roles in CoV infection. Among a series of novel use cases, we gather evidence for hypotheses that SARS2 infection efficiently represses E2F family target genes encoding key drivers of DNA replication and the cell cycle; that progesterone receptor signaling antagonizes SARS2-induced inflammatory signaling in the airway epithelium; and that SARS2 HCTs are enriched for genes involved in epithelial to mesenchymal transition. The CoV infection consensomes and HCT intersection analyses are freely accessible through the Signaling Pathways Project knowledgebase, and as Cytoscape-style networks in the Network Data Exchange repository.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Scott A Ochsner", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Rudolf T Pillich", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Neil McKenna", - "author_inst": "Baylor College of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.04.24.056259", "rel_title": "Expression of ACE2 and TMPRSS2, the SARS2-CoV-2 receptor and co-receptor, in prostate epithelial cells", @@ -1498752,6 +1502001,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.21.20074641", + "rel_title": "Association between rRT-PCR test results upon admission and outcome in hospitalized chest CT-Positive COVID-19 patients; a provincial retrospective cohort with active follow-up", + "rel_date": "2020-04-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20074641", + "rel_abs": "BackgroundThe Covid-19 pandemic imposed the most devastating challenge on healthcare systems worldwide. Iran was among the first countries that had to confront serious shortages in RT-PCR testing for SARS-CoV-2 and ventilators availabilities throughout the COVID-19 outbreak. This study aimed to investigate the clinical course of hospitalized COVID-19 patients with different rRT-PCR test results during the first 3 weeks of the outbreak in Qazvin province, Iran.\n\nMethodsFor this retrospective cohort study, data of hospitalized patients primarily diagnosed as having COVID-19 in all 12 centers across the whole Qazvin province during Feb 20-Mar 11, 2020 was analyzed. A multivariate logistic regression model was applied to assess the independent associates of death among COVID-19 patients.\n\nResults998 patients (57% male, median age 54 years) with positive chest CT-scan changes were included in this study. Among them, 558 patients were examined with rRT-PCR test and 73{middle dot}8% tested positive. Case fatality rate was 20{middle dot}68% and 7{middle dot}53% among test-positive and test negative hospitalized patients, respectively. While only 5{middle dot}2% of patients were ICU admitted, case fatality rates outside ICU were 17{middle dot}70% and 4{middle dot}65% in test-positive and test-negative non-ICU admitted patients, correspondingly. The independent associates of death were age [≥] 70 years, testing positive with rRT-PCR test, having immunodeficiency disorders and ICU admission.\n\nConclusionsHospitalized COVID-19 patients with mild symptoms despite positive chest CT changes and major comorbidities were more probable to have negative rRT-PCR test result, hence lower case fatality rate and a more favorable outcome.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Saeed Nemati", + "author_inst": "Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Hamid Reza Najari", + "author_inst": "1. Department of Internal Medicine, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran; 2. Deputy of health, Qazvin University of Medical S" + }, + { + "author_name": "Anita Eftekharzadeh", + "author_inst": "Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti Universiy School of Medicine, Tehran, Iran" + }, + { + "author_name": "Amir Mohammad Kazemifar", + "author_inst": "Department of Internal Medicine, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran" + }, + { + "author_name": "Ali Qandian", + "author_inst": "Office of Communicable Disease, Deputy of health, Qazvin University of Medical Sciences, Qazvin, Iran" + }, + { + "author_name": "Pedram Fattahi", + "author_inst": "Cancer Research Center, Cancer Research Institute, Tehran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Maedeh Zokaei Nikoo", + "author_inst": "Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran" + }, + { + "author_name": "Shiva Leghaei", + "author_inst": "Office of Communicable Disease, Deputy of health, Qazvin University of Medical Sciences, Qazvin, Iran" + }, + { + "author_name": "Mohammad Reza Rouhollahi", + "author_inst": "1. Cancer Research Center, Cancer Research Institute, Tehran University of Medical Sciences, Tehran, Iran; 2. Clinical Cancer Research Center (CCRC), Milad Hosp" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.21.20074757", "rel_title": "Knowledge, attitude, practice and perception regarding COVID-19 among students in Bangladesh: Survey in Rajshahi University", @@ -1498837,37 +1502137,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.22.20075267", - "rel_title": "Knowledge and Beliefs of General Public of India on COVID-19: A Web-based Cross-sectional Survey", - "rel_date": "2020-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20075267", - "rel_abs": "ContextDespite many awareness programs conducted by the governments and other agencies, there are certain false beliefs among the general public of India towards the transmission, prevention, and treatment of COVID-19.\n\nAimsTo assess the knowledge and beliefs of the general public of India on COVID-19.\n\nMaterials and MethodsA web-based cross-sectional survey was conducted between 20th March and 15th April 2020. A 17-item questionnaire was developed, validated, and used for the study. The questionnaire was randomly distributed among the public using Google forms through social media networks. Descriptive analysis was performed to represent the study characteristics, Chi-square test for assessing the associations among the study variables, and logistic regression analysis for identifying the factors influencing the beliefs.\n\nResultsA total of 462 participants with a mean (SD) age of 30.66 (11.31) years were responded to the questionnaire. Study participants are having fairly good knowledge of the basic aspects of COVID-19. However, a considerable fraction of participants were having false beliefs towards the transmission of new coronavirus, and prevention & treatment of COVID-19. It was observed that the participants who were aged 31-60 years and >60 years, education level of intermediate or diploma and high school certificate, and occupation as the unskilled workers had more of false beliefs towards COVID-19 compared to their counterparts.\n\nConclusionThough the overall knowledge on COVID-19 was good enough among the general public of India, still there is a need for education to avoid false beliefs especially among the people who are elderly, having a low level of education, and non-professional workers.\n\nKey MessagesA cross-sectional web-based online survey was conducted to assess the knowledge and beliefs of general public of India on COVID-19. It was identified that the knowledge among the general public on COVID-19 is fairly good. However, still there are some false beliefs among the population towards transmission of new coronavirus, and prevention & treatment of COVID-19, especially among the people who are elderly, having low level of education, and non-professional workers.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Puvvada Rahul Krishna", - "author_inst": "College of Science Health and Engineering, La Trobe University, Australia" - }, - { - "author_name": "Krishna Undela", - "author_inst": "JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru" - }, - { - "author_name": "Balaji Sathyanarayana Gupta", - "author_inst": "JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru" - }, - { - "author_name": "Shilpa Palaksha", - "author_inst": "JSS College of Pharmacy, JSS Academy of Higher Education & Research, Mysuru" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.22.20075382", "rel_title": "Chest computed tomography (CT) scan findings in patients with COVID-19: a systematic review and meta-analysis", @@ -1500150,6 +1503419,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.24.059576", + "rel_title": "Introductions and early spread of SARS-CoV-2 in France", + "rel_date": "2020-04-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.24.059576", + "rel_abs": "Following the emergence of coronavirus disease (COVID-19) in Wuhan, China in December 2019, specific COVID-19 surveillance was launched in France on January 10, 2020. Two weeks later, the first three imported cases of COVID-19 into Europe were diagnosed in France. We sequenced 97 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from samples collected between January 24 and March 24, 2020 from infected patients in France. Phylogenetic analysis identified several early independent SARS-CoV-2 introductions without local transmission, highlighting the efficacy of the measures taken to prevent virus spread from symptomatic cases. In parallel, our genomic data reveals the later predominant circulation of a major clade in many French regions, and implies local circulation of the virus in undocumented infections prior to the wave of COVID-19 cases. This study emphasizes the importance of continuous and geographically broad genomic sequencing and calls for further efforts with inclusion of asymptomatic infections.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Fabiana Gambaro", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Artem Baidaliuk", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Sylvie Behillil", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Flora Donati", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Melanie Albert", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Andreea Alexandru", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Maud Vanpeene", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Meline Bizard", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Angela Brisebarre", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Marion Barbet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Fawzi Derrar", + "author_inst": "Institut Pasteur of Algiers" + }, + { + "author_name": "Sylvie van der Werf", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Vincent Enouf", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Etienne Simon-Loriere", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.04.20.20064899", "rel_title": "Epidemiological characteristics of COVID-19 in medical staff members of neurosurgery departments in Hubei province: A multicentre descriptive study", @@ -1500307,57 +1503647,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.22.055863", - "rel_title": "Genomic, geographic and temporal distributions of SARS-CoV-2 mutations", - "rel_date": "2020-04-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.22.055863", - "rel_abs": "The COVID-19 pandemic is the most significant public health issue in recent history. Its causal agent, SARS-CoV-2, has evolved rapidly since its first emergence in December 2019. Mutations in the viral genome have critical impacts on the adaptation of viral strains to the local environment, and may alter the characteristics of viral transmission, disease manifestation, and the efficacy of treatment and vaccination. Using the complete sequences of 1,932 SARS-CoV-2 genomes, we examined the genomic, geographic and temporal distributions of aged, new, and frequent mutations of SARS-CoV-2, and identified six phylogenetic clusters of the strains, which also exhibit a geographic preference in different continents. Mutations in the form of single nucleotide variations (SNVs) provide a direct interpretation for the six phylogenetic clusters. Linkage disequilibrium, haplotype structure, evolutionary process, global distribution of mutations unveiled a sketch of the mutational history. Additionally, we found a positive correlation between the average mutation count and case fatality, and this correlation had strengthened with time, suggesting an important role of SNVs on disease outcomes. This study suggests that SNVs may become an important consideration in virus detection, clinical treatment, drug design, and vaccine development to avoid target shifting, and that continued isolation and sequencing is a crucial component in the fight against this pandemic.\n\nSignificance StatementMutation is the driving force of evolution for viruses like SARS-CoV-2, the causal agent of COVID-19. In this study, we discovered that the genome of SARS-CoV-2 is changing rapidly from the originally isolated form. These mutations have been spreading around the world and caused more than 2.5 million of infected cases and 170 thousands of deaths. We found that fourteen frequent mutations identified in this study can characterize the six main clusters of SARS-CoV-2 strains. In addition, we found the mutation burden is positively correlated with the fatality of COVID-19 patients. Understanding mutations in the SARS-CoV-2 genome will provide useful insight for the design of treatment and vaccination.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Hsin-Chou Yang", - "author_inst": "Institute of Statistical Science, Academia Sinica" - }, - { - "author_name": "Chun-houh Chen", - "author_inst": "Institute of Statistical Science, Academia Sinica" - }, - { - "author_name": "Jen-Hung Wang", - "author_inst": "Institute of Statistical Science, Academia Sinica" - }, - { - "author_name": "Hsiao-Ch Liao", - "author_inst": "Institute of Statistical Science, Academia Sinica" - }, - { - "author_name": "Chih-Ting Yang", - "author_inst": "Institute of Statistical Science, Academia Sinica" - }, - { - "author_name": "Chia-Wei Chen", - "author_inst": "Institute of Statistical Science, Academia Sinica" - }, - { - "author_name": "Yin-Chun Lin", - "author_inst": "Institute of Statistical Science, Academia Sinica" - }, - { - "author_name": "Chiun-How Kao", - "author_inst": "Institute of Statistical Science, Academia Sinica" - }, - { - "author_name": "James C. Liao", - "author_inst": "Institute of Biological Chemistry, Academia Sinica" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.24.058933", "rel_title": "Evolution and molecular characteristics of SARS-CoV-2 genome", @@ -1502068,6 +1505357,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.20.20072157", + "rel_title": "Multiple drivers of the COVID-19 spread: role of climate, international mobility, and region-specific conditions", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20072157", + "rel_abs": "The novel Coronavirus Disease 2019 (COVID-19) has spread quickly across the globe. Here, we evaluated the role of climate (temperature and precipitation), region-specific susceptibility (BCG vaccination, malaria infection, and elderly population) and international traveller population (human mobility) in shaping the geographical patterns of COVID-19 cases across 1,055 countries/regions, and examined the sequential shift of multiple drivers of the accumulated cases from December, 2019 to April 12, 2020. The accumulated numbers of COVID-19 cases (per 1 million population) were well explained by a simple regression model. The explanatory power (R2) of the model increased up to > 70% in April 2020 as the COVID-19 spread progressed. Climate, host mobility, and host susceptibility largely explained the variance of the COVID-19 cases (per 1 million population), and their explanatory power improved as the pandemic progressed; the relative importance of host mobility and host susceptibility have been greater than that of climate. The number of days from outbreak onset showed greater explanatory power in the earlier stages of COVID-19 spread but rapidly lost its influence. Our findings demonstrate that the COVID-19 pandemic is deterministically driven by climate suitability, cross-border human mobility, and region-specific susceptibility. The present distribution of COVID-19 cases has not reached an equilibrium and is changing daily, especially in the Southern Hemisphere. Nevertheless, the present results, based on mapping the spread of COVID-19 and identifying multiple drivers of this outbreak trajectory, may contribute to a better understanding of the COVID-19 disease transmission risk and the measures against long-term epidemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Yasuhiro Kubota", + "author_inst": "University of the Ryukyus" + }, + { + "author_name": "Takayuki Shiono", + "author_inst": "University of the Ryukyus" + }, + { + "author_name": "Buntarou Kusumoto", + "author_inst": "University of the Ryukyus" + }, + { + "author_name": "Junichi Fujinuma", + "author_inst": "University of the Ryukyus" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.22.20076141", "rel_title": "COVID-19: Public Compliance with and Public Support for Stay-at-Home Mitigation Strategies", @@ -1502185,49 +1505505,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.04.18.20069955", - "rel_title": "The impact of current and future control measures on the spread of COVID-19 in Germany", - "rel_date": "2020-04-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.18.20069955", - "rel_abs": "The novel coronavirus (SARS-CoV-2), identified in China at the end of December 2019 and causing the disease COVID-19, has meanwhile led to outbreaks all over the globe with about 2.2 million confirmed cases and more than 150,000 deaths as of April 17, 2020 [37]. In view of most recent information on testing activity [32], we present here an update of our initial work [4]. In this work, mathematical models have been developed to study the spread of COVID-19 among the population in Germany and to asses the impact of non-pharmaceutical interventions. Systems of differential equations of SEIR type are extended here to account for undetected infections, as well as for stages of infections and age groups. The models are calibrated on data until April 5, data from April 6 to 14 are used for model validation. We simulate different possible strategies for the mitigation of the current outbreak, slowing down the spread of the virus and thus reducing the peak in daily diagnosed cases, the demand for hospitalization or intensive care units admissions, and eventually the number of fatalities. Our results suggest that a partial (and gradual) lifting of introduced control measures could soon be possible if accompanied by further increased testing activity, strict isolation of detected cases and reduced contact to risk groups.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Maria Vittoria Barbarossa", - "author_inst": "Frankfurt Institute of Advanced Studies" - }, - { - "author_name": "Jan Fuhrmann", - "author_inst": "Juelich Supercomputing Centre, Forschungszentrum Juelich" - }, - { - "author_name": "Jan H Meinke", - "author_inst": "Julich Supercomputing Centre, Forschungszentrum Julich" - }, - { - "author_name": "Stefan Krieg", - "author_inst": "Julich Supercomputing Centre, Forschungszentrum Julich," - }, - { - "author_name": "Hridya V Varma", - "author_inst": "Interdisciplinary Center for Scientific Computing, Heidelberg" - }, - { - "author_name": "Noemi Castelletti", - "author_inst": "Institute of Radiation Medicine, Helmholtz Zentrum Muenchen, Neuherberg" - }, - { - "author_name": "Thomas Lippert", - "author_inst": "Julich Supercomputing Centre, Forschungszentrum Julich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.21.20073916", "rel_title": "Biased and unbiased estimation of the average lengths of stay in intensive care units in the COVID-19 pandemic", @@ -1503370,6 +1506647,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.20.20072892", + "rel_title": "Estimation of Undetected Covid-19 Infections in India", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20072892", + "rel_abs": "Background and ObjectivesWhile the number of detected COVID-19 infections are widely available, an understanding of the extent of undetected COVID-19 cases is urgently needed for an effective tackling of the pandemic and as a guide to lifting the lockdown. The aim of this work is to estimate and predict the true number of COVID-19 (detected and undetected) infections in India for short to medium forecast horizons. In particular, using publicly available COVID-19 infection data upto 16th April 2020, we predict the true number of infections in India during and upto the end of the formal lockdown period (21st April 2020).\n\nMethodsThe high death rate observed in most COVID-19 hit countries is suspected to be a function of the undetected infections existing in the population. An estimate of the age weighted infection fatality rate (IFR) of the disease of 0.41%, specifically calculated by taking into account the age structure of Indian population, is already available in the literature. In addition, the recorded case fatality rate (CFR= 0.70%) of Kerala, the only state in India to report single digit new infections over the second week of April, is used as a second estimate of the IFR. These estimates are used to formulate a relationship between deaths recorded and the true number of infections. The estimated undetected and detected cases time series based on these two IFR estimates are then used to fit a discrete time multivariate infection model to predict the total infections at the end of the formal lockdown period.\n\nResultsIn two consecutive fortnights during the lockdown, it was noted that the rise in detected infections has decreased by 2.7 times. For an IFR of 0.41%, the rise in undetected infections decreased by 3.2 times and the predicted number of total infections in India is 3.14 lakhs. While for an IFR of 0.70%, the rise in undetected cases decreased by 3.3 times and the total number of infections predicted on 21st April is 1.75 lakhs.\n\nInterpretation and ConclusionsThe behaviour of the undetected cases over time effectively illustrates the effects of lockdown and increased testing. From our estimates, it is found that the lockdown has brought down the undetected to detected cases ratio, and has consequently dampened the increase in the number of total cases. However, even though the rate of rise in total infections has fallen, the lifting of the lockdown should be done keeping in mind that 1.75 to 3 lakhs undetected cases will already exist in the population on 21st April.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Siuli Mukhopadhyay", + "author_inst": "Department of Mathematics, Indian Institute of Technology Bombay" + }, + { + "author_name": "Debraj Chakraborty", + "author_inst": "Indian Institute of Technology Bombay" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.20.20072462", "rel_title": "ESTIMATING R0 OF SARS-COV-2 IN HEALTHCARE SETTINGS", @@ -1503475,69 +1506775,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.19.20071548", - "rel_title": "Current Understanding of COVID-19 Clinical Course and Investigational Treatments", - "rel_date": "2020-04-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071548", - "rel_abs": "ImportanceCurrently, there is no unified framework linking disease progression to established viral levels, clinical tests, inflammatory markers, and investigational treatment options.\n\nObjectiveIt may take many weeks or months to establish a standard treatment approach. Given the growing morbidity and mortality with respect to COVID-19, we present a treatment approach based on a thorough review of scholarly articles and clinical reports. Our focus is on staged progression, clinical algorithms, and individualized treatment.\n\nEvidence ReviewWe followed the protocol for a quality review article proposed by Heyn et. al.1 A literature search was conducted to find all relevant studies related to COVID-19. The search was conducted between April 1, 2020 and April 13, 2020 using the following electronic databases: PubMed (1809 to present), Google Scholar (1900 to present), MEDLINE (1946 to present), CINAHL (1937 to present), and Embase (1980 to present). Keywords used included COVID-19, 2019-nCov, SARS-CoV-2, SARS-CoV, and MERS-CoV, with terms such as efficacy, seroconversion, microbiology, pathophysiology, viral levels, inflammation, survivability, and treatment and pharmacology. No language restriction was placed on the search. Reference lists were manually scanned for additional studies.\n\nFindingsOf the articles found in the literature search, 70 were selected for inclusion in this study (67 cited in the body of the manuscript and 3 additional unique references in the Figures).\n\nThe articles represent work from China, Japan, Taiwan, Vietnam, Rwanda, Israel, France, the United Kingdom, the Netherlands, Canada, and the United States. Most of the articles were cohort or case studies, but we also drew upon information found in guidelines from hospitals and clinics instructing their staff on procedures to follow. In addition, we based some decisions on data collected by agencies such as the CDC, FDA, IHME, ISDA, and Worldometer. None of the case studies or cohort studies used a large number of participants. The largest group of participants numbered less than 500 and some case studies had fewer than 30 patients. However, the review of the literature revealed the need for individualized treatment protocols due to the variability of patient clinical presentation and survivability. A number of factors appear to influence mortality: the stage at which the patient first presented for care, pre-existing health conditions, age, and the viral load the patient carried.\n\nConclusion and RelevanceCOVID-19 can be divided into three distinct Stages, beginning at the time of infection (Stage I), sometimes progressing to pulmonary involvement (Stage II, with or without hypoxemia) and less frequently to systemic inflammation (Stage III). In addition to modeling the stages of disease progression, we have also created a treatment algorithm which considers age, comorbidities, clinical presentation, and disease progression to suggest drug classes or treatment modalities. This paper presents the first evidence-based recommendations for individualized treatment for COVID-19.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat are the most effective treatment recommendations for COVID-19?\n\nFindingsCOVID-19 can be divided into three distinct Stages, beginning at the time of infection (Stage I), sometimes progressing to pulmonary involvement (Stage II, with or without hypoxemia) and less frequently to systemic inflammation (Stage III). In addition to modeling the stages of disease progression, we also created a treatment algorithm which considers age, comorbidities, clinical presentation, and disease progression to suggest drug classes or treatment modalities.\n\nMeaningThis paper presents the first evidence-based recommendations for individualized treatment for COVID-19.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Richard B Aguilar", - "author_inst": "Cano Health" - }, - { - "author_name": "Patrick Hardigan", - "author_inst": "Nova Southeastern University" - }, - { - "author_name": "Bindu Mayi", - "author_inst": "Nova Southeastern University" - }, - { - "author_name": "Darby Sider", - "author_inst": "Cleveland Clinic Florida" - }, - { - "author_name": "Jared Piotrkowski", - "author_inst": "Cleveland Clinic Florida" - }, - { - "author_name": "Jinesh Mehta", - "author_inst": "Cleveland Clinic Florida" - }, - { - "author_name": "Jenankan Dev", - "author_inst": "Cleveland Clinic Florida" - }, - { - "author_name": "Yelenis Seijo", - "author_inst": "Cleveland Clinic Florida" - }, - { - "author_name": "Antonio Lewis Camargo", - "author_inst": "Cleveland Clinic Florida" - }, - { - "author_name": "Luis Andux", - "author_inst": "Cano Health" - }, - { - "author_name": "Kathleen Hagen", - "author_inst": "Nova Southeastern University" - }, - { - "author_name": "Marlow B Hernandez", - "author_inst": "Cano Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.17.20070276", "rel_title": "Early epidemiological and clinical manifestations of COVID-19 in Japan", @@ -1504940,6 +1508177,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.23.057810", + "rel_title": "TARGETED PROTEOMICS FOR THE DETECTION OF SARS-COV-2 PROTEINS.", + "rel_date": "2020-04-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.23.057810", + "rel_abs": "The rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. In this proof-of-concept study, we explored the potential of targeted mass spectrometry based (MS) proteomics for the detection of SARS-CoV-2 proteins in both research samples and clinical specimens. First, we assessed the limit of detection for several SARS-CoV-2 proteins by parallel reaction monitoring (PRM) MS in infected Vero E6 cells. For tryptic peptides of Nucleocapsid protein, the limit of detection was in the mid-attomole range (9E-13 g). Next, this PRM methodology was applied to the detection of viral proteins in various COVID-19 patient clinical specimens, such as sputum and nasopharyngeal swabs. SARS-CoV-2 proteins were detected in these samples with high sensitivity in all specimens with PCR Ct values <24 and in several samples with higher CT values. A clear relationship was observed between summed MS peak intensities for SARS-CoV-2 proteins and Ct values reflecting the abundance of viral RNA. Taken together, these results suggest that targeted MS based proteomics may have the potential to be used as an additional tool in COVID-19 diagnostics.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Karel Bezstarosti", + "author_inst": "Erasmus University Medical Center" + }, + { + "author_name": "Mart M Lamers", + "author_inst": "Erasmus University Medical Center" + }, + { + "author_name": "Wouter AS Doff", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Peter C Wever", + "author_inst": "Jeroen Bosch Hospital" + }, + { + "author_name": "Khoa TD Thai", + "author_inst": "Star-shl diagnostic laboratories" + }, + { + "author_name": "Jeroen JA van Kampen", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Bart L Haagmans", + "author_inst": "Erasmus University Medical Center" + }, + { + "author_name": "Jeroen AA Demmers", + "author_inst": "Erasmus University Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.04.22.046565", "rel_title": "Functional and Genetic Analysis of Viral Receptor ACE2 Orthologs Reveals Broad Potential Host Range of SARS-CoV-2", @@ -1505233,81 +1508517,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.04.21.054387", - "rel_title": "Identification of potential treatments for COVID-19 through artificial intelligence-enabled phenomic analysis of human cells infected with SARS-CoV-2", - "rel_date": "2020-04-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.21.054387", - "rel_abs": "To identify potential therapeutic stop-gaps for SARS-CoV-2, we evaluated a library of 1,670 approved and reference compounds in an unbiased, cellular image-based screen for their ability to suppress the broad impacts of the SARS-CoV-2 virus on phenomic profiles of human renal cortical epithelial cells using deep learning. In our assay, remdesivir is the only antiviral tested with strong efficacy, neither chloroquine nor hydroxychloroquine have any beneficial effect in this human cell model, and a small number of compounds not currently being pursued clinically for SARS-CoV-2 have efficacy. We observed weak but beneficial class effects of {beta}-blockers, mTOR/PI3K inhibitors and Vitamin D analogues and a mild amplification of the viral phenotype with {beta}-agonists.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Katie Heiser", - "author_inst": "Recursion" - }, - { - "author_name": "Peter F. McLean", - "author_inst": "Recursion" - }, - { - "author_name": "Chadwick T. Davis", - "author_inst": "Recursion" - }, - { - "author_name": "Ben Fogelson", - "author_inst": "Recursion" - }, - { - "author_name": "Hannah B. Gordon", - "author_inst": "Recursion" - }, - { - "author_name": "Pamela Jacobson", - "author_inst": "Recursion" - }, - { - "author_name": "Brett L. Hurst", - "author_inst": "Utah State University" - }, - { - "author_name": "Ben J. Miller", - "author_inst": "Recursion" - }, - { - "author_name": "Ronald W. Alfa", - "author_inst": "Recursion" - }, - { - "author_name": "Berton A. Earnshaw", - "author_inst": "Recursion" - }, - { - "author_name": "Mason L. Victors", - "author_inst": "Recursion" - }, - { - "author_name": "Yolanda T. Chong", - "author_inst": "Recursion" - }, - { - "author_name": "Imran S. Haque", - "author_inst": "Recursion" - }, - { - "author_name": "Adeline S. Low", - "author_inst": "Recursion" - }, - { - "author_name": "Christopher C Gibson", - "author_inst": "Recursion" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.04.22.056127", "rel_title": "Heterogeneous expression of the SARS-Coronavirus-2 receptor ACE2 in the human respiratory tract", @@ -1506830,6 +1510039,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.19.20071654", + "rel_title": "A study on control of novel corona-virus (2019-nCoV) disease process by using PID controller", + "rel_date": "2020-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071654", + "rel_abs": "BackgroundIn this paper, the SEIR dynamic model will be used to model the epidemic of coronvirus (2019-nCoV)disease. The SEIR model has been used to model infectious diseases in Malaysia.Then, the spread and control of the disease is simulated applying a PID controller. The results of this study show that the implementation of strict restrictions such as quarantine, social distancing and closure of gathering centers is effective in controlling the disease. Using the results and analyzing them, it was found that early and strict implementation of strict restrictions such as quarantine, social distance and closure of centers with a high percentage of community is very important to control this disease and prevent irreparable economic losses and depreciation of medical staff.\n\nObjectiveModeling the prevalence and control of corona-virus (2019-nCoV)and the impact of government actions using control engineering methods.\n\nMethodIn this study, the SEIR dynamic model was used and the common data on the prevalence of the virus in Wuhan, China and Malaysia were used. As an example, the use of control target schemes is simulated in this paper.\n\nResultsThe findings of this study use control methods and forecasting in control engineering to provide a clear picture of macro-decisions for different governments in the field of infectious diseases.\n\nConclusionManagement and control schemes such as travel restrictions, quarantine, social distance and closure of offices, higher education institutions must be implemented immediately to prevent major economic and social losses. The implementation of these restrictions should not be delayed during the outbreak of corona-virus(2019-nCoV) infectious diseases.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "habibollah arasteh rad", + "author_inst": "Institute of applied Inteligent Systems Of University of Tehran" + }, + { + "author_name": "arshia badi", + "author_inst": "Institute of applied Inteligent Systems Of University of Tehran" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.18.20070821", "rel_title": "Estimating the Prevalence of COVID-19 in the United States: Three Complementary Approaches", @@ -1507027,141 +1510259,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.19.20068015", - "rel_title": "Impaired type I interferon activity and exacerbated inflammatory responses in severe Covid-19 patients", - "rel_date": "2020-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20068015", - "rel_abs": "BackgroundCoronavirus disease 2019 (Covid-19) is a major global threat that has already caused more than 100,000 deaths worldwide. It is characterized by distinct patterns of disease progression implying a diverse host immune response. However, the immunological features and molecular mechanisms involved in Covid-19 severity remain so far poorly known.\n\nMethodsWe performed an integrated immune analysis that included in-depth phenotypical profiling of immune cells, whole-blood transcriptomic and cytokine quantification on a cohort of fifty Covid19 patients with a spectrum of disease severity. All patient were tested 8 to 12 days following first symptoms and in absence of anti-inflammatory therapy.\n\nResultsA unique phenotype in severe and critically ill patients was identified. It consists in a profoundly impaired interferon (IFN) type I response characterized by a low interferon production and activity, with consequent downregulation of interferon-stimulated genes. This was associated with a persistent blood virus load and an exacerbated inflammatory response that was partially driven by the transcriptional factor NFB. It was also characterized by increased tumor necrosis factor (TNF)- and interleukin (IL)-6 production and signaling as well as increased innate immune chemokines.\n\nConclusionWe propose that type-I IFN deficiency in the blood is a hallmark of severe Covid-19 and could identify and define a high-risk population. Our study provides a rationale for testing IFN administration combined with adapted anti-inflammatory therapy targeting IL-6 or TNF- in most severe patients. These data also raise concern for utilization of drugs that interfere with the IFN pathway.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Jerome Hadjadj", - "author_inst": "Imagine institute, laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, Universite de Paris, F-75015, Paris" - }, - { - "author_name": "Nader Yatim", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Laura Barnabei", - "author_inst": "Imagine institute, laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, Universite de Paris, F-75015, Paris" - }, - { - "author_name": "Aurelien Corneau", - "author_inst": "Sorbonne Universite, Faculte de medecine, UMS037, PASS, Plateforme de cytometrie de la Pitie-Salpetriere CyPS, F-75013, Paris" - }, - { - "author_name": "Jeremy Boussier", - "author_inst": "Laboratory of Dendritic Cell Immunobiology, Department of Immunology, Institut Pasteur, F-75015, Paris" - }, - { - "author_name": "Helene Pere", - "author_inst": "Department of Virology, APHP-CUP, Universite de Paris, F-75015, Paris" - }, - { - "author_name": "Bruno Charbit", - "author_inst": "Centre for Translational Research, Institut Pasteur, F-75015, Paris" - }, - { - "author_name": "Vincent Bondet", - "author_inst": "Laboratory of Dendritic Cell Immunobiology, Department of Immunology, Institut Pasteur, F-75015, Paris" - }, - { - "author_name": "Camille Chenevier-Gobeaux", - "author_inst": "Department of Automated Diagnostic Biology, APHP. Centre-Universite de Paris, F-75014" - }, - { - "author_name": "Paul Breillat", - "author_inst": "Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hopitaux de Paris-Centre (APHP-CUP), Univer" - }, - { - "author_name": "Nicolas Carlier", - "author_inst": "Department of Pulmonology, APHP-CUP, Institut Cochin, UMR 1016, CESP U1018, Universite de Paris, F-75014, Paris" - }, - { - "author_name": "Remy Gauzit", - "author_inst": "Equipe Mobile Infectiologie, APHP Centre-Universite de Paris, F-75014, Paris" - }, - { - "author_name": "Caroline Morbieu", - "author_inst": "Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hopitaux de Paris-Centre (APHP-CUP), Univer" - }, - { - "author_name": "Frederic Pene", - "author_inst": "Medical intensive care unit, APHP-CUP, Institut Cochin, INSERM U1016, CNRS UMR 8104, Universite de Paris, F-75014, Paris" - }, - { - "author_name": "Nathalie Marin", - "author_inst": "Medical intensive care unit, APHP-CUP, Institut Cochin, INSERM U1016, CNRS UMR 8104, Universite de Paris, F-75014, Paris" - }, - { - "author_name": "Nicolas Roche", - "author_inst": "9Department of Pulmonology, APHP-CUP, Institut Cochin, UMR 1016, CESP U1018, Universite de Paris, F-75014, Paris" - }, - { - "author_name": "Tali-Anne Szwebel", - "author_inst": "Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hopitaux de Paris-Centre (APHP-CUP), Univer" - }, - { - "author_name": "Nikaia Smith", - "author_inst": "Laboratory of Dendritic Cell Immunobiology, Department of Immunology, Institut Pasteur, F-75015, Paris" - }, - { - "author_name": "Sarah Merkling", - "author_inst": "Insect-Virus Interactions Unit, Institut Pasteur, UMR2000, CNRS, Paris" - }, - { - "author_name": "Jean-Marc Treluyer", - "author_inst": "Centre Regional de Pharmacovigilance, APHP-CUP, Universite de Paris, F-75014, Paris" - }, - { - "author_name": "David Veyer", - "author_inst": "Department of Virology, APHP-CUP, Universite de Paris, F-75015, Paris" - }, - { - "author_name": "Luc Mouthon", - "author_inst": "Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hopitaux de Paris-Centre (APHP-CUP), Univer" - }, - { - "author_name": "Catherine Blanc", - "author_inst": "Sorbonne Universite, Faculte de medecine, UMS037, PASS, Plateforme de cytometrie de la Pitie-Salpetriere CyPS, F-75013, Paris" - }, - { - "author_name": "Pierre-Louis Tharaux", - "author_inst": "PARCC, INSERM U970, Paris" - }, - { - "author_name": "Flore Rozenberg", - "author_inst": "Department of Virology, APHP-CUP, Universite de Paris, F-75014, Paris" - }, - { - "author_name": "Alain Fischer", - "author_inst": "Imagine institute, laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, Universite de Paris, F-75015, Paris" - }, - { - "author_name": "Darragh Duffy", - "author_inst": "Laboratory of Dendritic Cell Immunobiology, Department of Immunology, Institut Pasteur, F-75015, Paris" - }, - { - "author_name": "Frederic Rieux-Laucat", - "author_inst": "Imagine institute, laboratory of Immunogenetics of Pediatric Autoimmune Diseases, INSERM UMR 1163, Universite de Paris, F-75015, Paris" - }, - { - "author_name": "Solen Kerneis", - "author_inst": "Epidemiologie et modelisation de la resistance aux antimicrobiens, Institut Pasteur, F-75015, Paris, France" - }, - { - "author_name": "Benjamin Terrier", - "author_inst": "Department of Internal Medicine, National Referral Center for Rare Systemic Autoimmune Diseases, Assistance Publique Hopitaux de Paris-Centre (APHP-CUP), Univer" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.18.20071167", "rel_title": "Repositioned chloroquine and hydroxychloroquine as antiviral prophylaxis for COVID-19: A protocol for rapid systematic review of randomized controlled trials", @@ -1508608,6 +1511705,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.04.17.20068601", + "rel_title": "The effect of BCG vaccination on COVID-19 examined by a statistical approach: no positive results from the Diamond Princess and cross-national differences previously reported by world-wide comparisons are flawed in several ways", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20068601", + "rel_abs": "Recently, the controversial hypothesis that past BCG (Bacillus Calmette-Guerin) vaccination reduces infection or severity of COVID-19 has been proposed. The present study examined this hypothesis using statistical approaches based on the public data. Three approaches were utilized: 1) comparing the infection and mortality ratio of people on the cruise ship Diamond Princess, 2) comparing the number of mortalities among nations, and 3) comparing the maximum daily increase rate of total mortalities among nations. The result of 1) showed that there is no significant difference in infection per person onboard or mortality-infection between Japanese citizens vs. US citizens and BCG obligatory nations vs. non-BCG obligatory nations on the Diamond Princess. The result of 2) showed that the number of mortalities among nations is similar to the previous studies, but this analysis also considered the timing of COVID-19 arrival in each nation. After correcting for arrival time, previously reported effect of BCG vaccination on decreasing total mortality disappeared. This is because nations that lack BCG vaccination are concentrated in Western Europe, which is near an epicenter of COVID-19. Therefore some previous reports are now considered to be affected by this artifact; the result may have been flawed by dispersal from an epicenter. However, some results showed weakly significant differences in the number of deaths at a particular time among BCG obligatory and non-BCG nations (especially the use of Japanese BCG strain Tokyo 172). However, these results are affected by the results of three countries and the effect of BCG vaccination remains inconclusive. The result of 3) showed that the maximum daily increasing rate in death among nations showed no significant difference among BCG vaccination policies. In the present study, although some results showed statistically significant differences among BCG vaccination policies, they may be affected by the impact of various other factors, such as national infection-control policies, social distancing, behavioral changes of people, possible previous local epidemics of closely related viruses, or inter-population differences in ACE2 or other genetic polymorphism. Further research is needed to better understand the underlying cause of the observed differences in infection and mortality of the disease among nations. Nevertheless, our results show that the effect of past BCG vaccination, if any, can be masked by many other factors. Therefore, the possible effect might be relatively small. In fact, in Japan, where almost all citizens have been vaccinated, COVID-19 cases are constantly increasing. Given the importance of peoples behavior in preventing viral propagation, the spread of optimism triggered by this hypothesis would be harmful to BCG vaccination nations.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Masakazu Asahara", + "author_inst": "Aichi Gakuin University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.17.20069716", "rel_title": "Years of life lost due to the psychosocial consequences of COVID19 mitigation strategies based on Swiss data", @@ -1508697,29 +1511813,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.04.17.20068916", - "rel_title": "Statistical and network-based analysis of Italian COVID-19 data: communities detection and temporal evolution", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20068916", - "rel_abs": "Coronavirus disease (COVID-19) outbreak started at Wuhan, China, and it has rapidly spread across China and many other countries. Italy is one of the European countries most affected by the COVID-19 disease, and it has registered high COVID-19 death rates and the death toll. In this article, we analyzed different Italian COVID-19 data at the regional level for the period February 24 to March 29, 2020. The analysis pipeline includes the following steps. After individuating groups of similar or dissimilar regions with respect to the ten types of available COVID-19 data using statistical test, we built several similarity matrices (reported in Supplementary file). Then, we mapped those similarity matrices into networks where nodes represent Italian regions and edges represent similarity relationships (edge length is inversely proportional to similarity). Then, network-based analysis was performed mainly discovering communities of regions that show similar behaviour. Then, network-based analysis was performed by running several community detection algorithms on those networks and by underlying communities of regions that show similar behaviour. The network-based analysis of Italian COVID-19 data is able to elegantly show how regions form communities, i.e. how they join and leave them, along time and how community consistency changes along time and with respect to the different available data.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Marianna Milano", - "author_inst": "University Magna Graecia of Catanzaro" - }, - { - "author_name": "Mario Cannataro", - "author_inst": "University Magna Graecia of Catanzaro" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.04.17.20069211", "rel_title": "A Web-based, Mobile Responsive Application to Screen Healthcare Workers for COVID Symptoms: Descriptive Study", @@ -1509978,6 +1513071,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.20.052290", + "rel_title": "Dynamical asymmetry exposes 2019-nCoV prefusion spike", + "rel_date": "2020-04-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.20.052290", + "rel_abs": "The novel coronavirus (2019-nCoV) spike protein is a smart molecular machine that instigates the entry of coronavirus to the host cell causing the COVID-19 pandemic. In this study, a structural-topology based model Hamiltonian of C3 symmetric trimeric spike is developed to explore its complete conformational energy landscape using molecular dynamic simulations. The study finds 2019-nCoV to adopt a unique strategy by undertaking a dynamic conformational asymmetry induced by a few unique inter-chain interactions. This results in two prevalent asymmetric structures of spike where one or two spike heads lifted up undergoing a dynamic transition likely to enhance rapid recognition of the host-cell receptor turning on its high-infectivity. The crucial interactions identified in this study are anticipated to potentially affect the efficacy of therapeutic targets.\n\nOne Sentence SummaryInter-chain-interaction driven rapid symmetry breaking strategy adopted by the prefusion trimeric spike protein likely to make 2019-nCoV highly infective.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Susmita Roy", + "author_inst": "Indian Institute of Science Education and Research Kolkata" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.04.16.20068163", "rel_title": "Projections for first-wave COVID-19 deaths across the US using social-distancing measures derived from mobile phones", @@ -1510091,49 +1513203,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.21.052639", - "rel_title": "Structural Basis of SARS-CoV-2 Spike Protein Priming by TMPRSS2", - "rel_date": "2020-04-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.21.052639", - "rel_abs": "Entry of SARS-CoV-2, etiological agent of COVID-19, in the host cell is driven by the interaction of its spike protein with human ACE2 receptor and a serine protease, TMPRSS2. Although complex between SARS-CoV-2 spike protein and ACE2 has been structurally resolved, the molecular details of the SARS-CoV-2 and TMPRSS2 complex are still elusive. TMPRSS2 is responsible for priming of the viral spike protein that entails cleavage of the spike protein at two potential sites, Arg685/Ser686 and Arg815/Ser816. The present study aims to investigate the conformational details of complex between TMPRSS2 and SARS-CoV-2 spike protein, in order to discern the finer details of the priming of viral spike and to point candidate drug targets. Briefly, full length structural model of TMPRSS2 was developed and docked against the resolved structure of SARS-CoV-2 spike protein with directional restraints of both cleavage sites. The docking simulations showed that TMPRSS2 interacts with the two different loops of SARS-CoV-2 spike protein, each containing different cleavage sites. Key functional residues of TMPRSS2 (His296, Ser441 and Ser460) were found to interact with immediate flanking residues of cleavage sites of SARS-CoV-2 spike protein. Compared to the N-terminal cleavage site (Arg685/Ser686), TMPRSS2 region that interact with C-terminal cleavage site (Arg815/Ser816) of the SARS-CoV-2 spike protein was predicted as relatively more druggable. In summary, the present study provide structural characteristics of molecular complex between human TMPRSS2 and SARS-CoV-2 spike protein and points to the candidate drug targets that could further be exploited to direct structure base drug designing.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Mushtaq Hussain", - "author_inst": "Dow College of Biotechnology, Dow University of Health Sciences" - }, - { - "author_name": "Nusrat Jabeen", - "author_inst": "Department of Microbiology, University of Karachi" - }, - { - "author_name": "Anusha Amanullah", - "author_inst": "Dow College of Biotechnology, Dow University of Health Sciences" - }, - { - "author_name": "Ayesha Ashraf Baig", - "author_inst": "Dow College of Biotechnology, Dow University of Health Sciences" - }, - { - "author_name": "Basma Aziz", - "author_inst": "Dow College of Biotechnology, Dow University of Health Sciences" - }, - { - "author_name": "Sanya Shabbir", - "author_inst": "Department of Microbiology, University of Karachi, Dow Research Institute of Biotechnology and Biomedical Sciences, Dow College of Biotechnology, Dow University" - }, - { - "author_name": "Fozia Raza", - "author_inst": "Dow College of Biotechnology, Dow University of Health Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.04.16.20068445", "rel_title": "A Novel Heuristic Global Algorithm to Predict the COVID-19 Pandemic Trend", @@ -1511428,6 +1514497,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.19.20071605", + "rel_title": "Spatial analysis of COVID-19 spread in Iran: Insights into geographical and structural transmission determinants at a province level", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071605", + "rel_abs": "The Islamic Republic of Iran reported its first COVID-19 cases by 19th February 2020, since then it has become one of the most affected countries, with more than 73,000 cases and 4,585 deaths at the date. Spatial modeling could be used to approach an understanding of structural and sociodemographic factors that have impacted COVID-19 spread at a province-level in Iran. In the present paper, we developed a spatial statistical approach to describe how COVID-19 cases are spatially distributed and to identify significant spatial clusters of cases and how the socioeconomic features of Iranian provinces might predict the number of cases. We identified a cluster of provinces with significantly higher rates of COVID-19 cases around Tehran, which indicated that the spread of COVID-19 within Iran was spatially correlated. Urbanized, highly connected provinces with older population structures and higher average temperatures were the most susceptible to present a higher number of COVID-19 cases. Interestingly, literacy is a protective factor that might be directly related to health literacy and compliance with public health measures. These features indicate that policies related to social distancing, protecting older adults, and vulnerable populations, as well as promoting health literacy, might be targeted to reduce SARS-CoV2 spread in Iran. Our approach could be applied to model COVID-19 outbreaks in other countries with similar characteristics or in case of an upturn in COVID-19 within Iran.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ricardo Ram\u00edrez-Aldana", + "author_inst": "Research Division, Instituto Nacional de Geriatr\u00eda (INGER), Anillo Perif. 2767, San Jeronimo Lidice, La Magdalena Contreras, 10200, Mexico City, Mexico." + }, + { + "author_name": "Juan Carlos Gomez-Verjan", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Omar Yaxmehen Bello-Chavolla", + "author_inst": "Instituto Nacional de Geriatria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.19.20071712", "rel_title": "Potential magnitude of COVID-19-induced healthcare resource depletion in Ontario, Canada", @@ -1511701,53 +1514797,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.04.19.20071639", - "rel_title": "How best to use limited tests? Improving COVID-19 surveillance in long-term care", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071639", - "rel_abs": "BackgroundLong-term care facilities (LTCFs) are vulnerable to COVID-19 outbreaks. Timely epidemiological surveillance is essential for outbreak response, but is complicated by a high proportion of silent (non-symptomatic) infections and limited testing resources.\n\nMethodsWe used a stochastic, individual-based model to simulate SARS-CoV-2 transmission along detailed inter-individual contact networks describing patient-staff interactions in real LTCF settings. We distributed nasopharyngeal swabs and RT-PCR tests using clinical and demographic indications, and evaluated the efficacy and resource-efficiency of a range of surveillance strategies, including group testing (sample pooling) and testing cascades, which couple (i) testing for multiple indications (symptoms, admission) with (ii) random daily testing.\n\nResultsIn the baseline scenario, randomly introducing SARS-CoV-2 into a 170-bed LTCF led to large outbreaks, with a cumulative 86 (6-224) infections after three weeks of unmitigated transmission. Efficacy of symptom-based screening was limited by (i) lags between infection and symptom onset, and (ii) silent transmission from asymptomatic and pre-symptomatic infections. Testing upon admission detected up to 66% of patients silently infected upon LTCF entry, but missed potential introductions from staff. Random daily testing was more effective when targeting patients than staff, but was overall an inefficient use of limited resources. At high testing capacity (>1 test/10 beds/day), cascades were most effective, with a 22-52% probability of detecting outbreaks prior to any nosocomial transmission, and 38-63% prior to first onset of COVID-19 symptoms. Conversely, at low capacity (<1 test/85 beds/day), pooling randomly selected patients in a daily group test was most effective (9-15% probability of detecting outbreaks prior to transmission; 30-44% prior to symptoms). The most efficient strategy compared to the reference was to pool individuals with any COVID-like symptoms, requiring only 5-7 additional tests and 17-24 additional swabs to detect outbreaks 5-6 days earlier, prior to an additional 14-18 infections.\n\nConclusionsGroup testing is an effective and efficient COVID-19 surveillance strategy for resource-limited LTCFs. Cascades are even more effective given ample testing resources. Increasing testing capacity and updating surveillance protocols accordingly could facilitate earlier detection of emerging outbreaks, informing a need for urgent intervention in settings with ongoing nosocomial transmission.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "David RM Smith", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Audrey Duval", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Koen B Pouwels", - "author_inst": "University of Oxford" - }, - { - "author_name": "Didier Guillemot", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Jerome Fernandes", - "author_inst": "Clinique de soins de suite et readaptation, Choisy-Le-Roi" - }, - { - "author_name": "Bich-Tram Huynh", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Laura Temime", - "author_inst": "Conservatoire national des arts et metiers" - }, - { - "author_name": "Lulla Opatowski", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.19.20071886", "rel_title": "Dynamics of Transmission and Control of COVID-19: A Real-time Estimation Using the Kalman Filter", @@ -1512750,6 +1515799,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.17.20064691", + "rel_title": "Development and validation of an early warning score (EWAS) for predicting clinical deterioration in patients with coronavirus disease 2019", + "rel_date": "2020-04-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20064691", + "rel_abs": "BackgroundSince the pandemic outbreak of coronavirus disease 2019 (COVID-19), the health system capacity in highly endemic areas has been overwhelmed. Approaches to efficient management are urgently needed. We aimed to develop and validate a score for early prediction of clinical deterioration of COVID-19 patients.\n\nMethodsIn this retrospective multicenter cohort study, we included 1138 mild to moderate COVID-19 patients admitted to 33 hospitals in Guangdong Province from December 27, 2019 to March 4, 2020 (N =818; training cohort), as well as two hospitals in Hubei Province from January 21 to February 22, 2020 (N =320; validation cohort) in the analysis.\n\nResultsThe 14-day cumulative incidences of clinical deterioration were 7.9% and 12.1% in the training and validation cohorts, respectively. An Early WArning Score (EWAS) (ranging from 0 to 4.5), comprising of age, underlying chronic disease, neutrophil to lymphocyte ratio, C-reactive protein, and D-dimer levels, was developed (AUROC: 0.857). By applying the EWAS, patients were categorized into low-, medium-, and high risk groups (cut-off values: two and three). The 14-day cumulative incidence of clinical deterioration in the low-risk group was 1.8%, which was significantly lower than the incidence rates in the medium-(14.4%) and high-risk (40.9%) groups (P <.001). The predictability of EWAS was similar in the validation cohort (AUROC =0.781), patients in the low-, medium-, and high-risk groups had 14-day cumulative incidences of 2.6%, 10.0%, and 25.7%, respectively (P <.001).\n\nConclusionThe EWAS, which is based on five common parameters, can predict COVID-19-related clinical deterioration and may be a useful tool for a rapid triage and establishing a COVID-19 hierarchical management system that will greatly focus clinical management and medical resources to reduce mortality in highly endemic areas.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Yabing Guo", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Yingxia Liu", + "author_inst": "National Clinical Research Centre for Infectious Disease, Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Tec" + }, + { + "author_name": "Jiatao Lu", + "author_inst": "Wuhan Hankou Hospital" + }, + { + "author_name": "Rong Fan", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Fuchun Zhang", + "author_inst": "Guangzhou Eighth People's Hospital" + }, + { + "author_name": "Xueru Yin", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Zhihong Liu", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Qinglang Zeng", + "author_inst": "Honghu People's Hospital" + }, + { + "author_name": "Jing Yuan", + "author_inst": "National Clinical Research Centre for Infectious Disease, Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Tec" + }, + { + "author_name": "Shufang Hu", + "author_inst": "Wuhan Hankou Hospital" + }, + { + "author_name": "Qiongya Wang", + "author_inst": "Wuhan Hankou Hospital" + }, + { + "author_name": "Baolin Liao", + "author_inst": "Guangzhou Eighth People's Hospital" + }, + { + "author_name": "Mingxing Huang", + "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Sichun Yin", + "author_inst": "The Ninth Dongguan People's Hospital" + }, + { + "author_name": "Xilin Zhang", + "author_inst": "The Fourth Foshan People's Hospital" + }, + { + "author_name": "Rui Xin", + "author_inst": "Guangdong Second Provincial General Hospital" + }, + { + "author_name": "Zhanzhou Lin", + "author_inst": "Huizhou Central People's Hospital" + }, + { + "author_name": "Changzheng Hu", + "author_inst": "Jiangmen Central Hospital" + }, + { + "author_name": "Boliang Zhao", + "author_inst": "The First Zhaoqing People's Hospital" + }, + { + "author_name": "Ridong He", + "author_inst": "Zhanjiang Central People's Hospital" + }, + { + "author_name": "Minfeng Liang", + "author_inst": "The First Foshan People's Hospital" + }, + { + "author_name": "Zheng Zhang", + "author_inst": "National Clinical Research Centre for Infectious Disease, Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Tec" + }, + { + "author_name": "Li Liu", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Jian Sun", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Lu Tang", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Lisi Deng", + "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Jinyu Xia", + "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Xiaoping Tang", + "author_inst": "Guangzhou Eighth People's Hospital" + }, + { + "author_name": "Lei Liu", + "author_inst": "National Clinical Research Centre for Infectious Disease, Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Tec" + }, + { + "author_name": "Jinlin Hou", + "author_inst": "Nanfang Hospital, Southern Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.15.20064931", "rel_title": "Sequencing analysis of the spread of SARS-CoV2 in the Greater New York City region", @@ -1513043,33 +1516227,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.16.20064709", - "rel_title": "Multi-task Deep Learning Based CT Imaging Analysis For COVID-19: Classification and Segmentation", - "rel_date": "2020-04-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20064709", - "rel_abs": "The fast spreading of the novel coronavirus COVID-19 has aroused worldwide interest and concern, and caused more than one million and a half confirmed cases to date. To combat this spread, medical imaging such as computed tomography (CT) images can be used for diagnostic. An automatic detection tools is necessary for helping screening COVID-19 pneumonia using chest CT imaging. In this work, we propose a multitask deep learning model to jointly identify COVID-19 patient and segment COVID-19 lesion from chest CT images. Our motivation is to leverage useful information contained in multiple related tasks to help improve both segmentation and classification performances. Our architecture is composed by an encoder and two decoders for reconstruction and segmentation, and a multi-layer perceptron for classification. The proposed model is evaluated and compared with other image segmentation and classification techniques using a dataset of 1044 patients including 449 patients with COVID-19, 100 normal ones, 98 with lung cancer and 397 of different kinds of pathology. The obtained results show very encouraging performance of our method with a dice coefficient higher than 0.78 for the segmentation and an area under the ROC curve higher than 93% for the classification.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Amine Amyar", - "author_inst": "University of Rouen" - }, - { - "author_name": "Romain Modzelewski", - "author_inst": "Henri Becquerel Center" - }, - { - "author_name": "Su Ruan", - "author_inst": "University of Rouen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.16.20067306", "rel_title": "Survival-Convolution Models for Predicting COVID-19 Cases and Assessing Effects of Mitigation Strategies", @@ -1514900,6 +1518057,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.04.20.051219", + "rel_title": "Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays", + "rel_date": "2020-04-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.20.051219", + "rel_abs": "SARS-CoV-2 enters cells using its Spike protein, which is also the main target of neutralizing antibodies. Therefore, assays to measure how antibodies and sera affect Spike-mediated viral infection are important for studying immunity. Because SARS-CoV-2 is a biosafety-level-3 virus, one way to simplify such assays is to pseudotype biosafety-level-2 viral particles with Spike. Such pseudotyping has now been described for single-cycle lentiviral, retroviral and VSV particles, but the reagents and protocols are not widely available. Here we detail how to effectively pseudotype lentiviral particles with SARS-CoV-2 Spike and infect 293T cells engineered to express the SARS-CoV-2 receptor, ACE2. We also make all the key experimental reagents available in the BEI Resources repository of ATCC and the NIH. Furthermore, we demonstrate how these pseudotyped lentiviral particles can be used to measure the neutralizing activity of human sera or plasma against SARS-CoV-2 in convenient luciferase-based assays, thereby providing a valuable complement to ELISA-based methods that measure antibody binding rather than neutralization.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Kate H.D. Crawford", + "author_inst": "University of Washington" + }, + { + "author_name": "Rachel Eguia", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Adam S Dingens", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Andrea N Loes", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Keara D Malone", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Caitlin R Wolf", + "author_inst": "University of Washington" + }, + { + "author_name": "Helen Y Chu", + "author_inst": "University of Washington" + }, + { + "author_name": "M. Alejandra Tortorici", + "author_inst": "University of Washington" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + }, + { + "author_name": "Michael Murphy", + "author_inst": "University of Washington" + }, + { + "author_name": "Deleah Pettie", + "author_inst": "University of Washington" + }, + { + "author_name": "Neil P King", + "author_inst": "University of Washington" + }, + { + "author_name": "Alejandro B Balazs", + "author_inst": "Ragon Institute" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "Fred Hutchinson Cancer Research Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.20.051581", "rel_title": "Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease", @@ -1515037,49 +1518265,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.14.20064618", - "rel_title": "Efficient high throughput SARS-CoV-2 testing to detect asymptomatic carriers", - "rel_date": "2020-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20064618", - "rel_abs": "The COVID-19 pandemic is rapidly spreading throughout the world. Recent reports suggest that 10-30% of SARS-CoV-2 infected patients are asymptomatic. Other studies report that some subjects have significant viral shedding prior to symptom onset. Since both asymptomatic and pre-symptomatic subjects can spread the disease, identifying such individuals is critical for effective control of the SARS-CoV-2 pandemic. Therefore, there is an urgent need to increase diagnostic testing capabilities in order to also screen asymptomatic carriers. In fact, such tests will be routinely required until a vaccine is developed. Yet, a major bottleneck of managing the COVID-19 pandemic in many countries is diagnostic testing, due to limited laboratory capabilities as well as limited access to genome-extraction and Polymerase Chain Reaction (PCR) reagents. We developed P-BEST - a method for Pooling-Based Efficient SARS-CoV-2 Testing, using a non-adaptive group-testing approach, which significantly reduces the number of tests required to identify all positive subjects within a large set of samples. Instead of testing each sample separately, samples are pooled into groups and each pool is tested for SARS-CoV-2 using the standard clinically approved PCR-based diagnostic assay. Each sample is part of multiple pools, using a combinatorial pooling strategy based on compressed sensing designed for maximizing the ability to identify all positive individuals. We evaluated P-BEST using leftover samples that were previously clinically tested for COVID-19. In our current proof-of-concept study we pooled 384 patient samples into 48 pools providing an 8-fold increase in testing efficiency. Five sets of 384 samples, containing 1-5 positive carriers were screened and all positive carriers in each set were correctly identified. P-BEST provides an efficient and easy-to-implement solution for increasing testing capacity that will work with any clinically approved genome-extraction and PCR-based diagnostic methodologies.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Noam Shental", - "author_inst": "Open University of Isarel" - }, - { - "author_name": "Shlomia Levy", - "author_inst": "Ben-Gurion University of the Negev" - }, - { - "author_name": "Shosh Skorniakov", - "author_inst": "Ben-Gurion University of the Negev" - }, - { - "author_name": "Vered Wuvshet", - "author_inst": "Ben-Gurion University of the Negev" - }, - { - "author_name": "Yonat Shemer-Avni", - "author_inst": "Soroka University Medical Center and Ben-Gurion University of the Negev" - }, - { - "author_name": "Angel Porgador", - "author_inst": "Ben-Gurion University of the Negev" - }, - { - "author_name": "Tomer Hertz", - "author_inst": "Ben-Gurion University of the Negev and Fred Hutch Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.14.20064535", "rel_title": "Proteome-wide analysis of differentially-expressed SARS-CoV-2 antibodies in early COVID-19 infection", @@ -1516494,6 +1519679,157 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.04.17.046375", + "rel_title": "Rapid development of an inactivated vaccine for SARS-CoV-2", + "rel_date": "2020-04-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.17.046375", + "rel_abs": "The COVID-19 pandemic caused by SARS-CoV-2 has brought about an unprecedented crisis, taking a heavy toll on human health, lives as well as the global economy. There are no SARS-CoV-2-specific treatments or vaccines available due to the novelty of this virus. Hence, rapid development of effective vaccines against SARS-CoV-2 is urgently needed. Here we developed a pilot-scale production of a purified inactivated SARS-CoV-2 virus vaccine candidate (PiCoVacc), which induced SARS-CoV-2-specific neutralizing antibodies in mice, rats and non-human primates. These antibodies potently neutralized 10 representative SARS-CoV-2 strains, indicative of a possible broader neutralizing ability against SARS-CoV-2 strains circulating worldwide. Immunization with two different doses (3g or 6 g per dose) provided partial or complete protection in macaques against SARS-CoV-2 challenge, respectively, without any antibody-dependent enhancement of infection. Systematic evaluation of PiCoVacc via monitoring clinical signs, hematological and biochemical index, and histophathological analysis in macaques suggests that it is safe. These data support the rapid clinical development of SARS-CoV-2 vaccines for humans.\n\nOne Sentence SummaryA purified inactivated SARS-CoV-2 virus vaccine candidate (PiCoVacc) confers complete protection in non-human primates against SARS-CoV-2 strains circulating worldwide by eliciting potent humoral responses devoid of immunopathology", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Qiang Gao", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Linlin Bao", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Haiyan Mao", + "author_inst": "Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Lin Wang", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Kangwei Xu", + "author_inst": "Division of Respiratory Virus Vaccines, National Institute for Food and Drug Control" + }, + { + "author_name": "minnan Yang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Yajing Li", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Ling Zhu", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Nan Wang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Zhe Lv", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Hong Gao", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Xiaoqin Ge", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Biao Kan", + "author_inst": "National Institute for Communicable Disease Control and Prevention, China CDC" + }, + { + "author_name": "Yaling Hu", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Jiangning Liu", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Fang Cai", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Deyu Jiang", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Yanhui Yin", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Chengfeng Qin", + "author_inst": "Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" + }, + { + "author_name": "Jing Li", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Xuejie Gong", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Xiuyu Lou", + "author_inst": "Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Wen Shi", + "author_inst": "Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Dongdong Wu", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Hengming Zhang", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Lang Zhu", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Wei Deng", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Yurong Li", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Jinxing Lu", + "author_inst": "National Institute for Communicable Diseases" + }, + { + "author_name": "Changgui Li", + "author_inst": "Division of Respiratory Virus Vaccines, National Institute for Food and Drug Control" + }, + { + "author_name": "Xiangxi Wang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Weidong Yin", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Yanjun Zhang", + "author_inst": "Zhejiang Center for Disease Control and Prevention" + }, + { + "author_name": "Chuan Qin", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.14.20060160", "rel_title": "Patient-derived mutations impact pathogenicity of SARS-CoV-2", @@ -1516615,85 +1519951,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.14.20064741", - "rel_title": "Health Education for Parents During the COVID-19 OutbreakPublic Health Education for Parents During the Outbreak of COVID-19: A Rapid Review", - "rel_date": "2020-04-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20064741", - "rel_abs": "BackgroundIt is well-known that public health education plays a crucial role in the prevention and control of emerging infectious diseases, but how health providers should advise families and parents to obtain health education information is a challenging question. With COVID-19 (Coronavirus disease 2019) spreading around the world, this rapid review aims to answer that question and thus to promote evidence-based decision making in health education policy and practice.\n\nMethodsWe systematically searched the literature on health education during COVID-19, SARS (severe acute respiratory syndrome) and MERS (middle east respiratory syndrome) epidemics in Medline (via PubMed), Cochrane Library, EMBASE, Web of Science, CBM (China Biology Medicine disc), CNKI (China National Knowledge Infrastructure), and Wanfang Data from their inception until March 31, 2020. The potential bias of the studies was assessed by Joanna Briggs Institute Prevalence Critical Appraisal Tool.\n\nResultsOf 1067 papers found, 24 cross-sectional studies with a total of 35,967 participants were included in this review. The general public lacked good knowledge of SARS and MERS at the early stage of epidemics. Some peoples knowledge, attitude and practice (KAP) of COVID-19 had been improved, but the health behaviors of some special groups including children and their parents need to be strengthened. Negative emotions including fear and stigmatization occurred during the outbreaks. Reliable health information was needed to improve public awareness and mental health for infectious diseases. Health information from nonprofit, government and academic websites was more accurate than privately owned commercial websites and media websites.\n\nConclusionsFor educating and cultivating children, parents should obtain information from the official websites of authorities such as the World Health Organization (WHO) and national Centers for Disease Control, or from other sources endorsed by these authorities, rather than from a general search of the internet or social media.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Weiguo Li", - "author_inst": "Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing 400014, China" - }, - { - "author_name": "Jing Liao", - "author_inst": "Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing 400014, China" - }, - { - "author_name": "Qinyuan Li", - "author_inst": "Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing 400014, China" - }, - { - "author_name": "Muna Baskota", - "author_inst": "Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing 400014, China" - }, - { - "author_name": "Xingmei Wang", - "author_inst": "Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing 400014, China" - }, - { - "author_name": "Yuyi Tang", - "author_inst": "Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing 400014, China" - }, - { - "author_name": "Qi Zhou", - "author_inst": "The First Clinical Medical College of Lanzhou University, Lanzhou, China" - }, - { - "author_name": "Xiaoqing Wang", - "author_inst": "Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing 400014, China" - }, - { - "author_name": "Xufei Luo", - "author_inst": "School of Public Health, Lanzhou University, Lanzhou 730000, China" - }, - { - "author_name": "Yanfang Ma", - "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" - }, - { - "author_name": "Toshio Fukuoka", - "author_inst": "Emergency and Critical Care Center, the Department of General Medicine, Department of Research and Medical Education at Kurashiki Central Hospital, Japan" - }, - { - "author_name": "Hyeong Sik Ahn", - "author_inst": "Department of Preventive Medicine, Korea University College of Medicine, Seoul, Korea" - }, - { - "author_name": "Myeong Soo Lee", - "author_inst": "Korea Institute of Oriental Medicine, Daejeon, Korea" - }, - { - "author_name": "Yaolong Chen", - "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China" - }, - { - "author_name": "Zhengxiu Luo", - "author_inst": "Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing 400014, China" - }, - { - "author_name": "Enmei Liu", - "author_inst": "Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing 400014, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.13.20064378", "rel_title": "Breastfeeding of Infants Born to Mothers with COVID-19: A Rapid Review", @@ -1518468,6 +1521725,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.14.20065466", + "rel_title": "Modelling strategies to predict hospital demand during the COVID-19 outbreak in Bogota, Colombia", + "rel_date": "2020-04-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065466", + "rel_abs": "Colombia, like many developing nations, does not have a strong health system able to respond to a pandemic of the magnitude of Covid-19. There is an increasing need to create a model that allows particular clinics and hospitals to estimate the number of patients that require Intensive Care Units-ICU care (critical), and the number of patients that require hospital care (severe), but not ICU care, in order to manage their limited resources.\n\nThis paper presents a prediction of the total number of ICU and regular beds that will be needed during the pandemic COVID-19 for Bogota-Colombia. We use a SEIR model that includes three different compartments of infection: those who can stay at home, those in regular hospital beds and those in need of ICU treatment. The model allows for a time varying transmission rate which we use to incorporate the measures introduced by the government over the period of one semester. The model predicts that by mid October 2020, the city will need 4 524 prevalent ICUs needed and 16 738 regular hospital beds needed. By the third week of July 2020, the number of patients that need ICUs will overpass the capacity set at 1 200 beds for ICU hospital beds in the city. The model predicts that the death toll by the same date will reach 1 752 people and the number of cases will be 30 216 inhabitants by then. We provide a Shiny app available in https://claudia-rivera-rodriguez.shinyapps.io/shinyappcovidclinic/. The original values in the app reproduce the results of this paper, but the parameters and starting values can be changed according to the users needs. COVID-19 has posed too many challenges to health systems around the globe, this model is an useful tool for cities, hospitals and clinics in Colombia that need to prepare for the excess demand of services that a pandemic like this one generates. Unfortunately, the model predicts that by the third week of July the projected capacity of the system in Bogota will not be enough. We expect the lockdown rules strength in the future days, so the death toll is not as bad as predicted by this model.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Claudia Rivera-Rodriguez", + "author_inst": "The University of Auckland" + }, + { + "author_name": "Beatriz Piedad Urdinola", + "author_inst": "National University of Colombia" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.14.20065706", "rel_title": "Has mortality due to other causes increased during the Covid-19 pandemic? Early evidence from England and Wales", @@ -1518561,61 +1521841,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.04.15.20066472", - "rel_title": "Objective olfactory testing in patients presenting with sudden onset olfactory dysfunction as the first manifestation of confirmed COVID-19 infection", - "rel_date": "2020-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20066472", - "rel_abs": "BackgroundThe aims of this study are to investigate the COVID-19 status of patients with initial sudden olfactory anosmia (ISOA) using nasopharyngeal swabs for RT-PCR analysis and to explore their olfactory dysfunctions with psychophysical olfactory evaluation.\n\nMethodologyThis prospective study included 78 ISOA patients who fulfilled a patient-reported outcome questionnaire and underwent a nasopharyngeal swabs. Among these, 46 patients performed psychophysical olfactory evaluation using sniffing tests. Based on the duration of the ISOA, two groups of patients were compared: patients with anosmia duration [≤]12 days (group 1) and those with duration >12 days (group 2).\n\nResultsAmong group 1, 42 patients (87.5%) had a positive viral load regarding RT-PCR while 6 patients (12.5%) were negative. In group 2, 7 patients (23%) had a positive viral load and 23 patients (77%) were negative. Among the 46 patients having performed a psychophysical olfactory evaluation, we observed anosmia in 52% (N=24), hyposmia in 24% (N=11) and normosmia in 24% (N=11) of patients. The viral load significantly decreased throughout the 14-days following the onset of the olfactory disorder.\n\nConclusionsOur results support that a high proportion of ISOA patients are Covid+. Our study supports the need to add anosmia to the list of symptoms used in screening tools for possible COVID-19 infection.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "jerome lechien", - "author_inst": "UMONS" - }, - { - "author_name": "pierre cabaraux", - "author_inst": "CHU Marie-Curie" - }, - { - "author_name": "carlos chiesa-estomba", - "author_inst": "Department of Otorhinolaryngology-Head & Neck Surgery, Hospital Universitario Donostia, San Sebastian, Spain." - }, - { - "author_name": "mohammad khalife", - "author_inst": "Epicura" - }, - { - "author_name": "jan plzak", - "author_inst": "University Hospital Motol, Prague, Czech Republic." - }, - { - "author_name": "stephane hans", - "author_inst": "Hopital Foch" - }, - { - "author_name": "delphine martiny", - "author_inst": "Laboratoire Hospitalier Universitaire de Bruxelles - Universitair Laboratorium Brussel (LHUB-ULB), Brussels, Belgium" - }, - { - "author_name": "christian Henriquez", - "author_inst": "Department of otolaryngology-Hospital Complex of Santiago de Compostela, Santiago de Compostela, Spain." - }, - { - "author_name": "Claire hopkins", - "author_inst": "Guy's and St Thomas NHS Foundation Trust, London, UK" - }, - { - "author_name": "sven saussez", - "author_inst": "University of Mons" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "otolaryngology" - }, { "rel_doi": "10.1101/2020.04.14.20065631", "rel_title": "Lack of coordination and medical disinformation in Canadian self-assessment tools for COVID-19", @@ -1519826,6 +1523051,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.16.044503", + "rel_title": "SARS-CoV-2 is transmitted via contact and via the air between ferrets.", + "rel_date": "2020-04-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.16.044503", + "rel_abs": "SARS-CoV-2, a coronavirus that newly emerged in China in late 2019 1,2 and spread rapidly worldwide, caused the first witnessed pandemic sparked by a coronavirus. As the pandemic progresses, information about the modes of transmission of SARS-CoV-2 among humans is critical to apply appropriate infection control measures and to slow its spread. Here we show that SARS-CoV-2 is transmitted efficiently via direct contact and via the air (via respiratory droplets and/or aerosols) between ferrets. Intranasal inoculation of donor ferrets resulted in a productive upper respiratory tract infection and long-term shedding, up to 11 to 19 days post-inoculation. SARS-CoV-2 transmitted to four out of four direct contact ferrets between 1 and 3 days after exposure and via the air to three out of four independent indirect recipient ferrets between 3 and 7 days after exposure. The pattern of virus shedding in the direct contact and indirect recipient ferrets was similar to that of the inoculated ferrets and infectious virus was isolated from all positive animals, showing that ferrets were productively infected via either route. This study provides experimental evidence of robust transmission of SARS-CoV-2 via the air, supporting the implementation of community-level social distancing measures currently applied in many countries in the world and informing decisions on infection control measures in healthcare settings 3.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Mathilde Richard", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Adinda Kok", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Dennis de Meulder", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Theo M. Bestebroer", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Mart M. Lamers", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Nisreen M.A. Okba", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Martje Fentener van Vlissingen", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Barry Rockx", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Bart L. Haagmans", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Marion P.G. Koopmans", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Ron A.M. Fouchier", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Sander Herfst", + "author_inst": "ErasmusMC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.14.20064733", "rel_title": "Chest Computed Tomography for the Diagnosis of Patients with Coronavirus Disease 2019 (COVID-19): A Rapid Review and Meta-Analysis", @@ -1520099,101 +1523387,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "toxicology" }, - { - "rel_doi": "10.1101/2020.04.17.046193", - "rel_title": "Shotgun proteomics of SARS-CoV-2 infected cells and its application to the optimisation of whole viral particle antigen production for vaccines", - "rel_date": "2020-04-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.17.046193", - "rel_abs": "Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) has resulted in a pandemic and continues to spread quickly around the globe. Currently, no effective vaccine is available to prevent COVID-19 and an intense global development activity is in progress. In this context, the different technology platforms face several challenges resulting from the involvement of a new virus still not fully characterised. Finding of the right conditions for virus amplification for the development of vaccines based on inactivated or attenuated whole viral particles is among them. Here, we describe the establishment of a workflow based on shotgun tandem mass spectrometry data to guide the optimisation of the conditions for viral amplification. In parallel, we analysed the dynamic of the host cell proteome following SARS-CoV-2 infection providing a global overview of biological processes modulated by the virus and that could be further explored to identify drug targets to address the pandemic.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Lucia Grenga", - "author_inst": "CEA" - }, - { - "author_name": "Fabrice Gallais", - "author_inst": "CEA" - }, - { - "author_name": "Olivier Pible", - "author_inst": "CEA" - }, - { - "author_name": "Jean-Charles Gaillard", - "author_inst": "CEA" - }, - { - "author_name": "Duarte Gouveia", - "author_inst": "CEA" - }, - { - "author_name": "Helene Batina", - "author_inst": "CEA" - }, - { - "author_name": "Niza Bazaline", - "author_inst": "CEA" - }, - { - "author_name": "Sylvie Ruat", - "author_inst": "CEA" - }, - { - "author_name": "Karen Culotta", - "author_inst": "CEA" - }, - { - "author_name": "Guylaine Miotello", - "author_inst": "CEA" - }, - { - "author_name": "Stephanie Debroas", - "author_inst": "CEA" - }, - { - "author_name": "Marie-Anne Roncato", - "author_inst": "CEA" - }, - { - "author_name": "Gerard Steinmetz", - "author_inst": "CEA" - }, - { - "author_name": "Charlotte Foissard", - "author_inst": "CEA" - }, - { - "author_name": "Anne Desplan", - "author_inst": "CEA" - }, - { - "author_name": "Beatrice Alpha-Bazin", - "author_inst": "CEA" - }, - { - "author_name": "Christine Almunia", - "author_inst": "CEA" - }, - { - "author_name": "Fabienne Gas", - "author_inst": "CEA" - }, - { - "author_name": "Laurent Bellanger", - "author_inst": "CEA" - }, - { - "author_name": "Jean Armengaud", - "author_inst": "CEA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.06.20055251", "rel_title": "Relationship between COVID-19 death toll doubling time and national BCG vaccination policy", @@ -1521468,6 +1524661,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.17.20067348", + "rel_title": "Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-qPCR", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20067348", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most widely used method of COVID-19 diagnostics is a reverse transcription polymerase chain reaction (RT-PCR) assay, to detect the presence of SARS-CoV-2 RNA in patient samples, typically from nasopharyngeal swabs. RNA extraction is a major bottleneck in current COVID-19 testing, in terms of turn-around, logistics, component availability and cost, which delays or completely precludes COVID-19 diagnostics in many settings. Efforts to simplify the current methods are critical, as increased diagnostic availability and efficiency would benefit patient care and infection control. Here, we describe methods to circumvent RNA extraction in COVID-19 testing by performing RT-PCR directly on heat-inactivated subject samples as well as samples lysed with readily available detergents. Our data, including benchmarking with 597 clinically diagnosed patient samples against a standardised and sensitive diagnostic system, show that direct RT-PCR is a viable option to extraction-based COVID-19 diagnostics. Furthermore, using controlled amounts of active SARS-CoV-2, we evaluated performance of generic buffers as sample medium for the direct RT-PCR assay, identifying several suitable formulations. We also confirmed the effectiveness of heat inactivation of SARS-CoV-2 by plaque assay. Significant savings in terms of time and cost can be achieved by embracing RNA-extraction-free protocols, that feed directly into the established PCR-based testing pipeline. This could aid the expansion of COVID-19 testing.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Ioanna Smyrlaki", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Martin Ekman", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Antonio Lentini", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Nuno Rufino de Sousa", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Natali Papanicoloau", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Martin Vondracek", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Johan Aarum", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Hamzah Safari", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Shaman Muradrasoli", + "author_inst": "Public Health Agency of Sweden" + }, + { + "author_name": "Antonio Gigliotti Rothfuchs", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Jan Albert", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Bj\u00f6rn H\u00f6gberg", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Bj\u00f6rn Reinius", + "author_inst": "Karolinska Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.14.20064501", "rel_title": "What influences COVID-19 infection rates: A statistical approach to identify promising factors applied to infection data from Germany", @@ -1521545,33 +1524805,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.14.20064949", - "rel_title": "Novel Coronavirus in Nigeria: Epidemiological analysis of the first 45 days of the pandemic", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20064949", - "rel_abs": "BackgroundOn December 31, 2019, the World Health Organization (WHO) was notified of a novel coronavirus in China that was later named COVID-19. On March 11, 2020, the outbreak of COVID-19 was declared a pandemic. The first instance of the virus in Nigeria was documented on February 27, 2020.\n\nMethodsThis study provides a preliminary epidemiological analysis of the first 45 days of COVID-19 outbreak in Nigeria quantifying. We estimated the early transmissibility via time-varying reproduction number based on Bayesian method that incorporates uncertainty in the distribution of serial interval (time interval between symptoms onset in an infected individual and the infector) and adjusted for disease importation.\n\nFindingsBy April 11, 2020, 318 confirmed cases and 10 deaths from COVID-19 have occurred in Nigeria. At day 45, the exponential growth rate was 0.07 (95% Confidence Interval (CI): 0.05 - 0.10) with doubling time of 9.84 days (95% CI: 7.28 - 15.18). Separately for travel related and local cases the doubling time was 12.88 days and 2.86 days, respectively. Furthermore, we estimated the reproduction number for each day of the outbreak using three-weekly window while adjusting for travel related cases. The estimated reproduction number was 4.98 (95% CrI: 2.65 - 8.41) at day 22 (March 19, 2020), peaking at 5.61 (95% CrI: 3.83 -7.88) at day 25 (March 22, 2020). The median reproduction number over the study period was 2.71 and the latest value at April 11, 2020 was 1.42 (95% CI: 1.26 - 1.58).\n\nInterpretationThese 45-day estimates suggested that cases of COVID-19 in Nigeria have been remarkably lower than expected and the preparedness to detect needs to be shifted to stop local transmission.\n\nFundingNone", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Oyelola Adegboye", - "author_inst": "James Cook University" - }, - { - "author_name": "Adeshina I Adekunle", - "author_inst": "James Cook University" - }, - { - "author_name": "Ezra Gayawan", - "author_inst": "Federal University of Technology" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.14.20065128", "rel_title": "Refined compartmental models, asymptomatic carriers and COVID-19", @@ -1522558,6 +1525791,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.16.20061044", + "rel_title": "EFFECTIVENESS OF BASELINE AND POST-PROCESSED CHEST X-RAY IN NONEARLY COVID-19 PATIENTS", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20061044", + "rel_abs": "BackgroundCT is a very sensitive technique to detect pneumonia in COVID-19 patients. However, it is impaired by high costs, logistic issues and high risk of exposure.\n\nChest x-ray (CXR) is a low-cost, low-risk, not time consuming technique and is emerging as the recommended imaging modality to use in COVID-19 pandemic.\n\nThis technique, although less sensitive than CT-scan, can provide useful information about pulmonary involvement.\n\nPurposeTo describe chest x-ray features of COVID-19 pneumonia and to evaluate the sensitivity of this technique in detecting pneumonia. A further scope is to assess the effectiveness of a post-processing algorithm in improving lung lesions detectability.\n\nMaterials and Methods72 patients with laboratory-confirmed COVID-19 underwent bedside chest X-ray.\n\nTwo radiologists were asked to express their opinion about: (i) presence of pneumonia (negative or positive); (ii) localization (unilateral or bilateral); (iii) topography (according to pulmonary fields); (iv) density (non consolidative ground-glass or inhomogeneous opacities; consolidative nodular-type or triangular; mixed consolidative e non-consolidative); and (v) presence of pleural effusion. The point (i) was evaluated separately, while the other points in consensus.\n\nA quality assessment of post-processed x-ray images was performed by two different readers.\n\nResultsThe agreement about presence of pneumonia was almost perfect with K value of 0.933 and p < 0.001.\n\nSensitivity was 69%.\n\nThe following findings were seen: unilateral lung involvement in 50%; lower lung lesions in 54%; peripheral distribution in 48%; and non-consolidative pattern in 44%.\n\nPost-processed images improved the detection of lesions in 7 out 72 patients ({cong}10%)\n\nConclusionCXR owns a good sensitivity in detecting COVID-19 lung involvement. Use of post-processing algorithm can improve detection of lesions. Our data support recommendations of the Radiological Society of North America (RSNA) to consider chest x-ray as first step imaging examination in Covid-19 patients.\n\nSUMMARYBedside CXR has a good sensitivity in evaluating COVID-19 lung involvement in hospitalized patients and should be considered as the first step imaging technique according to RSNA recommendations.\n\nKEY RESULTSO_LIBedside CXR has a good sensitivity in evaluating COVID-19 lung involvement in non-early clinical cases.\nC_LIO_LIThe most common findings of lung involvement were slight different from the well-described CT-ones, with less common patterns of bilateral and peripheral distribution.\nC_LIO_LIPost-processing algorithm enhances detection of pulmonary lesions.\nC_LI", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Michele Gaeta", + "author_inst": "University of Messina" + }, + { + "author_name": "Giuseppe Cicero", + "author_inst": "University of Messina" + }, + { + "author_name": "Maria Adele Marino", + "author_inst": "University of Messina" + }, + { + "author_name": "Tommaso D'Angelo", + "author_inst": "University of Messina" + }, + { + "author_name": "Enrico Maria Mormina", + "author_inst": "University of Messina" + }, + { + "author_name": "Silvio Mazziotti", + "author_inst": "University of Messina" + }, + { + "author_name": "Alfredo Blandino", + "author_inst": "University of Messina" + }, + { + "author_name": "Giulio Siracusano", + "author_inst": "University of Catania" + }, + { + "author_name": "Aurelio La Corte", + "author_inst": "University of Catania" + }, + { + "author_name": "Massimo Chiappini", + "author_inst": "Instituto Nazionale di Geofisica e Vulcanologia" + }, + { + "author_name": "Giovanni Finocchio", + "author_inst": "University of Messina" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.04.12.20062695", "rel_title": "Shut it down: a cross country panel analysis on the efficacy of lockdown measures", @@ -1522631,29 +1525923,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.11.20061804", - "rel_title": "Ivermectin as a potential COVID-19 treatment from the pharmacokinetic point of view", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20061804", - "rel_abs": "The broad-spectrum antiparasitic agent ivermectin has been very recently found to inhibit SARS-CoV-2 in vitro and proposed as a candidate for drug repurposing in COVID-19. In the present report the in vitro antiviral activity end-points are analyzed from the pharmacokinetic perspective. The available pharmacokinetic data from clinically relevant and excessive dosing studies indicate that the SARS-CoV-2 inhibitory concentrations are not likely to be attainable in humans.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Georgi Momekov", - "author_inst": "Faculty of Pharmacy; Medical University of Sofia" - }, - { - "author_name": "Denitsa Momekova", - "author_inst": "Faculty of Pharmacy, Medical University of Sofia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.11.20061838", "rel_title": "The Estimated Time-Varying Reproduction Numbers during the Ongoing Epidemic of the Coronavirus Disease 2019 (COVID-19) in China", @@ -1523788,6 +1527057,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.13.20063644", + "rel_title": "Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20063644", + "rel_abs": "BackgroundAs governments across Europe have issued non-pharmaceutical interventions (NPIs) such as social distancing and school closing, the mobility patterns in these countries have changed. It is likely different countries and populations respond differently to the same NPIs and that these differences are reflected in the epidemic development.\n\nMethodsWe build a Bayesian model that estimates the number of deaths on a given day dependent on changes in the basic reproductive number, R0, due to changes in mobility patterns. We utilize mobility data from Google mobility reports using five different categories: retail and recreation, grocery and pharmacy, transit stations, workplace and residential. The importance of each mobility category for predicting changes in R0 is estimated through the model.\n\nFindingsThe changes in mobility have a large overlap with the introduction of governmental NPIs, highlighting the importance of government action for population behavioural change. The grocery and pharmacy sector is estimated to account for 97 % of the reduction in R0 (95% confidence interval [0{middle dot}79,0{middle dot}99]).\n\nInterpretationOur model predicts three-week epidemic forecasts, using real-time observations of changes in mobility patterns, which can provide governments with direct feedback on the effects of their NPIs. The model predicts the changes in a majority of the countries accurately but overestimates the impact of NPIs in Sweden and Denmark and underestimates them in France and Belgium.\n\nFundingFinancial support: Swedish Research Council for Natural Science, grant No. VR-2016-06301 and Swedish E-science Research Center. Computational resources: Swedish National Infrastructure for Computing, grant No. SNIC-2019/3-319.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Patrick Bryant", + "author_inst": "Stockholm University/Science for Life Laboratory" + }, + { + "author_name": "Arne Elofsson", + "author_inst": "Stockholm University/Science for Life Laboratory" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.13.20063610", "rel_title": "The December 2019 New Corona Virus Disease (SARS-CoV-2) Outbreak: A Behavioral Infectious Disease Policy Model", @@ -1523861,33 +1527153,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.13.20063511", - "rel_title": "Estimating the Fraction of Unreported Infections in Epidemics with a Known Epicenter: an Application to COVID-19", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20063511", - "rel_abs": "We develop a simple analytical method to estimate the fraction of unreported infections in epidemics with a known epicenter and estimate the number of unreported COVID-19 infections in the US during the first half of March 2020. Our method utilizes the covariation in initial reported infections across US regions and the number of travelers to these regions from the epicenter, along with the results of a randomized testing study in Iceland. We estimate that 4-14% (1.5%-10%) of actual infections had been reported in US up to March 16, accounting for an assumed reporting lag of 8 (5) days.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ali Hortacsu", - "author_inst": "Department of Economics, University of Chicago" - }, - { - "author_name": "Jiarui Liu", - "author_inst": "Department of Economics, University of Chicago" - }, - { - "author_name": "Timothy Schwieg", - "author_inst": "Becker Friedman Institute, University of Chicago" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.13.20063354", "rel_title": "SimCOVID: An Open-Source Simulation Program for theCOVID-19 Outbreak", @@ -1524806,6 +1528071,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.11.20061721", + "rel_title": "COVID-19-related mortality by age groups in Europe: A meta-analysis", + "rel_date": "2020-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20061721", + "rel_abs": "Background and ObjectivesTo date, more than 1,000,000 confirmed cases and 65,000 deaths due to coronavirus disease 2019 (COVID-19) have been reported globally. Early data have indicated that older patients are at higher risk of dying from COVID-19 than younger ones, but precise international estimates of the age-breakdown of COVID-19-related deaths are lacking.\n\nMaterials and MethodsWe evaluated the distribution of COVID-19-related fatalities by age groups in Europe. On April 6, 2020, we systematically reviewed COVID-19-related mortality data from 32 European countries (European Union/European Economic Area and the United Kingdom). We collated official reports provided by local Public Health or Ministry of Health websites. We included countries if they provided data regarding more than 10 COVID-19-related deaths stratified by age according to pre-specified groups (i.e., < 40, 40-69, [≥] 70 years). We used random-effects meta-analysis to estimate the proportion of age groups among all COVID-19-related fatalities.\n\nResultsThirteen European countries were included in the review, for a total of 31,864 COVID-19-related deaths (range: 27-14,381 per country). In the main meta-analysis (including data from Germany, Hungary, Italy, Netherlands, Portugal, Spain, Switzerland; 21,522 COVID-19-related fatalities), the summary proportions of persons < 40, 40-69, and [≥] 70 years of age among all COVID-19-related deaths were 0.1% (0.0-0.2%; I2 24%), 12.8% (10.3-15.6%; I2 94%), and 84.8% (81.3-88.1%; I2 96%), respectively.\n\nConclusionsPeople under 40 years of age represent a small fraction of the total number of COVID-19-related deaths in Europe. These results may help health authorities respond to public concerns and guide future physical distancing and mitigation strategies.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "J\u00e9r\u00e9mie F. Cohen", + "author_inst": "Inserm UMR 1153, Universite de Paris" + }, + { + "author_name": "Dani\u00ebl A. Korevaar", + "author_inst": "Department of Respiratory Medicine, Amsterdam University Medical Center, University of Amsterdam, PO Box 22700, 1100 DE, Amsterdam, The Netherlands" + }, + { + "author_name": "Soraya Matczak", + "author_inst": "Department of General Pediatrics and Pediatric Infectious Diseases, AP-HP, Necker Hospital for Sick Children, Universite de Paris, 75015, Paris, France" + }, + { + "author_name": "Jos\u00e9phine Brice", + "author_inst": "Department of General Pediatrics and Pediatric Infectious Diseases, AP-HP, Necker Hospital for Sick Children, Universite de Paris, 75015, Paris, France" + }, + { + "author_name": "Martin Chalumeau", + "author_inst": "Department of General Pediatrics and Pediatric Infectious Diseases, AP-HP, Necker Hospital for Sick Children, Universite de Paris, 75015, Paris, France" + }, + { + "author_name": "Julie Toubiana", + "author_inst": "Department of General Pediatrics and Pediatric Infectious Diseases, AP-HP, Necker Hospital for Sick Children, Universite de Paris, 75015, Paris, France" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.12.20062869", "rel_title": "Cardiovascular Diseases and COVID-19 Mortality and Intensive Care Unit Admission: A Systematic Review and Meta-analysis", @@ -1524939,29 +1528243,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.13.20063529", - "rel_title": "Impact of population mask wearing on Covid-19 post lockdown", - "rel_date": "2020-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20063529", - "rel_abs": "COVID-19, caused by SARS-CoV2 is a rapidly spreading global pandemic. Although precise transmission routes and dynamics are unknown, SARS-CoV2 is thought primarily to spread via contagious respiratory droplets. Unlike with SARS-CoV, maximal viral shedding occurs in the early phase of illness, and this is supported by models that suggest 40-80% of transmission events occur from pre- and asymptomatic individuals. One widely-discussed strategy to limit transmission of SARS-CoV2, particularly from presymptomatic individuals, has been population-level wearing of masks. Modelling for pandemic influenza suggests some benefit in reducing total numbers infected with even 50% mask-use. COVID-19 has a higher hospitalization and mortality rate than influenza, and the impacts on these parameters, and critically, at what point in the pandemic trajectory mask-use might exert maximal benefit are completely unknown. We derived a simplified SIR model to investigate the effects of near-universal mask-use on COVID-19 assuming 8 or 16% mask efficacy. We decided to model, in particular, the impact of masks on numbers of critically-ill patients and cumulative mortality, since these are parameters that are likely to have the most severe consequences in the COVID-19 pandemic. Whereas mask use had a relatively minor benefit on critical-care and mortality rates when transmissibility (Reff) was high, the reduction on deaths was dramatic as the effective R approached 1, as might be expected after aggressive social-distancing measures such as wide-spread lockdowns. One major concern with COVID-19 is its potential to overwhelm healthcare infrastructures, even in resource-rich settings, with one third of hospitalized patients requiring critical-care. We incorporated this into our model, increasing death rates for when critical-care resources have been exhausted. Our simple model shows that modest efficacy of masks could avert substantial mortality in this scenario. Importantly, the effects on mortality became hyper-sensitive to mask-wearing as the effective R approaches 1, i.e. near the tipping point of when the infection trajectory is expected to revert to exponential growth, as would be expected after effective lockdown. Our model suggests that mask-wearing might exert maximal benefit as nations plan their post-lockdown strategies and suggests that mask-wearing should be included in further more sophisticated models of the current pandemic.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Babak Javid", - "author_inst": "Tsinghua University School of Medicine" - }, - { - "author_name": "Nathalie Q Balaban", - "author_inst": "Hebrew University of Jerusalem" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.12.20061002", "rel_title": "Estimating the Final Epidemic Size for COVID-19 Outbreak using Improved Epidemiological Models", @@ -1526079,6 +1529360,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.10.20060905", + "rel_title": "COVID-19: A model correlating BCG vaccination to protection from mortality implicates trained immunity", + "rel_date": "2020-04-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060905", + "rel_abs": "O_LIWe use a data quality model to demonstrate that BCG vaccination is correlated with protection from death from COVID19\nC_LIO_LIFrom a mechanistic perspective, BCG is well described to elicit its protective non-specific effects through the process of trained immunity.\nC_LIO_LITherapeutically enhancing trained immunity may therefore be an important mechanism in protection from the lethal effects of COVID19\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Cameron M. Green", + "author_inst": "Fresh Software A.G." + }, + { + "author_name": "Stephanie Fanucchi", + "author_inst": "Division of Chemical, Systems & Synthetic Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town" + }, + { + "author_name": "Ezio T. Fok", + "author_inst": "Epigenomics & Single Cell Biophysics Group, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, The Netherlands" + }, + { + "author_name": "Simone J.C.F.M. Moorlag", + "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands" + }, + { + "author_name": "Jorge Dominguez-Andres", + "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands" + }, + { + "author_name": "Yutaka Negishi", + "author_inst": "Epigenomics & Single Cell Biophysics Group, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, The Netherlands" + }, + { + "author_name": "Leo A.B. Joosten", + "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands" + }, + { + "author_name": "Mihai G. Netea", + "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands" + }, + { + "author_name": "Musa M. Mhlanga", + "author_inst": "Radboud University, Radboud Institute for Molecular Life Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.11.20062372", "rel_title": "Self-Collected Oral Fluid and Nasal Swabs Demonstrate Comparable Sensitivity to Clinician Collected Nasopharyngeal Swabs for Covid-19 Detection", @@ -1526184,29 +1529516,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.10.20061374", - "rel_title": "Covid-19 clinical data analysis using Ball Mapper", - "rel_date": "2020-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20061374", - "rel_abs": "In this note we provide a result of analysis of blood test data from patients with SARS-Cov-2 using Ball Mapper Algorithm. We observe that patients with the virus and in particularly patients who end up in Intensive Care Unit have quite narrow values of those parameters. Please note that this is a preliminary work and it need to be validated on much larger dataset which we are trying to acquire at the moment.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Pawel Dlotko", - "author_inst": "Swansea University" - }, - { - "author_name": "Simon Rudkin", - "author_inst": "Swansea University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.04.11.20061739", "rel_title": "Clinical Efficacy of Intravenous Immunoglobulin Therapy in Critical Patients with COVID-19: A multicenter retrospective cohort study", @@ -1527629,6 +1530938,57 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.04.14.041962", + "rel_title": "De novo 3D models of SARS-CoV-2 RNA elements and small-molecule-binding RNAs to guide drug discovery", + "rel_date": "2020-04-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.14.041962", + "rel_abs": "The rapid spread of COVID-19 is motivating development of antivirals targeting conserved SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA elements that offer potential small-molecule drug targets, but most of their 3D structures have not been experimentally characterized. Here, we provide a compilation of chemical mapping data from our and other labs, secondary structure models, and 3D model ensembles based on Rosettas FARFAR2 algorithm for SARS-CoV-2 RNA regions including the individual stems SL1-8 in the extended 5 UTR; the reverse complement of the 5 UTR SL1-4; the frameshift stimulating element (FSE); and the extended pseudoknot, hypervariable region, and s2m of the 3 UTR. For eleven of these elements (the stems in SL1-8, reverse complement of SL1-4, FSE, s2m, and 3 UTR pseudoknot), modeling convergence supports the accuracy of predicted low energy states; subsequent cryo-EM characterization of the FSE confirms modeling accuracy. To aid efforts to discover small molecule RNA binders guided by computational models, we provide a second set of similarly prepared models for RNA riboswitches that bind small molecules. Both datasets ( FARFAR2-SARS-CoV-2, https://github.com/DasLab/FARFAR2-SARS-CoV-2; and FARFAR2-Apo-Riboswitch, at https://github.com/DasLab/FARFAR2-Apo-Riboswitch) include up to 400 models for each RNA element, which may facilitate drug discovery approaches targeting dynamic ensembles of RNA molecules.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ramya Rangan", + "author_inst": "Stanford University" + }, + { + "author_name": "Andrew M. Watkins", + "author_inst": "Stanford University" + }, + { + "author_name": "Jose Chacon", + "author_inst": "Stanford University" + }, + { + "author_name": "Wipapat Kladwang", + "author_inst": "Stanford University" + }, + { + "author_name": "Ivan N. Zheludev", + "author_inst": "Stanford University" + }, + { + "author_name": "Jill Townley", + "author_inst": "Eterna Massive Open Laboratory" + }, + { + "author_name": "Mats Rynge", + "author_inst": "University of Southern California" + }, + { + "author_name": "Gregory Thain", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Rhiju Das", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.04.08.20058180", "rel_title": "Impact of COVID-19 pandemic on severity of illness and resources required during intensive care in the greater New York City area", @@ -1527726,85 +1531086,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.04.09.20059352", - "rel_title": "Analysis of factors associated early diagnosis in coronavirus disease 2019 (COVID-19)", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059352", - "rel_abs": "BackgroundThe pandemic of coronavirus disease 2019 (COVID-19) has become the first concern in international affairs as the novel coronavirus (SARS-CoV-2) is spreading all over the world at a terrific speed. The accuracy of early diagnosis is critical in the control of the spread of the virus. Although the real-time RT-PCR detection of the virus nucleic acid is the current golden diagnostic standard, it has high false negative rate when only apply single test.\n\nObjectiveSummarize the baseline characteristics and laboratory examination results of hospitalized COVID-19 patients. Analyze the factors that could interfere with the early diagnosis quantitatively to support the timely confirmation of the disease.\n\nMethodsAll suspected patients with COVID-19 were included in our study until Feb 9th, 2020. The last day of follow-up was Mar 20th, 2020. Throat swab real-time RT-PCR test was used to confirm SARS-CoV-2 infection. The difference between the epidemiological profile and first laboratory examination results of COVID-19 patients and non-COVID-19 patients were compared and analyzed by multiple logistic regression. Receiver operating characteristic (ROC) curve and area under curve (AUC) were used to assess the potential diagnostic value in factors, which had statistical differences in regression analysis.\n\nResultsIn total, 315 hospitalized patients were included. Among them, 108 were confirmed as COVID-19 patients and 207 were non-COVID-19 patients. Two groups of patients have significance in comparing age, contact history, leukocyte count, lymphocyte count, C-reactive protein, erythrocyte sedimentation rate (p<0.10). Multiple logistic regression analysis showed age, contact history and decreasing lymphocyte count could be used as individual factor that has diagnostic value (p<0.05). The AUC of first RT-PCR test was 0.84 (95% CI 0.73-0.89), AUC of cumulative two times of RT-PCR tests was 0.92 (95% CI 0.88-0.96) and 0.96 (95% CI 0.93-0.99) for cumulative three times of RT-PCR tests. Ninety-six patients showed typical pneumonia radiological features in first CT scan, AUC was 0.74 (95% CI 0.60-0.73). The AUC of patients age, contact history with confirmed people and the decreased lymphocytes were 0.66 (95% CI 0.60-0.73), 0.67 (95% CI 0.61-0.73), 0.62 (95% CI 0.56-0.69), respectively. Taking chest CT scan diagnosis together with patients age and decreasing lymphocytes, AUC would be 0.86 (95% CI 0.82-0.90). The age threshold to predict COVID-19 was 41.5 years, with a diagnostic sensitivity of 0.70 (95% CI 0.61-0.79) and a specificity of 0.59 (95% CI 0.52-0.66). Positive and negative likelihood ratios were 1.71 and 0.50, respectively. Threshold of lymphocyte count to diagnose COVID-19 was 1.53x109/L, with a diagnostic sensitivity of 0.82 (95% CI 0.73-0.88) and a specificity of 0.50 (95% CI 0.43-0.57). Positive and negative likelihood ratios were 1.64 and 0.37, respectively.\n\nConclusionSingle RT-PCR test has relatively high false negative rate. When first RT-PCR test show negative result in suspected patients, the chest CT scan, contact history, age and lymphocyte count should be used combinedly to assess the possibility of SARS-CoV-2 infection.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Jinwei Ai", - "author_inst": "Xiangyang No.1 Peoples Hospital" - }, - { - "author_name": "Junyan Gong", - "author_inst": "Xiangyang No.1 Peoples Hospital" - }, - { - "author_name": "Limin Xing", - "author_inst": "Xiangyang No.1 Peoples Hospital" - }, - { - "author_name": "Renjiao He", - "author_inst": "Xiangyang No.1 Peoples Hospital" - }, - { - "author_name": "Fangtao Tian", - "author_inst": "Xiangyang No.1 Peoples Hospital" - }, - { - "author_name": "Juan Wang", - "author_inst": "Xiangyang No.1 Peoples Hospital" - }, - { - "author_name": "Jun Wang", - "author_inst": "Xiangyang No.1 Peoples Hospital" - }, - { - "author_name": "Shengduo Polo Pei", - "author_inst": "Karolinska Institute" - }, - { - "author_name": "Dongxuan Chen", - "author_inst": "Leiden University" - }, - { - "author_name": "Guoxin Huang", - "author_inst": "Xiangyang No.1 Peoples Hospital" - }, - { - "author_name": "Meiling Zhang", - "author_inst": "Xiangyang No.1 Peoples Hospital" - }, - { - "author_name": "Gaojing Qu", - "author_inst": "Xiangyang No.1 Peoples Hospital" - }, - { - "author_name": "Wufeng Fan", - "author_inst": "Xiangyang No.1 Peoples Hospital" - }, - { - "author_name": "Hongming Lin", - "author_inst": "Xiangyang No.1 Peoples Hospital" - }, - { - "author_name": "Desheng Li", - "author_inst": "Xiangyang No.1 Peoples Hospital" - }, - { - "author_name": "Bin Pei", - "author_inst": "Xiangyang No.1 Peoples Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.04.09.20059758", "rel_title": "A Scalable Method of Applying Heat and Humidity for Decontamination of N95 Respirators During the COVID-19 Crisis", @@ -1528759,6 +1532040,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.10.20060616", + "rel_title": "Chaos, Percolation and the Coronavirus Spread: the Italian case", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060616", + "rel_abs": "A model based on chaotic maps and turbulent flows is applied to the spread of Coronavirus for each Italian region in order to obtain useful information and help to contrast it. We divide the regions into different risk categories and discuss anomalies. The worst cases are confined between the Appenine and the Alps mountain ranges but the situation seem to improve closer to the sea. The Veneto region gave the most efficient response so far and some of their resources could be diverted to other regions, in particular more tests to the Lombardia, Liguria, Piemonte, Marche and V. Aosta regions, which seem to be worst affected. We noticed worrying anomalies in the Lazio, Campania and Sicilia regions to be monitored. We stress that the number of fatalities we predicted on March 12 has been confirmed daily by the bulletins. This suggests a change of strategy in order to reduce such number maybe moving the weaker population (and negative to the virus test) to beach resorts, which should be empty presently. The ratio deceased/positives on April 4, 2020 is 5.4% worldwide, 12.3% in Italy, 1.4% in Germany, 2.7% in the USA, 10.3% in the UK and 4.1% in China. These large fluctuations should be investigated starting from the Italian regions, which show similar large fluctuations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Aldo Bonasera", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Giacomo Bonasera", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Suylatu Zhang", + "author_inst": "Inner Mongolia University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.10.20060673", "rel_title": "COVID-19 lockdowns cause global air pollution declines with implications for public health risk", @@ -1528836,85 +1532144,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.08.20047134", - "rel_title": "Calcium channel blocker amlodipine besylate is associated with reduced case fatality rate of COVID-19 patients with hypertension", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20047134", - "rel_abs": "The coronavirus disease (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread to more than 100 countries posing as a serious threat to the public health on a global scale. Patients with comorbidity such as hypertension suffer more severe infection with elevated case fatality rate. Development of effective anti-viral drug is in urgent need to treat COVID-19 patients. Here we report that calcium channel blockers (CCBs), a type of anti-hypertension drugs that are widely used in the clinics, can significantly inhibit the post-entry replication events of SARS-CoV-2 in vitro. Comparison with two other major types of anti-hypertension drugs, the angiotensin converting enzyme inhibitors (ACEI) and angiotensin II receptor blockers (ARB), showed that only CCBs display significant anti-SARS-CoV-2 efficacy. Combined treatment with chloroquine and CCBs significantly enhanced the anti-SARS-CoV-2 efficacy. Retrospective clinical investigation of COVID-19 patients revealed that the CCB amlodipine besylate administration was associated with reduced case fatality rate of patients with hypertension. Results from this study suggest that CCB administration for COVID-19 patients with hypertension as the comorbidity might improve the disease outcome.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Leike Zhang", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, P. R. China" - }, - { - "author_name": "Yuan Sun", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, P. R. China" - }, - { - "author_name": "Hao-Long Zeng", - "author_inst": "Department of Laboratory Medicine Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430071, P. R. China" - }, - { - "author_name": "Yudong Peng", - "author_inst": "Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China." - }, - { - "author_name": "Xiaming Jiang", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, P. R. China" - }, - { - "author_name": "Wei-Juan Shang", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, P. R. China" - }, - { - "author_name": "Yan Wu", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, P. R. China" - }, - { - "author_name": "Shufen Li", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, P. R. China" - }, - { - "author_name": "Yu-Lan Zhang", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, P. R. China" - }, - { - "author_name": "Liu Yang", - "author_inst": "Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology." - }, - { - "author_name": "Hongbo Chen", - "author_inst": "Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P. R. China" - }, - { - "author_name": "Runming Jin", - "author_inst": "Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P. R. China" - }, - { - "author_name": "Wei Liu", - "author_inst": "Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, P. R. China" - }, - { - "author_name": "Hao Li", - "author_inst": "Beijing Institute of Microbiology and Epidemiology, State Key Laboratory of Pathogen and Biosecurity, Beijing 100071, P. R. China" - }, - { - "author_name": "Ke Peng", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, P. R. China" - }, - { - "author_name": "Gengfu Xiao", - "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, 430071, P. R. China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.04.09.20053223", "rel_title": "Comparative Analysis of COVID-19 Transmission Patterns in Three Chinese Regions vs. South Korea,Italy and Iran", @@ -1530173,6 +1533402,25 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2020.04.11.20061432", + "rel_title": "Application of COVID-19 pneumonia diffusion data to predict epidemic situation", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20061432", + "rel_abs": "ObjectiveTo evaluate novel coronavirus pneumonia cases by establishing the mathematical model of the number of confirmed cases daily, and to assess the current situation and development of the epidemic situation, so as to provide a digital basis for decision-making.\n\nMethodsThe number of newly confirmed covid-19 cases per day was taken as the research object, and the seven-day average value (M) and the sequential value (R) of M were calculated to study the occurrence and development of covid-19 epidemic through the analysis of charts and data.\n\nResultsM reflected the current situation of epidemic development; R reflected the current level of infection and the trend of epidemic development.\n\nConclusionThe current data can be used to evaluate the number of people who have been infected, and when R < 1, the peak of epidemic can be predicted.\n\nPrefaceIn December 2019, a number of cases of pneumonia with unknown causes were found in some hospitals in Wuhan, Hubei province, China. On 11 March 2020, the director-general of the world health organization (WHO), Tedros Adhanom Ghebreyesus, announced that based on the assessment, WHO believes that the current outbreak of COVID-19 can be called a global pandemic. By early April 2020, there were more than one million confirmed cases worldwide.\n\nCOVID-19 has developed from sporadic cases to pandemic in a short period of 3 months. The analysis and research of its infectious data will help to prevent and control the next stage of epidemic prevention and other infectious diseases in the future.\n\nIn this paper, COVID-19 rounded average of seven days (M), and Ms ring ratio (R) are used to predict the current potential patients data, and the relative state of epidemic prevention and control is judged through the graphic features and characteristic data, so as to provide evidence for the prevention and control decisions.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Zhenguo Wu", + "author_inst": "Xi'an Jioatong University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.12.037580", "rel_title": "Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection", @@ -1530442,45 +1533690,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.09.20060053", - "rel_title": "COVID-19 pandemics modeling with SEIR(+CAQH), social distancing, and age stratification. The effect of vertical confinement and release in Brazil.", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20060053", - "rel_abs": "The ongoing COVID-19 epidemics poses a particular challenge to low and middle income countries, making some of them consider the strategy of \"vertical confinement\". In this strategy, contact is reduced only to specific groups (like age groups) that are at increased risk of severe disease following SARS-CoV-2 infection. We aim to assess the feasibility of this scenario as an exit strategy for the current lockdown in terms of its ability to keep the number of cases under the health care system capacity. We developed a modified SEIR model, including confinement, asymptomatic transmission, quarantine and hospitalization. The population is subdivided into 9 age groups, resulting in a system of 72 coupled nonlinear differential equations. The rate of transmission is dynamic and derived from the observed delayed fatality rate; the parameters of the epidemics are derived with a Markov chain Monte Carlo algorithm. We used Brazil as an example of middle income country, but the results are easily generalizable to other countries considering a similar strategy. We find that starting from 60% horizontal confinement, an exit strategy on May 1st of confinement of individuals older than 60 years old and full release of the younger population results in 400 000 hospitalizations, 50 000 ICU cases, and 120 000 deaths in the 50-60 years old age group alone. The health care system avoids collapse if the 50-60 years old are also confined, but our model assumes an idealized lockdown where the confined are perfectly insulated from contamination, so our numbers are a conservative lower bound. Our results discourage confinement by age as an exit strategy.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Wladimir Lyra", - "author_inst": "Department of Astronomy, New Mexico State University, PO Box 30001, MSC 4500, Las Cruces, NM 88003-8001, USA" - }, - { - "author_name": "Jose Dias do Nascimento", - "author_inst": "Dep. de Fisica Teorica e Experimental, DFTE, Universidade Federal do Rio Grande do Norte, Avenida Senador Salgado Filho, 3000. Campus Universitario. 59078-970 L" - }, - { - "author_name": "Jaber Belkhiria", - "author_inst": "One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, USA." - }, - { - "author_name": "Leandro de Almeida", - "author_inst": "Dep. de Fisica Teorica e Experimental, DFTE, Universidade Federal do Rio Grande do Norte, Avenida Senador Salgado Filho, 3000. Campus Universitario. 59078-970 L" - }, - { - "author_name": "Pedro Paulo Chrispim", - "author_inst": "Instituto Alicerce Ensino Pesquisa e Inovacao em Saude, R Cinco De Julho, 176/101, Rio De Janeiro, RJ, CEP 22051030, Brazil" - }, - { - "author_name": "Ion de Andrade", - "author_inst": "Departamento de Saude Coletiva, Universidade Federal do Rio Grande do Norte, Avenida Senador Salgado Filho, 3000. Campus Universitario. 59078-970 Lagoa Nova. Na" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.13.039941", "rel_title": "High-surety isothermal amplification and detection of SARS-CoV-2, including with crude enzymes", @@ -1531643,6 +1534852,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.10.036533", + "rel_title": "Structural interactions between pandemic SARS-CoV-2 spike glycoprotein and human Furin protease", + "rel_date": "2020-04-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.10.036533", + "rel_abs": "The SARS-CoV-2 pandemic is an urgent global public health emergency and warrants investigating molecular and structural studies addressing the dynamics of viral proteins involved in host cell adhesion. The recent comparative genomic studies highlight the insertion of Furin protease site in the SARS-CoV-2 spike glycoprotein alerting possible modification in the viral spike protein and its eventual entry to host cell and presence of Furin site implicated to virulence. Here we structurally show how Furin interacts with the SARS-CoV-2 spike glycoprotein homotrimer at S1/S2 region, which underlined the mechanism and mode of action, which is a key for host cell entry. Unravelling the structural features of biding site opens the arena in rising bonafide antibodies targeting to block the Furin cleavage and have great implications in the development of Furin inhibitors or therapeutics.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Naveen Vankadari", + "author_inst": "Monash University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.04.10.036020", "rel_title": "Analysis of Ten Microsecond simulation data of SARS-CoV-2 dimeric main protease", @@ -1531872,57 +1535100,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.10.035824", - "rel_title": "Scutellaria baicalensis extract and baicalein inhibit replication of SARS-CoV-2 and its 3C-like protease in vitro", - "rel_date": "2020-04-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.10.035824", - "rel_abs": "COVID-19 has become a global pandemic that threatens millions of people worldwide. There is an urgent call for developing effective drugs against the virus (SARS-CoV-2) causing this disease. The main protease of SARS-CoV-2, 3C-like protease (3CLpro), is highly conserved across coronaviruses and is essential for the maturation process of viral polyprotein. Scutellariae radix (Huangqin in Chinese), the root of Scutellaria baicalensis has been widely used in traditional Chinese medicine to treat viral infection related symptoms. The extracts of S. baicalensis have exhibited broad spectrum antiviral activities. We studied the anti-SARS-CoV-2 activity of S. baicalensis and its ingredient compounds. We found that the ethanol extract of S. baicalensis inhibits SARS-CoV-2 3CLpro activity in vitro and the replication of SARS-CoV-2 in Vero cells with an EC50 of 0.74 g/ml. Among the major components of S. baicalensis, baicalein strongly inhibits SARS-CoV-2 3CLpro activity with an IC50 of 0.39 M. We further identified four baicalein analogue compounds from other herbs that inhibit SARS-CoV-2 3CLpro activity at microM concentration. Our study demonstrates that the extract of S. baicalensis has effective anti-SARS-CoV-2 activity and baicalein and analogue compounds are strong SARS-CoV-2 3CLpro inhibitors.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Hongbo Liu", - "author_inst": "College of Chemistry and Molecular Engineering, Peking University" - }, - { - "author_name": "Fei Ye", - "author_inst": "National Institute for Viral Disease Control and Prevention, China CDC" - }, - { - "author_name": "Qi Sun", - "author_inst": "College of Chemistry and Molecular Engineering, Peking University" - }, - { - "author_name": "Hao Liang", - "author_inst": "College of Chemistry and Molecular Engineering, Peking University" - }, - { - "author_name": "Chunmei Li", - "author_inst": "College of Chemistry and Molecular Engineering, Peking University" - }, - { - "author_name": "Roujian Lu", - "author_inst": "National Institute for Viral Disease Control and Prevention, China CDC" - }, - { - "author_name": "Baoying Huang", - "author_inst": "National Institute for Viral Disease Control and Prevention, China CDC" - }, - { - "author_name": "Wenjie Tan", - "author_inst": "National Institute for Viral Disease Control and Prevention, China CDC" - }, - { - "author_name": "Luhua Lai", - "author_inst": "College of Chemistry and Molecular Engineering, Peking University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.04.11.037093", "rel_title": "BIP4COVID19: Releasing impact metrics data for articles relevant to COVID-19", @@ -1533049,6 +1536226,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.04.08.20054023", + "rel_title": "There are asymptomatic and pre-symptomatic patients infected with COVID-19. So what? Pandemic response implications", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20054023", + "rel_abs": "Asymptomatic but infectious people have been reported in many infectious diseases. Asymptomatic and pre-symptomatic carriers would be a hidden reservoir of COVID-19.\n\nAimThis review identifies primary empirical evidence about the ability of asymptomatic carriers to infect others with COVID-19 pandemic and reflects on the implications for control measures.\n\nMethodsA systematic review is followed by a narrative report and commentary inclusion criteria were: studies reporting primary data on asymptomatic or pre-symptomatic patients, who were considered to have passed on COVID-19 infection; and published in indexed journals or in peer review between January 1 and March 31, 2020.\n\nResultsNine articles reported on 83 asymptomatic or pre-symptomatic persons.\n\nConclusionsThe evidence confirms COVID-19 transmission from people who were asymptomatic at the time. A series of implications for health service response are laid out.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Nelson Aguirre-Duarte", + "author_inst": "The University of Auckland" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.09.20059014", "rel_title": "How much India detecting SARS-CoV-2 Infections? A model-based estimation", @@ -1533134,25 +1536330,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.10.20056697", - "rel_title": "Predication of Pandemic COVID-19 situation in Maharashtra, India", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20056697", - "rel_abs": "Presently, the world is infected by COVID 19 virus which has created an emergency for public health. For controlling the spreading of the virus, we have to prepare for precaution and futuristic calculation for infection spreading. The coronavirus affects the population of the world including Inia. Here, we are the study the virus spreading rate on the Maharashtra state which is part of India. We are predicting the infected people by the SIR model. SIR model is one of the most effective models which can predict the spreading rate of the virus. We have validated the model with the current spreading rate with this SIR model. This study will help to stop the epidemic spreading because it is in the early stage in the Maharashtra region.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "SUNNY KUMAR", - "author_inst": "MAULANA AJAD NATIONAL INSTITUTE OF TECHNOLOGY BHOPAL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.06.20055848", "rel_title": "The efficiency in the ordinary hospital bed management in Italy: an in-depth analysis of intensive care unit in the areas affected by COVID-19 before the outbreak", @@ -1534319,6 +1537496,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.08.20057851", + "rel_title": "Age-stratified Infection Probabilities Combined with Quarantine-Modified SEIR Model in the Needs Assessments for COVID-19", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20057851", + "rel_abs": "We use the age-stratified COVID-19 infection and death distributions from China (more than 44,672 infectious as of February 11, 2020) as an estimate for a study areas infection and morbidity probabilities at each age group. We then apply these probabilities into the actual age-stratified population to predict infectious individuals and deaths at peak. Testing with different countries shows the predicted infectious skewing with the countrys median age and age stratification, as expected. We added a Q parameter to the classic SEIR compartmental model to include the effect of quarantine (Q-SEIR). The projections from the age-stratified probabilities give much lower predicted incidences of infection than the Q-SEIR model. As expected, quarantine tends to delay the peaks for both Exposed and Infectious, and to flatten the curve or lower the predicted values for each compartment. These two estimates were used as a range to inform planning and response to the COVID-19 threat.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vena Pearl Bongolan", + "author_inst": "Department of Computer Science, UP Diliman, Philippines" + }, + { + "author_name": "Jose Marie Antonio Minoza", + "author_inst": "Department of Computer Science, UP Diliman, Philippines" + }, + { + "author_name": "Romulo de Castro", + "author_inst": "Center for Informatics, University of San Agustin, Iloilo City, Philippines" + }, + { + "author_name": "Jesus Emmanuel Sevilleja", + "author_inst": "National Center for Mental Health, Mandaluyong City, Philippines" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.08.20058040", "rel_title": "Blood glucose is a representative of the clustered indicators of multi-organ injury for predicting mortality of COVID-19 in Wuhan, China", @@ -1534452,65 +1537660,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.09.034942", - "rel_title": "Analysis of the mutation dynamics of SARS-CoV-2 reveals the spread history and emergence of RBD mutant with lower ACE2 binding affinity", - "rel_date": "2020-04-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.09.034942", - "rel_abs": "Monitoring the mutation dynamics of SARS-CoV-2 is critical for the development of effective approaches to contain the pathogen. By analyzing 106 SARS-CoV-2 and 39 SARS genome sequences, we provided direct genetic evidence that SARS-CoV-2 has a much lower mutation rate than SARS. Minimum Evolution phylogeny analysis revealed the putative original status of SARS-CoV-2 and the early-stage spread history. The discrepant phylogenies for the spike protein and its receptor binding domain proved a previously reported structural rearrangement prior to the emergence of SARS-CoV-2. Despite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a receptor binding domain mutation that leads to weaker ACE2 binding capability based on in silico simulation, which concerns a SARS-CoV-2 sample collected on 27th January 2020 from India. This represents the first report of a significant SARS-CoV-2 mutant, and requires attention from researchers working on vaccine development around the world.\n\nHighlightsO_LIBased on the currently available genome sequence data, we provided direct genetic evidence that the SARS-COV-2 genome has a much lower mutation rate and genetic diversity than SARS during the 2002-2003 outbreak.\nC_LIO_LIThe spike (S) protein encoding gene of SARS-COV-2 is found relatively more conserved than other protein-encoding genes, which is a good indication for the ongoing antiviral drug and vaccine development.\nC_LIO_LIMinimum Evolution phylogeny analysis revealed the putative original status of SARS-CoV-2 and the early-stage spread history.\nC_LIO_LIWe confirmed a previously reported rearrangement in the S protein arrangement of SARS-COV-2, and propose that this rearrangement should have occurred between human SARS-CoV and a bat SARS-CoV, at a time point much earlier before SARS-COV-2 transmission to human.\nC_LIO_LIWe provided first evidence that a mutated SARS-COV-2 with reduced human ACE2 receptor binding affinity have emerged in India based on a sample collected on 27th January 2020.\nC_LI", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "YONG JIA", - "author_inst": "Murdoch University" - }, - { - "author_name": "Gangxu Shen", - "author_inst": "I-Shou University;National Changhua University of Education" - }, - { - "author_name": "Stephanie Nguyen", - "author_inst": "Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia" - }, - { - "author_name": "Yujuan Zhang", - "author_inst": "Murdoch University" - }, - { - "author_name": "Keng-Shiang Huang", - "author_inst": "I-Shou University" - }, - { - "author_name": "Hsing-Ying Ho", - "author_inst": "Guo-Yuan Clinic, Taichung, Taiwan" - }, - { - "author_name": "Wei-Shio Hor", - "author_inst": "TOPO Pharmaceutical Co., Ltd, Taichung, Taiwan" - }, - { - "author_name": "Chih-Hui Yang", - "author_inst": "I-Shou University" - }, - { - "author_name": "John B Bruning", - "author_inst": "Institute of Photonics and Advanced Sensing (IPAS), School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia" - }, - { - "author_name": "Chengdao Li", - "author_inst": "Murdoch University; Department of Primary Industry and Regional Development, Government of Western Australia, South Perth, WA, 6155, Australia" - }, - { - "author_name": "Wei-Lung Wang", - "author_inst": "National Changhua University of Education" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2020.04.08.20058636", "rel_title": "Brief Analysis of the ARIMA model on the COVID-19 in Italy", @@ -1535528,6 +1538677,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.04.08.20057679", + "rel_title": "COVID-19 Epidemic Analysis using Machine Learning and Deep Learning Algorithms", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20057679", + "rel_abs": "The catastrophic outbreak of Severe Acute Respiratory Syndrome - Coronavirus (SARS-CoV-2) also known as COVID-2019 has brought the worldwide threat to the living society. The whole world is putting incredible efforts to fight against the spread of this deadly disease in terms of infrastructure, finance, data sources, protective gears, life-risk treatments and several other resources. The artificial intelligence researchers are focusing their expertise knowledge to develop mathematical models for analyzing this epidemic situation using nationwide shared data. To contribute towards the well-being of living society, this article proposes to utilize the machine learning and deep learning models with the aim for understanding its everyday exponential behaviour along with the prediction of future reachability of the COVID-2019 across the nations by utilizing the real-time information from the Johns Hopkins dashboard.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Narinder Singh Punn", + "author_inst": "Indian Institute of Information Technology Allahabad" + }, + { + "author_name": "Sanjay Kumar Sonbhadra", + "author_inst": "Indian Institute of Information Technology Allahabad" + }, + { + "author_name": "Sonali Agarwal", + "author_inst": "Indian Institute of Information Technology Allahabad" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.04.07.20057224", "rel_title": "UV light dosage distribution over irregular respirator surfaces. Methods and implications for safety", @@ -1535633,161 +1538809,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.08.20056929", - "rel_title": "Introductions and early spread of SARS-CoV-2 in the New York City area", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20056929", - "rel_abs": "New York City (NYC) has emerged as one of the epicenters of the current SARS-CoV2 pandemic. To identify the early events underlying the rapid spread of the virus in the NYC metropolitan area, we sequenced the virus causing COVID19 in patients seeking care at the Mount Sinai Health System. Phylogenetic analysis of 84 distinct SARS-CoV2 genomes indicates multiple, independent but isolated introductions mainly from Europe and other parts of the United States. Moreover, we find evidence for community transmission of SARS-CoV2 as suggested by clusters of related viruses found in patients living in different neighborhoods of the city.", - "rel_num_authors": 35, - "rel_authors": [ - { - "author_name": "Ana S Gonzalez-Reiche", - "author_inst": "Icahn school of Medicine at Mount Sinai" - }, - { - "author_name": "Matthew M Hernandez", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Mitchell Sullivan", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Brianne Ciferri", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Hala Alshammary", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ajay Obla", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Shelcie Fabre", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Giulio Kleiner", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Jose Polanco", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Zenab Khan", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Bremy Alburquerque", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Adriana van de Guchte", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Jayeeta Dutta", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Nancy Francoeur", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Betsaida Salom Melo", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Irina Oussenko", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Gintaras Deikus", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Juan Soto", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Shwetha Hara Sridhar", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ying-Chih Wang", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Kathryn Twyman", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Andrew Kasarskis", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Deena Rose Altman", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Melissa Smith", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Robert Sebra", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Judith Aberg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Adolfo Garcia-Sarstre", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Marta Luksza", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Gopi Patel", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Alberto Paniz-Mondolfi", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Melissa Gitman", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Emilia Mia Sordillo", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Viviana Simon", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Harm van Bakel", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.07.20056788", "rel_title": "Treatment with ACE-inhibitors is associated with less severe disease with SARS-Covid-19 infection in a multi-site UK acute Hospital Trust", @@ -1536710,6 +1539731,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.09.20056291", + "rel_title": "Risk factors for mortality of adult inpatients with Coronavirus disease 2019 (COVID-19): a systematic review and meta-analysis of retrospective studies", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20056291", + "rel_abs": "PurposeCoronavirus disease 2019 (COVID-19) is an emerging disease that was first reported in Wuhan city, the capital of Hubei province in China, and has subsequently spread worldwide. Risk factors for mortality have not been well summarized. Current meta-analysis of retrospective cohort studies was done to summarize available findings on the association between age, gender, comorbidities and risk of death from COVID-19 infection.\n\nMethodsOnline databases including Web of Science, PubMed, Scopus, Cochrane Library and Google scholar were searched to detect relevant publications up to 1 May 2020, using relevant keywords. To pool data, random-effects model was used. Furthermore, sensitivity analysis and publication bias test were also done.\n\nResultsIn total, 14 studies with 29,909 COVID-19 infected patients and 1,445 cases of death were included in the current meta-analysis. Significant associations were found between older age ([≥]65 vs <65 years old) (pooled ORs=4.59, 95% CIs=2.61-8.04, p<0.001), gender (male vs female) (pooled ORs=1.50, 95% CIs=1.06-2.12, p=0.021) and risk of death from COVID-19 infection. In addition, hypertension (pooled ORs=2.70, 95% CIs= 1.40-5.24, p=0.003), cardiovascular diseases (CVDs) (pooled ORs=3.72, 95% CIs=1.77-7.83, p=0.001), diabetes (pooled ORs=2.41, 95% CIs=1.05-5.51, p=0.037), chronic obstructive pulmonary disease (COPD) (pooled ORs=3.53, 95% CIs=1.79-6.96, p<0.001) and cancer (pooled ORs=3.04, 95% CIs=1.80-5.14, p<0.001), were associated with higher risk of mortality.\n\nConclusionOlder age ([≥]65 years old), male gender, hypertension, CVDs, diabetes, COPD and malignancies were associated with greater risk of death from COVID-19 infection. These findings could help clinicians to identify patients with poor prognosis at an early stage.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Mohammad Parohan", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Sajad Yaghoubi", + "author_inst": "Iranshahr University of Medical Sciences" + }, + { + "author_name": "Asal Seraji", + "author_inst": "Islamic Azad University, Damavand Branch" + }, + { + "author_name": "Mohammad Hassan Javanbakht", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Payam Sarraf", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Mahmoud Djalali", + "author_inst": "Tehran University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.07.20055723", "rel_title": "SARS-CoV-2 infection in Health Care Workers in a large public hospital in Madrid, Spain, during March 2020", @@ -1536807,137 +1539867,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.08.20056861", - "rel_title": "Epidemiological characteristics of COVID-19 cases in Italy and estimates of the reproductive numbers one month into the epidemic", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20056861", - "rel_abs": "BackgroundIn February 2020, a locally-acquired COVID-19 case was detected in Lombardia, Italy. This was the first signal of ongoing transmission of SARS-CoV-2 in the country. The outbreak rapidly escalated to a national level epidemic, amid the WHO declaration of a pandemic.\n\nMethodsWe analysed data from the national case-based integrated surveillance system of all RT-PCR confirmed COVID-19 infections as of March 24th 2020, collected from all Italian regions and autonomous provinces. Here we provide a descriptive epidemiological summary on the first 62,843 COVID-19 cases in Italy as well as estimates of the basic and net reproductive numbers by region.\n\nFindingsOf the 62,843 cases of COVID-19 analysed, 71.6% were reported from three Regions (Lombardia, Veneto and Emilia-Romagna). All cases reported after February 20th were locally acquired. Estimates of R0 varied between 2.5 (95%CI: 2.18-2.83) in Toscana and 3 (95%CI: 2.68-3.33) in Lazio, with epidemic doubling time of 3.2 days (95%CI: 2.3-5.2) and 2.9 days (95%CI: 2.2-4.3), respectively. The net reproduction number showed a decreasing trend starting around February 20-25, 2020 in Northern regions. Notably, 5,760 cases were reported among health care workers. Of the 5,541 reported COVID-19 associated deaths, 49% occurred in people aged 80 years or above with an overall crude CFR of 8.8%. Male sex and age were independent risk factors for COVID-19 death.\n\nInterpretationThe COVID-19 infection in Italy emerged with a clustering onset similar to the one described in Wuhan, China and likewise showed worse outcomes in older males with comorbidities. Initial R0 at 2.96 in Lombardia, explains the high case-load and rapid geographical spread observed. Overall Rt in Italian regions is currently decreasing albeit with large diversities across the country, supporting the importance of combined non-pharmacological control measures.\n\nFundingroutine institutional funding was used to perform this work.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Flavia Riccardo", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Marco Ajelli", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Xanthi Andrianou", - "author_inst": "Istituto Superiore di Sanita; Cyprus University of Technology" - }, - { - "author_name": "Antonino Bella", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Martina Del Manso", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Massimo Fabiani", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Stefania Bellino", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Stefano Boros", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Alberto Mateo Urdiales", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Valentina Marziano", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Maria Cristina Rota", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Antonietta Filia", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Fortunato (Paolo) D'Ancona", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Andrea Siddu", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Ornella Punzo", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Filippo Trentini", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Giorgio Guzzetta", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Piero Poletti", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Paola Stefanelli", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Maria Rita Castrucci", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Alessandra Ciervo", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Corrado Di Benedetto", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Marco Tallon", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Andrea Piccioli", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Silvio Brusaferro", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Giovanni Rezza", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Stefano Merler", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Patrizio Pezzotti", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "COVID-19 working group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.07.20055772", "rel_title": "A Very Flat Peak: Exponential growth phase of COVID-19 is mostly followed by a prolonged linear growth phase, not an immediate saturation", @@ -1538004,6 +1540933,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.09.033522", + "rel_title": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein harbors a conserved BH3-like motif", + "rel_date": "2020-04-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.09.033522", + "rel_abs": "Disclaimer textThe authors have withdrawn their manuscript whilst they perform additional experiments to test some of their conclusions further. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vincent Navratil", + "author_inst": "PRABI, Rhone Alpes Bioinformatics Center, UCBL, Lyon1, Universite de Lyon, Lyon, France" + }, + { + "author_name": "Sonia Longhi", + "author_inst": "AFMB lab, CNRS & Aix-Marseille University" + }, + { + "author_name": "Marie Hardwick", + "author_inst": "W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, U" + }, + { + "author_name": "Christophe Combet", + "author_inst": "Centre de Recherche en Cancerologie de Lyon, UMR Inserm U1052, CNRS 5286, Universite Claude Bernard Lyon 1, Centre Leon Berard, Lyon, France" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.07.20057315", "rel_title": "Clinical analysis and early differential diagnosis of suspected pediatric patients with 2019 novel coronavirus infection", @@ -1538089,61 +1541049,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.08.031963", - "rel_title": "BioLaboro: A bioinformatics system for detecting molecular assay signature erosion and designing new assays in response to emerging and reemerging pathogens", - "rel_date": "2020-04-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.08.031963", - "rel_abs": "BackgroundEmerging and reemerging infectious diseases such as the novel Coronavirus disease, COVID-19 and Ebola pose a significant threat to global society and test the public health communitys preparedness to rapidly respond to an outbreak with effective diagnostics and therapeutics. Recent advances in next generation sequencing technologies enable rapid generation of pathogen genome sequence data, within 24 hours of obtaining a sample in some instances. With these data, one can quickly evaluate the effectiveness of existing diagnostics and therapeutics using in silico approaches. The propensity of some viruses to rapidly accumulate mutations can lead to the failure of molecular detection assays creating the need for redesigned or newly designed assays.\n\nResultsHere we describe a bioinformatics system named BioLaboro to identify signature regions in a given pathogen genome, design PCR assays targeting those regions, and then test the PCR assays in silico to determine their sensitivity and specificity. We demonstrate BioLaboro with two use cases: Bombali Ebolavirus (BOMV) and the novel Coronavirus 2019 (SARS-CoV-2). For the BOMV, we analyzed 30 currently available real-time reverse transcription-PCR assays against the three available complete genome sequences of BOMV. Only two met our in silico criteria for successful detection and neither had perfect matches to the primer/probe sequences. We designed five new primer sets against BOMV signatures and all had true positive hits to the three BOMV genomes and no false positive hits to any other sequence. Four assays are closely clustered in the nucleoprotein gene and one is located in the glycoprotein gene. Similarly, for the SARS-CoV-2, we designed five highly specific primer sets that hit all 145 whole genomes (available as of February 28, 2020) and none of the near neighbors.\n\nConclusionsHere we applied BioLaboro in two real-world use cases to demonstrate its capability; 1) to identify signature regions, 2) to assess the efficacy of existing PCR assays to detect pathogens as they evolve over time, and 3) to design new assays with perfect in silico detection accuracy, all within hours, for further development and deployment. BioLaboro is designed with a user-friendly graphical user interface for biologists with limited bioinformatics experience.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Mitchell Holland", - "author_inst": "Noblis" - }, - { - "author_name": "Daniel Negron", - "author_inst": "Noblis" - }, - { - "author_name": "Shane Mitchell", - "author_inst": "Noblis" - }, - { - "author_name": "Nate Dellinger", - "author_inst": "Noblis" - }, - { - "author_name": "Mychal Ivancich", - "author_inst": "Noblis" - }, - { - "author_name": "Tyler Barrus", - "author_inst": "Noblis" - }, - { - "author_name": "Sterling Thomas", - "author_inst": "Noblis" - }, - { - "author_name": "Katharine W Jennings", - "author_inst": "Noblis" - }, - { - "author_name": "Bruce G Goodwin", - "author_inst": "DBPAO, CBRND-EB, JPEO" - }, - { - "author_name": "Shanmuga Sozhamannan", - "author_inst": "CBRND-Enabling Biotechnologies, JPEO" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.04.07.20057117", "rel_title": "Global access to handwashing: implications for COVID-19 control in low-income countries", @@ -1539634,6 +1542539,121 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.04.07.023903", + "rel_title": "Structural and functional analysis of a potent sarbecovirus neutralizing antibody", + "rel_date": "2020-04-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.07.023903", + "rel_abs": "SARS-CoV-2 is a newly emerged coronavirus responsible for the current COVID-19 pandemic that has resulted in more than one million infections and 73,000 deaths1,2. Vaccine and therapeutic discovery efforts are paramount to curb the pandemic spread of this zoonotic virus. The SARS-CoV-2 spike (S) glycoprotein promotes entry into host cells and is the main target of neutralizing antibodies. Here we describe multiple monoclonal antibodies targeting SARS-CoV-2 S identified from memory B cells of a SARS survivor infected in 2003. One antibody, named S309, potently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2 by engaging the S receptor-binding domain. Using cryo-electron microscopy and binding assays, we show that S309 recognizes a glycan-containing epitope that is conserved within the sarbecovirus subgenus, without competing with receptor attachment. Antibody cocktails including S309 along with other antibodies identified here further enhanced SARS-CoV-2 neutralization and may limit the emergence of neutralization-escape mutants. These results pave the way for using S309 and S309-containing antibody cocktails for prophylaxis in individuals at high risk of exposure or as a post-exposure therapy to limit or treat severe disease.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Dora Pinto", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Young-Jun Park", + "author_inst": "University of Washington" + }, + { + "author_name": "Martina Beltramello", + "author_inst": "Humabs BioMed SA" + }, + { + "author_name": "Alexandra C. Walls", + "author_inst": "University of Washington" + }, + { + "author_name": "M. Alejandra Tortorici", + "author_inst": "University of Washington" + }, + { + "author_name": "Siro Bianchi", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Stefano Jaconi", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Katja Culap", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Fabrizia Zatta", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Anna De Marco", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Alessia Peter", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Barbara Guarino", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Roberto Spreafico", + "author_inst": "Vir Biotechnology" + }, + { + "author_name": "Elisabetta Cameroni", + "author_inst": "Humabs Biomed" + }, + { + "author_name": "James Brett Case", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Rita E. Chen", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Colin Havenar-Daughton", + "author_inst": "Vir Biotehcnology" + }, + { + "author_name": "Gyorgy Snell", + "author_inst": "Vir Biotechnology" + }, + { + "author_name": "Amalio Telenti", + "author_inst": "Vir Biotechnology" + }, + { + "author_name": "Herbert W. Virgin", + "author_inst": "Vir Biotechnology" + }, + { + "author_name": "Antonio Lanzavecchia", + "author_inst": "Institute for Research in Biomedicine" + }, + { + "author_name": "Michael S. Diamond", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Katja Fink", + "author_inst": "Humabs Biomed" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + }, + { + "author_name": "Davide Corti", + "author_inst": "Humabs Biomed SA, subsidiary of Vir Biotechnology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.04.07.028589", "rel_title": "The IMPDH inhibitor merimepodib suppresses SARS-CoV-2 replication in vitro.", @@ -1539811,81 +1542831,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.04.07.029884", - "rel_title": "Immunoglobulin fragment F(ab')2 against RBD potently neutralizes SARS-CoV-2 in vitro", - "rel_date": "2020-04-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.07.029884", - "rel_abs": "COVID-19 caused by the emerging human coronavirus, SARS-CoV-2, has become a global pandemic, leading a serious threat to human health. So far, there is none vaccines or specific antiviral drugs approved for that. Therapeutic antibodies for SARS-CoV-2, was obtained from hyper immune equine plasma in this study. Herein, SARS-CoV-2 RBD with gram level were obtained through Chinese hamster ovary cells high-density fermentation. The binding of RBD to SARS-CoV-2 receptor, human ACE2, was verified and the efficacy of RBD in vivo was tested on mice and then on horses. As a result, RBD triggered high-titer neutralizing antibodies in vivo, and immunoglobulin fragment F(ab)2 was prepared from horse antisera through removing Fc. Neutralization test demonstrated that RBD-specific F(ab)2 inhibited SARS-CoV-2 with EC50 at 0.07 g/ml, showing a potent inhibitory effect on SARS-CoV-2. These results highlights as RBD-specific F(ab)2 as therapeutic candidate for SARS-CoV-2.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Xiaoyan Pan", - "author_inst": "Wuhan institute of virology, Chinese academy of sciences" - }, - { - "author_name": "Pengfei Zhou", - "author_inst": "Wuhan YZY Biopharma Co., Ltd" - }, - { - "author_name": "Tiejiong Fan", - "author_inst": "Shanghai Serum Bio-technology Co., LTD." - }, - { - "author_name": "Yan Wu", - "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences" - }, - { - "author_name": "Jing Zhang", - "author_inst": "Wuhan YZY Biopharma Co., Ltd" - }, - { - "author_name": "Xiaoyue Shi", - "author_inst": "Shanghai Serum Bio-technology Co., LTD." - }, - { - "author_name": "Weijuan Shang", - "author_inst": "Wuhan institute of virology, Chinese academy of sciences" - }, - { - "author_name": "Lijuan Fang", - "author_inst": "Wuhan YZY Biopharma Co., Ltd" - }, - { - "author_name": "Xiaming Jiang", - "author_inst": "University of the Chinese Academy of Sciences" - }, - { - "author_name": "Jian Shi", - "author_inst": "Wuhan YZY Biopharma Co., Ltd" - }, - { - "author_name": "Yuan Sun", - "author_inst": "University of the Chinese Academy of Sciences" - }, - { - "author_name": "Shaojuan Zhao", - "author_inst": "University of the Chinese Academy of Sciences" - }, - { - "author_name": "Rui Gong", - "author_inst": "Wuhan institute of virology, Chinese academy of sciences" - }, - { - "author_name": "Ze Chen", - "author_inst": "Shanghai Serum Bio-technology Co., LTD." - }, - { - "author_name": "Gengfu Xiao", - "author_inst": "Chinese Academy of Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.04.07.030734", "rel_title": "Reversal of Infected Host Gene Expression Identifies Repurposed Drug Candidates for COVID-19", @@ -1541227,6 +1544172,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.04.20052308", + "rel_title": "The basic reproduction number and prediction of the epidemic size of the novel coronavirus (COVID-19) in Shahroud, Iran", + "rel_date": "2020-04-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.04.20052308", + "rel_abs": "ObjectivesTo estimate the basic reproduction number (R0) of COVID-19 in the early stage of the epidemic and predict the expected number of new cases in Shahroud, Northeast of Iran.\n\nMethodsThe R0 of COVID-19 was estimated using the serial interval distribution and the number of incidence cases. The serial interval was fit with a gamma distribution. The probable incidence and cumulative incidence in the next 30 days were predicted using the assumption that daily incidence follows a Poisson distribution determined by daily infectiousness. Data analysis was done using \"earlyR\" and \"projections\" packages in R software.\n\nResultsThe maximum-likelihood value of R0 was 2.7 (95% confidence interval (CI): 2.1 to 3.4) for the COVID-19 epidemic in the early 14 days and decreased to 1.13 (95% CI: 1.03 to 1.25) by the end of the day 41. The expected average number of new cases in Shahroud is 9.0{+/-}3.8 case/day, which means an estimated total of 271 (95% CI: 178-383) new cases in the next 30 days.\n\nConclusionsIt is essential to reduce the R0 to values below one. Therefore, we strongly recommend enforcing and continuing the current preventive measures, restricting travel, and providing screening tests for a larger proportion of the population.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ahmad Khosravi", + "author_inst": "Ophthalmic Epidemiology Research Center, Shahroud University of Medical Sciences, Shahroud, Iran" + }, + { + "author_name": "Reza Chaman", + "author_inst": "Department of Epidemiology, School of Public Health, Shahroud University of Medical Sciences, Shahroud, Iran" + }, + { + "author_name": "Marzieh Rohani-Rasaf", + "author_inst": "Department of Epidemiology, School of Public Health, Shahroud University of Medical Sciences, Shahroud, Iran" + }, + { + "author_name": "Fariba Zare", + "author_inst": "Center for Health Related Social and Behavioral Sciences Research, Shahroud University of Medical Sciences, Shahroud, Iran." + }, + { + "author_name": "Shiva Mehravaran", + "author_inst": "ASCEND Center for Biomedical Research, Morgan State University, Baltimore, USA" + }, + { + "author_name": "Mohammad Hassan Emamian", + "author_inst": "Ophthalmic Epidemiology Research Center, Shahroud University of Medical Sciences, Shahroud, Iran" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.03.20052845", "rel_title": "Use Crow-AMSAA Method to predict the cases of the Coronavirus 19 in Michigan and U.S.A", @@ -1541304,53 +1544288,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.06.20054320", - "rel_title": "Derivation of the effective reproduction number R for COVID-19 in relation to mobility restrictions and confinement", - "rel_date": "2020-04-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20054320", - "rel_abs": "The spread of COVID-19 is posing an unprecedented threat to health systems worldwide1. The fast propagation of the disease combined with the existence of covert contagions by asymptomatic individuals make the controlling of this disease particularly challenging. The key parameter to track the progression of the epidemics is the effective reproduction number [R], defined as the number of secondary infections generated by an infected individual2. The suppression of the epidemics is directly related to this value, and is attained when [R] < 1. Here, we find an analytical expression for [R] as a function of mobility restrictions and confinement measures, using an epidemic model tailored for COVID-19. This expression for [R] is an extremely useful tool to design containment policies that are able to suppress the epidemics. We applied our epidemic model for the case of Spain, successfully forecasting both the observed incidence in each region and the overload of the health system. The expression for [R] allowed us to determine the precise reduction of mobility{kappa} 0 needed to bend the curve of epidemic incidence, which turned out to be{kappa} 0 [~] 0.7. This value, for the case of Spain, translates to a total lockdown with the exception of the mobility associated to essential services, a policy that was finally enforced on March 28.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Alex Arenas", - "author_inst": "Universitat Rovira i Virgili" - }, - { - "author_name": "Wesley Cota", - "author_inst": "Universidade Federal de Vicosa" - }, - { - "author_name": "Jesus Gomez-Gardenes", - "author_inst": "Universidad de Zaragoza" - }, - { - "author_name": "Sergio Gomez", - "author_inst": "Universitat Rovira i Virgili" - }, - { - "author_name": "Clara Granell", - "author_inst": "Universidad de Zaragoza" - }, - { - "author_name": "Joan T. Matamalas", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "David Soriano-Panos", - "author_inst": "Universidad de Zaragoza" - }, - { - "author_name": "Benjamin Steinegger", - "author_inst": "Universitat Rovira i Virgili" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.05.026435", "rel_title": "Validation of a Lysis Buffer Containing 4 M Guanidinium Thiocyanate (GITC)/ Triton X-100 for Extraction of SARS-CoV-2 RNA for COVID-19 Testing: Comparison of Formulated Lysis Buffers Containing 4 to 6 M GITC, Roche External Lysis Buffer and Qiagen RTL Lysis Buffer", @@ -1542577,6 +1545514,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.04.04.20052696", + "rel_title": "Face mask use in the general population and optimal resource allocation during the COVID-19 pandemic", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.04.20052696", + "rel_abs": "The ongoing novel coronavirus disease (COVID-19) pandemic has rapidly spread in early 2020, causing tens of thousands of deaths, over a million cases and widespread socioeconomic disruption. With no vaccine available and numerous national healthcare systems reaching or exceeding capacity, interventions to limit transmission are urgently needed. While there is broad agreement that travel restrictions and closure of non-essential businesses and schools are beneficial in limiting local and regional spread, recommendations around the use of face masks for the general population are less consistent internationally. In this study, we examined the role of face masks in mitigating the spread of COVID-19 in the general population, using epidemic models to estimate the total reduction of infections and deaths under various scenarios. In particular, we examined the optimal deployment of face masks when resources are limited, and explored a range of supply and demand dynamics. We found that face masks, even with a limited protective effect, can reduce infections and deaths, and can delay the peak time of the epidemic. We consistently found that a random distribution of masks in the population was a suboptimal strategy when resources were limited. Prioritizing coverage among the elderly was more beneficial, while allocating a proportion of available resources for diagnosed infected cases provided further mitigation under a range of scenarios. In summary, face mask use, particularly for a pathogen with relatively common asymptomatic carriage, can effectively provide some mitigation of transmission, while balancing provision between vulnerable healthy persons and symptomatic persons can optimize mitigation efforts when resources are limited.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Colin J Worby", + "author_inst": "Broad Institute" + }, + { + "author_name": "Hsiao-Han Chang", + "author_inst": "National Tsing Hua University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.03.20052720", "rel_title": "Mitigating COVID-19 outbreak via high testing capacity and strong transmission-intervention in the United States", @@ -1542682,33 +1545642,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, - { - "rel_doi": "10.1101/2020.04.03.20047175", - "rel_title": "Corona Epidemic in Indian context: Predictive Mathematical Modelling", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20047175", - "rel_abs": "The novel Coronavirus pathogen Covid-19 is a cause of concern across the world as the human-to-human infection caused by it is spreading at a fast pace. The virus that first manifested in Wuhan, China has travelled across continents. The increase in number of deaths in Italy, Iran, USA, and other countries has alarmed both the developed and developing countries. Scientists are working hard to develop a vaccine against the virus, but until now no breakthrough has been achieved. India, the second most populated country in the world, is working hard in all dimensions to stop the spread of community infection. Health care facilities are being updated; medical and paramedical staffs are getting trained, and many agencies are raising awareness on the issues related to this virus and its transmission. The administration is leaving no stone unturned to prepare the country to mitigate the adverse effects. However, as the number of infected patients, and those getting cured is changing differently in different states everyday it is difficult to predict the spread of the virus and its fate in Indian context. Different states have adopted measures to stop the community spread. Considering the vast size of the country, the population size and other socio-economic conditions of the states, a single uniform policy may not work to contain the disease. In this paper, we discuss a predictive mathematical model that can give us some idea of the fate of the virus, an indicative data and future projections to understand the further course this pandemic can take. The data can be used by the health care agencies, the Government Organizations and the Planning Commission to make suitable arrangements to fight the pandemic. Though the model is preliminary, it can be used at regional level to manage the health care system in the present scenario. The recommendations can be made, and advisories prepared based on the predictive results that can be implemented at regional levels.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jyoti Bhola", - "author_inst": "Hansraj College, University of Delhi" - }, - { - "author_name": "Vandana Revathi Venkateswaran", - "author_inst": "Max Plank Institute for Evolutionary Biology, Germany" - }, - { - "author_name": "Monika Koul", - "author_inst": "Hansraj College, University of Delhi" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.04.02.20050740", "rel_title": "Comparison of transmissibility of coronavirus between symptomatic and asymptomatic patients: Reanalysis of the Ningbo Covid-19 data", @@ -1543743,6 +1546676,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.06.20053918", + "rel_title": "Thoughts on Higher Medical Education Under Major Public Health Emergencies: Thinking Ahead After COVID-19 Outbreak", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20053918", + "rel_abs": "ImportanceThe spread of coronavirus disease 2019 (COVID-19) has posed great threat to peoples health and several medical schools in the world suspended classes as a precaution against the virus. China has also adopted precautionary measures to keep medical schools running without suspending classes. Thinking ahead after COVID-19 Outbreak is important.\n\nObjectiveTo explore the most suitable teaching and learning pattern in medical school during COVID-19 Outbreak.\n\nDesignThis study is a case-control study. We had tried to apply a new blended teaching model based on 5G network that combined team-based learning (TBL) and online interaction to the students before the outbreak and then universities responded to the COVID-19 outbreak by closing campuses and shifting to other forms of distance learning. In other word, the courses started using blended teaching model before COVID-19 outbreak and might last using other forms of distance learning throughout the pandemic. Five Point Likert Scale Questionnaires which contains 20 items were used, and the effect of the two kinds of teaching patterns was compared by evaluating the indicators of core competencies of students including professionalism, attitude towards learning, knowledge and learning skills, teamwork skills, motivation in learning, adaptability and acceptance of the courses and network environment.\n\nSettingOur study based on a single center.\n\nParticipantsFifty fourth-year medical students receiving the \"5+3\" pattern courses regarding internal medicine were enrolled in the study.\n\nExposure(s) (for observational studies)The teaching and learning patter started using blended teaching model before COVID-19 outbreak and might last using other forms of distance learning throughout the pandemic.\n\nMain Outcome(s)According to the descriptive statistical analysis of the first part of the questionnaire (question 1-16), the average score of adaptability and acceptance of the courses is 2.60 lower than 3, indicating that students are more adapted to other forms of distance learning during COVID-19 outbreak; the average score of the rest of the questions is higher than 3, indicating that blended teaching model based on 5G network is superior to other forms of distance learning. The number of male students who are inclined to the blended teaching model based on 5G network is 0.13 times as much as that of female students (95%CI:0.028[~]0.602, p=0.009).\n\nResultsOnline forms of distance learning were accepted by the students. Female students had higher expectations on the course and were more likely to adapt well to the change during the COVID-19 outbreak. However, all students preferred the blended teaching model based on 5G network that combined team-based learning (TBL) and online interaction before the pandemic.\n\nConclusionIt indicates that medical education based on 5G network that combined team-based learning (TBL) and online interaction is a more suitable option to teach medical students online. Chinas experience in online higher medical education may serve as a reference to other countries during the pandemic.\n\nKey pointO_ST_ABSQuestionsC_ST_ABSWhat are the reflections on approaches to teaching and learning during COVID-19 Outbreak?\n\nFindingsFifty fourth-year medical students receiving the \"5+3\" pattern courses regarding internal medicine were enrolled. Five Point Likert Scale Questionnaires which contains 20 items were used. This study indicates that medical education based on 5G network that combined team-based learning (TBL) and online interaction is a more suitable option to teach medical students online during COVID-19 outbreak.\n\nMeaningChinas experience in online higher medical education may serve as a reference to other countries during the pandemic.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Wei Lin", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Yan Chen", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Songchang Shi", + "author_inst": "Fujian Provincial Hospital South Branch" + }, + { + "author_name": "Jixing Liang", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Huibin Huang", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Liantao Li", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Liangchun Cai", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Liyao Zong", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Nengying Wang", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Junping Wen", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Gang Chen", + "author_inst": "Fujian Provincial Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "medical education" + }, { "rel_doi": "10.1101/2020.04.03.20052936", "rel_title": "An \"Infodemic\": Leveraging High-Volume Twitter Data to Understand Public Sentiment for the COVID-19 Outbreak", @@ -1543844,45 +1546836,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.04.04.20053058", - "rel_title": "Indoor transmission of SARS-CoV-2", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.04.20053058", - "rel_abs": "BackgroundBy early April 2020, the COVID-19 pandemic had infected nearly one million people and had spread to nearly all countries worldwide. It is essential to understand where and how SARS-CoV-2 is transmitted.\n\nMethodsCase reports were extracted from the local Municipal Health Commissions of 320 prefectural cities (municipalities) in China, not including Hubei province, between 4 January and 11 February 2020. We identified all outbreaks involving three or more cases and reviewed the major characteristics of the enclosed spaces in which the outbreaks were reported and associated indoor environmental issues.\n\nResultsThree hundred and eighteen outbreaks with three or more cases were identified, involving 1245 confirmed cases in 120 prefectural cities. We divided the venues in which the outbreaks occurred into six categories: homes, transport, food, entertainment, shopping, and miscellaneous. Among the identified outbreaks, 53{middle dot}8% involved three cases, 26{middle dot}4% involved four cases, and only 1{middle dot}6% involved ten or more cases. Home outbreaks were the dominant category (254 of 318 outbreaks; 79{middle dot}9%), followed by transport (108; 34{middle dot}0%; note that many outbreaks involved more than one venue category). Most home outbreaks involved three to five cases. We identified only a single outbreak in an outdoor environment, which involved two cases.\n\nConclusionsAll identified outbreaks of three or more cases occurred in an indoor environment, which confirms that sharing indoor space is a major SARS-CoV-2 infection risk.\n\nFundingThe work was supported by the Research Grants Council of Hong (no 17202719, C7025-16G), and National Natural Science Foundation of China (no 41977370).", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Hua Qian", - "author_inst": "Southeast University" - }, - { - "author_name": "Te Miao", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Li LIU", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Xiaohong Zheng", - "author_inst": "Southeast University" - }, - { - "author_name": "Danting Luo", - "author_inst": "Southeast University" - }, - { - "author_name": "Yuguo Li", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.03.20052860", "rel_title": "Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-Co2 virus detection", @@ -1545097,6 +1548050,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.03.31.20048652", + "rel_title": "Widespread use of face masks in public may slow the spread of SARS CoV-2: an ecological study", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20048652", + "rel_abs": "BackgroundThe reasons for the large differences between countries in the sizes of their SARS CoV-2 epidemics is unknown. Individual level studies have found that the use of face masks was protective for the acquisition and transmission of a range of respiratory viruses including SARS CoV-1. We hypothesized that population level usage of face masks may be negatively associated SARS CoV-2 spread.\n\nMethodsAt a country level, linear regression was used to assess the association between COVID-19 diagnoses per inhabitant and the national promotion of face masks in public (coded as a binary variable), controlling for the age of the COVID-19 epidemic and testing intensity.\n\nResultsEight of the 49 countries with available data advocated wearing face masks in public - China, Czechia, Hong Kong, Japan, Singapore, South Korea, Thailand and Malaysia. In multivariate analysis face mask use was negatively associated with number of COVID-19 cases/inhabitant (coef. -326, 95% CI -601- -51, P=0.021). Testing intensity was positively associated with COVID-19 cases (coef. 0.07, 95% CI 0.05-0.08, P<0.001).\n\nConclusionWhilst these results are susceptible to residual confounding, they do provide ecological level support to the individual level studies that found face mask usage to reduce the transmission and acquisition of respiratory viral infections.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Chris Kenyon", + "author_inst": "Institute of Tropical Medicine, Antwerp" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.30.20048165", "rel_title": "Association of BCG vaccination policy with prevalence and mortality of COVID-19", @@ -1545174,49 +1548146,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.02.20051334", - "rel_title": "Rapid implementation of mobile technology for real-time epidemiology of COVID-19", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20051334", - "rel_abs": "The rapid pace of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic (COVID-19) presents challenges to the robust collection of population-scale data to address this global health crisis. We established the COronavirus Pandemic Epidemiology (COPE) consortium to bring together scientists with expertise in big data research and epidemiology to develop a COVID-19 Symptom Tracker mobile application that we launched in the UK on March 24, 2020 and the US on March 29, 2020 garnering more than 2.25 million users to date. This mobile application offers data on risk factors, herald symptoms, clinical outcomes, and geographical hot spots. This initiative offers critical proof-of-concept for the repurposing of existing approaches to enable rapidly scalable epidemiologic data collection and analysis which is critical for a data-driven response to this public health challenge.\n\nOne Sentence SummaryCOVID-19 symptom tracker for smartphones", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "David A. Drew", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Long H. Nguyen", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Claire J. Steves", - "author_inst": "King's College London" - }, - { - "author_name": "Jonathan Wolf", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Tim D. Spector", - "author_inst": "King's College London" - }, - { - "author_name": "Andrew T. Chan", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "COPE Consortium", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.02.20051417", "rel_title": "Cryptic transmission of SARS-CoV-2 in Washington State", @@ -1546467,6 +1549396,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.31.20049387", + "rel_title": "The impacts of diagnostic capability and prevention measures on transmission dynamics of COVID-19 in Wuhan", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20049387", + "rel_abs": "BackgroundAlthough by late February 2020 the COVID-19 epidemic was effectively controlled in Wuhan, China, the virus has since spread around the world and been declared a pandemic on March 11. Estimating the effects of interventions, such as transportation restrictions and quarantine measures, on the early COVID-19 transmission dynamics in Wuhan is critical for guiding future virus containment strategies. Since the exact number of COVID-19 infected cases is unknown, the number of documented cases was used by many disease transmission models to infer epidemiological parameters. However, this means that it would not be possible to adequately estimate epidemiological parameters and the effects of intervention measures, because the percentage of all infected cases that were documented changed during the first 2 months of the epidemic as a consequence of a gradually increasing diagnostic capability.\n\nMethodsTo overcome the limitations, we constructed a stochastic susceptible-exposed-infected-quarantined-recovered (SEIQR) model, accounting for intervention measures and temporal changes in the proportion of new documented infections out of total new infections, to characterize the transmission dynamics of COVID-19 in Wuhan across different stages of the outbreak. Pre-symptomatic transmission was taken into account in our model, and all epidemiological parameters were estimated using Particle Markov-chain Monte Carlo (PMCMC) method.\n\nResultsOur model captured the local Wuhan epidemic pattern as a two-peak transmission dynamics, with one peak on February 4 and the other on February 12, 2020. The impact of intervention measures determined the timing of the first peak, leading to an 86% drop in the Re from 3.23 (95% CI, 2.22 to 4.20) to 0.45 (95% CI, 0.20 to 0.69). An improved diagnostic capability led to the second peak and a higher proportion of documented infections. Our estimated proportion of new documented infections out of the total new infections increased from 11% (95% CI 1% - 43%) to 28% (95% CI 4% - 62%) after January 26 when more detection kits were released. After the introduction of a new diagnostic criterion (case definition) on February 12, a higher proportion of daily infected cases were documented (49% (95% CI 7% - 79%)).", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jingbo LIANG", + "author_inst": "Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China" + }, + { + "author_name": "Hsiang-Yu Yuan", + "author_inst": "Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China" + }, + { + "author_name": "Lindsey Wu", + "author_inst": "Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, United Kingdom" + }, + { + "author_name": "Dirk Udo Pfeiffer", + "author_inst": "Centre for Applied One Health Research and Policy Advice, City University of Hong Kong, Hong Kong, China" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.31.20049452", "rel_title": "A Covid-19 case mortality rate without time delay systematics", @@ -1546584,29 +1549544,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.02.20050351", - "rel_title": "Capacities and predicted demands of Brazil's health system in view of the novel coronavirus disease outbreak", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20050351", - "rel_abs": "ObjectiveTo estimate surge capacities and demands of Brazils health system in view of severe cases of the novel coronavirus disease.\n\nMethodsThree types of hospital equipments demanded by severe COVID-19 patients are considered: available intensive care unit (ICU) beds, existing surgery operating rooms and respirators located in other hospital areas. They are taken into account on a cumulative basis forming three levels of hospital equipment usage. Based on a mean duration of hospitalization for the disease, it is estimated the daily admission capacity of infected patients per state and for the entire country for each level of hospital equipment usage. Furthermore, an exponential regression model is fitted by means of the daily national number of new documented patients. The prediction intervals for the number of new patients for certain days in the immediate future are then calculated and compared to the admissible daily demand for the three incremental groups of equipments. The data are made publicly available by the Brazilian federal government and are gathered and analyzed by means of the Python programming language.\n\nResults41% of the (adult) ICU beds in Brazil were available during 2019, indicating that this hospital equipment is not on average operating near capacity in national numbers. Nevertheless, there is a marked heterogeneity in the absolute and relative numbers of available and existing ICU beds and existing surgery operating rooms and extra respirators between its states.\n\nConclusionsThe remarkable differences between states reflect into the number of possible daily admissions of COVID-19 patients with respiratory failure for the three considered levels of hospital equipment usage. In national numbers, Brazils health system is estimated to be capable of daily admitting 693, 1243 and 2166 severe patients under the three studied scenarios. The fitted model predicted that only the first limit, if any, would be reached.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Eric Luis Barroso Cavalcante", - "author_inst": "Brazilian Federal Court of Accounts" - }, - { - "author_name": "Juliana Cristina Cardoso Ferreira", - "author_inst": "Federal University of S\u00e3o Paulo" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.04.02.20051078", "rel_title": "A Model for Supply-Chain Decisions for Resource Sharing with an Application to Ventilator Allocation to Combat COVID-19", @@ -1547561,6 +1550498,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.04.02.20050773", + "rel_title": "Exponential phase of covid19 expansion is not driven by climate at global scale", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20050773", + "rel_abs": "The pandemic state of COVID-19 caused by the SARS CoV-2 put the world in quarantine, led to hundreds of thousands of deaths and is causing an unprecedented economic crisis. However, COVID-19 is spreading in different rates at different countries. Here, we tested the effect of three classes of predictors, i.e., socioeconomic, climatic and transport, on the rate of daily increase of COVID-19. We found that global connections, represented by countries importance in the global air transportation network, is the main explanation for the growth rate of COVID-19 in different countries. Climate, geographic distance and socioeconomics had a milder effect in this big picture analysis. Geographic distance and climate were significant barriers in the past but were surpassed by the human engine that allowed us to colonize most of our planet land surface. Our results indicate that the current claims that the growth rate of COVID-19 may be lower in warmer and humid tropical countries should be taken very carefully, at risk to disturb well-established and effective policy of social isolation that may help to avoid higher mortality rates due to the collapse of national health systems.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Marco Tulio Pacheco Coelho", + "author_inst": "Universidade Federal de Goias" + }, + { + "author_name": "Joao Fabricio Mota Rodrigues", + "author_inst": "Universidade Federal de Goias" + }, + { + "author_name": "Anderson Matos Medina", + "author_inst": "Universidade Federal da Bahia" + }, + { + "author_name": "Paulo Scalco", + "author_inst": "Universidade Federal de Goias" + }, + { + "author_name": "Levi Carina Terribile", + "author_inst": "Universidade Federal de Jatai" + }, + { + "author_name": "Bruno Vilela", + "author_inst": "Universidade Federal da Bahia" + }, + { + "author_name": "Jose Alexandre Felizola Diniz-Filho", + "author_inst": "Universidade Federal de Goias" + }, + { + "author_name": "Ricardo Dobrovolski", + "author_inst": "Universidade Federal da Bahia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.02.20050922", "rel_title": "Inferring COVID-19 spreading rates and potential change points for case number forecasts", @@ -1547658,29 +1550642,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.04.02.20050468", - "rel_title": "Using network science to propose strategies for effectively dealing with pandemics: The COVID-19 example", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20050468", - "rel_abs": "The global spread of Coronavirus Disease 2019 (COVID-19) is overwhelming many health-care systems. As a result, epidemiological models are being used to inform policy on how to effectively deal with this pandemic. The majority of existing models assume random diffusion but do not take into account differences in the amount of interactions between individuals, i.e. the underlying human interaction network, whose structure is known to be scale-free. Here, we demonstrate how this network of interactions can be used to predict the spread of the virus and to inform policy on the most successful mitigation and suppression strategies. Using stochastic simulations in a scale-free network, we show that the epidemic can propagate for a long time at a low level before the number of infected individuals suddenly increases markedly, and that this increase occurs shortly after the first hub is infected. We further demonstrate that mitigation strategies that target hubs are far more effective than strategies that randomly decrease the number of connections between individuals. Although applicable to infectious disease modelling in general, our results emphasize how network science can improve the predictive power of current COVID-19 epidemiological models.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Helena A Herrmann", - "author_inst": "University of Manchester" - }, - { - "author_name": "Jean-Marc Schwartz", - "author_inst": "University of Manchester" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.04.03.20051813", "rel_title": "Separate Fever Clinics Prevent the Spread of COVID-19 and Offload Emergency Resources: Analysis from a large tertiary hospital in China", @@ -1548827,6 +1551788,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.02.022384", + "rel_title": "One-step RNA extraction for RT-qPCR detection of 2019-nCoV", + "rel_date": "2020-04-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.02.022384", + "rel_abs": "The global outbreak of coronavirus disease 2019 (COVID-19) has placed an unprecedented burden on healthcare systems as the virus spread from the initial 27 reported cases in the city of Wuhan, China to a global pandemic in under three month[1]. Resources essential to monitoring virus transmission have been challenged with a demand for expanded surveillance. The CDC 2019-nCoV Real-Time Diagnostic Panel uses a real-time reverse transcription polymerase chain reaction (RT-PCR) consisting of two TaqMan probe and primer sets specific for the 2019-nCoV N gene, which codes for the nucleocapsid structural protein that encapsulates viral RNA, for the qualitative detection of 2019-nCoV viral RNA in respiratory samples. To isolate RNA from respiratory samples, the CDC lists RNA extraction kits from four manufacturers. In anticipation of a limited supply chain of RNA extraction kits and the need for test scalability, we sought to identify alternative RNA extraction methods. Here we show that direct lysis of respiratory samples can be used in place of RNA extraction kits to run the CDC 2019-nCoV Real-Time Diagnostic assay with the additional benefits of higher throughput, lower cost, faster turnaround and possibly higher sensitivity and improved safety.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Monica Sentmanat", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Evguenia Kouranova", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Xiaoxia Cui", + "author_inst": "Washington University in St. Louis" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.04.02.019075", "rel_title": "Rapid community-driven development of a SARS-CoV-2 tissue simulator", @@ -1549092,61 +1552080,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.02.021469", - "rel_title": "LY6E Restricts the Entry of Human Coronaviruses, including the currently pandemic SARS-CoV-2", - "rel_date": "2020-04-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.02.021469", - "rel_abs": "C3A is a sub-clone of human hepatoblastoma HepG2 cell line with the strong contact inhibition of growth. We fortuitously found that C3A was more susceptible to human coronavirus HCoV-OC43 infection than HepG2, which was attributed to the increased efficiency of virus entry into C3A cells. In an effort to search for the host cellular protein(s) mediating the differential susceptibility of the two cell lines to HCoV-OC43 infection, we found that ADAP2, GILT and LY6E, three cellular proteins with known activity of interfering virus entry, expressed at significantly higher levels in HepG2 cells. Functional analyses revealed that ectopic expression of LY6E, but not GILT or ADAP2, in HEK 293 cells inhibited the entry of HCoV-OC43. While overexpression of LY6E in C3A and A549 cells efficiently inhibited the infection of HCoV-OC43, knockdown of LY6E expression in HepG2 significantly increased its susceptibility to HCoV-OC43 infection. Moreover, we found that LY6E also efficiently restricted the entry mediated by the envelope spike proteins of other human coronaviruses, including the currently pandemic SARS-CoV-2. Interestingly, overexpression of serine protease TMPRSS2 or amphotericin treatment significantly neutralized the IFITM3 restriction of human coronavirus entry, but did not compromise the effect of LY6E on the entry of human coronaviruses. The work reported herein thus demonstrates that LY6E is a critical antiviral immune effector that controls CoV infection and pathogenesis via a distinct mechanism.\n\nImportanceVirus entry into host cells is one of the key determinants of host range and cell tropism and is subjected to the control by host innate and adaptive immune responses. In the last decade, several interferon inducible cellular proteins, including IFITMs, GILT, ADAP2, 25CH and LY6E, had been identified to modulate the infectious entry of a variety of viruses. Particularly, LY6E was recently identified as host factors to facilitate the entry of several human pathogenic viruses, including human immunodeficiency virus, influenza A virus and yellow fever virus. Identification of LY6E as a potent restriction factor of coronaviruses expands the biological function of LY6E and sheds new light on the immunopathogenesis of human coronavirus infection.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Xuesen Zhao", - "author_inst": "Institute of Infectious disease, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China." - }, - { - "author_name": "Shuangli Zheng", - "author_inst": "Institute of Infectious disease, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China." - }, - { - "author_name": "Danying Chen", - "author_inst": "Institute of Infectious disease, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China." - }, - { - "author_name": "Mei Zheng", - "author_inst": "Institute of Infectious disease, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China" - }, - { - "author_name": "Xinglin Li", - "author_inst": "Institute of Infectious disease, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China." - }, - { - "author_name": "Guoli Li", - "author_inst": "Institute of Infectious disease, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China." - }, - { - "author_name": "Hanxin Lin", - "author_inst": "Department of Pathology and Laboratory Medicine, Western University, 1151 Richmond Street, London, Ontario, Canada." - }, - { - "author_name": "Jinhong Chang", - "author_inst": "Baruch S. Blumberg Institute, Hepatitis B Foundation, 3805 Old Easton Road, Doylestown, PA 18902. USA" - }, - { - "author_name": "Hui Zeng", - "author_inst": "Institute of Infectious disease, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China." - }, - { - "author_name": "Ju-Tao Guo", - "author_inst": "Baruch S. Blumberg Institute, Hepatitis B Foundation, 3805 Old Easton Road, Doylestown, PA 18902. USA." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.01.017624", "rel_title": "Indomethacin has a potent antiviral activity against SARS CoV-2 in vitro and canine coronavirus in vivo", @@ -1550313,6 +1553246,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.01.20049668", + "rel_title": "Spatial variability in the risk of death from COVID-19 in Italy, 2020", + "rel_date": "2020-04-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20049668", + "rel_abs": "ObjectivesItaly has been disproportionately affected by the COVID-19 pandemic, becoming the nation with the third highest death toll in the world as of May 10th, 2020. We analyzed the severity of COVID-19 pandemic across 20 Italian regions.\n\nMethodWe manually retrieved the daily cumulative numbers of laboratory-confirmed cases and deaths attributed to COVID-19 across 20 Italian regions. For each region, we estimated the crude case fatality ratio and time-delay adjusted case fatality ratio (aCFR). We then assessed the association between aCFR and sociodemographic, health care and transmission factors using multivariate regression analysis.\n\nResultsThe overall aCFR in Italy was estimated at 17.4%. Lombardia exhibited the highest aCFR (24.7%) followed by Marche (19.3%), Emilia Romagna (17.7%) and Liguria (17.6%). Our aCFR estimate was greater than 10% for 12 regions. Our aCFR estimates were statistically associated with population density and cumulative morbidity rate in a multivariate analysis.\n\nConclusionOur aCFR estimates for overall Italy and for 7 out of 20 regions exceeded those reported for the most affected region in China. Our findings highlight the importance of social distancing to suppress incidence and reduce the death risk by preventing saturating the health care system.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kenji Mizumoto", + "author_inst": "Kyoto University" + }, + { + "author_name": "Sushma Dahal", + "author_inst": "Georgia State University School of Public Health" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.31.20049007", "rel_title": "Harmonizing heterogeneous endpoints in COVID-19 trials without loss of information - an essential step to facilitate decision making", @@ -1550422,45 +1553382,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.31.20049304", - "rel_title": "COVID-19 infection during pregnancy: a systematic review to summarize possible symptoms, treatments, and pregnancy outcomes", - "rel_date": "2020-04-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20049304", - "rel_abs": "BackgroundWith the exponential increase in coronavirus disease 2019 (COVID-19) worldwide, an increasing proportion of pregnant women are now infected during their pregnancy. The aims of this systematic review were to summarize the possible symptoms, treatments, and pregnancy outcomes of women infected with COVID-19 during their pregnancy.\n\nMethodsFour databases (Medline, Web of Science, Scopus, and CINAHL) were searched on March 25, 2020, using the following keywords: \"COVID-19\", \"nCoV-2019\", and \"coronavirus.\" Articles included if they reported either the symptoms, treatments for the women who had been infected with the COVID-19 during their pregnancy or pregnancy outcomes. The selected articles results were summarized employing a narrative synthesis approach.\n\nResultsA total of nine studies were selected for this study, comprising 101 infected pregnant women. Other than the infected general population, infected pregnant women reported different symptoms; however, fever (66.7%), cough (39.4%), fatigue (15.2%), and breathing difficulties (14.1%) were common. Infected pregnant women were given different treatments than the general infected population. The C-section was a common (83.9%) mode of delivery among infected pregnant women, and a higher proportion of births were preterm births (30.4%) and low birth weight (17.9%).\n\nConclusionsPregnant infected women had different symptoms, and they were given dissimilar treatments than the general infected population. Healthcare providers may have appropriately informed about these symptoms and treatments. They, therefore, would be able to handle infection during pregnancy effectively, which would reduce common adverse consequences among infected pregnant women.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Md. Mostaured Ali Khan", - "author_inst": "University of Rajshahi" - }, - { - "author_name": "Md Nuruzzaman Khan", - "author_inst": "Jatiya Kabi Kazi Nazrul Islam University" - }, - { - "author_name": "Md. Golam Mustagir", - "author_inst": "University of Rajshahi" - }, - { - "author_name": "Juwel Rana", - "author_inst": "University of Massachusetts Amherst" - }, - { - "author_name": "Md. Rajwanul Haque", - "author_inst": "MEL and Research, Practical Action" - }, - { - "author_name": "Md. Mosfequr Rahman", - "author_inst": "University of Rajshahi" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.31.20049239", "rel_title": "A flexible load sharing system and implementation to anticipate and organise transfers based on ICU demand in the context of COVID-19 pandemic", @@ -1551403,6 +1554324,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.03.31.20048439", + "rel_title": "Research on the Influence of Information Diffusion on the Transmission of the Novel Coronavirus (COVID-19)", + "rel_date": "2020-04-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20048439", + "rel_abs": "With the rapid development of mobile Internet in China, the information of the epidemic is full-time and holographic, and the role of information diffusion in epidemic control is increasingly prominent. At the same time, the publicity of all kinds of big data also provides the possibility to explore the impact of media information diffusion on disease transmission. This paper explores the mechanism of the influence of information diffusion on the spread of the novel coronavirus, develops a model of the interaction between information diffusion and disease transmission based on the SIR model, and empirically tests the role and mechanism of information diffusion in the spread of COCID-19 by using econometric method. The result shows that there was a significant negative correlation between the information diffusion and the spread of the novel coronavirus; The result of robust test shows that the spread of both epidemic information and protection information hindered the further spread of the epidemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lin Shanlang", + "author_inst": "School of Economics and Management, Tongji University, China" + }, + { + "author_name": "Ma Chao", + "author_inst": "School of Economics and Management, Tongji University, China" + }, + { + "author_name": "Lin Ruofei", + "author_inst": "School of Economics and Management, Tongji University, China" + }, + { + "author_name": "Huang Junpei", + "author_inst": "School of Economics and Management, Tongji University, China" + }, + { + "author_name": "Xu Ruohan", + "author_inst": "School of Economics and Management, Tongji University, China" + }, + { + "author_name": "Yuan Aini", + "author_inst": "School of Economics and Management, Tongji University, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.03.31.20047142", "rel_title": "Clinical features and outcomes of 2019 novel coronavirus-infected patients with high plasma BNP levels", @@ -1551528,45 +1554488,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.30.20047688", - "rel_title": "Growth rate and acceleration analysis of the COVID-19 pandemic reveals the effect of public health measures in real time", - "rel_date": "2020-04-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20047688", - "rel_abs": "BackgroundEnding the COVID-19 pandemic is arguably one of the most prominent challenges in recent human history. Following closely the growth dynamics of the disease is one of the pillars towards achieving that goal.\n\nObjectiveWe aimed at developing a simple framework to facilitate the analysis of the growth rate (cases/day) and growth acceleration (cases/day2) of COVID-19 cases in real-time.\n\nMethodsThe framework was built using the Moving Regression (MR) technique and a Hidden Markov Model (HMM). The dynamics of the pandemic was initially modeled via combinations of four different growth stages: lagging (beginning of the outbreak), exponential (rapid growth), deceleration (growth decay) and stationary (near zero growth). A fifth growth behavior, namely linear growth (constant growth above zero), was further introduced to add more flexibility to the framework. An R Shiny application was developed, which can be accessed at http://www.theguarani.com.br/covid-19 or downloaded from https://github.com/adamtaiti/SARS-CoV-2. The framework was applied to data from the European Center for Disease Prevention and Control (ECDC), which comprised 853,200 cases reported worldwide as of April 2nd 2020.\n\nResultsWe found that the impact of public health measures on the prevalence of COVID-19 could be perceived in seemingly real-time by monitoring growth acceleration curves. Restriction to human mobility produced detectable decline in growth acceleration within few days, deceleration within [~]2 weeks and near-stationary growth within [~]6 weeks. Countries exhibiting different permutations of the five growth stages indicated that the evolution of COVID-19 prevalence is more complex and dynamic than previously appreciated.\n\nConclusionsThese results corroborate that mass social isolation is a highly effective measure against the dissemination of SARS-CoV-2, as previously suggested. Apart from the analysis of prevalence partitioned by country, the proposed framework is easily applicable to city, state, region and arbitrary territory data, serving as an asset to monitor the local behavior of COVID-19 cases.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Yuri Tani Utsunomiya", - "author_inst": "Department of Support, Production and Animal Health, School of Veterinary Medicine of Aracatuba, Sao Paulo State University (Unesp), 16050-680 R. Clovis Pestana" - }, - { - "author_name": "Adam Taiti Harth Utsunomiya", - "author_inst": "International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Aracatuba/S" - }, - { - "author_name": "Rafaela Beatriz Pintor Torrecilha", - "author_inst": "International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Aracatuba/S" - }, - { - "author_name": "Silvana Cassia Paulan", - "author_inst": "International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Aracatuba/S" - }, - { - "author_name": "Marco Milanesi", - "author_inst": "International Atomic Energy Agency (IAEA) Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clovis Pestana 793 - Dona Amelia, Aracatuba/S" - }, - { - "author_name": "Jose Fernando Garcia", - "author_inst": "Department of Support, Production and Animal Health, School of Veterinary Medicine of Aracatuba, Sao Paulo State University (Unesp), 16050-680 R. Clovis Pestana" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.30.20043612", "rel_title": "Covid-19 Outbreak Progression in Italian Regions: Approaching the Peak by March 29th", @@ -1552709,6 +1555630,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.30.20047589", + "rel_title": "The Institutional and Cultural Context of Cross-National Variation in COVID-19 Outbreaks", + "rel_date": "2020-04-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20047589", + "rel_abs": "BackgroundThe COVID-19 pandemic poses an unprecedented and cascading threat to the health and economic prosperity of the worlds population.\n\nObjectivesTo understand whether the institutional and cultural context influences the COVID-19 outbreak.\n\nMethodsAt the ecological level, regression coefficients are examined to figure out contextual variables influencing the pandemics exponential growth rate across 96 countries.\n\nResultsWhile a strong institutional context is negatively associated with the outbreak (B = -0.55 ... -0.64, p < 0.001), the pandemics growth rate is steeper in countries with a quality education system (B = 0.33, p < 0.001). Countries with an older population are more affected (B = 0.46, p < 0.001). Societies with individualistic (rather than collectivistic) values experience a flatter rate of pathogen proliferation (B = -0.31, p < 0.001), similarly for higher levels of power distance (B = -0.32, p < 0.001). Hedonistic values, that is seeking indulgence and not enduring restraints, are positively related to the outbreak (B = 0.23, p = 0.001).\n\nConclusionsThe results emphasize the need for public policy makers to pay close attention to the institutional and cultural context in their respective countries when instigating measures aimed at constricting the pandemics growth.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Wolfgang Messner", + "author_inst": "University of South Carolina" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.30.20047894", "rel_title": "Forecasting the CoViD19 Diffusion in Italy and the Related Occupancy of Intensive Care Units", @@ -1552818,49 +1555758,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.03.29.20046490", - "rel_title": "Early surveillance and public health emergency disposal measures between novel coronavirus disease 2019 and avian influenza in China: a case-comparison study", - "rel_date": "2020-04-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.29.20046490", - "rel_abs": "BackgroundThe novel coronavirus disease 2019 (COVID-19) outbreak is spreading rapidly throughout China and the world. Hence, early surveillance and public health emergency disposal are considered crucial to curb this emerging infectious disease. However, studies that investigated the early surveillance and public health emergency disposal for the prevention and control of the COVID-19 outbreak in China are relatively few. We aimed to compare the strengths and weaknesses of early surveillance and public health emergency disposal for prevention and control between COVID-19 and H7N9 avian influenza, which was commended by the international community, in China.\n\nMethodsA case-comparison study was conducted using a set of six key time nodes to form a reference framework for evaluating early surveillance and public health emergency disposal between H7N9 avian influenza (2013) in Shanghai, China and COVID-19 in Wuhan, China.\n\nFindingsA report to the local Center for Disease Control and Prevention, China, for the first hospitalized patient was sent after 6 and 20 days for H7N9 avian influenza and COVID-19, respectively. In contrast, the pathogen was identified faster in the case of COVID-19 than in the case of H7N9 avian influenza (12 days vs. 31 days). The government response regarding COVID-19 was 10 days later than that regarding avian influenza. The entire process of early surveillance and public health emergency disposal lasted 5 days longer in COVID-19 than in H7N9 avian influenza (46 days vs. 41 days).\n\nConclusionsThe identification of the unknown pathogen improved in China between the outbreaks of avian influenza and COVID-19. The longer emergency disposal period in the case of COVID-19 could be attributed to the governments slower response to the epidemic. Improving public health emergency management could lessen the adverse social effects of emerging infectious diseases and public health crisis in the future.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Tiantian Zhang", - "author_inst": "School of Public Health, Fudan University" - }, - { - "author_name": "Wenming Shi", - "author_inst": "School of Public Health, Fudan University" - }, - { - "author_name": "Ying Wang", - "author_inst": "School of Public Health, Fudan University" - }, - { - "author_name": "Ge Bai", - "author_inst": "School of Public Health, Fudan University" - }, - { - "author_name": "Ruiming Dai", - "author_inst": "School of Public Health, Fudan University" - }, - { - "author_name": "Qian Wang", - "author_inst": "School of Public Health, Fudan University" - }, - { - "author_name": "Li Luo", - "author_inst": "School of Public Health, Fudan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.03.29.20046011", "rel_title": "A phased lift of control: a practical strategy to achieve herd immunity against Covid-19 at the country level", @@ -1553779,6 +1556676,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.29.20043547", + "rel_title": "Health Communication Through News Media During the Early Stage of the COVID-19 Outbreak in China: A Digital Topic Modeling Approach", + "rel_date": "2020-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.29.20043547", + "rel_abs": "BackgroundIn December 2019, some COVID-19 cases were first reported and soon the disease broke out. As this dreadful disease spreads rapidly, the mass media has been active in community education on COVID-19 by delivering health information about this novel coronavirus.\n\nMethodsWe adopted the Huike database to extract news articles about coronavirus from major press media, between January 1st, 2020, to February 20th, 2020. The data were sorted and analyzed by Python software and Python package Jieba. We sought a suitable topic number using the coherence number. We operated Latent Dirichlet Allocation (LDA) topic modeling with the suitable topic number and generated corresponding keywords and topic names. We divided these topics into different themes by plotting them into two-dimensional plane via multidimensional scaling.\n\nFindingsAfter removing duplicates, 7791 relevant news reports were identified. We listed the number of articles published per day. According to the coherence value, we chose 20 as our number of topics and obtained their names and keywords. These topics were categorized into nine primary themes based on the topic visualization figure. The top three popular themes were prevention and control procedures, medical treatment and research, global/local social/economic influences, accounting for 32{middle dot}6%, 16{middle dot}6%, 11{middle dot}8% of the collected reports respectively.\n\nInterpretationThe Chinese mass media news reports lag behind the COVID-19 outbreak development. The major themes accounted for around half the content and tended to focus on the larger society than on individuals. The COVID-19 crisis has become a global issue, and society has also become concerned about donation and support as well as mental health. We recommend that future work should address the mass medias actual impact on readers during the COVID-19 crisis through sentiment analysis of news data.\n\nFundingNational Social Science Foundation of China (18CXW021)\n\nEvidence before this studyThe novel coronavirus related news reports have engaged public attention in China during the COVID-19 crisis. Topic modeling of these news articles can produce useful information about the significance of mass media for early health communication. We searched the Huike database, the most professional Chinese media content database, using the search term \"coronavirus\" for related news articles published from January 1st, 2020, to February 20th, 2020. We found that these articles can be classified into different themes according to their emphasis, however, we found no other studies apply topic modeling method to study them.\n\nAdded value of this studyTo our knowledge, this study is the first to investigate the patterns of health communications through media and the role the media have played and are still playing in the light of the current COVID-19 crisis in China with topic modeling method. We compared the number of articles each day with the outbreak development and identified theres a delay in reporting COVID-19 outbreak progression for Chinese mass media. We identify nine main themes for 7791 collected news reports and detail their emphasis respectively.\n\nImplications of all the available evidenceOur results show that the mass media news reports play a significant role in health communication during the COVID-19 crisis, government can strengthen the report dynamics and enlarge the news coverage next time another disease strikes. Sentiment analysis of news data are needed to assess the actual effect of the news reports.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Qian Liu", + "author_inst": "School of Journalism and Communication, National Media Experimental Teaching Demonstration Center, Jinan University, Guangzhou, China; Department of Communicati" + }, + { + "author_name": "Zequan Zheng", + "author_inst": "International School, Jinan University, China; Faculty of Medicine, Jinan University, China" + }, + { + "author_name": "Jiabin Zheng", + "author_inst": "International School, Jinan University, China; Faculty of Medicine, Jinan University, China" + }, + { + "author_name": "Qiuyi Chen", + "author_inst": "School of Journalism and Communication, National Media Experimental Teaching Demonstration Center, Jinan University, Guangzhou, China" + }, + { + "author_name": "Guan Liu", + "author_inst": "Faculty of Computer Centre, Jinan University, China" + }, + { + "author_name": "Sihan Chen", + "author_inst": "International School, Jinan University, China" + }, + { + "author_name": "Bojia Chu", + "author_inst": "International School, Jinan University, China" + }, + { + "author_name": "Hongyu Zhu", + "author_inst": "International School, Jinan University, China" + }, + { + "author_name": "Babatunde Akinwunmi", + "author_inst": "Pulmonary and Critical Care Medicine Unit, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard University, Boston, Massachuset" + }, + { + "author_name": "Jian Huang", + "author_inst": "MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk" + }, + { + "author_name": "Casper J. P. Zhang", + "author_inst": "School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China" + }, + { + "author_name": "Wai-kit Ming", + "author_inst": "Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.03.29.20046565", "rel_title": "Eco-epidemiological assessment of the COVID-19 epidemic in China, January-February 2020", @@ -1553876,37 +1556836,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.26.20044610", - "rel_title": "The diagnostic evaluation of Convolutional NeuralNetwork (CNN) for the assessment of chest X-ray ofpatients infected with COVID-19", - "rel_date": "2020-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044610", - "rel_abs": "IntroductionThe main target of COVID-19 is the lungs where it may cause pneumonia in severely ill patients. Chest X-ray is an important diagnostic test to assess the lung for the damaging effects of COVID-19. Many other microbial pathogens can also cause damage to lungs leading to pneumonia but there are certain radiological features which can favor the diagnosis of pneumonia caused by COVID-19. With the rising number of cases of COVID-19, it would be imperative to develop computer programs which may assist the health professionals in the prevailing scenario.\n\nMaterials & MethodsA total of two hundred and seventy eight (278) images of chest X-rays have been assessed by applying ResNet-50 convolutional neural network architectures in the present study. The digital images were acquired from the public repositories provided by University of Montreal and National Institutes of Health. These digital images of Chest X-rays were divided into three groups labeled as normal, pneumonia and COVID-19. The third group contains digital images of chest X-rays of patients diagnosed with COVID-19 infection while the second group contains images of lung with pneumonia caused by other pathogens.\n\nResultsThe radiological images included in the data set are 89 images of lungs with COVID-19 infection, 93 images of lungs without any radiological abnormality and 96 images of patient with pneumonia caused by other pathogens. In this data set, 80% of the images were employed for training, and 20% for testing. A pre-trained (on ImageNet data set) ResNet-50 architecture was used to diagnose the cases of COVID-19 infections on lung X-ray images. The analysis of the data revealed that computer vision based program achieved diagnostic accuracy of 98.18 %, and F1-score of 98.19.\n\nConclusionThe performance of convolutional neural network regarding the differentiation of pulmonary changes caused by COVID-19 from the other type of pneumonias on digital images of the chest X-rays is excellent and it may be an extremely useful adjunct tool for the health professionals.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Syed Usama Khalid Bukhari", - "author_inst": "The University of Lahore" - }, - { - "author_name": "Syed Safwan Khalid Bukhari", - "author_inst": "COMSATS University, Islamabad, Pakistan" - }, - { - "author_name": "Asmara Syed", - "author_inst": "Northern Border University" - }, - { - "author_name": "SYED SAJID HUSSAIN SHAH", - "author_inst": "Northern Border University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.27.20045427", "rel_title": "The Novel Severe Acute Respiratory Syndrome Coronavirus 2(SARS-CoV-2) Directly Decimates Human Spleens and Lymph Nodes", @@ -1555300,6 +1558229,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.27.20043299", + "rel_title": "Failed detection of the full-length genome of SARS-CoV-2 by ultra-deep sequencing from the recovered and discharged patients retested viral PCR positive", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20043299", + "rel_abs": "Over 10 percent of recovered and discharged patients retested positive for SARS-CoV-2, raising a public health concern whether they could be potential origins of infection. In this study, we found that detectable viral genome in discharged patients might only mean the presence of viral fragments, and could hardly form an infection origin for its extremely low concentration.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Fengyu Hu", + "author_inst": "Guangzhou Eighth People Hospital" + }, + { + "author_name": "Fengjuan Chen", + "author_inst": "Guangzhou Eighth People Hospital" + }, + { + "author_name": "Yaping Wang", + "author_inst": "Guangzhou Eighth People Hospital" + }, + { + "author_name": "Teng Xu", + "author_inst": "Vision Medicals" + }, + { + "author_name": "Xiaoping Tang", + "author_inst": "Guangzhou Eighth People Hospital" + }, + { + "author_name": "Feng Li", + "author_inst": "Guangzhou Eighth People Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.25.20043505", "rel_title": "Machine Learning Approach for Confirmation of COVID-19 Cases: Positive, Negative, Death and Release", @@ -1555393,89 +1558361,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.26.20043943", - "rel_title": "A Multi-hospital Study in Wuhan, China\uff1aProtective Effects of Non-menopause and Female Hormones on SARS-CoV-2 infection", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20043943", - "rel_abs": "ImportanceHow to explain the better prognosis of female coronavirus disease 2019 (COVID-19) patients than that of males?\n\nObjectiveTo determine the correlation between menstruation status/sex hormones and prognosis of COVID-19, and to identify potential protective factors for female patients.\n\nDesign, Setting, and ParticipantsA cross-sectional study of COVID-19 patients who were hospitalized at Tongji and Mobile Cabin Hospitals from Jan 28, 2020 to March 8, 2020.\n\nExposuresConfirmed SARS-CoV-2 infection.\n\nMain Outcomes and MeasuresSex differences in severity and composite endpoints (admission to intensive care unit (ICU), use of mechanical ventilation, or death) of COVID-19 patients were compared. The correlation analysis and cox/logistic regression modeling of menstruation status/sex hormones and prognosis were conducted. Correlation between cytokines related to immunity and inflammation and disease severity or estradiol (E2) was revealed.\n\nResultsChi square test indicated significant differences in distribution of composite endpoints (p<0.01) and disease severity (p=0.05) between male and female patients (n=1902). 435 female COVID-19 patients with menstruation records were recruited. By the end of Mar 8, 111 patients recovered and discharged (25.3%). Multivariate Cox regression model adjusted for age and severity indicated that post-menopausal patients show the greater risk of hospitalization time than non-menopausal patients (relative hazard [RH], 1.91; 95% confidence interval [CI], 1.06-3.46) Logistic regression model showed that higher anti-mullerian hormone (AMH) as a control for age increases the risk of severity of COVID-19 (HR=0.146,95%CI = (0.026-0.824) p=0.029). E2 showed protective effect against disease severity (HR= 0.335, 95%CI = (0.105-1.070), p= 0.046). In the Mann-Whitney U test, the higher levels of IL6 and IL8 were found in severe group (p= 0.040, 0.033). The higher levels of IL2R, IL6, IL8 and IL10 were also observed in patients with composite end points (p<0.001, <0.001, 0.009, 0.040). E2 levels were negatively correlated with IL2R, IL6, IL8 and TNF in luteal phase (Pearson Correlation=-0.592, -0.558, -0.545, -0.623; p=0.033, 0.048, 0.054, 0.023) and with C3 in follicular phase (Pearson Correlation=-0.651; p=0.030).\n\nConclusions and RelevanceMenopause is an independent risk factor for COVID-19. E2 and AMH are negatively correlated with COVID-19s severity probably due to their regulation of cytokines related to immunity and inflammation.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSAny differences in the outcomes between hospitalized female and male COVID-19 patients? If so, why?\n\nFindingsFemale patients display better prognosis than male patients. Non-menopausal women have shorter length of hospital stays, and AMH and E2 are negatively correlated with COVID-19s severity. There is a negative correlation between E2 and the levels of IL6, IL8, IL2R and TNF-, which are significantly correlated with disease severity or composite endpoint.\n\nMeaningNon-menopause and female sex hormones, especially E2 and AMH, are potential protective factors for females COVID-19 patients. E2 supplements could be potentially used for COVID-19 patients.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Ting Ding", - "author_inst": "Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; National Clinical Research Cent" - }, - { - "author_name": "Jinjin Zhang", - "author_inst": "Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; National Clinical Research Cent" - }, - { - "author_name": "Tian Wang", - "author_inst": "Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; National Clinical Research Cent" - }, - { - "author_name": "Pengfei Cui", - "author_inst": "Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; National Clinical Research Cent" - }, - { - "author_name": "Zhe Chen", - "author_inst": "Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; National Clinical Research Cent" - }, - { - "author_name": "Jingjing Jiang", - "author_inst": "Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; National Clinical Research Cent" - }, - { - "author_name": "Su Zhou", - "author_inst": "Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; National Clinical Research Cent" - }, - { - "author_name": "Jun Dai", - "author_inst": "Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; National Clinical Research Cent" - }, - { - "author_name": "Bo Wang", - "author_inst": "Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; National Clinical Research Cent" - }, - { - "author_name": "Suzhen Yuan", - "author_inst": "Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; National Clinical Research Cent" - }, - { - "author_name": "Wenqing Ma", - "author_inst": "Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; National Clinical Research Cent" - }, - { - "author_name": "Lingwei Ma", - "author_inst": "Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; National Clinical Research Cent" - }, - { - "author_name": "Yueguang Rong", - "author_inst": "Department of Pathogen Biology, School of Basic Medicine, Huazhong University of Science and Technology, Wuhan, 430030, China" - }, - { - "author_name": "Jiang Chang", - "author_inst": "Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of" - }, - { - "author_name": "Xiaoping Miao", - "author_inst": "Department of Epidemiology and Biostatistics, Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of" - }, - { - "author_name": "Xiangyi Ma", - "author_inst": "Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; National Clinical Research Cent" - }, - { - "author_name": "Shixuan Wang", - "author_inst": "Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; National Clinical Research Cent" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.27.20043661", "rel_title": "Clinical characteristics associated with COVID-19 severity in California", @@ -1556626,6 +1559511,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.27.20045252", + "rel_title": "Estimation of protection for COVID-19 in children from epidemiological information and estimate effect of policy in Japan", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20045252", + "rel_abs": "BackgroundIncidence in children was much less than in adults during the COVID-19 outbreak. Sports and entertainment events were canceled (VEC) in Japan for two weeks during 26 February - 13 March. Most schools were closed (SC).\n\nObjectWe construct a susceptible-infected-recovered model using three age classes and estimate the basic reproduction number (R0) and protection level among children simultaneously. Then we simulate SC and VEC effects.\n\nMethodWe used data of patients with symptoms in Japan during 14 January to assess SC and VEC introduction. Effects of SC and VEC were incorporated into the model through change in the contact pattern or frequencies among age classes.\n\nResultsResults suggest R0 as 2.86 [95%CI of 2.73, 2.97]. The protection level was estimated as 0.4 [0.2, 0.7]. SC and VEC can reduce the total number of patients significantly, by 6-7%.\n\nDiscussion and ConclusionThe estimated R0 was similar to that found from other studies in China and Japan. We found a significant protection level among children, and by effects of SC and VEC. Introduction", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Junko Kurita", + "author_inst": "Center for Medical Sciences, Ibaraki Prefectural University of Health Sciences, Ibaraki, Japan" + }, + { + "author_name": "Yoshiyuki Sugishita", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + }, + { + "author_name": "Tamie Sugawara", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + }, + { + "author_name": "Yasushi Ohkusa", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.03.27.20044958", "rel_title": "Research on the Influence of Effective Distance Between Cities on the Cross-regional Transmission of COVID-19", @@ -1556759,85 +1559675,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.24.20042374", - "rel_title": "What is required to prevent a second major outbreak of the novel coronavirus SARS-CoV-2 upon lifting the metropolitan-wide quarantine of Wuhan city, China", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042374", - "rel_abs": "BackgroundThe Chinese government implemented a metropolitan-wide quarantine of Wuhan city on 23rd January 2020 to curb the epidemic of the coronavirus COVID-19. Lifting of this quarantine is imminent. We modelled the effects of two key health interventions on the epidemic when the quarantine is lifted.\n\nMethodWe constructed a compartmental dynamic model to forecast the trend of the COVID-19 epidemic at different quarantine lifting dates and investigated the impact of different rates of public contact and facial mask usage on the epidemic.\n\nResultsWe estimated that at the end of the epidemic, a total of 65,572 (46,156-95,264) individuals would be infected by the virus, among which 16,144 (14,422-23,447, 24.6%) would be infected through public contacts, 45,795 (32,390-66,395, 69.7%) through household contact, 3,633 (2,344-5,865, 5.5%) through hospital contacts (including 783 (553-1,134) non-COVID-19 patients and 2,850 (1,801-4,981) medical staff members). A total of 3,262 (1,592-6,470) would die of COVID-19 related pneumonia in Wuhan. For an early lifting date (21st March), facial mask needed to be sustained at a relatively high rate ([≥]85%) if public contacts were to recover to 100% of the pre-quarantine level. In contrast, lifting the quarantine on 18th April allowed public person-to-person contact adjusted back to the pre-quarantine level with a substantially lower level of facial mask usage (75%). However, a low facial mask usage (<50%) combined with an increased public contact (>100%) would always lead a significant second outbreak in most quarantine lifting scenarios. Lifting the quarantine on 25th April would ensure a smooth decline of the epidemics regardless of the combinations of public contact rates and facial mask usage.\n\nConclusionThe prevention of a second epidemic is viable after the metropolitan-wide quarantine is lifted but requires a sustaining high facial mask usage and a low public contact rate.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Lei Zhang", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Mingwang Shen", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Xiaomeng Ma", - "author_inst": "University of Toronto" - }, - { - "author_name": "Shu Su", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Wenfeng Gong", - "author_inst": "Bill and Melinda Gates Foundation" - }, - { - "author_name": "Jing Wang", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Yusha Tao", - "author_inst": "Monash University" - }, - { - "author_name": "Zhuoru Zou", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Rui Zhao", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Joseph Lau", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Wei Li", - "author_inst": "Southeast University" - }, - { - "author_name": "Feng Liu", - "author_inst": "10.\tShaanxi Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Kai Ye", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Youfa Wang", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Guihua Zhuang", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Christopher K Fairley", - "author_inst": "Monash University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.24.20042366", "rel_title": "Role of Chloroquine and Hydroxychloroquine in the Treatment of COVID-19 Infection- A Systematic Literature Review", @@ -1558044,6 +1560881,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2020.03.26.20044388", + "rel_title": "The more I fear about COVID-19, the more I wear medical masks: A survey on risk perception and medical masks uses", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044388", + "rel_abs": "The legal behaviors in using medical masks in public have been finally promulgated by the Vietnamese Government after 47 days since the WHO declared the Public Health Emergency of International Concern (PHEIC) due to the COVID-19 pandemic. From a sample of 345 Vietnamese respondents aged from 15 to 47 years, this brief note found that the risk perception of COVID-19 danger significantly increases the likelihood of wearing the medical masks. In addition, there is a weak evidence about the differences in age under the COVID-19 outbreaks. More noticeably, those who use masks before COVID-19 pandemic tend to maintain their behaviors. Our results offer the insightful into Vietnamese citizens responses in terms of using medical masks; even the uses of this method are still controversial. Our results are robust by performing Exploratory Factor Analysis for five features and further regressions.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Toan D Huynh", + "author_inst": "University of Economics HCMC" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.03.28.20046110", "rel_title": "Which Measures are Effective in Containing COVID-19?Empirical Research Based on Prevention and Control Cases in China", @@ -1558125,29 +1560981,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.03.25.20043331", - "rel_title": "A Machine Learning Model Reveals Older Age and Delayed Hospitalization as Predictors of Mortality in Patients with COVID-19", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.25.20043331", - "rel_abs": "ObjectiveThe recent pandemic of novel coronavirus disease 2019 (COVID-19) is increasingly causing severe acute respiratory syndrome (SARS) and significant mortality. We aim here to identify the risk factors associated with mortality of coronavirus infected persons using a supervised machine learning approach.\n\nResearch Design and MethodsClinical data of 1085 cases of COVID-19 from 13th January to 28th February, 2020 was obtained from Kaggle, an online community of Data scientists. 430 cases were selected for the final analysis. Random Forest classification algorithm was implemented on the dataset to identify the important predictors and their effects on mortality.\n\nResultsThe Area under the ROC curve obtained during model validation on the test dataset was 0.97. Age was the most important variable in predicting mortality followed by the time gap between symptom onset and hospitalization.\n\nConclusionsPatients aged beyond 62 years are at higher risk of fatality whereas hospitalization within 2 days of the onset of symptoms could reduce mortality in COVID-19 patients.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Jit Sarkar", - "author_inst": "CSIR-Indian Institute of Chemical Biology" - }, - { - "author_name": "Partha Chakrabarti", - "author_inst": "CSIR-Indian Institute of Chemical Biology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.25.006213", "rel_title": "Comparative Genomic Analysis of Rapidly Evolving SARS CoV-2 Viruses Reveal Mosaic Pattern of Phylogeographical Distribution", @@ -1559370,6 +1562203,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.26.20044651", + "rel_title": "A deductive approach to modeling the spread of COVID-19", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044651", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), previously known as 2019-nCoV, is responsible for the atypical pneumonia pandemic designated as Coronavirus Disease 2019 (COVID-19). The number of cases continues to grow exponentially reaching 492,000 people in 175 countries as of March 25, 2020. 22,169 people ([~]4.5%) infected with SARS-COV-2 virus have died. We have developed an exponential regression model using the COVID-19 case data (Jan 22 - Mar 22, 2020). Our primary model uses designated Phase 1 countries, who exceed 2500 cases on Mar 22. The model is then applied to Phase 2 countries: those that escaped the initial Phase 1 global expansion of COVID-19. With the exception of stabilizing countries (South Korea, Japan, and Iran) all Phase 1 countries are growing exponentially, as per I2500(t) = 120.4 x e0.238t, with a rate, r = 0.238 {+/-} 0.068. Excluding China, the BRICS developing nations and Australia are in Phase 2. Case data from Phase 2 countries are following the model derived from Phase 1 countries. In the absence of measures employed to flatten the curve including social distancing, quarantine, and healthcare expansion, our model projects over 274,000 cases and 12,300 deaths in the US by Mar 31. India can expect 123,000 cases by April 16. By flattening the curve to the growth rate of stabilizing countries (r = 0.044 {+/-} 0.062), the US would prevent 8,500 deaths by Mar 31, and India would prevent 5,500 deaths by April 16.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Pranav Kumar Mishra", + "author_inst": "Kasturba Medical College, Manipal; Manipal Academy of Higher Education" + }, + { + "author_name": "Shekhar Mishra", + "author_inst": "Discovery Science and Innovation Management" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.25.20043927", "rel_title": "Dangers of ACE inhibitor and ARB usage in COVID-19: evaluating the evidence", @@ -1559435,29 +1562291,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.03.28.20044578", - "rel_title": "Government Responses Matter: Predicting Covid-19 cases in US under an empirical Bayesian time series framework", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.28.20044578", - "rel_abs": "Since the Covid-19 outbreak, researchers have been predicting how the epidemic will evolve, especially the number in each country, through using parametric extrapolations based on the history. In reality, the epidemic progressing in a particular country depends largely on its policy responses and interventions. Since the outbreaks in some countries are earlier than United States, the prediction of US cases can benefit from incorporating the similarity in their trajectories. We propose an empirical Bayesian time series framework to predict US cases using different countries as prior reference. The resultant forecast is based on observed US data and prior information from the reference country while accounting for different population sizes. When Italy is used as prior in the prediction, which the US data resemble the most, the cases in the US will exceed 300,000 by the beginning of April unless strong measures are adopted.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ziyue Liu", - "author_inst": "Indiana University" - }, - { - "author_name": "Wensheng Guo", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.03.27.20044495", "rel_title": "An alternative workflow for molecular detection of SARS-CoV-2 - escape from the NA extraction kit-shortage", @@ -1560708,6 +1563541,29 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2020.03.26.009605", + "rel_title": "Re-analysis of SARS-CoV-2 infected host cell proteomics time-course data by impact pathway analysis and network analysis. A potential link with inflammatory response.", + "rel_date": "2020-03-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.26.009605", + "rel_abs": "The disease known as coronavirus disease 19 (COVID-19), potentially caused by an outbreak of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in Wuhan, China, has hit the world hard, and has led to an unprecedent health and economic crisis. In order to develop treatment options able to stop or ameliorate SARS-CoV-2 effects, we need to understand the biology of the virus inside cells, but this kind of studies are still scarce. A recent study investigated translatome and proteome host cell changes induced in vitro by SARS-CoV-2. In the present study, we use the publicly available proteomics data from this study to re-analyze the mechanisms altered by the virus infection by impact pathways analysis and network analysis. Proteins linked to inflammatory response, but also proteins related to chromosome segregation during mitosis, were found to be regulated. The up-regulation of the inflammatory-related proteins observed could be linked to the propagation of inflammatory reaction and lung injury that is observed in advanced stages of COVID-19 patients.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ignacio Ortea", + "author_inst": "Instituto de Investigacion e Innovacion Biomedica de Cadiz (INiBICA)" + }, + { + "author_name": "Jens-Ole Bock", + "author_inst": "Cobo Technologies Aps" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.03.27.012906", "rel_title": "RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses", @@ -1560777,57 +1563633,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2020.03.22.20040923", - "rel_title": "Scarce COVID-19 Testing Capabilities at Urgent Care Centers in States with Greatest Disease Burden", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.22.20040923", - "rel_abs": "As of March 22, 2020, the number of confirmed COVID-19 cases in the U.S. has reached nearly 30,000.1 While rapid and accessible diagnosis is paramount to monitoring and reducing the spread of disease, COVID-19 testing capabilities across the U.S. remain constrained. For many individuals, urgent care centers (UCCs) may offer the most accessible avenue to be tested. Using a phone survey, we describe the COVID-19 testing capabilities of UCCs in states with the greatest disease burden.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Walter R Hsiang", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Howard P Forman", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Siddharth Jain", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Akshay Khunte", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Grace Jin", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Laurie Yousman", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Alison Mosier-Mills", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Michael Najem", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Daniel Wiznia", - "author_inst": "Yale School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.03.23.20041814", "rel_title": "Population-Level Mortality Rates from Novel Coronavirus (COVID-19) in South Korea", @@ -1562206,6 +1565011,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.24.20042234", + "rel_title": "Mechanical Ventilator Milano (MVM):A Novel Mechanical Ventilator Designed for Mass Scale Production in response to the COVID-19 Pandemics", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042234", + "rel_abs": "We present here the design of the Mechanical Ventilator Milano (MVM), a novel mechanical ventilator designed for mass scale production in response to the COVID-19 pandemics, to compensate for the dramatic shortage of such ventilators in many countries. This ventilator is an electro-mechanical equivalent of the old, reliable Manley Ventilator. Our design is optimized to permit large sale production in short time and at a limited cost, relying on off-the-shelf components, readily available worldwide from hardware suppliers. Operation of the MVM requires only a source of compressed oxygen (or compressed medical air) and electrical power. The MVM control and monitoring unit can be connected and networked via WiFi so that no additional electrical connections are necessary other than the connection to the electrical power.\n\nAt this stage the MVM is not a certified medical device. Construction of the first prototypes is starting with a team of engineers, scientists and computing experts. The purpose of this paper is to disseminate the conceptual design of the MVM broadly and to solicit feed-back from the scientific and medical community to speed the process of review, improvement and possible implementation.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Galbiati Cristiano", + "author_inst": "Physics Department, Princeton University, Princeton, NJ 08544, USA" + }, + { + "author_name": "Walter Bonivento", + "author_inst": "INFN Cagliari, Cagliari 09042, Italy" + }, + { + "author_name": "Mauro Caravati", + "author_inst": "INFN Cagliari, Cagliari 09042, Italy" + }, + { + "author_name": "Marco Razeti", + "author_inst": "INFN Cagliari, Cagliari 09042, Italy" + }, + { + "author_name": "Sandro DeCecco", + "author_inst": "Physics Department, Sapienza Universit`a di Roma, Roma 00185, Italy and INFN Sezione di Roma, Roma 00185, Italy" + }, + { + "author_name": "Giuliana Fiorillo", + "author_inst": "Physics Department, Universita degli Studi Federico II di Napoli, Napoli 80126, Italy and INFN Napoli, Napoli 80126, Italy" + }, + { + "author_name": "Federico Gabriele", + "author_inst": "INFN Laboratori Nazionali del Gran Sasso, Assergi (AQ) 67100, Italy" + }, + { + "author_name": "Roberto Tartaglia", + "author_inst": "INFN Laboratori Nazionali del Gran Sasso, Assergi (AQ) 67100, Italy" + }, + { + "author_name": "Alessandro Razeto", + "author_inst": "INFN Laboratori Nazionali del Gran Sasso, Assergi (AQ) 67100, Italy" + }, + { + "author_name": "Davide Sablone", + "author_inst": "INFN Laboratori Nazionali del Gran Sasso, Assergi (AQ) 67100, Italy" + }, + { + "author_name": "Eugenio Scapparone", + "author_inst": "INFN Bologna, Bologna 40126, Italy" + }, + { + "author_name": "Gemma Testera", + "author_inst": "INFN Genova, Genova 16146, Italy" + }, + { + "author_name": "Marco Rescigno", + "author_inst": "INFN Sezione di Roma, Roma 00185, Italy" + }, + { + "author_name": "Davide Franco", + "author_inst": "APC, Universite Paris Diderot, CNRS/IN2P3, CEA/Irfu, Obs de Paris, USPC, Paris 75205, France" + }, + { + "author_name": "Iza Kochanek", + "author_inst": "INFN Laboratori Nazionali del Gran Sasso, Assergi (AQ) 67100, Italy" + }, + { + "author_name": "Cary Kendziora", + "author_inst": "Fermi National Accelerator Laboratory, Batavia, IL 60510, USA" + }, + { + "author_name": "Stephen H. Pordes", + "author_inst": "Fermi National Accelerator Laboratory, Batavia, IL 60510, USA" + }, + { + "author_name": "Hanguo Wang", + "author_inst": "Physics and Astronomy Department, University of California, Los Angeles, CA 90095, USA" + }, + { + "author_name": "Andrea Ianni", + "author_inst": "Physics Department, Princeton University, Princeton, NJ 08544, USA" + }, + { + "author_name": "Art McDonald", + "author_inst": "Department of Physics, Engineering Physics and Astronomy, Queen s University, Kingston, ON K7L 3N6, Canada" + }, + { + "author_name": "L. Molinari Tosatti", + "author_inst": "CNR STIIMA, Milano 20133, Italy" + }, + { + "author_name": "T. Dinon", + "author_inst": "CNR STIIMA, Milano 20133, Italy" + }, + { + "author_name": "M. Malosio", + "author_inst": "CNR STIIMA, Milano 20133, Italy" + }, + { + "author_name": "D. Minuzzo", + "author_inst": "AZ Pneumatica S.r.l., Misinto (MB) 20826, Italy" + }, + { + "author_name": "A. Zardoni", + "author_inst": "AZ Pneumatica S.r.l., Misinto (MB) 20826, Italy" + }, + { + "author_name": "A. Prini", + "author_inst": "CNR STIIMA, Milano 20133, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.03.23.004176", "rel_title": "Structure-based modeling of SARS-CoV-2 peptide/HLA-A02 antigens", @@ -1562347,29 +1565271,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.03.24.006007", - "rel_title": "Automatic Identification of SARS Coronavirus using Compression-Complexity Measures", - "rel_date": "2020-03-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.24.006007", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWFinding vaccine or specific antiviral treatment for global pandemic of virus diseases (such as the ongoing COVID-19) requires rapid analysis, annotation and evaluation of metagenomic libraries to enable a quick and efficient screening of nucleotide sequences. Traditional sequence alignment methods are not suitable and there is a need for fast alignment-free techniques for sequence analysis. Information theory and data compression algorithms provide a rich set of mathematical and computational tools to capture essential patterns in biological sequences. In 2013, our research group (Nagaraj et al., Eur. Phys. J. Special Topics 222(3-4), 2013) has proposed a novel measure known as Effort-To-Compress (ETC) based on the notion of compression-complexity to capture the information content of sequences. In this study, we propose a compression-complexity based distance measure for automatic identification of SARS coronavirus strains from a set of viruses using only short fragments of nucleotide sequences. We also demonstrate that our proposed method can correctly distinguish SARS-CoV-2 from SARS-CoV-1 viruses by analyzing very short segments of nucleotide sequences. This work could be extended further to enable medical practitioners in automatically identifying and characterizing SARS coronavirus strain in a fast and efficient fashion using short and/or incomplete segments of nucleotide sequences. Potentially, the need for sequence assembly can be circumvented.\n\nNoteThe main ideas and results of this research were first presented at the International Conference on Nonlinear Systems and Dynamics (CNSD-2013) held at Indian Institute of Technology, Indore, December 12, 2013. In this manuscript, we have extended our preliminary analysis to include SARS-CoV-2 virus as well.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Karthi Balasubramanian", - "author_inst": "Amrita School of Engineering, Coimbatore" - }, - { - "author_name": "Nithin Nagaraj", - "author_inst": "National Institute of Advanced Studies" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.03.24.006197", "rel_title": "In-Silico evidence for two receptors based strategy of SARS-CoV-2", @@ -1563556,6 +1566457,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.03.23.20041889", + "rel_title": "Coincidence of COVID-19 epidemic and olfactory dysfunction outbreak", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.23.20041889", + "rel_abs": "BackgroundRecent surge of olfactory dysfunction in patients who were referred to ENT clinics and concurrent COVID-19epidemic in Iran motivated us to evaluate anosmic/hyposmic patients to find any relation between these two events.\n\nMethodsThis is a cross-sectional study with an online checklist on voluntary cases in all provinces of Iran between the 12th and 17th March, 2020. Cases was defined as self-reported anosmia/hyposmia in responders fewer than 4 weeks later (from start the of COVID-19 epidemic in Iran). Variables consist of clinical presentations, related past medical history, family history of recent respiratory tract infection and hospitalization.\n\nResultsIn this study 10069 participants aged 32.5{+/-}8.6 (7-78) years, 71.13% female and 81.68% non-smoker completed online checklist. They reported 10.55% a history of a trip out of home town and 1.1% hospitalization due to respiratory problems recently. From family members 12.17% had a history of severe respiratory disease in recent days and 48.23% had anosmia/hyposmia.\n\nCorrelation between the number of olfactory disorder and reported COVID-19 patients in all 31 provinces till 16th March 2020 was highly significant (Spearman correlation coefficient=0.87, p-Value<0.001). The onset of anosmia was sudden in 76.24% and till the time of filling the questionnaire in 60.90% of patients decreased sense of smell was constant. Also 83.38 of this patients had decreased taste sensation in association with anosmia.\n\nConclusionsIt seems that we have a surge in outbreak of olfactory dysfunction happened in Iran during the COVID-19 epidemic. The exact mechanism of anosmia/hyposmia in COVID-19 patients needs further investigations.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Seyed Hamid Reza Bagheri", + "author_inst": "ENT and Head & Neck Research center and department, The five senses Institute, Iran University of Medical Sciences" + }, + { + "author_name": "Ali Mohammad Asghari", + "author_inst": "Skull base research center, The five senses institute, Iran University of Medical Sciences" + }, + { + "author_name": "Mohammad Farhadi", + "author_inst": "ENT and Head & Neck Research center and department, The five senses Institute, Iran University of Medical Sciences" + }, + { + "author_name": "Ahmad Reza Shamshiri", + "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences" + }, + { + "author_name": "Ali Kabir", + "author_inst": "Minimally Invasive Surgery Research Center, Iran University of Medical Sciences" + }, + { + "author_name": "Seyed Kamran Kamrava", + "author_inst": "ENT and Head & Neck Research center and department, The five senses Institute, Iran University of Medical Sciences" + }, + { + "author_name": "Maryam Jalessi", + "author_inst": "Skull base research center, The five senses institute, Iran University of Medical Sciences" + }, + { + "author_name": "Alireza Mohebbi", + "author_inst": "ENT and Head & Neck Research center and department, The five senses Institute, Iran University of Medical Sciences" + }, + { + "author_name": "Rafieh Alizadeh", + "author_inst": "ENT and Head & Neck Research center and department, The five senses Institute, Iran University of Medical Sciences, Tehran" + }, + { + "author_name": "Ali Asghar Honarmand", + "author_inst": "Electronic learning Committee, Iran Medical Council" + }, + { + "author_name": "Babak Ghalehbaghi", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Alireza Salimi", + "author_inst": "Department of anesthesiology, Shahid Beheshti University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "otolaryngology" + }, { "rel_doi": "10.1101/2020.03.24.20042796", "rel_title": "Reproducibility and reporting practices in COVID-19 preprint manuscripts", @@ -1563705,81 +1566669,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.26.20039438", - "rel_title": "Evaluation of COVID-19 RT-qPCR test in multi-sample pools", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20039438", - "rel_abs": "The recent emergence of SARS-CoV-2 lead to a current pandemic of unprecedented levels. Though diagnostic tests are fundamental to the ability to detect and respond, many health systems are already experiencing shortages of reagents associated with this test. Here, testing a pooling approach for the standard RT-qPCR test, we find that a single positive sample can be detected even in pools of up to 32 samples, with an estimated false negative rate of 10%. Detection of positive samples diluted in even up to 64 samples may also be attainable, though may require additional amplification cycles. As it uses the standard protocols, reagents and equipment, this pooling method can be applied immediately in current clinical testing laboratories. We hope that such implementation of a pool test for COVID-19 would allow expanding current screening capacities thereby enabling the expansion of detection in the community, as well as in close integral groups, such as hospital departments, army units, or factory shifts.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Idan Yelin", - "author_inst": "Technion - Israel Institute of Technology" - }, - { - "author_name": "Noga Aharony", - "author_inst": "Technion - Israel Institute of Technology" - }, - { - "author_name": "Einat Shaer-Tamar", - "author_inst": "Technion - Israel Institute of Technology" - }, - { - "author_name": "Amir Argoetti", - "author_inst": "Technion - Israel Institute of Technology" - }, - { - "author_name": "Esther Messer", - "author_inst": "Technion - Israel Institute of Technology" - }, - { - "author_name": "Dina Berenbaum", - "author_inst": "Technion - Israel Institute of Technology" - }, - { - "author_name": "Einat Shafran", - "author_inst": "Rambam Health Care Campus" - }, - { - "author_name": "Areen Kuzli", - "author_inst": "Rambam Health Care Campus" - }, - { - "author_name": "Nagam Gandali", - "author_inst": "Rambam Health Care Campus" - }, - { - "author_name": "Tamar Hashimshony", - "author_inst": "Technion - Israel Institute of Technology" - }, - { - "author_name": "Yael Mandel-Gutfreund", - "author_inst": "Technion - Israel Institute of Technology" - }, - { - "author_name": "Michael Halberthal", - "author_inst": "Rambam Health Care Campus" - }, - { - "author_name": "Yuval Geffen", - "author_inst": "Rambam Health Care Campus" - }, - { - "author_name": "Moran Szwarcwort-Cohen", - "author_inst": "Rambam Health Care Campus" - }, - { - "author_name": "Roy Kishony", - "author_inst": "Technion - Israel Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.23.20041608", "rel_title": "Multiple-Input Deep Convolutional Neural Network Model for COVID-19 Forecasting in China", @@ -1565130,6 +1568019,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.24.20042291", + "rel_title": "Fundamental principles of epidemic spread highlight the immediate need forlarge-scale serological surveys to assess the stage of the SARS-CoV-2 epidemic", + "rel_date": "2020-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042291", + "rel_abs": "The spread of a novel pathogenic infectious agent eliciting protective immunity is typically characterised by three distinct phases: (I) an initial phase of slow accumulation of new infections (often undetectable), (II) a second phase of rapid growth in cases of infection, disease and death, and (III) an eventual slow down of transmission due to the depletion of susceptible individuals, typically leading to the termination of the (first) epidemic wave. Before the implementation of control measures (e.g. social distancing, travel bans, etc) and under the assumption that infection elicits protective immunity, epidemiological theory indicates that the ongoing epidemic of SARS-CoV-2 will conform to this pattern.\n\nHere, we calibrate a susceptible-infected-recovered (SIR) model to data on cumulative reported SARS-CoV-2 associated deaths from the United Kingdom (UK) and Italy under the assumption that such deaths are well reported events that occur only in a vulnerable fraction of the population. We focus on model solutions which take into consideration previous estimates of critical epidemiological parameters such as the basic reproduction number (R0), probability of death in the vulnerable fraction of the population, infectious period and time from infection to death, with the intention of exploring the sensitivity of the system to the actual fraction of the population vulnerable to severe disease and death.\n\nOur simulations are in agreement with other studies that the current epidemic wave in the UK and Italy in the absence of interventions should have an approximate duration of 2-3 months, with numbers of deaths lagging behind in time relative to overall infections. Importantly, the results we present here suggest the ongoing epidemics in the UK and Italy started at least a month before the first reported death and have already led to the accumulation of significant levels of herd immunity in both countries. There is an inverse relationship between the proportion currently immune and the fraction of the population vulnerable to severe disease.\n\nThis relationship can be used to determine how many people will require hospitalisation (and possibly die) in the coming weeks if we are able to accurately determine current levels of herd immunity. There is thus an urgent need for investment in technologies such as virus (or viral pseudotype) neutralization assays and other robust assays which provide reliable read-outs of protective immunity, and for the provision of open access to valuable data sources such as blood banks and paired samples of acute and convalescent sera from confirmed cases of SARS-CoV-2 to validate these. Urgent development and assessment of such tests should be followed by rapid implementation at scale to provide real-time data. These data will be critical to the proper assessment of the effects of social distancing and other measures currently being adopted to slow down the case incidence and for informing future policy direction.\n\nDisclaimer(a) This material is not final and is subject to be updated any time. (b) Code used will be made available as soon as possible. (c) Contact for press enquiries: Cairbre Sugrue, cairbre@sugruecomms.com, +44 (0)7502 203 769.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jose Lourenco", + "author_inst": "University of Oxford" + }, + { + "author_name": "Robert Paton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Craig Thompson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Paul Klenerman", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sunetra Gupta", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.24.20042705", "rel_title": "Mathematical modeling of COVID-19 transmission and mitigation strategies in the population of Ontario, Canada", @@ -1565227,165 +1568151,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.25.20043828", - "rel_title": "Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology", - "rel_date": "2020-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.25.20043828", - "rel_abs": "Since its emergence and detection in Wuhan, China in late 2019, the novel coronavirus SARS-CoV-2 has spread to nearly every country around the world, resulting in hundreds of thousands of infections to date. The virus was first detected in the Pacific Northwest region of the United States in January, 2020, with subsequent COVID-19 outbreaks detected in all 50 states by early March. To uncover the sources of SARS-CoV-2 introductions and patterns of spread within the U.S., we sequenced nine viral genomes from early reported COVID-19 patients in Connecticut. Our phylogenetic analysis places the majority of these genomes with viruses sequenced from Washington state. By coupling our genomic data with domestic and international travel patterns, we show that early SARS-CoV-2 transmission in Connecticut was likely driven by domestic introductions. Moreover, the risk of domestic importation to Connecticut exceeded that of international importation by mid-March regardless of our estimated impacts of federal travel restrictions. This study provides evidence for widespread, sustained transmission of SARS-CoV-2 within the U.S. and highlights the critical need for local surveillance.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Joseph R Fauver", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Mary E. Petrone", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Emma B Hodcroft", - "author_inst": "University of Basel" - }, - { - "author_name": "Kayoko Shioda", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Hanna Y Ehrlich", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Alexander G. Watts", - "author_inst": "BlueDot" - }, - { - "author_name": "Chantal B.F. Vogels", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Anderson F. Brito", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Tara Alpert", - "author_inst": "Yale University" - }, - { - "author_name": "Anthony Muyombwe", - "author_inst": "Connecticut State Department of Public Health" - }, - { - "author_name": "Jafar Razeq", - "author_inst": "Connecticut State Department of Public Health" - }, - { - "author_name": "Randy Downing", - "author_inst": "Connecticut State Department of Public Health" - }, - { - "author_name": "Nagarjuna R. Cheemarla", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Anne L Wyllie", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Chaney C. Kalinich", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Isabel Ott", - "author_inst": "Yale University" - }, - { - "author_name": "Josh Quick", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Nicholas J. Loman", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Karla M. Neugebauer", - "author_inst": "Yale University" - }, - { - "author_name": "Alexander L. Greninger", - "author_inst": "University of Washington" - }, - { - "author_name": "Keith R. Jerome", - "author_inst": "University of Washington" - }, - { - "author_name": "Pavitra Roychoundhury", - "author_inst": "University of Washington" - }, - { - "author_name": "Hong Xie", - "author_inst": "University of Washington" - }, - { - "author_name": "Lasata Shrestha", - "author_inst": "University of Washington" - }, - { - "author_name": "Meei-Li Huang", - "author_inst": "University of Washington" - }, - { - "author_name": "Virginia E. Pitzer", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Akiko Iwasaki", - "author_inst": "Yale University" - }, - { - "author_name": "Saad B. Omer", - "author_inst": "Yale Institute of Global Health" - }, - { - "author_name": "Kamran Khan", - "author_inst": "BlueDot" - }, - { - "author_name": "Isaac Bogoch", - "author_inst": "University of Toronto" - }, - { - "author_name": "Richard A. Martinello", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Ellen F. Foxman", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Marie-Louise Landry", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Richard A Neher", - "author_inst": "University of Basel" - }, - { - "author_name": "Albert I Ko", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Nathan D. Grubaugh", - "author_inst": "Yale School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.03.24.20042432", "rel_title": "Early chest computed tomography to diagnose COVID-19 from suspected patients: A multicenter retrospective study", @@ -1566812,6 +1569577,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.21.20040139", + "rel_title": "Tracking and forecasting milepost moments of the epidemic in the early-outbreak: framework and applications to the COVID-19", + "rel_date": "2020-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.21.20040139", + "rel_abs": "BackgroundThe outbreak of the 2019 novel coronavirus (COVID-19) has attracted global attention. In the early stage of the outbreak, the most important question concerns some meaningful milepost moments, including (1) the time when the number of daily confirmed cases decreases, (2) the time when the number of daily confirmed cases becomes smaller than that of the daily removed (recovered and death), (3) the time when the number of daily confirmed cases becomes zero, and (4) the time when the number of patients treated in hospital is zero, which indicates the end of the epidemic. Intuitively, the former two can be regarded as two important turning points which indicate the alleviation of epidemic to some extent, while the latter two as two \"zero\" points, respectively. Unfortunately, it is extremely difficult to make right and precise prediction due to the limited amount of available data at a early stage of the outbreak.\n\nMethodTo address it, in this paper, we propose a flexible framework incorporating the effectiveness of the government control to forecast the whole process of a new unknown infectious disease in its early-outbreak. Specially, we first establish the iconic indicators to characterize the extent of epidemic spread, yielding four periods of the whole process corresponding to the four meaningful milepost moments: two turning points and two \"zero\" points. Then we develop the tracking and forecasting procedure with mild and reasonable assumption. Finally we apply it to analyze and evaluate the COVID-19 using the public available data for mainland China beyond Hubei Province from the China Centers for Disease Control (CDC) during the period of Jan 29th, 2020, to Feb 29th, 2020, which shows the effectiveness of the proposed procedure.\n\nResultsResults show that our model can clearly outline the development of the epidemic at a very early stage. The first prediction results on Jan 29th reveal that the first and second milepost moments for mainland China beyond Hubei Province would appear on Jan 31st and Feb 14th respectively, which are only one day and three days behind the real world situations. Forecasting results indicate that the number of newly confirmed cases will become zero in the mid-late March, and the number of patients treated in the hospital will become zero between mid-March and mid-April in mainland China beyond Hubei Province. The framework proposed in this paper can help people get a general understanding of the epidemic trends in counties where COVID-19 are raging as well as any other outbreaks of new and unknown infectious diseases in the future.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Huiwen Wang", + "author_inst": "School of Economics and Management, Beihang University, Beijing, China" + }, + { + "author_name": "Yanwen Zhang", + "author_inst": "School of Economics and Management, Beihang University, Beijing, China" + }, + { + "author_name": "Shan Lu", + "author_inst": "School of Statistics and Mathematics, Central University of Finance and Economics, Beijing, China" + }, + { + "author_name": "Shanshan Wang", + "author_inst": "School of Economics and Management, Beihang University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.22.20034504", "rel_title": "High risk of infection caused posttraumatic stress symptoms in individuals with poor sleep quality: A study on influence of coronavirus disease (COVID-19) in China", @@ -1567005,25 +1569801,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.03.21.20031336", - "rel_title": "Characterizing occupations that cannot work from home: a means to identify susceptible worker groups during the COVID-19 pandemic", - "rel_date": "2020-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.21.20031336", - "rel_abs": "ObjectivesNot all workers are employed in occupations in which working from home is possible. These workers are at an increased risk for exposure to infectious disease during a pandemic event, and are more likely to experience events of job displacement and disruption during all types of public health emergencies. Here, I characterized which occupational sectors in the United States are most able to work from home during a public health emergency such as COVID-19.\n\nMethods2018 national employment and wage data maintained by the U.S. Bureau of Labor Statistics (BLS) was merged with measures from the BLS O*NET survey data. The measures utilized rank the importance of using a computer at work, and the importance of working with or performing for the public, which relate to the ability to complete work at home.\n\nResultsAbout 25% (35.6 M) of the U.S. workforce are employed in occupations which could be done from home, primarily in sectors such as technology, computer, management, administrative, financial, and engineering. The remaining 75% of U.S. workers (including healthcare, manufacturing, retail and food services, et al.) are employed in occupations where working from home would be difficult.\n\nConclusionsThe majority of U.S. workers are employed in occupations that cannot be done at home, putting 108.4 M U.S. workers at increased risk for adverse health outcomes related to working during a public health emergency. These workers tend to be lower paid than workers who can work from home. During COVID-19, this could result in a large increase in the burden of mental health disorders in the U.S., in addition to increased cases of COVID-19 due to workplace transmission. Public health guidance to \"work from home\" is not applicable to the majority of the U.S. workforce, emphasizing the need for additional guidance for workers during public health emergencies.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Marissa G. Baker", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.03.21.20037051", "rel_title": "Infection Control of 2019 Novel Corona Virus Disease (COVID-19) in Cancer Patients undergoing Radiotherapy in Wuhan", @@ -1568470,6 +1571247,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.19.20032532", + "rel_title": "Geo temporal distribution of 1,688 Chinese healthcare workers infected with COVID-19 in severe conditions, a secondary data analysis", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.19.20032532", + "rel_abs": "IntroductionThe COVID-19 outbreak is posing an unprecedented challenge to healthcare workers. This study analyzes the geo-temporal effects on disease severity for the 1,688 Chinese healthcare workers infected with COVID-19.\n\nMethodUsing the descriptive results recently reported by the Chinese CDC, we compare the percentage of infected healthcare workers in severe conditions over time and across three areas in China, and the fatality rate of infected healthcare workers with all the infected individuals in China aged 22-59 years.\n\nResultsAmong the infected Chinese healthcare workers whose symptoms onset appeared during the same ten-day period, the percentage of those in severe conditions decreased statistical significantly from 19.7% (Jan 11 - 20) to 14.4% (Jan 21 - 31) to 8.7% (Feb 1 - 11). Across the country, there was also a significant difference in the disease severity among patients symptoms onset during the same period, with Wuhan being the most severe (17%), followed by Hubei Province (10.4%), and the rest of China (7.0%). The case fatality rate for the 1,688 infected Chinese healthcare workers was significantly lower than that for the 29,798 infected patients aged 20-59 years--0.3% (5/1,688) vs. 0.65% (193/29,798), respectively.\n\nConclusionThe disease severity improved considerably over a short period of time in China. The more severe conditions in Wuhan compared to the rest of the country may be attributable to the draconian lockdown. The clinical outcomes of infected Chinese healthcare workers may represent a more accurate estimation of the severity of COVID-19 for those who have access to quality healthcare.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Wayne Gao", + "author_inst": "Taipei Medical University" + }, + { + "author_name": "Mattia Sanna", + "author_inst": "Taipei Medical University" + }, + { + "author_name": "Chi Pang Wen", + "author_inst": "National Health Research Institute; China Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.19.20039404", "rel_title": "Healthcare worker absenteeism, child care costs, and COVID-19 school closures: a simulation analysis", @@ -1568587,53 +1571391,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.03.18.20038455", - "rel_title": "ACE-2 Expression in the Small Airway Epithelia of Smokers and COPD Patients: Implications for COVID-19", - "rel_date": "2020-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.18.20038455", - "rel_abs": "IntroductionCoronavirus disease 2019 (COVID-19) is a respiratory infection caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This virus uses the angiotensin converting enzyme II (ACE-2) as the cellular entry receptor to infect the lower respiratory tract. Because individuals with chronic obstructive pulmonary disease (COPD) are at increased risk of severe COVID-19, we determined whether ACE-2 expression in the lower airways was related to COPD and cigarette smoking.\n\nMethodsUsing RNA-seq, we determined gene expression levels in bronchial epithelia obtained from cytologic brushings of 6th to 8th generation airways in individuals with and without COPD. We eternally validated these results from two additional independent cohorts, which used microarray technologies to measure gene expression levels from 6th to 12th generation airways.\n\nResultsIn the discovery cohort (n=42 participants), we found that ACE-2 expression levels were increased by 48% in the airways of COPD compared with non-COPD subjects (COPD=2.52{+/-}0.66 log2 counts per million reads (CPM) versus non-COPD= 1.70{+/-}0.51 CPM, p=7.62x10-4). There was a significant inverse relationship between ACE-2 gene expression and FEV1% of predicted (r=-0.24; p=0.035). Current smoking also significantly increased ACE-2 expression levels compared with never smokers (never current smokers=2.77{+/-}0.91 CPM versus smokers=1.78{+/-}0.39 CPM, p=0.024). These findings were replicated in the two eternal cohorts.\n\nConclusionsACE-2 expression in lower airways is increased in patients with COPD and with current smoking. These data suggest that these two subgroups are at increased risk of serious COVID-19 infection and highlight the importance of smoking cessation in reducing the risk.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Janice M Leung", - "author_inst": "University of British Columbia (UBC) Centre for Heart Lung Innovation" - }, - { - "author_name": "Chen Xi Yang", - "author_inst": "University of British Columbia (UBC) Centre for Heart Lung Innovation" - }, - { - "author_name": "Anthony Tam", - "author_inst": "University of British Columbia (UBC) Centre for Heart Lung Innovation" - }, - { - "author_name": "Tawimas Shaipanich", - "author_inst": "Department of Medicine (Division of Respirology), University of British Columbia" - }, - { - "author_name": "Tillie L Hackett", - "author_inst": "Department of Anesthesia, Pharmacology and Therapeutics, University of British Columbia" - }, - { - "author_name": "Gurpreet K Singhera", - "author_inst": "University of British Columbia (UBC) Centre for Heart Lung Innovation" - }, - { - "author_name": "Delbert R Dorscheid", - "author_inst": "University of British Columbia (UBC) Centre for Heart Lung Innovation" - }, - { - "author_name": "Don D Sin", - "author_inst": "University of British Columbia (UBC) Centre for Heart Lung Innovation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.03.19.20038364", "rel_title": "Supervised Machine Learning for the Early Prediction of Acute Respiratory Distress Syndrome (ARDS)", @@ -1569892,6 +1572649,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.20.20039818", + "rel_title": "Potential Factors for Prediction of Disease Severity of COVID-19 Patients", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.20.20039818", + "rel_abs": "ObjectiveCoronavirus disease 2019 (COVID-19) is an escalating global epidemic caused by SARS-CoV-2, with a high mortality in critical patients. Effective indicators for predicting disease severity in SARS-CoV-2 infected patients are urgently needed.\n\nMethodsIn this study, 43 COVID-19 patients admitted in Chongqing Public Health Medical Center were involved. Demographic data, clinical features, and laboratory examinations were obtained through electronic medical records. Peripheral blood specimens were collected from COVID-19 patients and examined for lymphocyte subsets and cytokine profiles by flow cytometry. Potential contributing factors for prediction of disease severity were further analyzed.\n\nResultsA total of 43 COVID-19 patients were included in this study, including 29 mild patients and 14 sever patients. Severe patients were significantly older (61.9{+/-}9.4 vs 44.4{+/-}15.9) and had higher incidence in co-infection with bacteria compared to mild group (85.7%vs27.6%). Significantly more severe patients had the clinical symptoms of anhelation (78.6%) and asthma (71.4%). For laboratory examination, 57.1% severe cases showed significant reduction in lymphocyte count. The levels of Interluekin-6 (IL6), IL10, erythrocyte sedimentation rate (ESR) and D-Dimer (D-D) were significantly higher in severe patients than mild patients, while the level of albumin (ALB) was remarkably lower in severe patients. Further analysis demonstrated that ESR, D-D, age, ALB and IL6 were the major contributing factors for distinguishing severe patients from mild patients. Moreover, ESR was identified as the most powerful factor to predict disease progression of COVID-19 patients.\n\nConclusionAge and the levels of ESR, D-D, ALB and IL6 are closely related to the disease severity of COVID-19 patients. ESR can be used as a valuable indicator for distinguishing severe COVID-19 patients in early stage, so as to increase the survival of severe patients.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "huizheng zhang", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "xiaoying wang", + "author_inst": "Chongqing Medical and Pharmaceutical College" + }, + { + "author_name": "zongqiang fu", + "author_inst": "Henan Province hospital of traditional chinese" + }, + { + "author_name": "ming luo", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "zhen zhang", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "ke zhang", + "author_inst": "Chongqing emergency center" + }, + { + "author_name": "ying he", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "dongyong wan", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "liwen zhang", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "jing wang", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "xiaofeng yan", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "mei han", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "yaokai chen", + "author_inst": "Chongqing Public Health Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.21.001933", "rel_title": "SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability", @@ -1570381,45 +1573205,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2020.03.16.20036723", - "rel_title": "Building a COVID-19 Vulnerability Index", - "rel_date": "2020-03-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.16.20036723", - "rel_abs": "COVID-19 is an acute respiratory disease that has been classified as a pandemic by the World Health Organization. Characterization of this disease is still in its early stages; however, it is known to have high mortality rates, particularly among individuals with preexisting medical conditions. Creating models to identify individuals who are at the greatest risk for severe complications due to COVID-19 will be useful for outreach campaigns to help mitigate the diseases worst effects. While information specific to COVID-19 is limited, a model using complications due to other upper respiratory infections can be used as a proxy to help identify those individuals who are at the greatest risk. We present the results for three models predicting such complications, with each model increasing predictive effectiveness at the expense of ease of implementation.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Dave DeCaprio", - "author_inst": "ClosedLoop.ai" - }, - { - "author_name": "Joseph A Gartner III", - "author_inst": "ClosedLoop.ai" - }, - { - "author_name": "Thadeus Burgess", - "author_inst": "ClosedLoop.ai" - }, - { - "author_name": "Sarthak Kothari", - "author_inst": "ClosedLoop.ai" - }, - { - "author_name": "Shaayaan Sayed", - "author_inst": "ClosedLoop.ai" - }, - { - "author_name": "Carol J McCall", - "author_inst": "ClosedLoop.ai" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.20.000794", "rel_title": "COVID-19 Vaccine Candidates: Prediction and Validation of 174 SARS-CoV-2 Epitopes", @@ -1571810,6 +1574595,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.16.20036939", + "rel_title": "COVID-19: Forecasting short term hospital needs in France", + "rel_date": "2020-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.16.20036939", + "rel_abs": "1Europe is now considered as the epicenter of the SARS-CoV-2 pandemic, France being among the most impacted country. In France, there is an increasing concern regarding the capacity of the healthcare system to sustain the outbreak, especially regarding intensive care units (ICU). The aim of this study was to estimate the dynamics of the epidemic in France, and to assess its impact on healthcare resources for each French metropolitan Region. We developed a deterministic, age-structured, Susceptible-Exposed-Infectious-Removed (SEIR) model based on catchment areas of each COVID-19 referral hospitals. We performed one month ahead predictions (up to April 14, 2020) for three different scenarios (R0 = 1.5, R0 = 2.25, R0 = 3), where we estimated the daily number of COVID-19 cases, hospitalizations and deaths, the needs in ICU beds per Region and the reaching date of ICU capacity limits. At the national level, the total number of infected cases is expected to range from 22,872 in the best case (R0 = 1.5) to 161,832 in the worst case (R0 = 3), while the total number of deaths would vary from 1,021 to 11,032, respectively. At the regional level, all ICU capacities may be overrun in the worst scenario. Only seven Regions may lack ICU beds in the mild scenario (R0 = 2.25) and only one in the best case. In the three scenarios, Corse may be the first Region to see its ICU capacities overrun. The two other Regions, whose capacity will be overrun shortly after are Grand-Est and Bourgogne-Franche-Comte. Our analysis shows that, even in the best case scenario, the French healthcare system will very soon be overwhelmed. While drastic social distancing measures may temper our results, a massive reorganization leading to an expansion of French ICU capacities seems to be necessary to manage the coming wave of critically affected COVID-19 patients.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Cl\u00e9ment Massonnaud", + "author_inst": "Univ Rennes, EHESP, REPERES - EA 7449; Rouen University Hospital, Department of Biostatistics" + }, + { + "author_name": "Jonathan Roux", + "author_inst": "Univ Rennes, EHESP, REPERES - EA 7449" + }, + { + "author_name": "Pascal Cr\u00e9pey", + "author_inst": "Univ Rennes, EHESP, REPERES - EA 7449" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.14.20035659", "rel_title": "Maximum entropy method for estimating the reproduction number: An investigation for COVID-19 in China", @@ -1571899,33 +1574711,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.16.20034934", - "rel_title": "Advance of Novel Coronavirus Registration Clinical Trial", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.16.20034934", - "rel_abs": "BackgroundTo analyze the characteristics and heterogeneity of clinical trials of Novel Coronavirus(COVID-19) registered in the China Clinical Trial Registry (ChiCTR), and provide data bases and information references for clinical treatment\n\nMethodsStatistics of COVID-19 clinical trials registered with ChiCTR as of February 24, 2020 were collected. Descriptive analysis of registration characteristics. The chi-square test is used to compare statistical differences between different study types, intervention methods, study stage, and Primary sponsor.\n\nResults232 COVID-19 studies registered at the ChiCTR were collected. The overall number of COVID-19 registrations was increased. Hubei Province, China has the largest number of registrations. There were significant differences between the number of participants(P=0.000), study duration(P=0.008), study assignment(P=0.000), and blind method(P=0.000) for different study types. Significant differences could be seen in the dimensions of multicenter study(P=0.022), of participants numbe(P=0.000), study duration(P=0.000) and study assignment(P=0.001) for the four intervention methods. There were significant differences in study assignment(P=0.043) between the early and late studies. CMT drugs with high research frequency are chloroquine, lopinavir / ritonavir, and I-IFN; BI was Cell therapy, plasma therapy, Thymosin, and M/P-AB.\n\nConclusionsDifferent study design characteristics have led to significant differences in some aspects of the COVID-19 clinical trial. Timely summary analysis can provide more treatment options and evidence for clinical practice.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "gao song", - "author_inst": "Puer Peoples Hospital" - }, - { - "author_name": "meng qun cheng", - "author_inst": "Puer Peoples Hospital" - }, - { - "author_name": "xian wen wei", - "author_inst": "Puer Peoples Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.17.20037408", "rel_title": "How to improve adherence with quarantine: Rapid review of the evidence", @@ -1573072,6 +1575857,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.16.20037135", + "rel_title": "Hydroxychloroquine and Azithromycin as a treatment of COVID-19: preliminary results of an open-label non-randomized clinical trial", + "rel_date": "2020-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.16.20037135", + "rel_abs": "BackgroundChloroquine and hydroxychloroquine have been found to be efficient on SARS-CoV-2, and reported to be efficient in Chinese COV-19 patients. We evaluate the role of hydroxychloroquine on respiratory viral loads.\n\nPatients and methodsPatients were included in a single arm protocol to receive 600mg of hydroxychloroquine daily and their viral load in nasal swabs was tested daily. Depending on their clinical presentation, azithromycin was added to the treatment. Untreated patients from another center and cases refusing the protocol were included as negative controls. Presence and absence of virus at Day6-post inclusion was considered the end point.\n\nResultsTwenty cases were treated in this study and showed a significant reduction of the viral carriage at D6-post inclusion compared to controls, and much lower average carrying duration than reported of untreated patients in the literature. Azithromycin added to hydroxychloroquine was significantly more efficient for virus elimination.\n\nConclusionHydroxychloroquine is significantly associated with viral load reduction/disappearance in COVID-19 patients and its effect is reinforced by azithromycin.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Philippe GAUTRET", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Jean Christophe LAGIER", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Philippe PAROLA", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Van Thuan HOANG", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Line MEDDED", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Morgan MAILHE", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Barbara DOUDIER", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Johan COURJON", + "author_inst": "Centre Hospitalier Universitaire de Nice" + }, + { + "author_name": "Valerie GIORDANENGO", + "author_inst": "Centre Hospitalier Universitaire de Nice" + }, + { + "author_name": "Vera ESTEVES VIEIRA", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Herve TISSOT DUPONT", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Stephane HONORE", + "author_inst": "Aix Marseille University" + }, + { + "author_name": "Philippe COLSON", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Eric CHABRIERE", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Bernard LA SCOLA", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Jean Marc ROLAIN", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Philippe BROUQUI", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Didier RAOULT Sr.", + "author_inst": "IHU Mediterrane Infection, Aix Marseille University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.19.20038844", "rel_title": "A framework for identifying regional outbreak and spread of COVID-19 from one-minute population-wide surveys", @@ -1573209,49 +1576081,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.18.20038117", - "rel_title": "Predicting the epidemic trend of COVID-19 in China and across the world using the machine learning approach", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.18.20038117", - "rel_abs": "BackgroundAlthough COVID-19 has been well controlled in China, it is rapidly spreading outside the country and may have catastrophic results globally without implementation of necessary mitigation measures. Because the COVID-19 outbreak has made comprehensive and profound impacts on the world, an accurate prediction of its epidemic trend is significant. Although many studies have predicted the COVID-19 epidemic trend, most have used early-stage data and focused on Chinese cases.\n\nMethodsWe first built models to predict daily numbers of cumulative confirmed cases (CCCs), new cases (NCs), and death cases (DCs) of COVID-19 in China based on data from January 20, 2020, to March 1, 2020. Based on these models, we built models to predict the epidemic trend across the world (outside China). We also built models to predict the epidemic trend in Italy, Spain, Germany, France, UK, and USA where COVID-19 is rapidly spreading.\n\nResultsThe COVID-19 outbreak will have peaked on February 22, 2020, in China and will peak on May 22, 2020, across the world. It will be basically under control in early April 2020 in China and late August 2020 across the world. The total number of COVID-19 cases will reach around 89,000 in China and 6,126,000 across the world during the epidemic. Around 4,000 and 290,000 people will die of COVID-19 in China and across the world, respectively. The COVID-19 outbreak will have peaked recently in Italy and will peak in Spain, Germany, France, UK, and USA within two weeks.\n\nConclusionThe COVID-19 outbreak is controllable in the foreseeable future if comprehensive and stringent control measures are taken.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Mengyuan Li", - "author_inst": "China Pharmaceutical University" - }, - { - "author_name": "Zhilan Zhang", - "author_inst": "China Pharmaceutical University" - }, - { - "author_name": "Shanmei Jiang", - "author_inst": "China Pharmaceutical University" - }, - { - "author_name": "Qian Liu", - "author_inst": "China Pharmaceutical University" - }, - { - "author_name": "Canping Chen", - "author_inst": "China Pharmaceutical University" - }, - { - "author_name": "Yue Zhang", - "author_inst": "Pinghu hospital of Shenzhen University" - }, - { - "author_name": "Xiaosheng Wang", - "author_inst": "China Pharmaceutical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.17.20037648", "rel_title": "Sentinel Event Surveillance to Estimate Total SARS-CoV-2 Infections, United States", @@ -1574710,6 +1577539,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.15.20036368", + "rel_title": "Coronavirus disease-19: The First 7,755 Cases in the Republic of Korea", + "rel_date": "2020-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.15.20036368", + "rel_abs": "We report the first 7,755 patients with confirmed COVID-19 in Korea as of March 13, 2020. A total of 66 deaths were identified, resulting case fatality proportion of 0.9%. Older people, and those with coexisting medical conditions were at risk for fatal outcomes. The highest number of cases were from Daegu, followed by Gyeongbuk, with elevated age-stratified case fatality. This summary may help to understand the disease dynamics in the early phase of COVID-19 outbreak, therefore, to guide future public health measures.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "- COVID-19 National Emergency Response Center Korea Centers for Disease Control and Prevention", + "author_inst": "-" + }, + { + "author_name": "Young June Choe", + "author_inst": "Hallym University College of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.15.20036350", "rel_title": "Coronavirus disease-19: Summary of 2,370 Contact Investigations of the First 30 Cases in the Republic of Korea", @@ -1574819,33 +1577671,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.13.20035345", - "rel_title": "Forecasting of COVID-19 Confirmed Cases in Different Countries with ARIMA Models", - "rel_date": "2020-03-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.13.20035345", - "rel_abs": "The epidemic of a novel coronavirus illness (COVID-19) becomes as a global threat. The aim of this study is first to find the best prediction models for daily confirmed cases in countries with high number of confirmed cases in the world and second to predict confirmed cases with these models in order to have more readiness in healthcare systems. This study was conducted based on daily confirmed cases of COVID-19 that were collected from the official website of Johns Hopkins University from January 22th, 2020 to March 1th, 2020. Auto Regressive Integrated Moving Average (ARIMA) model was used to predict the trend of confirmed cases. Stata version 12 and R version 3.6.2 were used. Parameters used for ARIMA were (2,1,0) for Mainland China, ARIMA(1,0,0) for South Korea, and ARIMA(3,1,0) for Thailand. Mainland China and Thailand were successful in haltering COVID-19 epidemic. Investigating their protocol in this control like quarantine should be in the first line of other countries program", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Tania Dehesh", - "author_inst": "Kerman University of Medical Sciences" - }, - { - "author_name": "H.A. Mardani-Fard", - "author_inst": "Yasuj University" - }, - { - "author_name": "Paria Dehesh", - "author_inst": "Iran University of Medical Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.13.20033290", "rel_title": "Mental health status among family members of health care workers in Ningbo, China during the Coronavirus Disease 2019 (COVID-19) outbreak: a Cross-sectional Study", @@ -1576284,6 +1579109,57 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.03.15.20035204", + "rel_title": "International expansion of a novel SARS-CoV-2 mutant", + "rel_date": "2020-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.15.20035204", + "rel_abs": "Letter to the editor. There is no abstract. The summary was showed: SARS-CoV-2 has inevitably mutated during its pandemic spread to cause unpredictable effects on COVID-19 and complicate epidemic control efforts. Here we report that a novel SARS-CoV-2 mutation (ORF3a) appears to be spreading worldwide, which deserves close attention.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Minjin Wang", + "author_inst": "Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China" + }, + { + "author_name": "Mengjiao Li", + "author_inst": "Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China" + }, + { + "author_name": "Ruotong Ren", + "author_inst": "1. Genskey Biotechnology Co., Ltd. 2. Department of Hematology, The First Hospital of Lanzhou University" + }, + { + "author_name": "Andreas Brave", + "author_inst": "Department of microbiology,Public Health Agency of Sweden" + }, + { + "author_name": "Sylvie van der Werf", + "author_inst": "Department of Virology,Molecular Genetics of RNA Viruses unit,CNRS UMR-3569, University of Paris, National Reference Center for Respiratory Viruses Institut Pas" + }, + { + "author_name": "En-Qiang Chen", + "author_inst": "Center of Infectious Diseases, West China Hospital of Sichuan University" + }, + { + "author_name": "Zhiyong Zong", + "author_inst": "Department of Infection Control and Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, China" + }, + { + "author_name": "Weimin Li", + "author_inst": "Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China" + }, + { + "author_name": "Binwu Ying", + "author_inst": "Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.10.986711", "rel_title": "Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols", @@ -1576485,29 +1579361,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.03.15.20034199", - "rel_title": "Temporal relationship between outbound traffic from Wuhan and the 2019 coronavirus disease (COVID-19) incidence in China", - "rel_date": "2020-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.15.20034199", - "rel_abs": "BackgroundThe city of Wuhan is the epicenter of the 2019 coronavirus disease (COVID-19) outbreak and a central Chinese hub for transportation and industry. Mass migration prior to the Chinese New Year may have accelerated the spread of COVID-19 across China. This analysis investigated the temporal relationship between daily outbound traffic from Wuhan and the incidence of COVID-19 in 31 Chinese provinces during January-February 2020.\n\nMethodsWe collected incidence of confirmed COVID-19 cases from National and Provincial Health Committee reports from January 10 to February 29, 2020. Volume of outbound traffic from Wuhan to other provinces was measured by Baidu Migration Index, a widely used metric that tracks migration based on cellphone location. We used cross-correlation function and autoregressive integrated moving average (ARIMA) model to examine time-lagged association between traffic volume and COVID-19 incidence by province. Contributors to the provincial variation in the temporal associations were investigated. Additionally, we estimated the reduction in cumulative incidence of COVID-19 cases following the travel ban for Wuhan.\n\nResultsCross-correlation function analyses suggested that the volume of outbound traffic from Wuhan was positively associated with COVID-19 incidence in all provinces, with correlation coefficients between 0.22-0.78 (all P<0.05). Approximately 42% of provinces showed <1 week of lag between traffic volume and COVID-19 incidence, 39% with 1 week, and 19% with 2-3 weeks. Migration had more prolonged impacts in provinces closer to Wuhan and with more passenger influx from Wuhan, but affected economically advantaged provinces to a lesser extent. We further estimated that the travel ban may have prevented approximately 19,768 COVID-19 cases (95% CI: 13,589, 25,946) outside of Wuhan by February 29, 2020.\n\nConclusionsOutflowing migration from Wuhan facilitated the COVID-19 transmission to other parts of China with varying time-lagged effects dependent on provincial characteristics. The travel ban led to a significant reduction in COVID-19 outside of Wuhan.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Zaixing Shi", - "author_inst": "State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China" - }, - { - "author_name": "Ya Fang", - "author_inst": "State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.15.20033472", "rel_title": "Blood single cell immune profiling reveals the interferon-MAPK pathway mediated adaptive immune response for COVID-19", @@ -1577734,6 +1580587,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.11.20034512", + "rel_title": "A Method to Model Outbreaks of New Infectious Diseases with Pandemic Potential such as COVID-19", + "rel_date": "2020-03-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.11.20034512", + "rel_abs": "The emergence of the novel coronavirus (a.k.a. COVID-19, SARS-CoV-2) out of Wuhan, Hubei Province, China caught the world by surprise. As the outbreak began to spread outside of China, too little was known about the virus to model its transmission with any acceptable accuracy. World governments responded to rampant misinformation about the virus leading to collateral disasters, such as plunging financial markets, that could have been avoided if better models of the outbreak had been available. This is an engineering approach to model the spread of a new infectious disease from sparse data when little is known about the infectious agent itself. The paper is not so much about the model itself - because there are many good scientific approaches to model an epidemic - as it is about crunching numbers when there are barely any numbers to crunch. The coronavirus outbreak in USA is used to illustrate the implementation of this modeling approach. A Monte Carlo approach is implemented by using incubation period and testing efficiency as variables. Among others it is demonstrated that imposing early travel restrictions from infected countries slowed down the outbreak in the USA by about 26 days.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Willem G Odendaal", + "author_inst": "Virginia Tech" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.11.20031096", "rel_title": "Relationship between the ABO Blood Group and the COVID-19 Susceptibility", @@ -1577874,73 +1580746,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.12.20034660", - "rel_title": "Impact assessment of non-pharmaceutical interventions against COVID-19 and influenza in Hong Kong: an observational study", - "rel_date": "2020-03-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.12.20034660", - "rel_abs": "BackgroundA range of public health measures have been implemented to delay and reduce local transmission of COVID-19 in Hong Kong, and there have been major changes in behaviours of the general public. We examined the effect of these interventions and behavioral changes on the incidence of COVID-19 as well as on influenza virus infections which may share some aspects of transmission dynamics with COVID-19.\n\nMethodsWe reviewed policy interventions and measured changes in population behaviours through two telephone surveys, on January 20-23 and February 11-14. We analysed data on laboratory-confirmed COVID-19 cases, influenza surveillance data in outpatients of all ages, and influenza hospitalisations in children. We estimated the daily effective reproduction number (Rt), for COVID-19 and influenza A(H1N1).\n\nFindingsCOVID-19 transmissibility has remained at or below 1, indicating successful containment to date. Influenza transmission declined substantially after the implementation of social distancing measures and changes in population behaviours in late January, with a 44% (95% confidence interval, CI: 34% to 53%) reduction in transmissibility in the community, and a 33% (95% CI: 24% to 43%) reduction in transmissibility based on paediatric hospitalization rates. In the two surveys we estimated that 74.5% and 97.5% of the general adult population wore masks when going out, and 61.3% and 90.2% avoided going to crowded places, respectively.\n\nImplicationsContainment measures, social distancing measures and changes in population behaviour have successfully prevented spread of COVID-19. The social distancing measures and behavioural changes led to a substantial reduction in influenza transmission in early February 2020. However, it may be challenging to avoid fatigue and sustain these measures and population behaviours as COVID-19 continues to spread globally.\n\nFundingHealth and Medical Research Fund, Hong Kong", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Benjamin J Cowling", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Sheikh Taslim Ali", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Tiffany W. Y. Ng", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Tim K Tsang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Julian C. M Li", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Min Whui Fong", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Qiuyan Liao", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Mike YW Kwan", - "author_inst": "Princess Margaret Hospital" - }, - { - "author_name": "So Lun Lee", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Susan S. Chiu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Joseph T. Wu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Peng Wu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Gabriel M. Leung", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.12.20034595", "rel_title": "Rational evaluation of various epidemic models based on the COVID-19 data of China", @@ -1579617,6 +1582422,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.09.20033126", + "rel_title": "Clinical features of imported cases of coronavirus disease 2019 in Tibetan patients in the Plateau area", + "rel_date": "2020-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.09.20033126", + "rel_abs": "Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has rapidly spread throughout China, but the clinical characteristics of Tibetan patients living in the Qinghai-Tibetan plateau are unknown. We aimed to investigate the epidemiological, clinical, laboratory and radiological characteristics of these patients. We included 67 Tibetan patients with confirmed SARS-CoV-2 infection. The patients were divided into two groups based on the presence of clinical symptoms at admission, with 31 and 36 patients in the symptomatic and asymptomatic groups, respectively. The epidemiological, clinical, laboratory and radiological characteristics were extracted and analysed. No patient had a history of exposure to COVID-19 patients from Wuhan or had travelled to Wuhan. The mean age of Tibetan patients was 39.3 years and 59% of the patients were male. Seven patients presented with fever on admission and lymphocytopenia was present in 20 patients. 47 patients had abnormal chest CTs at admission instead of stating that 20 were unchanged. Lactate dehydrogenase levels were increased in 31 patients. Seven patients progressed to severe COVID-19; however, after treatment, their condition was stable. No patients died. Of the 36 asymptomatic patients, the mean age was younger than the symptomatic group (34.4{+/-}17.3vs 44.9{+/-}18.1 years, P=0.02). Lymphocyte count and prealbumin levels were higher in the asymptomatic group than the group with clinical symptoms (1.6{+/-}0.5 vs 1.3{+/-}0.6 and 241.8{+/-}68.2 vs 191.9{+/-}60.3, respectively; P<0.05). Imported cases of COVID-19 in Tibetan patients were generally mild in this high-altitude area. Absence of fever or radiologic abnormalities on initial presentation were common.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Yu Lei", + "author_inst": "sichuan academy of medical sciences&sichuan provincial people's hospital" + }, + { + "author_name": "yunping lan", + "author_inst": "sichuan academy of medical sciences&sichuan provincial people's hospital" + }, + { + "author_name": "jianli lu", + "author_inst": "363 hospital of chengdu" + }, + { + "author_name": "xiaobo huang", + "author_inst": "sichuan academy of medical sciences&sichuan provincial people's hospital" + }, + { + "author_name": "bamu silang", + "author_inst": "daofu people's hospital" + }, + { + "author_name": "fan zeng", + "author_inst": "sichuan academy of medical sciences&sichuan provincial people's hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.11.20033159", "rel_title": "Prolonged presence of SARS-CoV-2 in feces of pediatric patients during the convalescent phase", @@ -1579762,45 +1582606,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.09.20033241", - "rel_title": "The demand for inpatient and ICU beds for COVID-19 in the US: lessons from Chinese cities", - "rel_date": "2020-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.09.20033241", - "rel_abs": "BackgroundSustained spread of SARS-CoV-2 has happened in major US cities. Capacity needs in Chinese cities could inform the planning of local healthcare resources.\n\nMethodsWe described the intensive care unit (ICU) and inpatient bed needs for confirmed COVID-19 patients in two Chinese cities (Wuhan and Guangzhou) from January 10 to February 29, 2020, and compared the timing of disease control measures in relation to the timing of SARS-CoV-2 community spread. We estimated the peak ICU bed needs in US cities if a Wuhan-like outbreak occurs.\n\nResultsIn Wuhan, strict disease control measures were implemented six weeks after sustained local transmission of SARS-CoV-2. Between January 10 and February 29, COVID-19 patients accounted for an average of 637 ICU patients and 3,454 serious inpatients on each day. During the epidemic peak, 19,425 patients (24.5 per 10,000 adults) were hospitalized, 9,689 (12.2 per 10,000 adults) were considered to be in serious condition, and 2,087 patients (2.6 per 10,000 adults) needed critical care per day. In Guangzhou, strict disease control measures were implemented within one week of case importation. Between January 24 and February 29, COVID-19 accounted for an average of 9 ICU patients and 20 inpatients on each day. During the epidemic peak, 15 patients were in critical condition, and 38 were classified as serious. If a Wuhan-like outbreak were to happen in a US city, the need for healthcare resources may be higher in cities with a higher prevalence of vulnerable populations.\n\nConclusionEven after the lockdown of Wuhan on January 23, the number of seriously ill COVID-19 patients continued to rise, exceeding local hospitalization and ICU capacities for at least a month. Plans are urgently needed to mitigate the effect of COVID-19 outbreaks on the local healthcare system in US cities.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ruoran Li", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Caitlin Rivers", - "author_inst": "Johns Hopkins Center for Health Security and the Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Qi Tan", - "author_inst": "Department of Global Health and Social Medicine, Harvard Medical School" - }, - { - "author_name": "Megan B Murray", - "author_inst": "Department of Global Health and Social Medicine, Harvard Medical School" - }, - { - "author_name": "Eric Toner", - "author_inst": "Johns Hopkins Center for Health Security and the Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Marc Lipsitch", - "author_inst": "Harvard T.H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.09.20033381", "rel_title": "Novel Coronavirus (COVID-19) Knowledge and Perceptions: A Survey on Healthcare workers", @@ -1581850,6 +1584655,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.03.08.980383", + "rel_title": "In silico approach to accelerate the development of mass spectrometry-based proteomics methods for detection of viral proteins: Application to COVID-19", + "rel_date": "2020-03-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.08.980383", + "rel_abs": "We describe a method for rapid in silico selection of diagnostic peptides from newly described viral pathogens and applied this approach to SARS-CoV-2/COVID-19. This approach is multi-tiered, beginning with compiling the theoretical protein sequences from genomic derived data. In the case of SARS-CoV-2 we begin with 496 peptides that would be produced by proteolytic digestion of the viral proteins. To eliminate peptides that would cause cross-reactivity and false positives we remove peptides from consideration that have sequence homology or similar chemical characteristics using a progressively larger database of background peptides. Using this pipeline, we can remove 47 peptides from consideration as diagnostic due to the presence of peptides derived from the human proteome. To address the complexity of the human microbiome, we describe a method to create a database of all proteins of relevant abundance in the saliva microbiome. By utilizing a protein-based approach to the microbiome we can more accurately identify peptides that will be problematic in COVID-19 studies which removes 12 peptides from consideration. To identify diagnostic peptides, another 7 peptides are flagged for removal following comparison to the proteome backgrounds of viral and bacterial pathogens of similar clinical presentation. By aligning the protein sequences of SARS-CoV-2 field isolates deposited to date we can identify peptides for removal due to their presence in highly variable regions that may lead to false negatives as the pathogen evolves. We provide maps of these regions and highlight 3 peptides that should be avoided as potential diagnostic or vaccine targets. Finally, we leverage publicly deposited proteomics data from human cells infected with SARS-CoV-2, as well as a second study with the closely related MERS-CoV to identify the two proteins of highest abundance in human infections. The resulting final list contains the 24 peptides most unique and diagnostic of SARS-CoV-2 infections. These peptides represent the best targets for the development of antibodies are clinical diagnostics. To demonstrate one application of this we model peptide fragmentation using a deep learning tool to rapidly generate targeted LCMS assays and data processing method for detecting CoVID-19 infected patient samples.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=156 HEIGHT=200 SRC=\"FIGDIR/small/980383v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (37K):\norg.highwire.dtl.DTLVardef@1d7fd4borg.highwire.dtl.DTLVardef@136563borg.highwire.dtl.DTLVardef@57641dorg.highwire.dtl.DTLVardef@16de9a4_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ben Orsburn", + "author_inst": "UVA School of Medicine" + }, + { + "author_name": "Conor Jenkins", + "author_inst": "Hood College Biology Department" + }, + { + "author_name": "Sierra D Miller", + "author_inst": "Millersville University" + }, + { + "author_name": "Benjamin A Neely", + "author_inst": "Proteomic und Genomic Sciences" + }, + { + "author_name": "Namandje M Bumpus", + "author_inst": "Johns Hopkins University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.03.10.985150", "rel_title": "A proposal of an alternative primer for the ARTIC Network's multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing", @@ -1581979,69 +1584819,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.03.06.20032425", - "rel_title": "Prevalence and Risk Factors of Acute Posttraumatic Stress Symptoms during the COVID-19 Outbreak in Wuhan, China", - "rel_date": "2020-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.06.20032425", - "rel_abs": "BackgroundTo exam the prevalence of and risk factors for acute posttraumatic stress disorder (PTSD) in Chinese people shortly after the COVID-19 outbreak.\n\nMethodsAn online questionnaire survey was conducted between 30 January and 3 February, 2020. The survey included two self-administered questionnaires: one was designed to require participants personal information (gender, age, education background), current location, recent epidemic area contact history, the classification of population, and subjective sleep quality; the other was the PTSD Checklist for DSM-5 (PCL-5).\n\nResultsA total of 2091 Chinese participated in this study. The prevalence of PTSD among the Chinese public one month after the COVID-19 outbreak was 4.6%. Multiple linear regression analysis revealed that gender (p < 0.001), epidemic area contact history (p = 0.047), classification of population (p < 0.001), and subjective sleep quality (p < 0.001) could be regarded as predictor factors for PTSD.\n\nLimitationsFirst, the majority of participants in this study were the general public, and confirmed or suspected patients being a small part. Second, the measurement of PTSD might be vulnerable to selection bias because of an online self-report study, such as participants recruitment. Third, the prevalence of PTSD in this study was estimated by an online questionnaire rather than a clinical interview.\n\nConclusionsThe results revealed that some Chinese showed acute PTSD during the COVID-19 outbreak. Therefore, comprehensive psychological intervention needs further implementation. Furthermore, females, people who having recent epidemic area contact history, those at high risk of infection or with poor sleep quality deserve special attention.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Luna Sun", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Zhuoer Sun", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Lili Wu", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Zhenwen Zhu", - "author_inst": "Fudan University" - }, - { - "author_name": "Fan Zhang", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Zhilei Shang", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Yanpu Jia", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Jingwen Gu", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Yaoguang Zhou", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Yan Wang", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Nianqi Liu", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Weizhi Liu", - "author_inst": "Naval Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.03.07.20032599", "rel_title": "Analysis of early renal injury in COVID-19 and diagnostic value of multi-index combined detection", @@ -1583340,6 +1586117,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.05.20031906", + "rel_title": "COVID-19 early warning score: a multi-parameter screening tool to identify highly suspected patients", + "rel_date": "2020-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.05.20031906", + "rel_abs": "BACKGROUNDCorona Virus Disease 2019 (COVID-19) is spreading worldwide. Effective screening for patients is important to limit the epidemic. However, some defects make the currently applied diagnosis methods are still not very ideal for early warning of patients. We aimed to develop a diagnostic model that allows for the quick screening of highly suspected patients using easy-to-get variables.\n\nMETHODSA total of 1,311 patients receiving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleicacid detection were included, whom with a positive result were classified into COVID-19 group. Multivariate logistic regression analyses were performed to construct the diagnostic model. Receiver operating characteristic (ROC) curve analysis were used for model validation.\n\nRESULTSAfter analysis, signs of pneumonia on CT, history of close contact, fever, neutrophil-to-lymphocyte ratio (NLR), Tmax and sex were included in the diagnostic model. Age and meaningful respiratory symptoms were enrolled into COVID-19 early warning score (COVID-19 EWS). The areas under the ROC curve (AUROC) indicated that both of the diagnostic model (training dataset 0.956 [95%CI 0.935-0.977, P < 0.001]; validation dataset 0.960 [95%CI 0.919-1.0, P < 0.001]) and COVID-19 EWS (training dataset 0.956 [95%CI 0.934-0.978, P < 0.001]; validate dataset 0.966 [95%CI 0.929-1, P < 0.001]) had good discrimination capacity. In addition, we also obtained the cut-off values of disease severity predictors, such as CT score, CD8+ T cell count, CD4+ T cell count, and so on.\n\nCONCLUSIONSThe new developed COVID-19 EWS was a considerable tool for early and relatively accurately warning of SARS-CoV-2 infected patients.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Cong-Ying Song", + "author_inst": "The First Affiliated Hospital, School of Medicine, Zhejiang University" + }, + { + "author_name": "Jia Xu", + "author_inst": "The First Affiliated Hospital, School of Medicine, Zhejiang University" + }, + { + "author_name": "Jian-Qin He", + "author_inst": "The First Affiliated Hospital, School of Medicine, Zhejiang University" + }, + { + "author_name": "Yuan-Qiang Lu", + "author_inst": "The First Affiliated Hospital, School of Medicine, Zhejiang University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.06.20031955", "rel_title": "Transmission of corona virus disease 2019 during the incubation period may lead to a quarantine loophole", @@ -1583585,37 +1586393,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.03.05.20031872", - "rel_title": "Role of temperature and humidity in the modulation of the doubling time of COVID-19 cases", - "rel_date": "2020-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.05.20031872", - "rel_abs": "COVID-19 is having a great impact on public health, mortality and economy worldwide, in spite of the efforts to prevent its epidemy. The SARS-CoV-2 genome is different from that of MERS-CoV and SARS-CoV, although also expected to spread differently according to meteorological conditions. Our main goal is to investigate the role of some meteorological variables on the expansion of this outbreak.\n\nIn this study, an exponential model relating the number of accumulated confirmed cases and time was considered. The rate of COVID-19 spread, using as criterion the doubling time of the number of confirmed cases, was used as dependent variable in a linear model that took four independent meteorological variables: temperature, humidity, precipitation and wind speed. Only China cases were considered, to control both cultural aspects and containment policies. Confirmed cases and the 4 meteorological variables were gathered between January 23 and March 1 (39 days) for the 31 provinces of Mainland China. Several periods of time were sampled for each province, obtaining more than one value for the rate of disease progression. Two different periods of time were tested, of 12 and 15 days, along with 3 and 5 different starting points in time, randomly chosen. The median value for each meteorological variable was computed, using the same time period; models with [Formula] were selected. The rate of progression and doubling time were computed and used to fit a linear regression model. Models were evaluated using = 0.05.\n\nResults indicate that the doubling time correlates positively with temperature and inversely with humidity, suggesting that a decrease in the rate of progression of COVID-19 with the arrival of spring and summer in the north hemisphere. A 20{degrees}C increase is expected to delay the doubling time in 1.8 days. Those variables explain 18% of the variation in disease doubling time; the remaining 82% may be related to containment measures, general health policies, population density, transportation or cultural aspects.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Barbara Oliveiros", - "author_inst": "Faculty of Medicine, University of Coimbra" - }, - { - "author_name": "Liliana Caramelo", - "author_inst": "Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Tras-os-Montes and Alto Douro, Vila Real, Portugal" - }, - { - "author_name": "Nuno C Ferreira", - "author_inst": "Faculty of Medicine, University of Coimbra" - }, - { - "author_name": "Francisco Caramelo", - "author_inst": "Faculty of Medicine, University of Coimbra, Portugal" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.03.05.20031898", "rel_title": "Emotional responses and coping strategies of nurses and nursing college students during COVID-19 outbreak", @@ -1584945,6 +1587722,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.02.20030148", + "rel_title": "Validity of Wrist and Forehead Temperature in Temperature Screening in the General Population During the Outbreak of 2019 Novel Coronavirus: a prospective real-world study", + "rel_date": "2020-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20030148", + "rel_abs": "AimsTemperature screening is important in the population during the outbreak of 2019 Novel Coronavirus (COVID-19). This study aimed to compare the accuracy and precision of wrist and forehead temperature with tympanic temperature under different circumstances.\n\nMethodsWe performed a prospective observational study in a real-life population. We consecutively collected wrist and forehead temperatures in Celsius ({degrees}C) using a non-contact infrared thermometer (NCIT). We also measured the tympanic temperature using a tympanic thermometers (IRTT) and defined fever as a tympanic temperature [≥]37.3{degrees}C.\n\nResultsWe enrolled a total of 528 participants including 261 indoor and 267 outdoor participants. We divided outdoor participants into four types according to their means of transportation to the hospital as walk, bicycle, electric vehicle, car, and inside the car. Under different circumstance, the mean difference ranged from -1.72 to -0.56{degrees}C in different groups for the forehead measurements, and -0.96 to -0.61{degrees}C for the wrist measurements. Both measurements had high fever screening abilities in inpatients (wrist: AUC 0.790; 95% CI: 0.725-0.854, P <0.001; forehead: AUC 0.816; 95% CI: 0.757-0.876, P <0.001). The cut-off value of wrist measurement for detecting tympanic temperature [≥]37.3{degrees}C was 36.2{degrees}C with a 86.4% sensitivity and a 67.0% specificity, and the best threshold of forehead measurement was also 36.2{degrees}C with a 93.2% sensitivity and a 60.0% specificity.\n\nConclusionsWrist measurement is more stable than forehead measurement under different circumstance. Both measurements have great fever screening abilities for indoor patients. The cut-off value of both measurements was 36.2{degrees}C. (ClinicalTrials.gov number: NCT04274621)", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ge Chen", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Jiarong Xie", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Guangli Dai", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Peijun Zheng", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Xiaqing Hu", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Hongpeng Lu", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Lei Xu", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Xueqin Chen", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Xiaomin Chen", + "author_inst": "Ningbo First Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.03.04.20031005", "rel_title": "Case fatality risk of novel coronavirus diseases 2019 in China", @@ -1585194,69 +1588022,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.04.20031047", - "rel_title": "How to differentiate COVID-19 pneumonia from heart failure with computed tomography at initial medical contact during epidemic period", - "rel_date": "2020-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.04.20031047", - "rel_abs": "OBJECTIVESTo compare chest CT findings in heart failure with those of Corona Virus Disease 2019 (COVID-19) pneumonia.\n\nBACKGROUNDDuring epidemic period, chest computed tomography (CT) has been highly recommended for screening patients with suspected COVID-19. However, the comparison of CT imaging between heart failure and COVID-19 pneumonia has not been fully elucidated.\n\nMETHODSPatients with heart failure (n=12), COVID-19 pneumonia (n=12) and one patient with both diseases were retrospectively enrolled. Clinical information and imaging of chest CT were collected and analyzed.\n\nRESULTSThere was no difference of ground glass opacity (GGO), consolidation, crazy paving pattern, lobes affected and septal thickening between heart failure and COVID-19 pneumonia. However, less rounded morphology (8.3% vs. 67%, p=0.003), more peribronchovascular thickening (75% vs. 33%, p=0.041) and fissural thickening (33% vs. 0%, p=0.028), less peripheral distribution (33% vs. 92%, p=0.003) were found in heart failure group than that in COVID-19 group. Importantly, there were also more patients with upper pulmonary vein enlargement (75% vs. 8.3%, p=0.001), subpleural effusion and cardiac enlargement in heart failure group than that in COVID-19 group (50% vs. 0%, p=0.005, separately). Besides, more fibrous lesions were found in COVID-19 group although there was no statistical difference (25% vs. 0%, P=0.064)\n\nCONCLUSIONSAlthough there are some overlaps of CT imaging between heart failure and COVID-19, CT is still a useful tool in differentiating COVID-19 pneumonia.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Zhaowei Zhu", - "author_inst": "the Second Xiangya Hospital of Central South University" - }, - { - "author_name": "Jianjun Tang", - "author_inst": "the Second Xiangya Hospital of Central South University" - }, - { - "author_name": "Xiangping Chai", - "author_inst": "the Second Xiangya Hospital of Central South University" - }, - { - "author_name": "Zhenfei Fang", - "author_inst": "the Second Xiangya Hospital of Central South University" - }, - { - "author_name": "Qiming Liu", - "author_inst": "the Second Xiangya Hospital of Central South University" - }, - { - "author_name": "Xinqun Hu", - "author_inst": "the Second Xiangya Hospital of Central South University" - }, - { - "author_name": "Danyan Xu", - "author_inst": "the Second Xiangya Hospital of Central South University" - }, - { - "author_name": "Jia He", - "author_inst": "the Second Xiangya Hospital of Central South University" - }, - { - "author_name": "Liang Tang", - "author_inst": "the Second Xiangya Hospital of Central South University" - }, - { - "author_name": "Shi Tai", - "author_inst": "the Second Xiangya Hospital of Central South University" - }, - { - "author_name": "Yuzhi Wu", - "author_inst": "the Second Xiangya Hospital of Central South University" - }, - { - "author_name": "Shenghua Zhou", - "author_inst": "the Second Xiangya Hospital of Central South University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.03.03.20030833", "rel_title": "Caution: The clinical characteristics of COVID-19 patients at admission are changing", @@ -1586559,6 +1589324,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.03.20030627", + "rel_title": "SOCRATES: An online tool leveraging a social contact data sharing initiative to assess mitigation strategies for COVID-19", + "rel_date": "2020-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.03.20030627", + "rel_abs": "ObjectiveEstablishing a social contact data sharing initiative and an interactive tool to assess mitigation strategies for COVID-19.\n\nResultsWe organized data sharing of published social contact surveys via online repositories and formatting guidelines. We analyzed this social contact data in terms of weighted social contact matrices, next generation matrices, relative incidence and R0. We incorporated location-specific isolation measures (e.g. school closure or telework) and capture their effect on transmission dynamics. All methods have been implemented in an online application based on R Shiny and applied to COVID-19 with age-specific susceptibility and infectiousness. Using our online tool with the available social contact data, we illustrate that social distancing could have a considerable impact on reducing transmission for COVID-19. The effect itself depends on assumptions made about disease-specific characteristics and the choice of intervention(s).", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lander Willem", + "author_inst": "Centre for Health Economic Research and Modelling Infectious Diseases,University of Antwerp, Antwerp, Belgium" + }, + { + "author_name": "Thang Van Hoang", + "author_inst": "Interuniversity Institute of Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium" + }, + { + "author_name": "Sebastian Funk", + "author_inst": "Centre for the Mathematical Modelling of Infectious Diseases,London School of Hygiene & Tropical Medicine, London, United Kingdom" + }, + { + "author_name": "Pietro Coletti", + "author_inst": "Interuniversity Institute of Biostatistics and statistical Bioinformatics, Data Science Institute,Hasselt University, Hasselt, Belgium" + }, + { + "author_name": "Philippe Beutels", + "author_inst": "(1) Centre for Health Economic Research and Modelling Infectious Diseases,University of Antwerp, Antwerp, Belgium; (2) School of Public health and Community Med" + }, + { + "author_name": "Niel Hens", + "author_inst": "(1) Centre for Health Economic Research and Modelling Infectious Diseases,University of Antwerp, Antwerp, Belgium; (2) Interuniversity Institute of Biostatistic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.03.20030593", "rel_title": "Evolving Epidemiology and Impact of Non-pharmaceutical Interventions on the Outbreak of Coronavirus Disease 2019 in Wuhan, China", @@ -1586812,25 +1589616,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.03.01.20028944", - "rel_title": "Epidemiologic Characteristics of COVID-19 in Guizhou, China", - "rel_date": "2020-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.01.20028944", - "rel_abs": "At the end of 2019, a coronavirus disease 2019 (COVID-19) outbroke in Wuhan, China, and spread to Guizhou province on January of 2020. To acquire the epidemiologic characteristics of COVID-19 in Guizhou, China, we collected data on 162 laboratory-confirmed cases related to COVID-19. We described the demographic characteristics of the cases and estimated the incubation period, serial interval and basic reproduction number. With an estimation of 8 days incubation period and 6 days serial interval, our results indicate that there may exist infectiousness during the incubation period for 2019-nCoV. This increases the difficulty of screening or identifying cases related to COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Kaike Ping", - "author_inst": "Guizhou Center for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.04.20026005", "rel_title": "Transmission and clinical characteristics of coronavirus disease 2019 in 104 outside-Wuhan patients, China", @@ -1588256,6 +1591041,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.02.973255", + "rel_title": "Evidence for RNA editing in the transcriptome of 2019 Novel Coronavirus", + "rel_date": "2020-03-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.02.973255", + "rel_abs": "The COVID-19 outbreak has become a global health risk and understanding the response of the host to the SARS-CoV-2 virus will help to contrast the disease. Editing by host deaminases is an innate restriction process to counter viruses, and it is not yet known whether it operates against Coronaviruses. Here we analyze RNA sequences from bronchoalveolar lavage fluids derived from infected patients. We identify nucleotide changes that may be signatures of RNA editing: Adenosine-to-Inosine changes from ADAR deaminases and Cytosine-to-Uracil changes from APOBEC ones. A mutational analysis of genomes from different strains of human-hosted Coronaviridae reveals mutational patterns compatible to those observed in the transcriptomic data. Our results thus suggest that both APOBECs and ADARs are involved in Coronavirus genome editing, a process that may shape the fate of both virus and patient.\n\nFor the casual ReaderJust to make a few things clear: - RNA editing and DNA editing are PHYSIOLOGICAL processes. Organisms uses them to (a) try to fight viruses, (b) increase heterogeneity inside cells (on many levels), (c) recognise their own RNA.\n- our work suggests that: (a) cells use RNA editing in trying to deal with Coronaviruses. We don't know to what extent they succeed (and it would be nice if we could help them). (b) Whatever happens, mutations inserted by RNA editing fuel viral evolution. We don't know whether viruses actively exploit this.\n- If you (scientist or not) think our work suggests ANYTHING ELSE, contact us. It can be a first step to help fight these !@#$ coronavirus, or towards a Nobel prize - but we need to discuss it thoroughly.\n- If you think these cellular processes are fascinating, join the club and contact us. We can have a nice cup of tea while chatting how wondrous nature is at coming up with extraordinary solutions...", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Salvatore Di Giorgio", + "author_inst": "Core Research Laboratory, ISPRO, Firenze, 50139, Italy; Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy" + }, + { + "author_name": "Filippo Martignano", + "author_inst": "Core Research Laboratory, ISPRO, Firenze, 50139, Italy; Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy" + }, + { + "author_name": "Maria Gabriella Torcia", + "author_inst": "Department of Experimental and Clinical Medicine, University of Florence, Firenze 50139, Italy" + }, + { + "author_name": "Giorgio Mattiuz", + "author_inst": "Core Research L 5 aboratory, ISPRO, Firenze, 50139, Italy; Department of Experimental and Clinical Medicine, University of Florence, Firenze 50139, Italy" + }, + { + "author_name": "Silvestro G Conticello", + "author_inst": "Institute for Cancer Research, Prevention and Clinical Network (ISPRO); Institute of Clinical Physiology, National Research Council, 56124, Pisa, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.02.28.20029025", "rel_title": "Clinical significance of IgM and IgG test for diagnosis of highly suspected COVID-19 infection", @@ -1588561,69 +1591381,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.29.20029520", - "rel_title": "Detectable serum SARS-CoV-2 viral load (RNAaemia) is closely associated with drastically elevated interleukin 6 (IL-6) level in critically ill COVID-19 patients", - "rel_date": "2020-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.29.20029520", - "rel_abs": "BackgroundAlthough the SARS-CoV-2 viral load detection of respiratory specimen has been widely used for novel coronavirus disease (COVID-19) diagnosis, it is undeniable that serum SARS-CoV-2 nucleic acid (RNAaemia) could be detected in a fraction of the COVID-19 patients. However, it is not clear that if the incidence of RNAaemia could be correlated with the occurrence of cytokine storm or with the specific class of patients.\n\nMethodsThis study enrolled 48 patients with COVID-19 admitted to the General Hospital of Central Theater Command, PLA, a designated hospital in Wuhan, China. The patients were divided into three groups according to the Diagnosis and Treatment of New Coronavirus Pneumonia (version 6) published by the National Health Commission of China. The clinical and laboratory data were collected. The serum viral load detection and serum IL-6 levels were determined. Except for routine statistical analysis, Generalized Linear Models (GLMs) analysis was used to establish a patient status prediction model based on real-time RT-PCR Ct value.\n\nFindingsThe Result showed that cases with RNAaemia were exclusively confirmed in critically ill patients group and appeared to reflect the illness severity. Further more, the inflammatory cytokine IL-6 levels were significantly elevated in critically ill patients, which is almost 10-folds higher than those in other patients. More importantly, the extremely high IL-6 level was closely correlated with the incidence of RNAaemia (R=0.902) and the vital signs of COVID-19 patients (R= -0.682).\n\nInterpretationSerum SARS-CoV-2 viral load (RNAaemia) is strongly associated with cytokine storm and can be used to predict the poor prognosis of COVID-19 patients. Moreover, our results strongly suggest that cytokine IL-6 should be considered as a therapeutic target in critically ill patients with excessive inflammatory response.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Xiaohua Chen", - "author_inst": "General Hospital of Central Theater Command, PLA" - }, - { - "author_name": "Binghong Zhao", - "author_inst": "General Hospital of Central Theater Command, PLA" - }, - { - "author_name": "Yueming Qu", - "author_inst": "Huazhong Agricultural University" - }, - { - "author_name": "Yurou Chen", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Jie Xiong", - "author_inst": "Wuhan University" - }, - { - "author_name": "Yong Feng", - "author_inst": "Wuhan University" - }, - { - "author_name": "Dong Men", - "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences" - }, - { - "author_name": "Qianchuan Huang", - "author_inst": "General Hospital of Central Theater Command, PLA" - }, - { - "author_name": "Ying Liu", - "author_inst": "General Hospital of Central Theater Command, PLA" - }, - { - "author_name": "Bo Yang", - "author_inst": "General Hospital of Central Theater Command, PLA" - }, - { - "author_name": "Jinya Ding", - "author_inst": "General Hospital of Central Theater Command, PLA" - }, - { - "author_name": "Feng Li", - "author_inst": "Wuhan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.02.20030189", "rel_title": "Antibody responses to SARS-CoV-2 in patients of novel coronavirus disease 2019", @@ -1590154,6 +1592911,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.02.20030080", + "rel_title": "Estimation of local novel coronavirus (COVID-19) cases in Wuhan, China from off-site reported cases and population flow data from different sources", + "rel_date": "2020-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20030080", + "rel_abs": "BackgroundsIn December 2019, a novel coronavirus (COVID-19) pneumonia hit Wuhan, Hubei Province, China and spread to the rest of China and overseas. The emergence of this virus coincided with the Spring Festival Travel Rush in China. It is possible to estimate total number of cases of COVID-19 in Wuhan, by 23 January 2020, given the cases reported in other cities and population flow data between cities.\n\nMethodsWe built a model to estimate the total number of cases in Wuhan by 23 January 2020, based on the number of cases detected outside Wuhan city in China, with the assumption that if the same screening effort used in other cities applied in Wuhan. We employed population flow data from different sources between Wuhan and other cities/regions by 23 January 2020. The number of total cases was determined by the maximum log likelihood estimation.\n\nFindingsFrom overall cities/regions data, we predicted 1326 (95% CI: 1177, 1484), 1151 (95% CI: 1018, 1292) and 5277 (95% CI: 4732, 5859) as total cases in Wuhan by 23 January 2020, based on different source of data from Changjiang Daily newspaper, Tencent, and Baidu. From separate cities/regions data, we estimated 1059 (95% CI: 918, 1209), 5214 (95% CI: 4659, 5808) as total cases in Wuhan in Wuhan by 23 January 2020, based on different sources of population flow data from Tencent and Baidu.\n\nConclusionSources of population follow data and methods impact the estimates of local cases in Wuhan before city lock down.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Zian Zhuang", + "author_inst": "Hong Kong Polytechnic University" + }, + { + "author_name": "Peihua Cao", + "author_inst": "Southern Medical University" + }, + { + "author_name": "Shi Zhao", + "author_inst": "Chinese University of Hong Kong" + }, + { + "author_name": "Yijun Lou", + "author_inst": "Hong Kong Polytechnic University" + }, + { + "author_name": "Weiming Wang", + "author_inst": "Huaiyin Normal University" + }, + { + "author_name": "Shu Yang", + "author_inst": "Chengdu University of Traditional Chinese Medicine, Chengdu, China" + }, + { + "author_name": "Lin Yang", + "author_inst": "The Hong Kong Polytechnic University" + }, + { + "author_name": "Daihai He", + "author_inst": "Hong Kong Polytechnic University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.28.20029173", "rel_title": "Analysis on the Clinical Characteristics of 36 Cases of Novel Coronavirus Pneumonia in Kunming", @@ -1590258,41 +1593062,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.26.20028431", - "rel_title": "Transmission characteristics of the COVID-19 outbreak in China: a study driven by data", - "rel_date": "2020-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.26.20028431", - "rel_abs": "The COVID-19 outbreak has been a serious public health threat worldwide. We use individually documented case descriptions of COVID-19 from China (excluding Hubei Province) to estimate the distributions of the generation time, incubation period, and periods from symptom onset to isolation and to diagnosis. The recommended 14-day quarantine period may lead to a 6.7% failure for quarantine. We recommend a 22-day quarantine period. The mean generation time is 3.3 days and the mean incubation period is 7.2 days. It took 3.7 days to isolate and 6.6 days to diagnose a patient after his/her symptom onset. Patients may become infectious on average 3.9 days before showing major symptoms. This makes contact tracing and quarantine ineffective. The basic reproduction number is estimated to be 1.54 with contact tracing, quarantine and isolation, mostly driven by super spreaders.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Meili Li", - "author_inst": "Donghua University" - }, - { - "author_name": "Pian Chen", - "author_inst": "Donghua University" - }, - { - "author_name": "Qianqian Yuan", - "author_inst": "Donghua University" - }, - { - "author_name": "Baojun Song", - "author_inst": "Montclair State University" - }, - { - "author_name": "Junling Ma", - "author_inst": "University of Victoria" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.27.20029009", "rel_title": "Clinical characteristics of 36 non-survivors with COVID-19 in Wuhan, China", @@ -1591767,6 +1594536,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.02.24.20027649", + "rel_title": "Transmission potential of the New Corona (COVID-19) onboard the Princess Cruises Ship, 2020", + "rel_date": "2020-02-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.24.20027649", + "rel_abs": "An outbreak of COVID-19 developed aboard the Princess Cruises Ship during January-February 2020. Using mathematical modeling and time-series incidence data describing the trajectory of the outbreak among passengers and crew members, we characterize how the transmission potential varied over the course of the outbreak. Our estimate of the mean reproduction number in the confined setting reached values as high as [~]11, which is higher than mean estimates reported from community-level transmission dynamics in China and Singapore (approximate range: 1.1-7). Our findings suggest that Rt decreased substantially compared to values during the early phase after the Japanese government implemented an enhanced quarantine control. Most recent estimates of Rt reached values largely below the epidemic threshold, indicating that a secondary outbreak of the novel coronavirus was unlikely to occur aboard the Diamond Princess Ship.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Kenji Mizumoto", + "author_inst": "Kyoto University" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.25.20025643", "rel_title": "Correlation Analysis Between Disease Severity and Inflammation-related Parameters in Patients with COVID-19 Pneumonia", @@ -1591928,57 +1594720,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.02.24.20027052", - "rel_title": "Clinical and radiographic features of cardiac injury in patients with 2019 novel coronavirus pneumonia", - "rel_date": "2020-02-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.24.20027052", - "rel_abs": "ObjectiveTo investigate the correlation between clinical characteristics and cardiac injury of COVID-2019 pneumonia.\n\nMethodsIn this retrospective, single-center study, 41 consecutive corona virus disease 2019 (COVID-2019) patients (including 2 deaths) of COVID-2019 in Beijing Youan Hospital, China Jan 21 to Feb 03, 2020, were involved in this study. The high risk factors of cardiac injury in different COVID-2019 patients were analyzed. Computed tomographic (CT) imaging of epicardial adipose tissue (EAT) has been used to demonstrate the cardiac inflammation of COVID-2019.\n\nResultsOf the 41 COVID-2019 patients, 2 (4.88%), 32 (78.05%), 4 (9.75%) and 3 (7.32%) patients were clinically diagnosed as light, mild, severe and critical cases, according to the 6th guidance issued by the National Health Commission of China. 10 (24.4%) patients had underlying complications, such as hypertension, CAD, type 2 diabetes mellites and tumor. The peak value of TnI in critical patients is 40-fold more than normal value. 2 patients in the critical group had the onset of atrial fibrillation, and the peak heart rates reached up to 160 bpm. CT scan showed low EAT density in severe and critical patients.\n\nConclusionOur results indicated that cardiac injury of COVID-2019 was rare in light and mild patients, while common in severe and critical patients. Therefore, the monitoring of the heart functions of COVID-2019 patients and applying potential interventions for those with abnormal cardiac injury related characteristics, is vital to prevent the fatality.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Hui Hui", - "author_inst": "CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences" - }, - { - "author_name": "Yingqian Zhang", - "author_inst": "Department of Cardiology, Chinese PLA General Hospital, China" - }, - { - "author_name": "Xin Yang", - "author_inst": "CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences" - }, - { - "author_name": "Xi Wang", - "author_inst": "Department of Cardiology, Chinese PLA General Hospital, China" - }, - { - "author_name": "Bingxi He", - "author_inst": "CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences" - }, - { - "author_name": "Li Li", - "author_inst": "Department of Radiology, Beijing Youan Hospital, Capital Medical University, China" - }, - { - "author_name": "Hongjun Li", - "author_inst": "Department of Radiology, Beijing Youan Hospital, Capital Medical University, China" - }, - { - "author_name": "Jie Tian", - "author_inst": "CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences" - }, - { - "author_name": "Yundai Chen", - "author_inst": "Department of Cardiology, Chinese PLA General Hospital, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.02.26.20026971", "rel_title": "Clinical Features of COVID-19 Related Liver Damage", @@ -1593393,6 +1596134,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.20.20025999", + "rel_title": "Generation of antibodies against COVID-19 virus for development of diagnostic tools", + "rel_date": "2020-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.20.20025999", + "rel_abs": "The COVID-19 China coronavirus started in Dec 2019 was challenged by the lack of accurate serological diagnostic tool for this deadly disease to quickly identify and isolate the infected patients. The generation of COVID-19-specific antibodies is essential for such tasks. Here we report that polyclonal and monoclonal antibodies were generated by immunizing animals with synthetic peptides corresponding to different areas of Nucleoprotein (N) of COVID-19. The specificities of the COVID-19 antibodies were assessed by Western Blot analysis against NPs from COVID-19, MERS and SARS. Antibodies were used for immunohistochemistry staining of the tissue sections from COVID-19 infected patient, as a potential diagnostic tool. A Sandwich ELISA kit was quickly assembled for quantitation of the virus/NP of COVID-19 concentrations in the vaccine preparations. Development of POCT is also aggressively undergoing.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Maohua Li", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Ronghua Jin", + "author_inst": "Beijing You'an Hospital, Capital Medical University" + }, + { + "author_name": "Ya Peng", + "author_inst": "Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University" + }, + { + "author_name": "Cuiyan Wang", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Wenlin Ren", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Fudong Lv", + "author_inst": "Beijing You'an Hospital, Capital Medical University" + }, + { + "author_name": "Sitao Gong", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Feng Fang", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Qianyun Wang", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Jianli Li", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Tong Shen", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Hunter Sun", + "author_inst": "AnyGo Technology Co., Ltd" + }, + { + "author_name": "Lei Zhou", + "author_inst": "State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences" + }, + { + "author_name": "Yali Cui", + "author_inst": "College of Life Sciences, Northwest University" + }, + { + "author_name": "Hao Song", + "author_inst": "Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences" + }, + { + "author_name": "Le Sun", + "author_inst": "AbMax Biotechnology Co., LTD" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.23.20026864", "rel_title": "Higher severity and mortality in male patients with COVID-19 independent of age and susceptibility", @@ -1593634,85 +1596454,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.23.20026856", - "rel_title": "Epidemiologic and Clinical Characteristics of 91 Hospitalized Patients with COVID-19 in Zhejiang, China: A retrospective, multi-centre case series", - "rel_date": "2020-02-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.23.20026856", - "rel_abs": "BackgroundRecent studies have focused initial clinical and Epidemiologic characteristics on the COVID-19, mainly revealing situation in Wuhan, Hubei.\n\nAimTo reveal more data on the epidemiologic and clinical characteristics of COVID-19 patients outside of Wuhan, in Zhejiang, China.\n\nDesignRetrospective case series.\n\nMethods88 cases of laboratory-confirmed and 3 cases of clinical-confirmed COVID-19 were admitted to five hospitals in Zhejiang province, China. Data were collected from 20 January 2020 to 11 February 2020.\n\nResultsOf all 91 patients, 88 (96.70%) were laboratory-confirmed COVID-19 with throat swab samples that tested positive for SARS-Cov-2 while 3 (3.30%) were clinical-diagnosed COVID-19 cases. The median age of the patients was 50 (36.5-57) years, and female accounted for 59.34%. In this sample 40 (43.96%) patients had contracted the diseases from local cases, 31 (34.07%) patients had been to Wuhan/Hubei, 8 (8.79%) cases had contacted with people from Wuhan, 11 (12.09%) cases were confirmed aircraft transmission. In particular within the city of Ningbo, 60.52% cases can be traced back to an event held in a temple. The most common symptoms were fever (71.43%), cough (60.44%) and fatigue (43.96%). The median of incubation period was 6 (IQR, 3-8) days and the median time from first visit to a doctor to confirmed diagnosis was 1 (1-2) days. According to the Chest computed tomography scans, 67.03% cases had bilateral pneumonia.\n\nConclusionsSocial activity cluster, family cluster and travel by airplane were how COVID-19 patients get transmitted and could be rapidly diagnosed COVID-19 in Zhejiang.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Guo-Qing Qian", - "author_inst": "Ningbo City First Hospital" - }, - { - "author_name": "Nai-Bin Yang", - "author_inst": "Ningbo City First Hospital" - }, - { - "author_name": "Feng Ding", - "author_inst": "Affiliated Hospital of Shaoxing University" - }, - { - "author_name": "Ada Hoi Yan Ma", - "author_inst": "University of Nottingham Ningbo China" - }, - { - "author_name": "Zong-Yi Wang", - "author_inst": "Ninghai County First Hospital" - }, - { - "author_name": "Yue-Fei Shen", - "author_inst": "Xiaoshan District People Hospital" - }, - { - "author_name": "Chun-Wei Shi", - "author_inst": "Xiaoshan District People Hospital" - }, - { - "author_name": "Xiang Lian", - "author_inst": "Xiangshan County People First Hospital" - }, - { - "author_name": "Jin-Guo Chu", - "author_inst": "Ningbo City First Hospital" - }, - { - "author_name": "Lei Chen", - "author_inst": "Ningbo City First Hospital" - }, - { - "author_name": "Zhi-Yu Wang", - "author_inst": "Ningbo City First Hospital" - }, - { - "author_name": "Da-Wei Ren", - "author_inst": "Ningbo City First Hospital" - }, - { - "author_name": "Guo-Xiang Li", - "author_inst": "Ningbo City First Hospital" - }, - { - "author_name": "Xue-Qin Chen", - "author_inst": "Ningbo City First Hospital" - }, - { - "author_name": "Hua-Jiang Shen", - "author_inst": "Affiliated Hospital of Shaoxing University" - }, - { - "author_name": "Xiao-Min Chen", - "author_inst": "Ningbo City First Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.22.20026815", "rel_title": "Applying chemical reaction transition theory to predict the latent transmission dynamics of coronavirus outbreak in China", @@ -1595111,6 +1597852,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.20.20025866", + "rel_title": "Estimating the Asymptomatic Ratio of 2019 Novel Coronavirus onboard the Princess Cruises Ship, 2020", + "rel_date": "2020-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.20.20025866", + "rel_abs": "The potential infectiousness of asymptomatic COVID-19 cases together with a substantial fraction of asymptomatic infections among all infections, have been highlighted in clinical studies. We conducted statistical modeling analysis to derive the delay-adjusted asymptomatic proportion of the positive COVID-19 infections onboard the Princess Cruises ship along with the timeline of infections. We estimated the asymptomatic proportion at 17.9% (95% CrI: 15.5%-20.2%), with most of the infections occurring before the start of the 2-week quarantine.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kenji Mizumoto", + "author_inst": "Kyoto University" + }, + { + "author_name": "Katsushi Kagaya", + "author_inst": "Kyoto University" + }, + { + "author_name": "Alexander Zarebski", + "author_inst": "Oxford University" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.22.20025460", "rel_title": "Development and Evaluation of A CRISPR-based Diagnostic For 2019-novel Coronavirus", @@ -1595264,41 +1598036,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.20.20025973", - "rel_title": "Assessing the impact of a symptom-based mass screening and testing intervention during a novel infectious disease outbreak: The case of COVID-19", - "rel_date": "2020-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.20.20025973", - "rel_abs": "A symptom-based mass screening and testing intervention (MSTI) can identify a large fraction of infected individuals during an infectious disease outbreak. China is currently using this strategy for the COVID-19 outbreak. However, MSTI might lead to increased transmission if not properly implemented. We investigate under which conditions MSTI is beneficial.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yang Ge", - "author_inst": "The University of Georgia" - }, - { - "author_name": "Brian Kenneth McKay", - "author_inst": "The University of Georgia" - }, - { - "author_name": "Shengzhi Sun", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Feng Zhang", - "author_inst": "University of Texas Health Science Center at Houston" - }, - { - "author_name": "Andreas Handel", - "author_inst": "The University of Georgia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.19.20025296", "rel_title": "Early Prediction of Disease Progression in 2019 Novel Coronavirus Pneumonia Patients Outside Wuhan with CT and Clinical Characteristics", @@ -1596656,6 +1599393,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.02.17.952895", + "rel_title": "Functional pangenome analysis provides insights into the origin, function and pathways to therapy of SARS-CoV-2 coronavirus", + "rel_date": "2020-02-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.17.952895", + "rel_abs": "The spread of the novel coronavirus (SARS-CoV-2) has triggered a global emergency, that demands urgent solutions for detection and therapy to prevent escalating health, social and economic impacts. The spike protein (S) of this virus enables binding to the human receptor ACE2, and hence presents a prime target for vaccines preventing viral entry into host cells1. The S proteins from SARS-CoV-1 and SARS-CoV-2 are similar2, but structural differences in the receptor binding domain (RBD) preclude the use of SARS-CoV-1-specific neutralizing antibodies to inhibit SARS-CoV-23. Here we used comparative pangenomic analysis of all sequenced Betacoronaviruses to reveal that, among all core gene clusters present in these viruses, the envelope protein E shows a variant shared by SARS and SARS-Cov2 with two completely-conserved key functional features, an ion-channel and a PDZ-binding Motif (PBM). These features trigger a cytokine storm that activates the inflammasome, leading to increased edema in lungs causing the acute respiratory distress syndrome (ARDS)4-6, the leading cause of death in SARS-CoV-1 and SARS-CoV-2 infection7,8. However, three drugs approved for human use may inhibit SARS-CoV-1 and SARS-CoV-2 Protein E, either acting upon the ion channel (Amantadine and Hexamethylene amiloride9,10) or the PBM (SB2035805), thereby potentially increasing the survival of the host, as already demonstrated for SARS-CoV-1in animal models. Hence, blocking the SARS protein E inhibits development of ARDS in vivo. Given that our results demonstrate that the protein E subcluster for the SARS clade is quasi-identical for the key functional regions of SARS-CoV-1 and SARS-CoV-2, we conclude that use of approved drugs shown to act as SARS E protein inhibitors can help prevent further casualties from COVID-2019 while vaccines and other preventive measures are being developed.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Intikhab Alam", + "author_inst": "King Abdullah University of Science and Technology (KAUST)" + }, + { + "author_name": "Allan K Kamau", + "author_inst": "King Abdullah University of Science and Technology (KAUST)" + }, + { + "author_name": "Maxat Kulmanov", + "author_inst": "King Abdullah University of Science and Technology" + }, + { + "author_name": "Stefan T Arold", + "author_inst": "King Abdullah University of Science and Technology" + }, + { + "author_name": "Arnab T Pain", + "author_inst": "King Abdullah University of Science and Technology (KAUST)" + }, + { + "author_name": "Takashi Gojobori", + "author_inst": "King Abdullah University of Science and Technology (KAUST)" + }, + { + "author_name": "Carlos M. Duarte", + "author_inst": "King Abdullah University of Science and Technology (KAUST)" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.02.21.959817", "rel_title": "Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform", @@ -1596857,45 +1599637,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.02.12.946087", - "rel_title": "Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology- and bioinformatic-based predictions", - "rel_date": "2020-02-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.12.946087", - "rel_abs": "Effective countermeasures against the recent emergence and rapid expansion of the 2019-Novel Coronavirus (2019-nCoV) require the development of data and tools to understand and monitor viral spread and immune responses. However, little information about the targets of immune responses to 2019-nCoV is available. We used the Immune Epitope Database and Analysis Resource (IEDB) resource to catalog available data related to other coronaviruses, including SARS-CoV, which has high sequence similarity to 2019-nCoV, and is the best-characterized coronavirus in terms of epitope responses. We identified multiple specific regions in 2019-nCoV that have high homology to SARS virus. Parallel bionformatic predictions identified a priori potential B and T cell epitopes for 2019-nCoV. The independent identification of the same regions using two approaches reflects the high probability that these regions are targets for immune recognition of 2019-nCoV.\n\nONE SENTENCE SUMMARYWe identified potential targets for immune responses to 2019-nCoV and provide essential information for understanding human immune responses to this virus and evaluation of diagnostic and vaccine candidates.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Alba Grifoni", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "John Sidney", - "author_inst": "La Jolla Insitute for immunology" - }, - { - "author_name": "Yun Zhang", - "author_inst": "J. Craig Venter Institute" - }, - { - "author_name": "Richard H. Scheuermann", - "author_inst": "J. Craig Venter Institute" - }, - { - "author_name": "Bjoern H. Peters", - "author_inst": "La Jolla Institute for Allergy and Immunology" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Immunology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.02.12.945576", "rel_title": "Aberrant pathogenic GM-CSF+ T cells and inflammatory CD14+CD16+ monocytes in severe pulmonary syndrome patients of a new coronavirus", @@ -1598186,6 +1600927,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.18.955195", + "rel_title": "Structure and immune recognition of the porcine epidemic diarrhea virus spike protein", + "rel_date": "2020-02-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.18.955195", + "rel_abs": "Porcine epidemic diarrhea virus is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a key target for the host antibody response and a good candidate for a protein-based vaccine immunogen. We used electron microscopy to evaluate the PEDV spike structure, as well as pig polyclonal antibody responses to viral infection. The structure of the PEDV spike reveals a configuration similar to that of HuCoV-NL63. Several PEDV protein-protein interfaces are mediated by non-protein components including a glycan at Asn264 and two bound palmitoleic acid molecules. The polyclonal antibody response to PEDV infection shows a dominance of epitopes in the S1 region. This structural and immune characterization provides new insights into coronavirus spike stability determinants and explores the immune landscape of viral spike proteins.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Robert Kirchdoerfer", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Mahesh Bhandari", + "author_inst": "Iowa State University" + }, + { + "author_name": "Olnita Martini", + "author_inst": "The Scripps Research Intitute" + }, + { + "author_name": "Leigh M Sewell", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Sandhya Bangaru", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Kyoung-Jin Yoon", + "author_inst": "Iowa State University" + }, + { + "author_name": "Andrew Ward", + "author_inst": "The Scripps Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.02.18.20021881", "rel_title": "Association between 2019-nCoV transmission and N95 respirator use", @@ -1598339,77 +1601123,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.17.20024018", - "rel_title": "COVID-19 in a Designated Infectious Diseases HospitalOutside Hubei Province,China", - "rel_date": "2020-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.17.20024018", - "rel_abs": "BackgroundA new type of novel coronavirus infection (COVID-19) occurred in Wuhan, Hubei Province. Previous investigations reported patients in Wuhan city often progressed into severe or critical and had a high mortality rate.The clinical characteristics of affected patients outside the epicenter of Hubei province are less well understood.\n\nMethodsAll confirmed COVID-19 case treated in the Third Peoples Hospital of Shenzhen,from January 11, 2020 to February 6, 2020, were included in this study. We analyzed the epidemiological and clinical features of these cases to better inform patient management in normal hospital settings.\n\nResultsAmong the 298 confirmed cases, 233(81.5%) had been to Hubei while 42(14%) had not clear epidemiological history. Only 192(64%) cases presented with fever as initial symptom. The lymphocyte count decreased in 38% patients after admission. The number (percent) of cases classified as non-severe and severe was 240(80.6%) and 58(19.4%) respectively. Thirty-two patients (10.7%) needed ICU care. Compared to the non-severe cases, severe cases were associated with older age, underlying diseases, as well as higher levels of CRP, IL-6 and ESR. The median (IRQ) duration of positive viral test were 14(10-19). Slower clearance of virus was associated with higher risk of progression to severe clinical condition. As of February 14, 2020, 66(22.1%) patients were discharged and the overall mortality rate remains 0.\n\nConclusionsIn a designated hospital outside the Hubei Province, COVID-19 patients were mainly characterized by mild symptoms and could be effectively manage by properly using the existing hospital system.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Qingxian Cai", - "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Deliang Huang", - "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Pengcheng Ou", - "author_inst": "The First Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Hong Yu", - "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Zhibin Zhu", - "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Zhang Xia", - "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Yinan Su", - "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Zhenghua Ma", - "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Yiming Zhang", - "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Zhiwei Li", - "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Qing He", - "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Yang Fu", - "author_inst": "Southern University of Science and Technology" - }, - { - "author_name": "Lei Liu", - "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Jun Chen", - "author_inst": "The Second Affiliated Hospital of Southern University of Science and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.02.16.20023614", "rel_title": "Utilize State Transition Matrix Model to Predict the Novel Corona Virus Infection Peak and Patient Distribution", @@ -1599580,6 +1602293,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.14.20022913", + "rel_title": "Estimating the Efficacy of Traffic Blockage and Quarantine for the Epidemic Caused by 2019-nCoV (COVID-19)", + "rel_date": "2020-02-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.14.20022913", + "rel_abs": "BackgroundSince the 2019-nCoV (COVID-19) outbreaks in Wuhan, China, the cumulative number of confirmed cases is increasing every day, and a large number of populations all over the world are at risk. The quarantine and traffic blockage can alleviate the risk of the epidemic and the infections, henceforth evaluating the efficacy of such actions is essential to inform policy makers and raise the public awareness of the importance of self-isolation and quarantine.\n\nMethodWe collected confirmed case data and the migration data, and introduced the quarantine factor and traffic blockage factor to the Flow-SEIR model. By varying the quarantine factor and traffic blockage factor, we simulated the change of the peak number and arrival time of infections, then the efficacy of these two intervation measures can be analyzed in our simulation. In our study, the self-protection at home is also included in quarantine.\n\nResultsIn the simulated results, the quarantine and traffic blockage are effective for epidemic control. For Hubei province, the current quarantine factor is estimaed to be 0.405, which means around 40.5% of suceptibles who are close contacting with are in quarantine, and the current traffic blockage factor is estimaed to be 0.66, which indicates around 34% of suceptibles who had flowed out from Hubei. For the other provinces outside Hubei, the current quarantine factor is estimated to be 0.285, and the current traffic blockage factor is estimated to be 0.26. With the quarantine and traffic blockage factor increasing, the number of infections decrease dramatically. We also simulated the start dates of quarantine and traffic blockage at four time points, the simulated results show that the early of warning is also effective for epidemic containing. However, provincial level traffic blockage can only alleviate 21.06% - 22.38% of the peak number of infections. In general, the quarantine is much more effective than the traffic blockage control.\n\nConclusionBoth of quarantine and traffic blockage are effective ways to control the spread of COVID-19. However, the eff icacy of quarantine is found to be much stronger than that of traffic blockage. Considering traffic blockage may also cause huge losses of economy, we propose to gradually deregulate the traffic blockage, and improve quarantine instead. Also, there might be a large number of asymptomatic carriers of COVID-19, the quarantine should be continued for a long time until the epidemic is totally under control.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Deqiang Li", + "author_inst": "Southeast University" + }, + { + "author_name": "Zhicheng Liu", + "author_inst": "Southeast University" + }, + { + "author_name": "Qinghe Liu", + "author_inst": "Southeast University" + }, + { + "author_name": "Zefei Gao", + "author_inst": "Southeast University" + }, + { + "author_name": "Junkai Zhu", + "author_inst": "Southeast University" + }, + { + "author_name": "Junyan Yang", + "author_inst": "Southeast University" + }, + { + "author_name": "Qiao Wang", + "author_inst": "Southeast University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.14.20021535", "rel_title": "Clinical Characteristics of 2019 Novel Infected Coronavirus Pneumonia\uff1aA Systemic Review and Meta-analysis", @@ -1599705,49 +1602461,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.02.14.20023127", - "rel_title": "Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (COVID-19)", - "rel_date": "2020-02-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.14.20023127", - "rel_abs": "BackgroundEstimation of the fraction and contagiousness of undocumented novel coronavirus (COVID-19) infections is critical for understanding the overall prevalence and pandemic potential of this disease. Many mild infections are typically not reported and, depending on their contagiousness, may support stealth transmission and the spread of documented infection.\n\nMethodsHere we use observations of reported infection and spread within China in conjunction with mobility data, a networked dynamic metapopulation model and Bayesian inference, to infer critical epidemiological characteristics associated with the emerging coronavirus, including the fraction of undocumented infections and their contagiousness.\n\nResultsWe estimate 86% of all infections were undocumented (95% CI: [82%-90%]) prior to the Wuhan travel shutdown (January 23, 2020). Per person, these undocumented infections were 52% as contagious as documented infections ([44%-69%]) and were the source of infection for two-thirds of documented cases. Our estimate of the reproductive number (2.23; [1.77-3.00]) aligns with earlier findings; however, after travel restrictions and control measures were imposed this number falls considerably.\n\nConclusionsA majority of COVID-19 infections were undocumented prior to implementation of control measures on January 23, and these undocumented infections substantially contributed to virus transmission. These findings explain the rapid geographic spread of COVID-19 and indicate containment of this virus will be particularly challenging. Our findings also indicate that heightened awareness of the outbreak, increased use of personal protective measures, and travel restriction have been associated with reductions of the overall force of infection; however, it is unclear whether this reduction will be sufficient to stem the virus spread.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ruiyun Li", - "author_inst": "Imperial College London" - }, - { - "author_name": "Sen Pei", - "author_inst": "Columbia University" - }, - { - "author_name": "Bin Chen", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Yimeng Song", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Tao Zhang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Wan Yang", - "author_inst": "Columbia University" - }, - { - "author_name": "Jeffrey Shaman", - "author_inst": "Columbia University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.11.944462", "rel_title": "Cryo-EM Structure of the 2019-nCoV Spike in the Prefusion Conformation", @@ -1600918,6 +1603631,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.10.20021725", + "rel_title": "Beyond R0: the importance of contact tracing when predicting epidemics", + "rel_date": "2020-02-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.10.20021725", + "rel_abs": "The basic reproductive number -- R0 -- is one of the most common and most commonly misapplied numbers in public health. Although often used to compare outbreaks and forecast pandemic risk, this single number belies the complexity that two different pathogens can exhibit, even when they have the same R0 [1-3]. Here, we show how to predict outbreak size using estimates of the distribution of secondary infections, leveraging both its average R0 and the underlying heterogeneity. To do so, we reformulate and extend a classic result from random network theory [4] that relies on contact tracing data to simultaneously determine the first moment (R0) and the higher moments (representing the heterogeneity) in the distribution of secondary infections. Further, we show the different ways in which this framework can be implemented in the data-scarce reality of emerging pathogens. Lastly, we demonstrate that without data on the heterogeneity in secondary infections for emerging infectious diseases like COVID-19, the uncertainty in outbreak size ranges dramatically. Taken together, our work highlights the critical need for contact tracing during emerging infectious disease outbreaks and the need to look beyond R0 when predicting epidemic size.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Laurent H\u00e9bert-Dufresne", + "author_inst": "University of Vermont" + }, + { + "author_name": "Benjamin M. Althouse", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Samuel V. Scarpino", + "author_inst": "Northeastern University" + }, + { + "author_name": "Antoine Allard", + "author_inst": "Universit\u00e9 Laval" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.11.20022095", "rel_title": "Primary Care Practitioners' Response to 2019 Novel Coronavirus Outbreak in China", @@ -1601051,61 +1603795,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2020.02.10.20021824", - "rel_title": "Distribution of the 2019-nCoV Epidemic and Correlation with Population Emigration from Wuhan, China", - "rel_date": "2020-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.10.20021824", - "rel_abs": "BACKGROUNDSThe ongoing new coronavirus (2019-nCoV) pneumonia outbreak is spreading in China and has not reached its peak. Five millions of people had emigrated from Wuhan before the city lockdown, which potentially represent a source of virus spreaders. Case distribution and its correlation with population emigration from Wuhan in early epidemic are of great importance for early warning and prevention of future outbreak.\n\nMETHODSThe officially reported cases of 2019-nCoV pneumonia were collected as of January 30, 2020. Time and location information of these cases were extracted analyzed with ArcGIS and WinBUGS. Population migration data of Wuhan City and Hubei province were extracted from Baidu Qianxi and analyzed for their correlation with case number.\n\nFINDINGSThe 2019-nCoV pneumonia cases were predominantly distributed in Hubei and other provinces of South China. Hot spot provinces included Sichuan and Yunnan provinces that are adjacent to Hubei. While Wuhan city has the highest number of cases, the time risk is relatively stable. Numbers of cases in some cities are relatively low, but the time risks are continuously rising. The case numbers of different provinces and cities of Hubei province were highly correlated with the emigrated populations from Wuhan. Lockdown of 19 cities of Hubei province, and implementation of nationwide control measures efficiently prevented the exponential growth of case number.\n\nINTERPRETATIONPopulation emigrated from Wuhan was the main infection source for other cities and provinces. Some cities with low case number but were in rapid increase. Due to the upcoming Spring Festival return transport wave, understanding of the trends of risks in different regions is of great significance for preparedness for both individuals and institutions.\n\nFUNDINGSNational Key Research and Development Program of China, National Major Project for Control and Prevention of Infectious Disease in China, State Key Program of National Natural Science of China.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Zeliang Chen", - "author_inst": "Sun Yat-Sen University" - }, - { - "author_name": "Qi Zhang", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Yi Lu", - "author_inst": "Boston University" - }, - { - "author_name": "Xi Zhang", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Wenjun Zhang", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Cheng Guo", - "author_inst": "Columbia University" - }, - { - "author_name": "Conghui Liao", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Qianlin Li", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Xiaohu Han", - "author_inst": "Shenyang Agricultural University" - }, - { - "author_name": "Jiahai Lu", - "author_inst": "Sun Yat-sen University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.11.20022111", "rel_title": "Healthcare-resource-adjusted vulnerabilities towards the 2019-nCoV epidemic across China", @@ -1602492,6 +1605181,57 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.02.07.20021071", + "rel_title": "Incorporating Human Movement Data to Improve Epidemiological Estimates for 2019-nCoV", + "rel_date": "2020-02-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.07.20021071", + "rel_abs": "Estimating the key epidemiological features of the novel coronavirus (2019-nCoV) epidemic proves to be challenging, given incompleteness and delays in early data reporting, in particular, the severe under-reporting bias in the epicenter, Wuhan, Hubei Province, China. As a result, the current literature reports widely varying estimates. We developed an alternative geo-stratified debiasing estimation framework by incorporating human mobility with case reporting data in three stratified zones, i.e., Wuhan, Hubei Province excluding Wuhan, and mainland China excluding Hubei. We estimated the latent infection ratio to be around 0.12% (18,556 people) and the basic reproduction number to be 3.24 in Wuhan before the citys lockdown on January 23, 2020. The findings based on this debiasing framework have important implications to prioritization of control and prevention efforts.\n\nOne Sentence SummaryA geo-stratified debiasing approach incorporating human movement data was developed to improve modeling of the 2019-nCoV epidemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Zhidong Cao", + "author_inst": "Institute of Automation, Chinese Academy of Sciences" + }, + { + "author_name": "Qingpeng Zhang", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Xin Lu", + "author_inst": "National University of Defense Technology" + }, + { + "author_name": "Dirk Pfeiffer", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Lei Wang", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Hongbing Song", + "author_inst": "Chinese PLA Center for Disease Control and Prevention" + }, + { + "author_name": "Tao Pei", + "author_inst": "Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Sciences" + }, + { + "author_name": "Zhongwei Jia", + "author_inst": "Peking University" + }, + { + "author_name": "Daniel Dajun Zeng", + "author_inst": "Institute of Automation, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.06.20020941", "rel_title": "Analysis of the epidemic growth of the early 2019-nCoV outbreak using internationally confirmed cases", @@ -1602721,73 +1605461,6 @@ "type": "contradictory results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.02.05.20020792", - "rel_title": "Preparedness and vulnerability of African countries against introductions of 2019-nCoV", - "rel_date": "2020-02-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.05.20020792", - "rel_abs": "BackgroundThe novel coronavirus (2019-nCoV) epidemic has spread to 23 countries from China. Local cycles of transmission already occurred in 7 countries following case importation. No African country has reported cases yet. The management and control of 2019-nCoV introductions heavily relies on countrys health capacity. Here we evaluate the preparedness and vulnerability of African countries against their risk of importation of 2019-nCoV.\n\nMethodsWe used data on air travel volumes departing from airports in the infected provinces in China and directed to Africa to estimate the risk of introduction per country. We determined the countrys capacity to detect and respond to cases with two indicators: preparedness, using the WHO International Health Regulation Monitoring and Evaluation Framework; and vulnerability, with the Infectious Disease Vulnerability Index. Countries were clustered according to the Chinese regions contributing the most to their risk.\n\nFindingsCountries at the highest importation risk (Egypt, Algeria, Republic of South Africa) have moderate to high capacity to respond to outbreaks. Countries at moderate risk (Nigeria, Ethiopia, Sudan, Angola, Tanzania, Ghana, Kenya) have variable capacity and high vulnerability. Three clusters of countries are identified that share the same exposure to the risk originating from the provinces of Guangdong, Fujian, and Beijing, respectively.\n\nInterpretationSeveral countries in Africa are stepping up their preparedness to detect and cope with 2019-nCoV importations. Resources and intensified surveillance and capacity capacity should be urgently prioritized towards countries at moderate risk that may be ill-prepared to face the importation and to limit onward transmission.\n\nFundingThis study was partially supported by the ANR project DATAREDUX (ANR-19-CE46-0008-03) to VC; the EU grant MOOD (H2020-874850) to MG, CP, MK, PYB, VC.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Marius Gilbert", - "author_inst": "Universite Libre de Bruxelles" - }, - { - "author_name": "Giulia Pullano", - "author_inst": "INSERM, Paris, France" - }, - { - "author_name": "Francesco Pinotti", - "author_inst": "INSERM, Paris, France" - }, - { - "author_name": "Eugenio Valdano", - "author_inst": "University of California Los Angeles, Los Angeles, United States" - }, - { - "author_name": "Chiara Poletto", - "author_inst": "INSERM, Paris, France" - }, - { - "author_name": "Pierre-Yves Boelle", - "author_inst": "INSERM, Paris, France" - }, - { - "author_name": "Eric D'Ortenzio", - "author_inst": "INSERM, Paris, France" - }, - { - "author_name": "Yazdan Yazdanpanah", - "author_inst": "INSERM, Paris, France" - }, - { - "author_name": "Serge Paul Eholie", - "author_inst": "Service des Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Treichville, Abidjan, Ivory Coast" - }, - { - "author_name": "Mathias Altmann", - "author_inst": "IDLIC, Bordeaux, France" - }, - { - "author_name": "Bernardo Gutierrez", - "author_inst": "Department of Zoology, University of Oxford" - }, - { - "author_name": "Moritz U. G. Kraemer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Vittoria Colizza", - "author_inst": "INSERM, Paris, France" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.02.05.20020545", "rel_title": "ACE2 expression by colonic epithelial cells is associated with viral infection, immunity and energy metabolism", @@ -1603914,6 +1606587,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.01.31.20019901", + "rel_title": "Early dynamics of transmission and control of 2019-nCoV: a mathematical modelling study", + "rel_date": "2020-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.01.31.20019901", + "rel_abs": "BackgroundAn outbreak of the novel coronavirus SARS-CoV-2 has led to 46,997 confirmed cases as of 13th February 2020. Understanding the early transmission dynamics of the infection and evaluating the effectiveness of control measures is crucial for assessing the potential for sustained transmission to occur in new areas.\n\nMethodsWe combined a stochastic transmission model with data on cases of novel coronavirus disease (COVID-19) in Wuhan and international cases that originated in Wuhan to estimate how transmission had varied over time during January and February 2020. Based on these estimates, we then calculated the probability that newly introduced cases might generate outbreaks in other areas.\n\nFindingsWe estimated that the median daily reproduction number, Rt, declined from 2.35 (95% CI: 1.15-4.77) one week before travel restrictions were introduced on 23rd January to 1.05 (95% CI: 0.413-2.39) one week after. Based on our estimates of Rt,we calculated that in locations with similar transmission potential as Wuhan in early January, once there are at least four independently introduced cases, there is a more than 50% chance the infection will establish within that population.\n\nInterpretationOur results show that COVID-19 transmission likely declined in Wuhan during late January 2020, coinciding with the introduction of control measures. As more cases arrive in international locations with similar transmission potential to Wuhan pre-control, it is likely many chains of transmission will fail to establish initially, but may still cause new outbreaks eventually.\n\nFundingWellcome Trust (206250/Z/17/Z, 210758/Z/18/Z), HDR UK (MR/S003975/1), Gates Foundation (INV-003174), NIHR (16/137/109)", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Adam J Kucharski", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Timothy W Russell", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Charlie Diamond", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Yang Liu", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "CMMID nCoV working group", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "John Edmunds", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Sebastian Funk", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Rosalind M Eggo", + "author_inst": "London School of Hygiene & Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.01.30.20019844", "rel_title": "Early evaluation of the Wuhan City travel restrictions in response to the 2019 novel coronavirus outbreak", @@ -1604079,57 +1606799,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.01.29.20019547", - "rel_title": "Real time estimation of the risk of death from novel coronavirus (2019-nCoV) infection: Inference using exported cases", - "rel_date": "2020-02-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.01.29.20019547", - "rel_abs": "The exported cases of 2019 novel coronavirus (COVID-19) infection that were confirmed outside of China provide an opportunity to estimate the cumulative incidence and confirmed case fatality risk (cCFR) in mainland China. Knowledge of the cCFR is critical to characterize the severity and understand the pandemic potential of COVID-19 in the early stage of the epidemic. Using the exponential growth rate of the incidence, the present study statistically estimated the cCFR and the basic reproduction number--the average number of secondary cases generated by a single primary case in a naive population. We modeled epidemic growth either from a single index case with illness onset on 8 December, 2019 (Scenario 1), or using the growth rate fitted along with the other parameters (Scenario 2) based on data from 20 exported cases reported by 24 January, 2020. The cumulative incidence in China by 24 January was estimated at 6924 cases (95% CI: 4885, 9211) and 19,289 cases (95% CI: 10,901, 30,158), respectively. The latest estimated values of the cCFR were 5.3% (95% CI: 3.5%, 7.5%) for Scenario 1 and 8.4% (95% CI: 5.3%, 12.3%) for Scenario 2. The basic reproduction number was estimated to be 2.1 (95% CI: 2.0, 2.2) and 3.2 (95% CI: 2.7, 3.7) for Scenarios 1 and 2, respectively. Based on these results, we argued that the current COVID-19 epidemic has a substantial potential for causing a pandemic. The proposed approach provides insights in early risk assessment using publicly available data.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sung-mok Jung", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Andrei R. Akhmetzhanov", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Katsuma Hayashi", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Natalie M. Linton", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Yichi Yang", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Baoyin Yuan", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Tetsuro Kobayashi", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Ryo Kinoshita", - "author_inst": "Hokkaido University" - }, - { - "author_name": "Hiroshi Nishiura", - "author_inst": "Hokkaido University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.01.30.20019836", "rel_title": "Transmission and epidemiological characteristics of Novel Coronavirus (2019-nCoV)-Infected Pneumonia(NCIP):preliminary evidence obtained in comparison with 2003-SARS", @@ -1605127,6 +1607796,121 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.01.25.919787", + "rel_title": "Transmission dynamics of 2019 novel coronavirus (2019-nCoV)", + "rel_date": "2020-01-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.25.919787", + "rel_abs": "RationaleSeveral studies have estimated basic production number of novel coronavirus pneumonia (NCP). However, the time-varying transmission dynamics of NCP during the outbreak remain unclear.\n\nObjectivesWe aimed to estimate the basic and time-varying transmission dynamics of NCP across China, and compared them with SARS.\n\nMethodsData on NCP cases by February 7, 2020 were collected from epidemiological investigations or official websites. Data on severe acute respiratory syndrome (SARS) cases in Guangdong Province, Beijing and Hong Kong during 2002-2003 were also obtained. We estimated the doubling time, basic reproduction number (R0) and time-varying reproduction number (Rt) of NCP and SARS.\n\nMeasurements and main resultsAs of February 7, 2020, 34,598 NCP cases were identified in China, and daily confirmed cases decreased after February 4. The doubling time of NCP nationwide was 2.4 days which was shorter than that of SARS in Guangdong (14.3 days), Hong Kong (5.7 days) and Beijing (12.4 days). The R0 of NCP cases nationwide and in Wuhan were 4.5 and 4.4 respectively, which were higher than R0 of SARS in Guangdong (R0=2.3), Hongkong (R0=2.3), and Beijing (R0=2.6). The Rt for NCP continuously decreased especially after January 16 nationwide and in Wuhan. The R0 for secondary NCP cases in Guangdong was 0.6, and the Rt values were less than 1 during the epidemic.\n\nConclusionsNCP may have a higher transmissibility than SARS, and the efforts of containing the outbreak are effective. However, the efforts are needed to persist in for reducing time-varying reproduction number below one.\n\nAt a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSSince December 29, 2019, pneumonia infection with 2019-nCoV, now named as Novel Coronavirus Pneumonia (NCP), occurred in Wuhan, Hubei Province, China. The disease has rapidly spread from Wuhan to other areas. As a novel virus, the time-varying transmission dynamics of NCP remain unclear, and it is also important to compare it with SARS.\n\nWhat This Study Adds to the FieldWe compared the transmission dynamics of NCP with SARS, and found that NCP has a higher transmissibility than SARS. Time-varying production number indicates that rigorous control measures taken by governments are effective across China, and persistent efforts are needed to be taken for reducing instantaneous reproduction number below one.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Tao Liu", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Jianxiong Hu", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Jianpeng Xiao", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Guanhao He", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Min Kang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Zuhua Rong", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Lifeng Lin", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Haojie Zhong", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Qiong Huang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Aiping Deng", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Weilin Zeng", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Xiaohua Tan", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Siqing Zeng", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Zhihua Zhu", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Jiansen Li", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Dexin Gong", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Donghua Wan", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Shaowei Chen", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Lingchuan Guo", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Yan Li", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Limei Sun", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Wenjia Liang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Tie Song", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Jianfeng He", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Wenjun Ma", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2020.01.25.919688", "rel_title": "Origin time and epidemic dynamics of the 2019 novel coronavirus", @@ -1605188,69 +1607972,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.01.24.919241", - "rel_title": "From SARS-CoV to Wuhan 2019-nCoV: Will History Repeat Itself?", - "rel_date": "2020-01-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.24.919241", - "rel_abs": "This manuscript has been withdrawn as it was submitted without the full consent of all the authors. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Zeliang Chen", - "author_inst": "School of Public Health, Sun Yat-sen University" - }, - { - "author_name": "Wenjun Zhang", - "author_inst": "School of Life Sciences, Sun Yat-sen University" - }, - { - "author_name": "Yi Lu", - "author_inst": "School of Public Health, Boston University" - }, - { - "author_name": "Cheng Guo", - "author_inst": "Mailman School of Public Health, Columbia University" - }, - { - "author_name": "Zhongmin Guo", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Conghui Liao", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "Xi Zhang", - "author_inst": "Shenyang Agricultural University" - }, - { - "author_name": "Yi Zhang", - "author_inst": "Shenyang Agricultural University" - }, - { - "author_name": "Xiaohu Han", - "author_inst": "Shenyang Agricultural University" - }, - { - "author_name": "Qianlin Li", - "author_inst": "Sun Yat-sen University" - }, - { - "author_name": "W. Ian Lipkin", - "author_inst": "Mailman School of Public Health, Columbia University" - }, - { - "author_name": "Jiahai Lu", - "author_inst": "Sun Yat-Sen University" - } - ], - "version": "1", - "license": "cc_no", - "type": "confirmatory results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.01.24.919183", "rel_title": "Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China",